Genome-Wide Identification of Cyclin Dependent Kinase (CDK) Family Genes Influencing Adipocyte Differentiation in Cattle

Genome-Wide Identification of Cyclin Dependent Kinase (CDK) Family Genes Influencing Adipocyte Differentiation in Cattle | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research article Genome-Wide Identification of Cyclin Dependent Kinase (CDK) Family Genes Influencing Adipocyte Differentiation in Cattle Cuili Pan, Zhaoxiong Lei, Shuzhe Wang, Xingping Wang, Dawei Wei, and 4 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-133585/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 12 Jul, 2021 Read the published version in BMC Genomics → Version 1 posted 9 You are reading this latest preprint version Abstract Background : The cyclin dependent kinases (CDKs) are protein kinases regulating important cellular processes such as cell cycle and transcription. A variety of studies have shown that many CDK genes also played a critical role during adipogenic differentiation. However, there is a lack of systematic research on the CDK gene family regulating bovine adipocyte differentiation.Therefore, this study aimed to characterize CDK family genes in bovine and study the expression pattern during adipocyte differentiation. Results : We performed a genome-wide analysis and identified 25, 25, 22, 21, 22, 24, 22 and 24 CDK genes in Bos taurus , Bos indicus , Hybrid-Bos taurus , Hybrid bos indicus , Bos grunniens , Bos mutus, Bison and Bubalus bubalis , respectively. All the CDK genes classified into 8 subfamilies through phylogenetic analysis. Chromosome localization displayed 25 bovine CDK genes distributed on 16 chromosomes. Collinearity analysis revealed that CDK family genes of Bos taurus were extensively homologous with Bos indicus , Hybrid-Bos taurus , Hybrid bos indicus , Bos grunniens and Bubalus bubalis . Tanscriptome analysis showed that several of the CDK family genes had relatively high expression levels in preadipocytes compared with differentiated adipocytes, which is generally similar to qPCR, indicating that it could have a significant function in the growth of the emerging lipid droplets. Conclusion: We performed a comprehensive analysis for the CDK family genes including identification, phylogenetic classification, structural characterization, chromosomal distribution, collinearity analysis and expression profile analysis by tanscriptome sequencing and qPCR. The results provide a basis for further study to determine the roles of CDK family genes in regulating adipocyte differentiation, which is beneficial for beef quality improvement. Epigenetics & Genomics CDK gene family Bovine Adipocytes differentiation Collinearity analysis Gene expression pattern Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Background With the improvement of people's living standard, high-quality beef would become the mainstream of consumption in the future.The intramuscular fat (IMF) content of beef is a crucial factor that affects the flavor, freshness, juiciness, tenderness and color, which plays an important role in the improvement of taste and nutritional value. So it is of great scientific significance to further reveal the molecular mechanism of IMF deposition in cattle. Adipogenic differentiation is a complex process regulated by many genes, among which C/EBPα and PPARγ are the key transcription factors in the regulatory network that could regulate the expression of a series of adipogenic phenotypic genes ( FABP1 , FABP4 , LPL , aP2 , CAP , Perilipin , etc.) through transcriptional activation [ 1 – 3 ]. A number of genes regulate adipocyte differentiation and lipid droplet formation by regulating C/EBPα and PPARγ directly or indirectly. For example, another important member of C/EBP gene family , C/EBPβ , could transactivate the expression of C/EBPα and PPARγ to promote adipocyte terminal differentiation [ 2 ]. In addition , C/EBPβ is involved in the regulation of C/EBPα and PPARγ through activating Klf5 , SREBP1c , Ebf1 , Xbp1 and Atg4b , respectively [ 2 ]. C/EBPβ can also activate some other transcriptional factors and inhibit the expression of Wnt10b which is an anti-adipogenic factor that can suppress PPARγ through β-catenin signaling pathway [ 4 , 5 ]. SREBP-1a , SREBP-1c and SREBP-2 are three members of SREBP gene family regulating de novo synthesis of fatty acids, the differentiation of adipocytes and synthesis of cholesterol, respectively, by targeting fatty acid metabolism-related genes including ACC , SCD , FASD , GPAT , etc. [ 6 ]. Besides, there are a variety of gene families that function in adipogenic differentiation such as KLFs , SMADs , RARs , DGATs and so on [ 7 ]. CDKs are a large family of serine/threonine protein kinases that were first discovered in the regulation of cell cycle, and they had diverse functions in various of biological processes in eukaryotes including mRNA processing, regulation of transcription [ 8 – 11 ]. Recently, they have been shown to regulate adipocyte differentiation and lipid droplet formation by phosphorylating a series of associated transcription factors or adipocyte-specific genes. CDK6 , a member of CDK family genes, was targeted by miR107 to inhibit Notch and its downstream gene Hes1 , thereby inhibiting glucose uptake and triglyceride synthesis in adipocytes [ 12 ]. MAPK and CDK2/cyclinA sequentially activated C/EBPβ by maintaining the phosphorylated state of Thr188 during the progression of mitotic clonal expansion (MCE) and adipocytes terminal differentiation [ 13 ]. Insulin activated the CCND3-CDK4 complex which in turn phosphorylated Ser388 of the insulin receptor IRS2 to maintain the active status of the insulin signaling pathway in adipocyte, eventually promoting de novo lipid synthesis [ 14 ]. In addition, CDK4 could phosphorylate Rb to release E2F leading to preadipocyte proliferation as well as phosphorylate PPARγ to regulate the terminal differentiation of adipocytes [ 15 ]. CDK5 could reduce the insulin sensitivity of adipocytes by phosphorylating Ser273 of PPARγ, and inhibition the phosphorylation of Ser273 would promote browning and thermogenesis of white adipose tissue [ 16 ]. CDK7 complex could inactivate PPARγ through the phosphorylation of PPARγ-S112 to inhibit adipogenesis [ 17 ]. CDK8 promotes the ubiquitination and degradation of SREBP-1c by phosphorylating its serine residues, thus inhibiting the adipogenesis [ 18 ]. These findings inspired our curiosity to explore the effects of CDK family genes on bovine adipocytes differentiation. However, the expression patterns and regulatory mechanisms of CDKs in bovine adipocytes have not been systematically studied and elucidated. Therefore, the present study aimed to detect CDK family genes in the bovine genome, and then perform a detailed analysis of the classification, physicochemical properties, phylogenetic analysis, structural features, and functional analysis. Furthermore, the expression pattern analysis by transcriptom and qPCR verification was performed in order to identify essential members of CDK family that affect adipogenic differentiation. Our study provided a deep insight into CDKs that influence adipogenic differentiation, which is essential for future study in improving IMF in the process of bovine breeding. Results Identification of the members in the CDK family To identify the CDK family members, 59 verified CDK amino acid sequences from cattle ( Bos taurus , 8), human ( Homo sapiens , 26) and mouse (Mus musculus , 25) were used as the query for genome-wide detection of the homologous sequences in Bos taurus , Bos indicus , Bos grunniens , Hybrid-Bos Indicus , Hybrid-Bos taurus , Bos mutus , Bison bison bison , and Bubalus bubalis . As a result, 25 non-redundant CDK protein sequences including CDK1-10,CDK11B, CDK12-20, CDKL1-5 were identified in Bos taurus (Table 1 ). In parallel, 22, 21, 22, 24, 22, 25 and 24 CDK family proteins were recognized in Bos grunniens, Hybrid-Bos Indicus, Hybrid-Bos taurus, Bos mutus, Bison bison bison, Bos indicus and Bubalus bubalis , respectively (Additional file 1) and the protein sequences of all the CDKs were provided in Additional file 2. Transcript ENSBIXT00000049337 is a newly identified member of CDK family in Hybrid-Bos taurus , which is named CDK20 according to the sequence similarity and collinearity. Table 1 Details of Genome-wide identified CDK family members in Bos taurus Protein Name gene ID transcript ID pI Mw/Da Amino acids description CDK1 ENSBTAG00000010109 ENSBTAT00000013337 8.38 34025.40 297 cyclin dependent kinase 1 CDK2 ENSBTAG00000004021 ENSBTAT00000005252 8.79 33873.46 298 cyclin dependent kinase 2 CDK3 ENSBTAG00000010509 ENSBTAT00000013885 8.13 34805.48 305 cyclin dependent kinase 3 CDK4 ENSBTAG00000007160 ENSBTAT00000009420 6.51 33646.73 303 cyclin dependent kinase 4 CDK5 ENSBTAG00000007766 ENSBTAT00000010212 7.57 33288.47 292 cyclin dependent kinase 5 CDK6 ENSBTAG00000044023 ENSBTAT00000061349 6.22 37014.40 326 cyclin dependent kinase 6 CDK7 ENSBTAG00000011046 ENSBTAT00000014667 8.67 38946.26 346 cyclin dependent kinase 7 CDK8 ENSBTAG00000016737 ENSBTAT00000022252 8.72 53282.71 464 cyclin dependent kinase 8 CDK9 ENSBTAG00000004695 ENSBTAT00000006162 9.04 42747.58 372 cyclin dependent kinase 9 CDK10 ENSBTAG00000033333 ENSBTAT00000047400 9.16 41046.93 361 cyclin dependent kinase 10 CDK11B ENSBTAG00000010737 ENSBTAT00000014227 5.34 89901.85 771 cyclin dependent kinase 11B CDK12 ENSBTAG00000013238 ENSBTAT00000002005 9.54 140641.60 1264 cyclin dependent kinase 12 CDK13 ENSBTAG00000001528 ENSBTAT00000002003 9.71 164717.14 1512 cyclin dependent kinase 13 CDK14 ENSBTAG00000048664 ENSBTAT00000068321 9.06 53169.98 470 cyclin dependent kinase 14 CDK15 ENSBTAG00000055073 ENSBTAT00000086547 6.68 45011.42 405 cyclin dependent kinase 15 CDK16 ENSBTAG00000016769 ENSBTAT00000022303 7.23 55758.68 496 cyclin dependent kinase 16 CDK17 ENSBTAG00000001510 ENSBTAT00000077282 9.1 59563.16 523 cyclin dependent kinase 17 CDK18 ENSBTAG00000012673 ENSBTAT00000085187 9.26 54126.19 471 cyclin dependent kinase 18 CDK19 ENSBTAG00000007288 ENSBTAT00000009583 8.66 56685.13 500 cyclin dependent kinase 19 CDK20 ENSBTAG00000015171 ENSBTAT00000020188 6.06 38546.53 346 cyclin dependent kinase 20 CDKL1 ENSBTAG00000004780 ENSBTAT00000036046 9.08 40735.16 352 cyclin dependent kinase like 1 CDKL2 ENSBTAG00000014038 ENSBTAT00000031574 8.76 64289.09 569 cyclin dependent kinase like 2 CDKL3 ENSBTAG00000010979 ENSBTAT00000014574 9.37 67477.82 591 cyclin dependent kinase like 3 CDKL4 ENSBTAG00000024044 ENSBTAT00000033135 8.88 39465.72 342 cyclin dependent kinase like 4 CDKL5 ENSBTAG00000007428 ENSBTAT00000076996 9.56 107236.16 960 cyclin dependent kinase like 5 Mw : molecular weight, pI : isoelectric point The length of amino acid sequences of 25 cattle CDK proteins ranged from 292 (CDK5) to 1512 (CDK13), and their molecular weight (Mw) was 33288.47-164717.14 Da, which correlated well with the protein length. The isoelectric points (pI) of most CDK family proteins was higher than 8.0, which containing more basic amino acids than acidic amino acids, except for 2 neutral proteins(CDK5 and CDK16), whose pI are 7.57 and 7.23, respectively , and 5 acidic proteins (CDK4, CDK6, CDK11B, CDK15 and CDK20), whose pI is between 5.34 and 6.68. Moreover, we detected all the 25 CDK proteins contained the Serine/Threonine Kinase conserved domain (Additional file 3). Structural features of bovine CDK family members To explore the structural characteristics of bovine CDK proteins and genes, the conserved motifs and gene structures were projected based on their phylogenetic relationships (Fig. 1 ). Results showed the CDKs of cattle initially categorized into three main subfamily according to the evolutionary clades. Among 25 bovine CDK family genes, the first subfamily contains 6 members including CDKL1, CDKL2, CDKL3, CDKL4, CDKL5 and CDK20. The second subfamily possesses CDK10 and CDK11B, and the other members belongs to the third subfamily. Six conserved domains(Motif 1, 3, 5, 6, 7, and 9), containing 29, 21, 21, 21, 21, and 21 amino acids respectively, were shared among all the CDK family proteins (Additional file 4). As a small branch in the third subfamily, CDK16, CDK17 and CDK18, have all of the ten motifs. CDK4, CDK15 and CDK20 all consists of eight motifs, while CDK4 lacks of Motif 4 and Motif 10, CDK15 is short for Motif 2 and Motif 10, and CDK20 is without Motif 4 and Motif 10. The rest CDK proteins comprise nine motifs lacking of CDK10, which indicates they all have the same conserved patterns. The items of introns, coding sequences (CDS) and untranslated region (UTR) were various among CDK family genes, for instance, the gene length CDKs ranged from 3599nt ( CDK4 ) to 678562nt ( CDK14 ), which is mainly due to the variation in intron. The number of CDS varied from 7 to 17 and the length and layout of 3’UTR and 5’UTR were also various in the noncoding areas. Although CDS, introns and UTRs varied greatly, analysis discovered that CDK family members in the same evolutionary branch tend to show similar gene structures and semblable conserved patterns in motifs. Phylogenetic relationship of CDK proteins in different organisms To assess evolutionary relationships of CDK proteins between cattle and other organisms, we conducted a phylogenetic analysis of animals in bovinae ( Bos taurus, Bos indicus, Bos grunniens, Hybrid-Bos Indicus, Hybrid-Bos taurus, Bos mutus, Bison bison bison, and Bubalus bubalis ). Besides, CDK proteins in Homo sapiens and Mus musculus were also included for they have been studied extensively as two model organisms. Accordingly, 236 amino acid sequences from 10 organisms were aligned to generate nonrooted Neighbor-Joining (NJ) tree (Fig. 2 ). Phylogenetic analyses revealed CDK family proteins were classified into eight major clades. Clade Ⅰ contained CDK4 and CDK6 and Clade Ⅱ included CDK5, CDK7 and CDK20. Then CDK14 and CDK15 coalesced into a single branch named Clade Ⅲ, CDK11A, CDK11B, CDK16, CDK17 and CDK18 got together named Clade Ⅳ, CDK1, CDK2 and CDK3 got together named Clade Ⅴ, CDK9 of the 10 species merged together named Clade Ⅵ, all the Cyclin Dependent Kinases Like proteins ( CDKL1, CDKL2, CDKL3, CDKL4 and CDKL5) classified into a category named Clade Ⅶ, and the rest (CDK8, CDK10, CDK12, CDK13 and CDK19) clustered into a branch named Clade Ⅷ. Chromosomal distribution and collinearity analysis of CDK genes CDK family genes were mapped on the chromosomes of six bovinae species (Fig. 3 ). 25 bovine CDKs distribute on 16 chromosomes including Chr 2, Chr 4, Chr 5, Chr 6, Chr 7, Chr 8, Chr 9, Chr 10, Chr 11, Chr 12, Chr 16, Chr 18, Chr 19, Chr 20, Chr 28 and Chr X. Among them, the CDKs of cattle have a similar position distribution with Bos indicus , whereas the arrangement of a few genes on chromesomes are different between cattle and the other species. For example, the order of CDK14 (7.94–8.62 Mb), CDK6 (9.94–10.19 Mb), CDK13 (80.95–81.08 Mb) and CDK5 (113.630-113.634 Mb) in Bos taurus Chr 4 was opposite from that in Hybrid-Bos Indicus, Hybrid-Bos taurus and Bos grunniens , which is CDK5 , CDK13 , CDK6 and CDK14 , respectively. CDK4 , CDK2 and CDK7 were three tandem genes in Bos taurus at the location of 29.66–29.69 Mb, 29.66–29.69 Mb and 29.72–29.92 Mb on Chr 5, while the arrangement of these three genes were reversed in Bos grunniens, Hybrid-Bos Indicus Chr 5 and Bubalus Chr 4. In addition, compared with Bos taurus , Bos grunniens lacks of CDK7 , CDK11B and CDK20 , Hybrid-Bos Indicus lacks of CDK11B , CDK16 , CDK20 and CDKL4 , Hybrid-Bos taurus is without CDK11B , CDK20 , CDKL4 and CDKL5 , and Bubalus is short of CDK11B . What’s more, CDKL5 is located on chromosome X in Bos taurus , while on chromosome Y in Bos grunniens. Collinearity analysis of the genome resulted in the identification of 31,691, 34,495, 33,570, 32,378 and 33,327 pairs of collinear genes between Bos taurus and Bos indicus , Hybrid-Bos Indicus , Hybrid-Bos taurus , Bos grunniens and Bubalus bubalis , respectively(Fig. 4 ). Results showed that there is a one-to-one correspondence between chromosomes of Bos taurus and Hybrid-Bos Indicus , Hybrid-Bos taurus , Bos indicus and Bos grunniens . A large chromosome homologous also existed between cattle (2 N = 60) and buffalo (2 N = 50), although the chromosome number is different of the two species.The syntenic blocks revealed that Chr1 of buffalo appears to be a fusion of cattle Chr1 and Chr 27, buffalo Chr 2 appears to be a combination of cattle Chr2 and Chr 23, buffalo Chr 3 amounts to cattle Chr 8 and Chr 19, buffalo Chr 4 equals cattle Chr 5 and Chr 28, and buffalo Chr 5 equals cattle Chr- 16 and Chr 29. The detailed syntenic relationships of CDK family genes between cattle and the other five species in bovinae was displayed in Table 2 . Table 2 Syntenic relationships of CDK family genes between cattle and the other five species Gene Bos indicus Hybrid-Bos taurus Hybrid-Bos Indicus Bos grunniens Bubalus bubalis CDK1 Y Y Y Y Y CDK2 Y Y Y Y Y CDK3 Y Y Y Y Y CDK4 Y Y Y Y Y CDK5 Y Y Y Y Y CDK6 Y Y Y Y Y CDK7 N Y Y - Y CDK8 Y Y Y Y Y CDK9 Y Y Y Y Y CDK10 Y Y Y Y Y CDK11B N - - - - CDK12 Y Y Y Y Y CDK13 Y Y Y Y Y CDK14 Y Y Y Y Y CDK15 Y Y Y Y Y CDK16 Y Y - Y Y CDK17 Y Y Y Y Y CDK18 Y Y Y Y Y CDK19 Y Y Y Y Y CDK20 Y Y - - Y CDKL1 Y Y Y Y Y CDKL2 Y Y Y Y Y CDKL3 Y Y Y Y Y CDKL4 Y - - Y Y CDKL5 Y - Y Y Y ‘Y’ represents the synteny of genes between two species, while ‘N’ means not and ‘-’ means lacking of the gene. The expression analysis of CDKs in different tissue The expression pattern of genes could provide important references for their function. To explore the expression pattern of the CDK gene family during adipogenic differentiation , we investigated the relative expression level in 163 samples of 60 tissue types includin g heart, liver, spleen, lung, kidney, muscle, fat , etc. The results showed that CDKs displayed differential expression patterns in diverse tissues (Fig. 5 a), which could be classified into 5 groups (A to E). As a marker gene for adipocyte differentiation , PPARγ had a high expression in Group B including omental fat, intramuscular fat, subcutaneous fat and mammary gland fat, indicating that the results is reliable. The 25 CDKs could be grouped into 4 categories according to their expression patterns and they all expressed in 60 tissues, suggesting that they may play a broad regulatory role in life activities. Group Ⅰ( CDK4 , CDK9 and CDK11B ) showed the highest expression levels, followed by Group Ⅲ( CDK3 , CDK5 , CDK7 , CDK8 , CDK10 , CDK18 , and CDK20 ) and Group Ⅳ ( CDK1 , CDK2 , CDK6 , CDK12 , CDK13 , CDK14 , CDK16 , and CDK17 ). Group Ⅱ comprised the rest members of CDKs , whose expression level was the lowest. Further analysis of the five different fat tissues revealed that CDK9 was highly expressed in all the fat tissues and its expression pattern was similar to PPARγ (Fig. 5 b). Expression analysis of CDKs in preadipocytes and differentiated adipocytes by RNA-seq Transcriptome analysis of 25 CDKs in preadipocytes and differentiated adipocytes reveal ed that CDKs showed a up-regulation trend in preadipocytes compared with differentiated adipocytes except for CDK1 , CDK3 , CDK6 , CDK19 , CDKL1 and CDKL4 (Fig. 6 ). CDK7 displayed a significant high expression, whereas CDK1 showed a significant low expression in preadipocytes within the 95% confidence interval. And CDK4 , CDK8 , CDK9 and CDK14 all displayed a significant high expression in preadipocytes within the 99% confidence interval. Expression analysis of CDKs during adipocyte differention by qPCR To further explore the expression pattern of CDK family genes, preadipocytes collected from perirenal adipose tissue of premature calves were induced differentiation. The results of oil red O staining showed that lipid droplet accumulation was significantly increased in adipocytes induced for 10 days compared to preadipocytes (Additional file 5), indicating that the induction and differentiation was successful. And we conducted qPCR to detect the expression of CDKs at 0, 2, 4, 6 and 10 days during adipocytes differentiation(Fig. 7 ). Results suggested that CDKs showed a relatively high expression in preadipocytes and then decreased as differentiation process went on in addition to CDK1 , CDK15 , CDK18 , CDKL3 and CDKL5 . The three members, CDK1 , CDKL3 and CDKL5 , all had the highest expression on the second day of differentiation and the lowest expression points were on the 6, 8 and 6 day, respectively. The expression level of CDK15 and CDK18 increased with adipocyte differentiation and reached the peak on the fourth day, then decreased. Discussion Cattle is known as an important species for supplying meat. The IMF content directly affects the taste and flavor of beef and it is of great scientific significance to reveal the molecular regulation mechanism of IMF deposition for meat quality improvement. The CDK family genes encoding functional proteins have been well studied in the regulation of transcription, metabolism and cell differentiation[ 8 – 10 ]. However, investigation of CDKs in adipocyte differentiation, especially in bovidae, was limited. Since cattle and several species of bovidae were sequenced, the vast amount of genetic resources might serve as references for exploring the evolution and function of CDK gene family and advancing genome science in bovidae. Structural features of bovine CDK family proteins and genes The activity of proteins depend on their functional motifs and domains[ 19 ]. Six conserved amino acid sequences including Motif 1, Motif 3, Motif 5, Motif 6, Motif 7 and Motif 9 were well-kept among all CDK family members in cattle, indicating the high conservation in motif distribution of CDK family proteins. These highly conserved motifs usually locate at the active sites of the enzymes, which may play essential roles in maintaining the structure, binding to substrate and catalyzing[ 20 , 21 ]. CDK16, CDK17 and CDK18, a small branch in a subfamily, have all of the ten motifs, meaning some specific functions may exist in the three members. It is speculated that Motif 10 is not located in the core of the catalytic domain due to the other 22 members of CDK family proteins lacking of Motif 10 show kinase activities as well. Several CDK proteins such as CDK4, CDK15 and CDK20 are short of Motif 4, Motif 2 and Motif 8, respectively, in addition to Motif 10, indicating some sequence loss occurred in the evolution. As a newly identified member in Hybrid-Bos tauru s, CDK20 possesses a conserved STKc domain and nine motifs (Additional file 6). The domain and motifs analysis revealed that it is consistant with the other CDK proteins. What’s more, the gene structural analysis showed that the distribution and number of CDSs, introns, and UTRs were various in CDKs . This divergence was mainly caused by the length and layout of introns and UTRs, while the gene coding sequences translated proteins were similar. In other words, the nucleic acid sequences of bovine CDK family members were less conversed compared with amino acid sequences. These results have suggested that the similarity of amino acid sequences, especially that in the conversed motifs, may play essential roles in keeping the kinase functions of CDK proteins. Phylogenetic relationship of CDK family proteins The phylogenetic analysis of CDK family proteins in ten species provided an in-deep insight for their evolutionary relationships[ 22 ]. The results revealed that CDK family proteins were classified into eight major clades and the same member from different species first clustered in one branch, indicating that they were conserved in sequences among the 10 species. Clade Ⅰ was separated out initially while Clade Ⅱ, Ⅲ and Ⅳ clustered into a subfamily and the others clustered into another subfamily, manifesting that they have been evolved asymmetrically and the evolutionary relationship between this three subfamilies may be relatively far. Notably, Clade Ⅶ includes all the Cyclin Dependent Kinases Like proteins ( CDKL1, CDKL2, CDKL3, CDKL4 and CDKL5), which is consistant with the study in human that divided the CDKs into CDK and CDKL[ 10 ]. As expected, members of the CDK proteins with a closer relationship tend to have a nearer evolutionary distance, which means that they may cluster together first. For example, Bos Indicus CDK1 first clustered with that of Bubalus bubalis , and then get together with Hybrid-Bos taurus , Bos taurus, Bos mutus, Hybrid-Bos Indicus , Bos grunniens, Bison , human and mouse in turn. Collinearity analysis of CDKs in bovidae The family genes may distribute on different chromosomes or co-locate on the same chromosome, which are generally defined as segmental duplication events in the former and tandem duplication events in the latter[ 23 – 25 ]. Chromosomal distributions of the CDK family genes showed that they located on 13 to 16 chromosomes in six species of bovidae, indicating both segmental and tandem duplication events have occurred for the expansion of CDK genes. The genomes of Bos taurus , Bos grunniens , Hybrid-Bos Indicus , Hybrid-Bos taurus , and Bos indicus consist of 29 autosomes and a pair sex chromosomes(XX/XY)[ 26 , 27 ], while Bubalus bubalis has 24 autosomes plus a pair sex chromosomes(XX/XY). The collinearity results showed a one-to-one correspondence between chromosomes of Bos taurus and Hybrid-Bos Indicus , Hybrid-Bos taurus , Bos indicus and Bos grunniens , and large homologous chromosomal regions between Bos taurus and Bubalus . The arrangement of genes in some syntenic chromosomes may be totally reversed between two species, such as Chr 1, Chr 2, Chr 4, etc. between bos taurus and Hybrid -Bos taurus , Chr 4, Chr 5, Chr 7, etc. between Bos taurus and Hybrid -Bos taurus , Chr 2, Chr 4, Chr 6, etc. between Bos taurus and Bos grunniens , and Chr 9, Chr 10, Chr 11, etc. between Bos taurus and Bubalus bubalis. The discrepancies may due to the opposite starting point for chromosome annotation. Since all the chromosomes were homologous in bovidae, the positions where CDKs located were either collinear (conserved in the same order) or syntenic (not necessarily in the same order) between each two species except for only a few gene pairs[ 28 ]. For example, CDK7 in Chr 20 and CDK11B in Chr 16 didn’t show synteny between Bos taurus and Bos indicus. The positions of CDKL4 and CDK9 are opposite between Bos taurus and Bos grunniens , which locate at 21.50-21.55 Mb and 98.46–98.47 Mb in Chr 11 of Bos taurus and 41.02–41.08 Mb and 7.13–7.14 Mb in Chr 9 of Bos grunniens. The deficiency and discrepancies of CDK genes might be caused by the sequence variation and chromosome rearrangement in the process of evolution[ 29 ]. In addition, Chr16 of Bos taurus showed syntenic relationship with Chr5 and scaffold NW_020228957.1 of Bubalus bubalis (Fig. 4 e), suggesting that NW_020228957.1, which hasn't been assembled yet, may be a part of Bubalus Chr5. Meanwhile, it was syntenic between CDK18 of Bos taurus Chr16 and that in scaffold NW_020228957.1 of Bubalus. In a word, the extensive homology provided rich perspectives for studying the function and evolution of CDK family genes in bovidae. CDK genes affecting adipocyte differentiation CDK family proteins, as a kind of phosphorylases, could regulate adipocytes differentiation by phosphorylating a series of transcription-related factors or adipocyte-specific genes [ 12 – 16 , 18 ]. To dissect the expression pattern of CDK family genes, we analyzed the expression values of the 25 members in 60 tissue types. As a results, CDK4 , CDK9 and CDK11B showed the highest expression in four types of fat tissues (omental fat, intramuscular fat, subcutaneous fat and mammary gland fat) in relative with other tissues. So we suspected the three genes may play more important and wide-ranging roles in adipose tissue compared with other members of CDK family. Previous studies have revealed that CDK4 could phosphorylate IRS2 and Rb to promote adipogenesis[ 14 , 15 ]. CDK9, a component of positive transcription elongation factor b (P-TEFb), could phosphorylate the C-terminal domain of RNA polymerase II and regulate the transcription of target genes by facilitating transcriptional elongation[ 30 ]. In 3T3-L1 cells, CDK9 increased the adipogenic potential by phosphorylating PPARγ directly and inducing its transcriptional activity[ 31 ]. CDK11B had similar expression patterns with CDK4 and CDK9 by tissue expression analysis, while it has not been reported to be involved in adipogenic differentiation by now. It would be valuable to further explore the function of CDK11B in the regulation of adipocytes differentiation. Adipogenic differentiation is a complicated and well-organized process regulated by multiple genes. Analyzing the expression patterns of CDK family genes during adipocytes differentiation is the basis of exploring their functions. Results of transcriptome analysis and qPCR validation both revealed that CDK4, CDK7, CDK8 and CDK9 showed significant high expression in preadipocytes. It is speculated that the four members may have important functions in targeting newly generated lipid droplets. The expression of CDK1, CDKL3 and CDKL5 reached the highest in the second day, while CDK15 and CDK18 reached the peak in the fourth day indicating that they may play regulatory roles during adipocyte differentiation in turn. The functions of CDK1, CDK4, CDK7, CDK8 and CDK9 in adipocytes differentiation have been preliminarily studied and need to be further explored[ 14 , 15 , 17 , 18 , 31 – 35 ]. Expression analysis revealed that CDK15, CDK18, CDKL3 and CDKL5, whose functions has not been studied, may also play significant roles. In addition, the expression trends of some members were inconsistent between RNA-seq and qPCR validation. For instance, there was no significant differences in the expression of CDK2, CDK6, CDK10, CDK11B, CDK12, CDK16, CDK17, CDK19 and CDKL1 by RNA-seq analysis, but they showed a significant down-regulation in qPCR detection. This discrepancy may caused by different sample sources. The samples for RNA-seq were separated from inguinal subcutaneous fat of two 1 year old male Qinchuan cattle, while samples for qPCR were from perirenal fat of a premature female Holstein calf. In summary, the functions of CDKs during adipocytes differentiation is complicated and need to be studied in depth and analyzed comprehensively. The CDK family genes and the interacted genes constructed an integrative network by literature mining using Agilent Literature Search plug-in of Cytoscape (Additional file 7)[ 36 ]. For example, CDK7 could directly activate CDK9 to maintain the high expression of MDM4 and MDM2 [ 34 , 35 ]. MDM2 facilitates adipocyte differentiation through CRTC-mediated activation of STAT3 [ 37 ]. Overall, the results revealed that CDK family genes encoding the enzymes directly or indirectly interact with each other or some other genes, playing non-redundant roles, collectively regulating the life activity including cell cycle, adipocyte differentiation, lipid metabolism etc. Conclusions This study conducted a comprehensive genome-wide analysis of CDK family genes in bovidae. A total of 185 CDK genes were identified and grouped into eight distinct clades. Collinearity analysis revealed that CDK family genes were homologous between cattle and other species in bovinae. The expression analysi s and functional prediction indicated that CDKs may play an significant and complicated role in regulating bovine adipocyte differentiation . The results provided an essential reference for further studies of CDK family genes in the regulation of adipocyte differentiation in cattle. Methods Ethics statement Animal experiments were conducted according to the guidelines of the Regulations for the Administration of Affairs Concerning Experimental Animals (Ministry of Science and Technology, China, 2004). All animal protocols were approved by Animal Ethics Committee of Ningxia University. A premature female calf of a Holstein pregnant cow used in the experiment was released and the primary adipocyte were isolated immediately. We made all efforts to minimize the calf’s suffering.The pregnant cow are not sampled and are still being raised in Zerui ecological breeding farm (yinchuan, China) after a period of recuperation. Genome-wide identification of CDK genes The genome and annotation of Bos taurus (ARS-UCD1.2.101 assembly), Bos grunniens (LU_Bosgru_v3.0.101 assembly), Hybrid-Bos Indicus ( Bos indicus × Bos taurus , UOA_Brahman_1.101 assembly), Hybrid-Bos taurus ( Bos indicus × Bos taurus , UOA_Angus_1.101 assembly), Bos mutus (BosGru_v2.0.101 assembly), Bison bison bison (Bison_UMD1.0.101 assembly), Homo sapiens (GRCh38.101 assembly) and Mus musculus (GRCm38.101 assembly) are from Ensembl database ( http://asia.ensembl.org/index.html ); Bos indicus (GCF_000247795.1 assembly) and Bubalus bubalis (ASM312139v1 assembly) are from NCBI database ( https://www.ncbi.nlm.nih.gov/ ). In order to identify all the possible CDKs in bovine, both Hidden Markov Model (HMM) search and Basic Local Alignment Search Tool (BLAST) were performed[ 38 ]. The number of 59 reviewed CDKs sequences of bovine (Bos taurus) , human ( Homo sapiens ) and mouse ( Mus musculus ) were obtained from UniProt database ( https://www.uniprot.org/ ). These protein sequences were taken as seeds to query the potential candidates of CDK gene family via BLASTP with a threshold of e-value = 10 − 5 . Besides, the HMM of CDKs (Pkinase) was downloaded from Pfam ( https://pfam.xfam.org/ )[ 39 ] and HMMER 3.3.1 ( http://hmmer.org/ )[ 40 ] was used to constructe HMM profiles in bovidae for detection of CDK family genes with the default setting. The candidate sequences obtained from two methods were further manual checked to confirm the CDK homolog sequences. Subsequently, the non-redundant CDK homologs were submitted to NCBI CD-search [ 41 ] to verify the presence of the conserved protein domain. The molecular weight and isoelectric point of bovine CDK proteins were calculated by ExPASy ( https://web.expasy.org/protparam/ )[ 42 ]. Phylogenetic analysis The known CDK amino acid sequences in the Homo sapiens and Mus musculus were downloaded from UniProt database ( https://www.uniprot.org/ ) (Additional file 2). The identified and known amino acid sequences of CDK in Bos taurus , Bos grunniens , Hybrid-Bos Indicus , Hybrid-Bos taurus , Bos mutus , Bison bison bison , Bos indicus and Bubalus bubalis , as well as the known CDKs from Homo sapiens and Mus musculus were aligned by ClusalW and constructed a Neighbor-Joining tree in MEGA 7.0[ 43 ]. The bootstrap was set as 1000 replication. FigTree software (version 1.4.3) was used to adjust and beautify the evolutionary tree. Structural features analysis To further evaluate the structural diversity of cattle CDK genes and proteins, a phylogenetic Neighbor-Joining tree was constructed and the conserved motifs were detected in MEME 5.0[ 44 ] and visualized in TBtools[ 45 ]. The minimum and maximum number of amino acids in each motif were 6 and 50. The motif number of each CDK protein was limited to 10. Also, coding sequences and corresponding genomic sequences of bovine CDKs were loaded into the TBtools to portray the numbers and positions of CDSs and introns graphically. Chromosomal distribution and collinearity analysis Positional information of predicted CDK genes of Bos taurus , Bos grunniens , Hybrid-Bos Indicus , Hybrid-Bos taurus , Bos indicus and Bubalus bubalis were extracted from the genomic sequence and annotation files and then were visualized in TBtools[ 45 ]. The identified CDKs of each species were mapping on chromosomes. Comparisons between each two genomes were determined by all-against-all BLASTP searches (e-value = 10 − 5 ) using the proteome sequences of Bos taurus as queries against those of other five bovine species above. The collinearity analysis between Bos taurus and other five species for orthologous genes was conducted using MCScanX toolkit[ 46 ]. The results of collinearity analysis and orthologous CDKs were visualized by TBtools[ 45 ]. Gene expression analysis by transcriptom The RNA-Seq data of preadipocytes and differentiated adipocytes was downloaded from the National Center for Biotechnology Information (NCBI) Sequence Read Archive(SRR3056892, SRR3064490, SRR3064491, SRR3064492)[ 47 ] and transformed into fastaq format by Fastq-dump.The sequencing quality was checked using FastQC[ 48 ]. Quality control of raw sequence data, including removal of the adapter sequences and low-quality sequences were performed using the Trim_galore. Clean reads were then mapped to the Bos taurus genome(ARS-UCD1.2.101) using STAR. The RSEM and FeatureCounts was used to calculate the expression of transcripts. Data was normalized by calculating the RPKM for each gene. These results were used to analyze the expression of CDKs between preadipocytes and differentiated adipocytes in cattle. The RNA-Seq data of 163 bovine tissue samples were downloaded from Ruminant Genome Database ( http://animal.nwsuaf.edu.cn/code/index.php/RGD )[ 49 ]. The SRR number and adjusted RPKM values of 163 tissue samples were provided in Additional file 8. The heatmap was performed in R software. Isolation, culture and induction differentiation of bovine primary adipocytes Primary adipocyte was isolated and cultured from the perirenal adipose tissue of premature calf in Zerui ecological breeding farm. Type Ⅰ collagenase digestion method was used for the isolation and cultivation of calf preadipocytes. The method described by Huang et al.[ 50 ] was adopted in the induction of preadipocytes differentiation, and the method described by Wang et al.[ 51 ] was applied for oil red O staining. Rna Extraction And Quantitative Rt-pcr (qrt-pcr) RNA extraction and quantitative RT-PCR (qRT-PCR) According to reference sequence from NCBI, quantitative primers of CDK family genes were designed used Primer Premier 5.0 software and the primer sequences were provided in Additional file 9. Total RNA were extracted at 0d, 2d, 4d, 6d and 10d during the differentiation of bovine preadipocytes by phenol-chloroform method using the TRIzol reagent (9109, Takara). RNA samples were measured for absorbance at 260 nm and 280 nm in the multifunctional full-wavelength Multiskan and the samples with an OD260/OD280 ratio between 1.8 and 2.0 was used in the subsequent experiment. Then, 1000 ng total RNA was reverse transcribed using random primers with Moloney murine leukemia virus reverse transcriptase (Takara Bio, Kyoto, Japan). Realtime PCR was carried out in a CFX96 Touch Real-Time PCR Detection System (Bio-Rad, Hercules, CA, USA) with SYBR Green Master Mix (Takara Bio, Kyoto, Japan). Statistical Analysis All qRT-PCR results were calculated using a 2 −∆∆Ct method. Three independent technical repetitions were processed for each test. Statistical significance was examined using Graphpad Prism 7.0 software. Abbreviations CDK: cyclin dependent kinases; CDS: coding sequences; HMM: Hidden Markov Model; Chr: Chromosome; IMF: intramuscular fat; pI: isoelectric points; Mw: molecular weight Declarations Acknowledgments We would like to thank all the participants in our study. We would also like to thank Li Qingfeng and Chen Chengjie for providing valuable advices in the research. Authors' contributions CLP and ZXL made the same contribution to the paper. Conceived and designed the research:YM and CLP; Analyzed the data and conducted the experiment: CLP and ZXL; Wrote the paper: CLP; Modified manuscript: YM, LW, ZXL, SZW, XPW, DWW, XYC, ZMLR. All authors read and approved the final manuscript. Funding This study was funded by the National Natural Science Foundation of China (32072720 and 31672403), the Leading Talents Fund in Science and Technology Innovation in Henan Province(No. 194200510022), the Key Research and Talent Introduction Project of Ningxia Hui Autonomous Region(2019YCZX0068) and the Science and Technology Innovation Team Projects of Ningxia Hui Autonomous Region(03010360052). The funding bodies played no role in the design of the study, collection, analysis, and interpretation of data and writing the manuscript. Availability of data and materials All data generated or analyzed during this study are included in this published article and its supplementary information files. Ethics approval and consent to participate The Animal Ethics Committees of Ningxia University approved the experimental design and animal sample collection for the present study (permit number NXUC20200618).We obtained the verbal informed consent to participate from the owners and the Ethics Committees of Zerui ecological breeding farm, because our laboratory has a long-term cooperation agreement with the farm about the experiment animals used in experimental research. And animal experiments were conducted strictly followed the guidelines of the Regulations for the Administration of Affairs Concerning Experimental Animals (Ministry of Science and Technology, China, 2004). Consent for publication Not applicable. Competing interests The authors declare that we have no competing interests. References Fox KE, Fankell DM, Erickson PF, Majka SM, Crossno JJ, Klemm DJ. Depletion of cAMP-response element-binding protein/ATF1 inhibits adipogenic conversion of 3T3-L1 cells ectopically expressing CCAAT/enhancer-binding protein (C/EBP) alpha, C/EBP beta, or PPAR gamma. J BIOL CHEM. 2006;281(52):40341–53. Guo L, Li X, Tang QQ. Transcriptional regulation of adipocyte differentiation: a central role for CCAAT/enhancer-binding protein (C/EBP) beta. J BIOL CHEM. 2015;290(2):755–61. Cristancho AG, Lazar MA. Forming functional fat: a growing understanding of adipocyte differentiation. Nat Rev Mol Cell Biol. 2011;12(11):722–34. Chung SS, Lee JS, Kim M, Ahn BY, Jung HS, Lee HM, Kim JW, Park KS. Regulation of Wnt/beta-catenin signaling by CCAAT/enhancer binding protein beta during adipogenesis. Obesity (Silver Spring). 2012;20(3):482–7. Rahman N, Jeon M, Kim YS. Delphinidin, a major anthocyanin, inhibits 3T3-L1 pre-adipocyte differentiation through activation of Wnt/beta-catenin signaling. BIOFACTORS. 2016;42(1):49–59. Horton JD, Shah NA, Warrington JA, Anderson NN, Park SW, Brown MS, Goldstein JL. Combined analysis of oligonucleotide microarray data from transgenic and knockout mice identifies direct SREBP target genes. Proc Natl Acad Sci U S A. 2003;100(21):12027–32. Liu S, Huang J, Wang X, Ma Y. Transcription factors regulate adipocyte differentiation in beef cattle. ANIM GENET. 2020;51(3):351–7. Malumbres M. Cyclin-dependent kinases. GENOME BIOL. 2014;15(6):122. Hochegger H, Takeda S, Hunt T. Cyclin-dependent kinases and cell-cycle transitions: does one fit all? Nat Rev Mol Cell Biol. 2008;9(11):910–6. Malumbres M, Harlow E, Hunt T, Hunter T, Lahti JM, Manning G, Morgan DO, Tsai LH, Wolgemuth DJ. Cyclin-dependent kinases: a family portrait. NAT CELL BIOL. 2009;11(11):1275–6. Malumbres M, Barbacid M. Mammalian cyclin-dependent kinases. TRENDS BIOCHEM SCI. 2005;30(11):630–41. Ahonen MA, Haridas P, Mysore R, Wabitsch M, Fischer-Posovszky P, Olkkonen VM. miR-107 inhibits CDK6 expression, differentiation, and lipid storage in human adipocytes. MOL CELL ENDOCRINOL. 2019;479:110–6. Li X, Kim JW, Gronborg M, Urlaub H, Lane MD, Tang QQ. Role of cdk2 in the sequential phosphorylation/activation of C/EBPbeta during adipocyte differentiation. Proc Natl Acad Sci U S A. 2007;104(28):11597–602. Lagarrigue S, Lopez-Mejia IC, Denechaud PD, Escote X, Castillo-Armengol J, Jimenez V, Chavey C, Giralt A, Lai Q, Zhang L et al: CDK4 is an essential insulin effector in adipocytes . J CLIN INVEST 2016, 126 ( 1 ): 335–348 . Abella A, Dubus P, Malumbres M, Rane SG, Kiyokawa H, Sicard A, Vignon F, Langin D, Barbacid M, Fajas L. Cdk4 promotes adipogenesis through PPARgamma activation. CELL METAB. 2005;2(4):239–49. Wang H, Liu L, Lin JZ, Aprahamian TR, Farmer SR. Browning of White Adipose Tissue with Roscovitine Induces a Distinct Population of UCP1(+) Adipocytes. CELL METAB. 2016;24(6):835–47. Helenius K, Yang Y, Alasaari J, Makela TP. Mat1 inhibits peroxisome proliferator-activated receptor gamma-mediated adipocyte differentiation. MOL CELL BIOL. 2009;29(2):315–23. Zhao X, Feng D, Wang Q, Abdulla A, Xie XJ, Zhou J, Sun Y, Yang ES, Liu LP, Vaitheesvaran B et al: Regulation of lipogenesis by cyclin-dependent kinase 8-mediated control of SREBP-1 . J CLIN INVEST 2012, 122 ( 7 ): 2417–2427 . Vallbracht M, Fuchs W, Klupp BG, Mettenleiter TC. Functional Relevance of the Transmembrane Domain and Cytoplasmic Tail of the Pseudorabies Virus Glycoprotein H for Membrane Fusion . J VIROL 2018, 92( 12 ). Ota M, Kinoshita K, Nishikawa K. Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation. J MOL BIOL. 2003;327(5):1053–64. van Montfort RL, Pijning T, Kalk KH, Hangyi I, Kouwijzer ML, Robillard GT, Dijkstra BW: The structure of the Escherichia coli phosphotransferase IIAmannitol reveals a novel fold with two conformations of the active site. STRUCTURE 1998, 6(3):377–88. Song L, Wu S, Tsang A. Phylogenetic Analysis of Protein Family. Methods Mol Biol. 2018;1775:267–75. Xie T, Chen C, Li C, Liu J, Liu C, He Y. Genome-wide investigation of WRKY gene family in pineapple: evolution and expression profiles during development and stress. BMC GENOMICS. 2018;19(1):490. Gerdol M, Greco S, Pallavicini A. Extensive Tandem Duplication Events Drive the Expansion of the C1q-Domain-Containing Gene Family in Bivalves . MAR DRUGS 2019, 17( 10 ). Krsticevic FJ, Arce DP, Ezpeleta J, Tapia E: Tandem Duplication Events in the Expansion of the Small Heat Shock Protein Gene Family in Solanum lycopersicum ( cv . Heinz 1706 ). G3 (Bethesda) 2016, 6 ( 10 ): 3027 – 3034 . Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, Hanrahan F, Pertea G, Van Tassell CP, Sonstegard TS et al: A whole-genome assembly of the domestic cow, Bos taurus . GENOME BIOL 2009, 10 ( 4 ): R42 . Hu Q, Ma T, Wang K, Xu T, Liu J, Qiu Q. The Yak genome database: an integrative database for studying yak biology and high-altitude adaption. BMC GENOMICS. 2012;13:600. Liu J, Wang Z, Li J, Li H, Yang L. Genome-wide identification of Diacylglycerol Acyltransferases (DGAT) family genes influencing Milk production in Buffalo. BMC GENET. 2020;21(1):26. Weckselblatt B, Rudd MK. Human Structural Variation: Mechanisms of Chromosome Rearrangements. TRENDS GENET. 2015;31(10):587–99. Parua PK, Kalan S, Benjamin B, Sanso M, Fisher RP. Distinct Cdk9-phosphatase switches act at the beginning and end of elongation by RNA polymerase II. NAT COMMUN. 2020;11(1):4338. Iankova I, Petersen RK, Annicotte JS, Chavey C, Hansen JB, Kratchmarova I, Sarruf D, Benkirane M, Kristiansen K, Fajas L. Peroxisome proliferator-activated receptor gamma recruits the positive transcription elongation factor b complex to activate transcription and promote adipogenesis. MOL ENDOCRINOL. 2006;20(7):1494–505. Mu RF, Niu YF, Wang Q, Zhou HM, Hu J, Qin WY, Xiong WY. Eriocalyxin B Inhibits Adipogenesis in 3T3-L1 Adipocytes by Cell Cycle Arrest. Nat Prod Bioprospect. 2020;10(3):131–40. Marquez MP, Alencastro F, Madrigal A, Jimenez JL, Blanco G, Gureghian A, Keagy L, Lee C, Liu R, Tan L et al: The Role of Cellular Proliferation in Adipogenic Differentiation of Human Adipose Tissue-Derived Mesenchymal Stem Cells . STEM CELLS DEV 2017, 26 ( 21 ): 1578–1595 . Stetkova M, Growkova K, Fojtik P, Valcikova B, Palusova V, Verlande A, Jorda R, Krystof V, Hejret V, Alexiou P et al: CDK9 activity is critical for maintaining MDM4 overexpression in tumor cells . CELL DEATH DIS 2020, 11 ( 9 ): 754 . Mbonye U, Wang B, Gokulrangan G, Shi W, Yang S, Karn J. Cyclin-dependent kinase 7 (CDK7)-mediated phosphorylation of the CDK9 activation loop promotes P-TEFb assembly with Tat and proviral HIV reactivation. J BIOL CHEM. 2018;293(26):10009–25. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. GENOME RES. 2003;13(11):2498–504. Hallenborg P, Siersbaek M, Barrio-Hernandez I, Nielsen R, Kristiansen K, Mandrup S, Grontved L, Blagoev B. MDM2 facilitates adipocyte differentiation through CRTC-mediated activation of STAT3. CELL DEATH DIS. 2016;7(6):e2289. Li Y, He L, Li J, Chen J, Liu C. Genome-Wide Identification, Characterization, and Expression Profiling of the Legume BZR Transcription Factor Gene Family. FRONT PLANT SCI. 2018;9:1332. El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, Qureshi M, Richardson LJ, Salazar GA, Smart A et al: The Pfam protein families database in 2019 . NUCLEIC ACIDS RES 2019, 47 ( D1 ): D427-D432 . Potter SC, Luciani A, Eddy SR, Park Y, Lopez R, Finn RD. HMMER web server: 2018 update. NUCLEIC ACIDS RES. 2018;46(W1):W200–4. Lu S, Wang J, Chitsaz F, Derbyshire MK, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Marchler GH, Song JS et al: CDD/SPARCLE: the conserved domain database in 2020 . NUCLEIC ACIDS RES 2020, 48 ( D1 ): D265-D268 . Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, de Castro E, Duvaud S, Flegel V, Fortier A, Gasteiger E et al: ExPASy: SIB bioinformatics resource portal . NUCLEIC ACIDS RES 2012, 40(Web Server issue) : W597-W603 . Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. MOL BIOL EVOL. 2016;33(7):1870–4. Bailey TL, Johnson J, Grant CE, Noble WS. The MEME Suite. NUCLEIC ACIDS RES. 2015;43(W1):W39–49. Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, He Y, Xia R. TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data. MOL PLANT. 2020;13(8):1194–202. Wang Y, Tang H, Debarry JD, Tan X, Li J, Wang X, Lee TH, Jin H, Marler B, Guo H et al: MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity . NUCLEIC ACIDS RES 2012, 40 ( 7 ): e49 . Cai H, Li M, Sun X, Plath M, Li C, Lan X, Lei C, Huang Y, Bai Y, Qi X et al: Global Transcriptome Analysis During Adipogenic Differentiation and Involvement of Transthyretin Gene in Adipogenesis in Cattle . FRONT GENET 2018, 9 : 463 . Wingett SW, Andrews S: FastQ Screen : A tool for multi - genome mapping and quality control . F1000Res 2018, 7 : 1338 . Chen L, Qiu Q, Jiang Y, Wang K, Lin Z, Li Z, Bibi F, Yang Y, Wang J, Nie W et al: Large - scale ruminant genome sequencing provides insights into their evolution and distinct traits . SCIENCE 2019, 364 ( 6446 ). Huang J, Zheng Q, Wang S, Wei X, Li F, Ma Y. High-Throughput RNA Sequencing Reveals NDUFC2-AS lncRNA Promotes Adipogenic Differentiation in Chinese Buffalo (Bubalus bubalis L) . Genes (Basel) 2019, 10( 9 ). Wang Y, Goulart RA, Pantanowitz L. Oil red O staining in cytopathology. DIAGN CYTOPATHOL. 2011;39(4):272–3. Supplementary Files Additionalfile1.xls.xlsx Additional file 1. Genome-wide identified CDK family members in bovidae. Additionalfile2.txt.fa Additional file 2. Protein sequences of CDK family members in ten species. Additionalfile3.pdf.pdf Additional file 3. Conserved domain prediction of bovine CDK protein sequences. Additionalfile4.pdf.pdf Additional file 4. Amino acid sequences logos of 10 identified motifs in bovine CDK proteins. Additionalfile5.pdf.pdf Additional file 5. Oil red O staining of preadipocytes and differentiated adipocytes. Additionalfile6.pdf.pdf Additional file 6. Conserved domain and motifs of hybrid-bos taurus CDK proteins. Additionalfile7.pdf.pdf Additional file 7. The interaction network for CDK genes constructed by Cytoscape. Additionalfile8.xls.xls Additional file 8. Expression values (RPKM) of 163 bovine samples in 60 tissue types. Additionalfile9.xls.xls Additional file 9. Primer sequences of 25 bovine CDK family genes. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-133585","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research article","associatedPublications":[],"authors":[{"id":6888774,"identity":"c7d09be7-b300-4451-ab16-16fa8de3e35a","order_by":0,"name":"Cuili Pan","email":"","orcid":"https://orcid.org/0000-0001-5443-8401","institution":"Ningxia university","correspondingAuthor":false,"prefix":"","firstName":"Cuili","middleName":"","lastName":"Pan","suffix":""},{"id":6888775,"identity":"905bede9-480d-4ad9-aa67-720e78fd4d0e","order_by":1,"name":"Zhaoxiong Lei","email":"","orcid":"","institution":"Ningxia University","correspondingAuthor":false,"prefix":"","firstName":"Zhaoxiong","middleName":"","lastName":"Lei","suffix":""},{"id":6888776,"identity":"df7b99bc-1457-4217-80c5-dc5fac9bd403","order_by":2,"name":"Shuzhe Wang","email":"","orcid":"","institution":"Ningxia University","correspondingAuthor":false,"prefix":"","firstName":"Shuzhe","middleName":"","lastName":"Wang","suffix":""},{"id":6888777,"identity":"fcce06af-5cd6-47e2-845e-21135378a543","order_by":3,"name":"Xingping Wang","email":"","orcid":"","institution":"Ningxia University","correspondingAuthor":false,"prefix":"","firstName":"Xingping","middleName":"","lastName":"Wang","suffix":""},{"id":6888778,"identity":"71d22e71-a69a-4324-b736-27e50def2f94","order_by":4,"name":"Dawei Wei","email":"","orcid":"","institution":"Ningxia University","correspondingAuthor":false,"prefix":"","firstName":"Dawei","middleName":"","lastName":"Wei","suffix":""},{"id":6888779,"identity":"3f61bd50-f8f2-4f9f-a645-abd411f6f078","order_by":5,"name":"Xiaoyan Cai","email":"","orcid":"","institution":"Ningxia University","correspondingAuthor":false,"prefix":"","firstName":"Xiaoyan","middleName":"","lastName":"Cai","suffix":""},{"id":6888780,"identity":"057426b6-33e8-4b41-92e0-8fb56dcf38bc","order_by":6,"name":"Zhuoma Luoreng","email":"","orcid":"","institution":"Ningxia University","correspondingAuthor":false,"prefix":"","firstName":"Zhuoma","middleName":"","lastName":"Luoreng","suffix":""},{"id":6888781,"identity":"f9de8fcc-c104-4834-b45c-60515cd24600","order_by":7,"name":"Lei Wang","email":"","orcid":"","institution":"Xinyang Teachers\\' College: Xinyang Normal University","correspondingAuthor":false,"prefix":"","firstName":"Lei","middleName":"","lastName":"Wang","suffix":""},{"id":6888782,"identity":"61331a48-fe26-4cfd-85ea-6e2ecb2d0b14","order_by":8,"name":"Yun Ma","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAxUlEQVRIiWNgGAWjYPACGzl+9sbGBx9I0JJmLNlzuNlwBglaDiUazEhvk+YgRq1u+xkz6QKGAwkGkg8bpBkY7OR0GwhoMTuTYyY9g+FOnrl0YoNxAUOysdkBQloOALXwMDwrtpyd2JA8g+FA4jaCWs6/AWk5nLjh5sGGwzxEabmRA9Vyg7GxmUgtz4qtecCBnNjMOMOAGL+cT954mwcclcef//hQYSdHUAsDA4cBA+M/GMeAoHIQYH9AlLJRMApGwSgYwQAA0WZDLGERdtUAAAAASUVORK5CYII=","orcid":"","institution":"Ningxia University","correspondingAuthor":true,"prefix":"","firstName":"Yun","middleName":"","lastName":"Ma","suffix":""}],"badges":[],"createdAt":"2020-12-21 21:13:07","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-133585/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-133585/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1186/s12864-021-07653-8","type":"published","date":"2021-07-12T15:02:35+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":4553398,"identity":"f7425cc8-0eec-4517-be34-6d33605a526a","added_by":"auto","created_at":"2020-12-28 19:19:29","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":190989,"visible":true,"origin":"","legend":"Characterizations of the identified CDK proteins and genes in Bos taurus. \nThe phylogenetic tree (left) was constructed by Neighbor Joining method. Structure of amino acid sequences (middle), rectangles with different colors represent ten conserved motifs. Gene structure map (right), green rectangle, black line and red rectangle represent CDS, intron and UTR, respectively. \n","description":"","filename":"Figure1.png","url":"https://assets-eu.researchsquare.com/files/rs-133585/v1/a730d75b50de8a4daf2922f1.png"},{"id":4553491,"identity":"311c4525-acc4-49d5-89f7-7711555eb49d","added_by":"auto","created_at":"2020-12-28 19:22:29","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":1505064,"visible":true,"origin":"","legend":"Phylogenetic Neighbor-Joining (NJ) tree of CDK proteins from ten organisms. \nIdentified CDKs in Bos taurus (BOSTA), Bos grunniens (BOSGR), Hybrid-Bos Indicus (BOSIH), Hybrid-Bos taurus (BOSTH), Bos mutus (BOSMU), Bison bison bison (BISOM), Bos indicus (BOSIN) and Bubalus bubalis (BUBBU) together with verified CDKs from Homo sapiens (HUMAN) and Mus musculus (MOUSE) were included in the analyses.The CDK proteins are grouped into eight clusters (Ⅰ-Ⅷ), which are represented by different colors. \n","description":"","filename":"Figure2.png","url":"https://assets-eu.researchsquare.com/files/rs-133585/v1/8063bbe4ef6abf73730e7603.png"},{"id":4553498,"identity":"e25b2048-5afe-4a56-a234-6814d4941d92","added_by":"auto","created_at":"2020-12-28 19:22:29","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":414572,"visible":true,"origin":"","legend":"Chromosomal distribution of CDK genes. The black font on the left represents chromosome numbers and the red font on the right represents CDK family genes.","description":"","filename":"Figure3.png","url":"https://assets-eu.researchsquare.com/files/rs-133585/v1/79ead37458633591831eb67f.png"},{"id":4553401,"identity":"741773ee-fda6-4dba-acbb-ed26840a50e9","added_by":"auto","created_at":"2020-12-28 19:19:29","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":925073,"visible":true,"origin":"","legend":"Collinearity analysis of CDK genes between cattle and other organisms. Each pair of linked genes by grey lines are syntenic genes and the red lines represent syntenic CDKs.","description":"","filename":"Figure4.png","url":"https://assets-eu.researchsquare.com/files/rs-133585/v1/d46e49adae0e9c09f57a1ddc.png"},{"id":4553647,"identity":"0dd72c93-114a-4c0b-9e3d-4d8db94f5dc9","added_by":"auto","created_at":"2020-12-28 19:25:29","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":384286,"visible":true,"origin":"","legend":"Expression analysis of CDK family genes in different bovine tissue types. \na. Expression analysis of CDK family genes in 60 bovine tissues. The tissues were classifed into 5 groups (A to E) and the 27 genes were classifed into 4 groups (Ⅰ-Ⅳ) according to their expression pattern. b. Expression analysis of CDK family genes in 5 bovine fat tissues. The horizontal axis represents 25 CDKs and 2 marker genes (PPARG and CEBPA) of adipocyte differentiation. The vertical axis represents different bovine tissues. \n","description":"","filename":"Figure5.png","url":"https://assets-eu.researchsquare.com/files/rs-133585/v1/08b502623efe617a034cbea9.png"},{"id":4553399,"identity":"1d15a6fa-e13f-44f8-b0cf-2d434ea5cda6","added_by":"auto","created_at":"2020-12-28 19:19:29","extension":"png","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":20973,"visible":true,"origin":"","legend":"Expression analysis of CDKs in preadipocytes and differentiated adipocytes by RNA-seq. \nError bars were obtained from two measurements. ‘*’ and ‘**’ above the bars indicate significant differences at 0.05 and 0.01 level between preadipocytes and differented adipocytes.\n","description":"","filename":"Figure6.png","url":"https://assets-eu.researchsquare.com/files/rs-133585/v1/5e0e97df672995518be0d54c.png"},{"id":4553407,"identity":"d44d65b9-e81f-4f87-8d60-7c444a28dcf2","added_by":"auto","created_at":"2020-12-28 19:19:30","extension":"png","order_by":7,"title":"Figure 7","display":"","copyAsset":false,"role":"figure","size":124067,"visible":true,"origin":"","legend":"Expression analysis of CDKs during adipocyte differention by qPCR. \nError bars were obtained from three measurements. ‘*’ and ‘**’ above the bars indicate significant differences at 0.05 and 0.01 level compared with preadipocytes (0 day). The line with ‘*’ and ‘**’ represents the significant differences between two labeled pillars.\n","description":"","filename":"Figure7.png","url":"https://assets-eu.researchsquare.com/files/rs-133585/v1/42aa069d29c60ed3144bfcd2.png"},{"id":13640462,"identity":"4da9c594-bc21-44fc-9ab1-631892c2577b","added_by":"auto","created_at":"2021-09-17 08:59:52","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":3855219,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-133585/v1/08daa0f9-5091-4e85-a79a-faf03c8cb055.pdf"},{"id":4553394,"identity":"ea9755b7-acfa-4f96-882a-9cddb5fb61cd","added_by":"auto","created_at":"2020-12-28 19:19:29","extension":"xlsx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":16438,"visible":true,"origin":"","legend":"Additional file 1. Genome-wide identified CDK family members in bovidae.","description":"","filename":"Additionalfile1.xls.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-133585/v1/79a0460de781381fe6bd1ae4.xlsx"},{"id":4553649,"identity":"ba1fbf53-b0c1-4517-a61a-a16cfd047a10","added_by":"auto","created_at":"2020-12-28 19:25:29","extension":"fa","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":131351,"visible":true,"origin":"","legend":"Additional file 2. Protein sequences of CDK family members in ten species.","description":"","filename":"Additionalfile2.txt.fa","url":"https://assets-eu.researchsquare.com/files/rs-133585/v1/625d3edc6cf38951bf39317d.fa"},{"id":4553496,"identity":"37432b14-3b73-4c10-a430-4c5bc9cd3551","added_by":"auto","created_at":"2020-12-28 19:22:29","extension":"pdf","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":4626,"visible":true,"origin":"","legend":"Additional file 3. Conserved domain prediction of bovine CDK protein sequences.","description":"","filename":"Additionalfile3.pdf.pdf","url":"https://assets-eu.researchsquare.com/files/rs-133585/v1/97380dbea3472e371f63277f.pdf"},{"id":4553492,"identity":"ba380701-0e18-464f-8036-772a67765f23","added_by":"auto","created_at":"2020-12-28 19:22:29","extension":"pdf","order_by":4,"title":"","display":"","copyAsset":false,"role":"supplement","size":617027,"visible":true,"origin":"","legend":"Additional file 4. Amino acid sequences logos of 10 identified motifs in bovine CDK proteins.","description":"","filename":"Additionalfile4.pdf.pdf","url":"https://assets-eu.researchsquare.com/files/rs-133585/v1/c89b63995b0223ee1c2adc06.pdf"},{"id":4553820,"identity":"d4e10e99-a10a-4800-98ff-6c17ba21e14c","added_by":"auto","created_at":"2020-12-28 19:28:30","extension":"pdf","order_by":5,"title":"","display":"","copyAsset":false,"role":"supplement","size":1115345,"visible":true,"origin":"","legend":"Additional file 5. Oil red O staining of preadipocytes and differentiated adipocytes.","description":"","filename":"Additionalfile5.pdf.pdf","url":"https://assets-eu.researchsquare.com/files/rs-133585/v1/dc6380f484bff8b949ccde8b.pdf"},{"id":4553409,"identity":"89c9acd8-2a56-4a2c-a05a-f0a48d7cb716","added_by":"auto","created_at":"2020-12-28 19:19:30","extension":"pdf","order_by":6,"title":"","display":"","copyAsset":false,"role":"supplement","size":548692,"visible":true,"origin":"","legend":"Additional file 6. Conserved domain and motifs of hybrid-bos taurus CDK proteins.","description":"","filename":"Additionalfile6.pdf.pdf","url":"https://assets-eu.researchsquare.com/files/rs-133585/v1/a9f9ae6eca574c8d8693c7b8.pdf"},{"id":4553648,"identity":"71a20efb-3e56-4c80-ba71-899eebd5586d","added_by":"auto","created_at":"2020-12-28 19:25:29","extension":"pdf","order_by":7,"title":"","display":"","copyAsset":false,"role":"supplement","size":15891,"visible":true,"origin":"","legend":"Additional file 7. The interaction network for CDK genes constructed by Cytoscape.","description":"","filename":"Additionalfile7.pdf.pdf","url":"https://assets-eu.researchsquare.com/files/rs-133585/v1/e50166a0258fc092752a0646.pdf"},{"id":4553501,"identity":"3bf80394-2a9b-441a-b2a6-10448cbac193","added_by":"auto","created_at":"2020-12-28 19:22:30","extension":"xls","order_by":8,"title":"","display":"","copyAsset":false,"role":"supplement","size":71680,"visible":true,"origin":"","legend":"Additional file 8. Expression values (RPKM) of 163 bovine samples in 60 tissue types.","description":"","filename":"Additionalfile8.xls.xls","url":"https://assets-eu.researchsquare.com/files/rs-133585/v1/bde13e68c86001545fae27e3.xls"},{"id":4553493,"identity":"341d4bb1-c25a-473f-8756-ceecedd81042","added_by":"auto","created_at":"2020-12-28 19:22:29","extension":"xls","order_by":9,"title":"","display":"","copyAsset":false,"role":"supplement","size":26624,"visible":true,"origin":"","legend":"Additional file 9. Primer sequences of 25 bovine CDK family genes.","description":"","filename":"Additionalfile9.xls.xls","url":"https://assets-eu.researchsquare.com/files/rs-133585/v1/c00a9559e74b3ec5f62c2174.xls"},{"id":4553500,"identity":"0a3adac1-3aae-4238-9104-7be805705342","added_by":"auto","created_at":"2020-12-28 19:22:30","extension":"pdf","order_by":10,"title":"","display":"","copyAsset":false,"role":"supplement","size":165211,"visible":true,"origin":"","legend":"","description":"","filename":"AuthorChecklistFull.pdf","url":"https://assets-eu.researchsquare.com/files/rs-133585/v1/16ea781b00f3522c48f89f8b.pdf"}],"financialInterests":"","formattedTitle":"\u003cp\u003eGenome-Wide\u0026nbsp;Identification of Cyclin Dependent Kinase (CDK) Family Genes Influencing Adipocyte Differentiation in\u0026nbsp;Cattle\u003c/p\u003e","fulltext":[{"header":"Background","content":" \u003cp\u003e \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eWith the improvement of people's living standard, high-quality beef would become the mainstream of consumption in the future.The intramuscular fat (IMF) content of beef is a crucial factor that affects the flavor, freshness, juiciness, tenderness and color, which plays an important role in the improvement of taste and nutritional value.\u003c/span\u003e So \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eit is of great scientific significance to further reveal the molecular mechanism of IMF deposition in cattle. Adipogenic differentiation is a complex process regulated by many genes, among which\u003c/span\u003e \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eC/EBPα\u003c/span\u003e \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eand\u003c/span\u003e \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003ePPARγ\u003c/span\u003e \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eare the key transcription factors in the regulatory network that could regulate the expression of a series of adipogenic phenotypic genes (\u003c/span\u003e\u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eFABP1\u003c/span\u003e, \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eFABP4\u003c/span\u003e, \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eLPL\u003c/span\u003e, \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eaP2\u003c/span\u003e, \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eCAP\u003c/span\u003e, \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003ePerilipin\u003c/span\u003e, \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eetc.) through transcriptional activation\u003c/span\u003e[\u003cspan additionalcitationids=\"CR2\" citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e].\u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eA number of genes regulate adipocyte differentiation and lipid droplet formation by regulating\u003c/span\u003e \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eC/EBPα\u003c/span\u003e \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eand\u003c/span\u003e \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003ePPARγ\u003c/span\u003e \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003edirectly or indirectly. For example, another important member of C/EBP gene family\u003c/span\u003e, \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eC/EBPβ\u003c/span\u003e, \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003ecould transactivate the expression of\u003c/span\u003e \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eC/EBPα\u003c/span\u003e \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eand\u003c/span\u003e \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003ePPARγ\u003c/span\u003e \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eto promote adipocyte terminal differentiation\u003c/span\u003e[\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e]. \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eIn addition\u003c/span\u003e, \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eC/EBPβ\u003c/span\u003e \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eis involved in the regulation of\u003c/span\u003e \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eC/EBPα\u003c/span\u003e \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eand\u003c/span\u003e \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003ePPARγ\u003c/span\u003e \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003ethrough activating\u003c/span\u003e \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eKlf5\u003c/span\u003e, \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eSREBP1c\u003c/span\u003e, \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eEbf1\u003c/span\u003e, \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eXbp1\u003c/span\u003e \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eand\u003c/span\u003e \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eAtg4b\u003c/span\u003e, \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003erespectively\u003c/span\u003e[\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e]. \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eC/EBPβ\u003c/span\u003e \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003ecan also activate some other transcriptional factors and inhibit the expression of\u003c/span\u003e \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eWnt10b\u003c/span\u003e \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003ewhich is an anti-adipogenic factor that can suppress\u003c/span\u003e \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003ePPARγ\u003c/span\u003e \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003ethrough β-catenin signaling pathway\u003c/span\u003e[\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e, \u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e]. \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eSREBP-1a\u003c/span\u003e, \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eSREBP-1c\u003c/span\u003e \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eand\u003c/span\u003e \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eSREBP-2\u003c/span\u003e \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eare three members of SREBP gene family regulating de novo synthesis of fatty acids, the differentiation of adipocytes and synthesis of cholesterol, respectively, by targeting fatty acid metabolism-related genes including\u003c/span\u003e \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eACC\u003c/span\u003e, \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eSCD\u003c/span\u003e, \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eFASD\u003c/span\u003e, \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eGPAT\u003c/span\u003e,\u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eetc.\u003c/span\u003e[\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e]. \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eBesides, there are a variety of gene families that function in adipogenic differentiation such as\u003c/span\u003e \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eKLFs\u003c/span\u003e, \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eSMADs\u003c/span\u003e, \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eRARs\u003c/span\u003e, \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eDGATs\u003c/span\u003e \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eand so on\u003c/span\u003e[\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e].\u003c/p\u003e \u003cp\u003e \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eCDKs are a large family of serine/threonine protein kinases that were first discovered in the regulation of cell cycle, and they had diverse functions in various of biological processes in eukaryotes including mRNA processing, regulation of transcription\u003c/span\u003e[\u003cspan additionalcitationids=\"CR9 CR10\" citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e]. \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eRecently, they have been shown to regulate adipocyte differentiation and lipid droplet formation by phosphorylating a series of associated transcription factors or\u003c/span\u003e adipocyte-specific genes. \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eCDK6\u003c/span\u003e, \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003ea member of CDK family genes, was targeted by miR107 to inhibit\u003c/span\u003e \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eNotch\u003c/span\u003e \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eand its downstream gene\u003c/span\u003e \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eHes1\u003c/span\u003e, \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003ethereby inhibiting glucose uptake and triglyceride synthesis in adipocytes\u003c/span\u003e[\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e]. \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eMAPK and CDK2/cyclinA sequentially activated C/EBPβ by maintaining the phosphorylated state of Thr188 during the progression of mitotic clonal expansion (MCE) and adipocytes terminal differentiation\u003c/span\u003e[\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e]. \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eInsulin activated the CCND3-CDK4 complex which in turn phosphorylated Ser388 of the insulin receptor IRS2 to maintain the active status of the insulin signaling pathway in adipocyte, eventually promoting de novo lipid synthesis\u003c/span\u003e[\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e]. \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eIn addition, CDK4 could phosphorylate Rb to release E2F leading to preadipocyte proliferation as well as phosphorylate PPARγ to regulate the terminal differentiation of adipocytes\u003c/span\u003e[\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]. \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eCDK5 could reduce the insulin sensitivity of adipocytes by phosphorylating Ser273 of PPARγ, and inhibition the phosphorylation of Ser273 would promote browning and thermogenesis of white adipose tissue\u003c/span\u003e[\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]. \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eCDK7 complex could inactivate PPARγ through the phosphorylation of PPARγ-S112 to inhibit adipogenesis\u003c/span\u003e[\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e]. \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eCDK8 promotes the ubiquitination and degradation of SREBP-1c by phosphorylating its serine residues, thus inhibiting the adipogenesis\u003c/span\u003e[\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e]. \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eThese findings inspired our curiosity to explore the effects of CDK family genes on bovine adipocytes differentiation. However, the expression patterns and regulatory mechanisms of\u003c/span\u003e \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eCDKs\u003c/span\u003e \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003ein bovine adipocytes have not been systematically studied and elucidated.\u003c/span\u003e\u003c/p\u003e \u003cp\u003e \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eTherefore, the present study aimed to detect CDK family genes in the bovine genome, and then perform a detailed analysis of the classification, physicochemical properties, phylogenetic analysis, structural features, and functional analysis. Furthermore, the expression pattern analysis by transcriptom and qPCR verification was performed in order to identify essential members of CDK family that affect adipogenic differentiation. Our study provided a deep insight into\u003c/span\u003e \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eCDKs\u003c/span\u003e \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003ethat influence adipogenic differentiation, which is essential for future study in improving IMF in the process of bovine breeding.\u003c/span\u003e\u003c/p\u003e "},{"header":"Results","content":" \u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003eIdentification of the members in the CDK family\u003c/h2\u003e \u003cp\u003eTo identify the CDK family members, 59 verified CDK amino acid sequences from cattle (\u003cem\u003eBos taurus\u003c/em\u003e, 8), human (\u003cem\u003eHomo sapiens\u003c/em\u003e, 26) and mouse (Mus \u003cem\u003emusculus\u003c/em\u003e, 25) were used as the query for genome-wide detection of the homologous sequences in \u003cem\u003eBos taurus\u003c/em\u003e, \u003cem\u003eBos indicus\u003c/em\u003e, \u003cem\u003eBos grunniens\u003c/em\u003e, \u003cem\u003eHybrid-Bos Indicus\u003c/em\u003e, \u003cem\u003eHybrid-Bos taurus\u003c/em\u003e, \u003cem\u003eBos mutus\u003c/em\u003e, \u003cem\u003eBison bison bison\u003c/em\u003e, and \u003cem\u003eBubalus bubalis\u003c/em\u003e. As a result, 25 non-redundant CDK protein sequences including CDK1-10,CDK11B, CDK12-20, CDKL1-5 were identified in \u003cem\u003eBos taurus\u003c/em\u003e (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). In parallel, 22, 21, 22, 24, 22, 25 and 24 CDK family proteins were recognized in \u003cem\u003eBos grunniens, Hybrid-Bos Indicus, Hybrid-Bos taurus, Bos mutus, Bison bison bison, Bos indicus\u003c/em\u003e and \u003cem\u003eBubalus bubalis\u003c/em\u003e, respectively (Additional file 1) and the protein sequences of all the CDKs were provided in Additional file 2. Transcript ENSBIXT00000049337 is a newly identified member of CDK family in \u003cem\u003eHybrid-Bos taurus\u003c/em\u003e, which is named \u003cem\u003eCDK20\u003c/em\u003e according to the sequence similarity and collinearity.\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eDetails of Genome-wide identified CDK family members in \u003cem\u003eBos taurus\u003c/em\u003e\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"7\"\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eProtein Name\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003egene ID\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003etranscript ID\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003epI\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003eMw/Da\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003eAmino acids\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c7\"\u003e \u003cp\u003edescription\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCDK1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eENSBTAG00000010109\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eENSBTAT00000013337\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e8.38\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e34025.40\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e297\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003ecyclin dependent kinase 1\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCDK2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eENSBTAG00000004021\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eENSBTAT00000005252\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e8.79\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e33873.46\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e298\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003ecyclin dependent kinase 2\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCDK3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eENSBTAG00000010509\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eENSBTAT00000013885\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e8.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e34805.48\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e305\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003ecyclin dependent kinase 3\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCDK4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eENSBTAG00000007160\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eENSBTAT00000009420\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e6.51\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e33646.73\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e303\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003ecyclin dependent kinase 4\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCDK5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eENSBTAG00000007766\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eENSBTAT00000010212\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e7.57\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e33288.47\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e292\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003ecyclin dependent kinase 5\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCDK6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eENSBTAG00000044023\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eENSBTAT00000061349\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e6.22\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e37014.40\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e326\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003ecyclin dependent kinase 6\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCDK7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eENSBTAG00000011046\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eENSBTAT00000014667\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e8.67\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e38946.26\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e346\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003ecyclin dependent kinase 7\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCDK8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eENSBTAG00000016737\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eENSBTAT00000022252\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e8.72\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e53282.71\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e464\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003ecyclin dependent kinase 8\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCDK9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eENSBTAG00000004695\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eENSBTAT00000006162\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e9.04\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e42747.58\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e372\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003ecyclin dependent kinase 9\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCDK10\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eENSBTAG00000033333\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eENSBTAT00000047400\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e9.16\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e41046.93\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e361\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003ecyclin dependent kinase 10\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCDK11B\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eENSBTAG00000010737\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eENSBTAT00000014227\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e5.34\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e89901.85\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e771\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003ecyclin dependent kinase 11B\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCDK12\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eENSBTAG00000013238\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eENSBTAT00000002005\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e9.54\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e140641.60\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e1264\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003ecyclin dependent kinase 12\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCDK13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eENSBTAG00000001528\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eENSBTAT00000002003\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e9.71\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e164717.14\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e1512\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003ecyclin dependent kinase 13\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCDK14\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eENSBTAG00000048664\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eENSBTAT00000068321\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e9.06\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e53169.98\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e470\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003ecyclin dependent kinase 14\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCDK15\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eENSBTAG00000055073\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eENSBTAT00000086547\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e6.68\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e45011.42\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e405\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003ecyclin dependent kinase 15\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCDK16\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eENSBTAG00000016769\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eENSBTAT00000022303\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e7.23\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e55758.68\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e496\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003ecyclin dependent kinase 16\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCDK17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eENSBTAG00000001510\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eENSBTAT00000077282\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e9.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e59563.16\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e523\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003ecyclin dependent kinase 17\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCDK18\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eENSBTAG00000012673\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eENSBTAT00000085187\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e9.26\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e54126.19\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e471\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003ecyclin dependent kinase 18\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCDK19\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eENSBTAG00000007288\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eENSBTAT00000009583\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e8.66\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e56685.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e500\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003ecyclin dependent kinase 19\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCDK20\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eENSBTAG00000015171\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eENSBTAT00000020188\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e6.06\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e38546.53\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e346\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003ecyclin dependent kinase 20\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCDKL1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eENSBTAG00000004780\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eENSBTAT00000036046\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e9.08\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e40735.16\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e352\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003ecyclin dependent kinase like 1\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCDKL2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eENSBTAG00000014038\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eENSBTAT00000031574\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e8.76\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e64289.09\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e569\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003ecyclin dependent kinase like 2\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCDKL3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eENSBTAG00000010979\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eENSBTAT00000014574\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e9.37\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e67477.82\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e591\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003ecyclin dependent kinase like 3\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCDKL4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eENSBTAG00000024044\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eENSBTAT00000033135\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e8.88\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e39465.72\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e342\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003ecyclin dependent kinase like 4\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCDKL5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eENSBTAG00000007428\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eENSBTAT00000076996\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e9.56\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e107236.16\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e960\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003ecyclin dependent kinase like 5\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003ctfoot\u003e \u003ctr\u003e\u003ctd colspan=\"7\"\u003e\u003cb\u003eMw\u003c/b\u003e: molecular weight, \u003cb\u003epI\u003c/b\u003e: isoelectric point\u003c/td\u003e\u003c/tr\u003e \u003c/tfoot\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003eThe length of amino acid sequences of 25 cattle CDK proteins ranged from 292 (CDK5) to 1512 (CDK13), and their molecular weight (Mw) was 33288.47-164717.14\u0026nbsp;Da, which correlated well with the protein length. The isoelectric points (pI) of most CDK family proteins was higher than 8.0, which containing more basic amino acids than acidic amino acids, except for 2 neutral proteins(CDK5 and CDK16), whose pI are 7.57 and 7.23, \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003erespectively\u003c/span\u003e, and 5 acidic proteins (CDK4, CDK6, CDK11B, CDK15 and CDK20), whose pI is between 5.34 and 6.68. Moreover, we detected all the 25 CDK proteins contained the Serine/Threonine Kinase conserved domain (Additional file 3).\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec4\" class=\"Section2\"\u003e \u003ch2\u003eStructural features of bovine CDK family members\u003c/h2\u003e \u003cp\u003eTo explore the structural characteristics of bovine CDK proteins and genes, the conserved motifs and gene structures were projected based on their phylogenetic relationships (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). Results showed the CDKs of cattle initially categorized into three main subfamily according to the evolutionary clades. Among 25 bovine CDK family genes, the first subfamily contains 6 members including CDKL1, CDKL2, CDKL3, CDKL4, CDKL5 and CDK20. The second subfamily possesses CDK10 and CDK11B, and the other members belongs to the third subfamily. Six conserved domains(Motif 1, 3, 5, 6, 7, and 9), containing 29, 21, 21, 21, 21, and 21 amino acids respectively, were shared among all the CDK family proteins (Additional file 4). As a small branch in the third subfamily, CDK16, CDK17 and CDK18, have all of the ten motifs. CDK4, CDK15 and CDK20 all consists of eight motifs, while CDK4 lacks of Motif 4 and Motif 10, CDK15 is short for Motif 2 and Motif 10, and CDK20 is without Motif 4 and Motif 10. The rest CDK proteins comprise nine motifs lacking of CDK10, which indicates they all have the same conserved patterns.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eThe items of introns, coding sequences (CDS) and untranslated region (UTR) were various among CDK family genes, for instance, the gene length \u003cem\u003eCDKs\u003c/em\u003e ranged from 3599nt (\u003cem\u003eCDK4\u003c/em\u003e) to 678562nt (\u003cem\u003eCDK14\u003c/em\u003e), which is mainly due to the variation in intron. The number of CDS varied from 7 to 17 and the length and layout of 3\u0026rsquo;UTR and 5\u0026rsquo;UTR were also various in the noncoding areas. Although CDS, introns and UTRs varied greatly, analysis discovered that CDK family members in the same evolutionary branch tend to show similar gene structures and semblable conserved patterns in motifs.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec5\" class=\"Section2\"\u003e \u003ch2\u003ePhylogenetic relationship of CDK proteins in different organisms\u003c/h2\u003e \u003cp\u003eTo assess evolutionary relationships of CDK proteins between cattle and other organisms, we conducted a phylogenetic analysis of animals in bovinae (\u003cem\u003eBos taurus, Bos indicus, Bos grunniens, Hybrid-Bos Indicus, Hybrid-Bos taurus, Bos mutus, Bison bison bison, and Bubalus bubalis\u003c/em\u003e). Besides, CDK proteins in \u003cem\u003eHomo sapiens\u003c/em\u003e and \u003cem\u003eMus musculus\u003c/em\u003e were also included for they have been studied extensively as two model organisms. Accordingly, 236 amino acid sequences from 10 organisms were aligned to generate nonrooted Neighbor-Joining (NJ) tree (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e). Phylogenetic analyses revealed CDK family proteins were classified into eight major clades. Clade Ⅰ contained CDK4 and CDK6 and Clade Ⅱ included CDK5, CDK7 and CDK20. Then CDK14 and CDK15 coalesced into a single branch named Clade Ⅲ, CDK11A, CDK11B, CDK16, CDK17 and CDK18 got together named Clade Ⅳ, CDK1, CDK2 and CDK3 got together named Clade Ⅴ, CDK9 of the 10 species merged together named Clade Ⅵ, all the \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eCyclin Dependent Kinases Like proteins (\u003c/span\u003eCDKL1, CDKL2, CDKL3, CDKL4 and CDKL5) classified into a category named Clade Ⅶ, and the rest (CDK8, CDK10, CDK12, CDK13 and CDK19) clustered into a branch named Clade Ⅷ.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec6\" class=\"Section2\"\u003e \u003ch2\u003eChromosomal distribution and collinearity analysis of CDK genes\u003c/h2\u003e \u003cp\u003eCDK family genes were mapped on the chromosomes of six bovinae species (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e). 25 bovine \u003cem\u003eCDKs\u003c/em\u003e distribute on 16 chromosomes including Chr 2, Chr 4, Chr 5, Chr 6, Chr 7, Chr 8, Chr 9, Chr 10, Chr 11, Chr 12, Chr 16, Chr 18, Chr 19, Chr 20, Chr 28 and Chr X. Among them, the \u003cem\u003eCDKs\u003c/em\u003e of cattle have a similar position distribution with \u003cem\u003eBos indicus\u003c/em\u003e, whereas the arrangement of a few genes on chromesomes are different between cattle and the other species. For example, the order of \u003cem\u003eCDK14\u003c/em\u003e (7.94\u0026ndash;8.62\u0026nbsp;Mb), \u003cem\u003eCDK6\u003c/em\u003e (9.94\u0026ndash;10.19\u0026nbsp;Mb), \u003cem\u003eCDK13\u003c/em\u003e (80.95\u0026ndash;81.08\u0026nbsp;Mb) and \u003cem\u003eCDK5\u003c/em\u003e (113.630-113.634\u0026nbsp;Mb) in \u003cem\u003eBos taurus\u003c/em\u003e Chr 4 was opposite from that in \u003cem\u003eHybrid-Bos Indicus, Hybrid-Bos taurus and Bos grunniens\u003c/em\u003e, which is \u003cem\u003eCDK5\u003c/em\u003e, \u003cem\u003eCDK13\u003c/em\u003e, \u003cem\u003eCDK6\u003c/em\u003e and \u003cem\u003eCDK14\u003c/em\u003e, respectively. \u003cem\u003eCDK4\u003c/em\u003e, \u003cem\u003eCDK2\u003c/em\u003e and \u003cem\u003eCDK7\u003c/em\u003e were three tandem genes in \u003cem\u003eBos taurus\u003c/em\u003e at the location of 29.66\u0026ndash;29.69\u0026nbsp;Mb, 29.66\u0026ndash;29.69\u0026nbsp;Mb and 29.72\u0026ndash;29.92\u0026nbsp;Mb on Chr 5, while the arrangement of these three genes were reversed in \u003cem\u003eBos grunniens, Hybrid-Bos Indicus\u003c/em\u003e Chr 5 and \u003cem\u003eBubalus\u003c/em\u003e Chr 4. In addition, compared with \u003cem\u003eBos taurus\u003c/em\u003e, \u003cem\u003eBos grunniens\u003c/em\u003e lacks of \u003cem\u003eCDK7\u003c/em\u003e, \u003cem\u003eCDK11B\u003c/em\u003e and \u003cem\u003eCDK20\u003c/em\u003e, \u003cem\u003eHybrid-Bos Indicus\u003c/em\u003e lacks of \u003cem\u003eCDK11B\u003c/em\u003e, \u003cem\u003eCDK16\u003c/em\u003e, \u003cem\u003eCDK20\u003c/em\u003e and \u003cem\u003eCDKL4\u003c/em\u003e, \u003cem\u003eHybrid-Bos taurus\u003c/em\u003e is without \u003cem\u003eCDK11B\u003c/em\u003e, \u003cem\u003eCDK20\u003c/em\u003e, \u003cem\u003eCDKL4\u003c/em\u003e and \u003cem\u003eCDKL5\u003c/em\u003e, and \u003cem\u003eBubalus\u003c/em\u003e is short of \u003cem\u003eCDK11B\u003c/em\u003e. What\u0026rsquo;s more, \u003cem\u003eCDKL5\u003c/em\u003e is located on chromosome X in \u003cem\u003eBos taurus\u003c/em\u003e, while on chromosome Y in \u003cem\u003eBos grunniens.\u003c/em\u003e\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eCollinearity analysis of the genome resulted in the identification of 31,691, 34,495, 33,570, 32,378 and 33,327 pairs of collinear genes between \u003cem\u003eBos taurus\u003c/em\u003e and \u003cem\u003eBos indicus\u003c/em\u003e, \u003cem\u003eHybrid-Bos Indicus\u003c/em\u003e, \u003cem\u003eHybrid-Bos taurus\u003c/em\u003e, \u003cem\u003eBos grunniens\u003c/em\u003e and \u003cem\u003eBubalus bubalis\u003c/em\u003e, respectively(Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e). Results showed that there is a one-to-one correspondence between chromosomes of \u003cem\u003eBos taurus\u003c/em\u003e and \u003cem\u003eHybrid-Bos Indicus\u003c/em\u003e, \u003cem\u003eHybrid-Bos taurus\u003c/em\u003e, \u003cem\u003eBos indicus\u003c/em\u003e and \u003cem\u003eBos grunniens\u003c/em\u003e. A large chromosome homologous also existed between cattle (2\u0026nbsp;\u003cem\u003eN\u003c/em\u003e\u0026thinsp;=\u0026thinsp;60) and buffalo (2\u0026nbsp;\u003cem\u003eN\u003c/em\u003e\u0026thinsp;=\u0026thinsp;50), although the chromosome number is different of the two species.The syntenic blocks revealed that Chr1 of buffalo appears to be a fusion of cattle Chr1 and Chr 27, buffalo Chr 2 appears to be a combination of cattle Chr2 and Chr 23, buffalo Chr 3 amounts to cattle Chr 8 and Chr 19, buffalo Chr 4 equals cattle Chr 5 and Chr 28, and buffalo Chr 5 equals cattle Chr- 16 and Chr 29. The detailed syntenic relationships of CDK family genes between cattle and the other five species in bovinae was displayed in Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab2\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 2\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eSyntenic relationships of CDK family genes between cattle and the other five species\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"6\"\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eGene\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eBos indicus\u003c/em\u003e\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cem\u003eHybrid-Bos taurus\u003c/em\u003e\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003e\u003cem\u003eHybrid-Bos Indicus\u003c/em\u003e\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cem\u003eBos grunniens\u003c/em\u003e\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003e\u003cem\u003eBubalus bubalis\u003c/em\u003e\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCDK1\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCDK2\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCDK3\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCDK4\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCDK5\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCDK6\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCDK7\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eN\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCDK8\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCDK9\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCDK10\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCDK11B\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eN\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCDK12\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCDK13\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCDK14\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCDK15\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCDK16\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCDK17\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCDK18\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCDK19\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCDK20\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCDKL1\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCDKL2\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCDKL3\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCDKL4\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCDKL5\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eY\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003ctfoot\u003e \u003ctr\u003e\u003ctd colspan=\"6\"\u003e\u0026lsquo;Y\u0026rsquo; represents the synteny of genes between two species, while \u0026lsquo;N\u0026rsquo; means not and \u0026lsquo;-\u0026rsquo; means lacking of the gene.\u003c/td\u003e\u003c/tr\u003e \u003c/tfoot\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cdiv id=\"Sec7\" class=\"Section3\"\u003e \u003ch2\u003e\u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eThe expression analysis of\u003c/span\u003e \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eCDKs\u003c/span\u003e \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003ein different tissue\u003c/span\u003e\u003c/h2\u003e \u003cp\u003eThe expression pattern of genes could provide important references for their function. To explore the expression pattern of the CDK gene family during \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eadipogenic differentiation\u003c/span\u003e, we investigated the relative expression level in 163 samples of 60 tissue types includin\u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eg heart, liver, spleen, lung, kidney, muscle, fat\u003c/span\u003e, etc. The results showed that \u003cem\u003eCDKs\u003c/em\u003e displayed differential expression patterns in diverse tissues (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003ea), which could be classified into 5 groups (A to E). As a marker gene for \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eadipocyte differentiation\u003c/span\u003e, \u003cem\u003ePPARγ\u003c/em\u003e had a high expression in Group B including omental fat, intramuscular fat, subcutaneous fat and mammary gland fat, indicating that the results is reliable. The 25 \u003cem\u003eCDKs\u003c/em\u003e could be grouped into 4 categories according to their expression patterns and they all expressed in 60 tissues, suggesting that they may play a broad regulatory role in life activities. Group Ⅰ(\u003cem\u003eCDK4\u003c/em\u003e, \u003cem\u003eCDK9\u003c/em\u003e and \u003cem\u003eCDK11B\u003c/em\u003e) showed the highest expression levels, followed by Group Ⅲ(\u003cem\u003eCDK3\u003c/em\u003e, \u003cem\u003eCDK5\u003c/em\u003e, \u003cem\u003eCDK7\u003c/em\u003e, \u003cem\u003eCDK8\u003c/em\u003e, \u003cem\u003eCDK10\u003c/em\u003e, \u003cem\u003eCDK18\u003c/em\u003e, and \u003cem\u003eCDK20\u003c/em\u003e) and Group Ⅳ (\u003cem\u003eCDK1\u003c/em\u003e, \u003cem\u003eCDK2\u003c/em\u003e, \u003cem\u003eCDK6\u003c/em\u003e, \u003cem\u003eCDK12\u003c/em\u003e, \u003cem\u003eCDK13\u003c/em\u003e, \u003cem\u003eCDK14\u003c/em\u003e, \u003cem\u003eCDK16\u003c/em\u003e, and \u003cem\u003eCDK17\u003c/em\u003e). Group Ⅱ comprised the rest members of \u003cem\u003eCDKs\u003c/em\u003e, whose expression level was the lowest. Further analysis of the five different fat tissues revealed that \u003cem\u003eCDK9\u003c/em\u003e was highly expressed in all the fat tissues and its expression pattern was similar to \u003cem\u003ePPARγ\u003c/em\u003e (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003eb).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cdiv id=\"Sec8\" class=\"Section4\"\u003e \u003ch2\u003e\u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eExpression analysis of\u003c/span\u003e \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eCDKs\u003c/span\u003e \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003ein preadipocytes and differentiated adipocytes by RNA-seq\u003c/span\u003e\u003c/h2\u003e \u003cp\u003eTranscriptome analysis of 25 \u003cem\u003eCDKs\u003c/em\u003e \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003ein preadipocytes and differentiated adipocytes reveal\u003c/span\u003eed that \u003cem\u003eCDKs\u003c/em\u003e showed a up-regulation trend in \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003epreadipocytes compared with differentiated adipocytes except for\u003c/span\u003e \u003cem\u003eCDK1\u003c/em\u003e, \u003cem\u003eCDK3\u003c/em\u003e, \u003cem\u003eCDK6\u003c/em\u003e, \u003cem\u003eCDK19\u003c/em\u003e, \u003cem\u003eCDKL1\u003c/em\u003e and \u003cem\u003eCDKL4\u003c/em\u003e (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003e). \u003cem\u003eCDK7\u003c/em\u003e displayed a significant high expression, \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003ewhereas\u003c/span\u003e \u003cem\u003eCDK1\u003c/em\u003e showed a significant low expression in \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003epreadipocytes within the 95% confidence interval. And\u003c/span\u003e \u003cem\u003eCDK4\u003c/em\u003e, \u003cem\u003eCDK8\u003c/em\u003e, \u003cem\u003eCDK9\u003c/em\u003e and \u003cem\u003eCDK14\u003c/em\u003e all displayed a significant high expression in \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003epreadipocytes within the 99% confidence interval.\u003c/span\u003e\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv id=\"Sec9\" class=\"Section3\"\u003e \u003ch2\u003e\u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eExpression analysis of\u003c/span\u003e \u003cspan type=\"ItalicSmallCaps\" class=\"ItalicSmallCaps\" name=\"Emphasis\"\u003eCDKs\u003c/span\u003e \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eduring adipocyte differention by qPCR\u003c/span\u003e\u003c/h2\u003e \u003cp\u003eTo further explore the expression pattern of CDK family genes, preadipocytes collected from perirenal adipose tissue of premature calves were induced differentiation. The results of oil red O staining showed that lipid droplet accumulation was significantly increased in adipocytes induced for 10 days compared to preadipocytes (Additional file 5), indicating that the induction and differentiation was successful. And we conducted qPCR to detect the expression of \u003cem\u003eCDKs\u003c/em\u003e at 0, 2, 4, 6 and 10 days during adipocytes differentiation(Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003e). Results suggested that \u003cem\u003eCDKs\u003c/em\u003e showed a relatively high expression in \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003epreadipocytes\u003c/span\u003e and then decreased as differentiation process went on in addition to \u003cem\u003eCDK1\u003c/em\u003e, \u003cem\u003eCDK15\u003c/em\u003e, \u003cem\u003eCDK18\u003c/em\u003e, \u003cem\u003eCDKL3\u003c/em\u003e and \u003cem\u003eCDKL5\u003c/em\u003e. The three members, \u003cem\u003eCDK1\u003c/em\u003e, \u003cem\u003eCDKL3\u003c/em\u003e and \u003cem\u003eCDKL5\u003c/em\u003e, all had the highest expression on the second day of differentiation and the lowest expression points were on the 6, 8 and 6\u0026nbsp;day, respectively. The expression level of \u003cem\u003eCDK15\u003c/em\u003e and \u003cem\u003eCDK18\u003c/em\u003e increased with adipocyte differentiation and reached the peak on the fourth day, then decreased.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e \u003c/div\u003e "},{"header":"Discussion","content":" \u003cp\u003eCattle is known as an important species for supplying meat. \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eThe IMF content directly affects the taste and flavor of beef and it is of great scientific significance to reveal the molecular regulation mechanism of IMF deposition for meat quality improvement.\u003c/span\u003e The CDK family genes encoding functional proteins have been well studied in the regulation of transcription, metabolism and cell differentiation[\u003cspan additionalcitationids=\"CR9\" citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e]. However, investigation of \u003cem\u003eCDKs\u003c/em\u003e in adipocyte differentiation, especially in bovidae, was limited. Since cattle and several species of bovidae were sequenced, the vast amount of genetic resources might serve as references for exploring the evolution and function of CDK gene family and advancing genome science in bovidae.\u003c/p\u003e \u003cdiv id=\"Sec11\" class=\"Section2\"\u003e \u003ch2\u003eStructural features of bovine CDK family proteins and genes\u003c/h2\u003e \u003cp\u003eThe activity of proteins depend on their functional motifs and domains[\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e]. Six conserved amino acid sequences including Motif 1, Motif 3, Motif 5, Motif 6, Motif 7 and Motif 9 were well-kept among all CDK family members in cattle, indicating the high conservation in motif distribution of CDK family proteins. These highly conserved motifs usually locate at the active sites of the enzymes, which may play essential roles in maintaining the structure, binding to substrate and catalyzing[\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e, \u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e]. CDK16, CDK17 and CDK18, a small branch in a subfamily, have all of the ten motifs, meaning some specific functions may exist in the three members. It is speculated that Motif 10 is not located in the core of the catalytic domain due to the other 22 members of CDK family proteins lacking of Motif 10 show kinase activities as well. Several CDK proteins such as CDK4, CDK15 and CDK20 are short of Motif 4, Motif 2 and Motif 8, respectively, in addition to Motif 10, indicating some sequence loss occurred in the evolution. As a newly identified member in \u003cem\u003eHybrid-Bos tauru\u003c/em\u003es, CDK20 possesses a conserved STKc domain and nine motifs (Additional file 6). The domain and motifs analysis revealed that it is consistant with the other CDK proteins.\u003c/p\u003e \u003cp\u003eWhat\u0026rsquo;s more, the gene structural analysis showed that the distribution and number of CDSs, introns, and UTRs were various in \u003cem\u003eCDKs\u003c/em\u003e. This divergence was mainly caused by the length and layout of introns and UTRs, while the gene coding sequences translated proteins were similar. In other words, the nucleic acid sequences of bovine CDK family members were less conversed compared with amino acid sequences. These results have suggested that the similarity of amino acid sequences, especially that in the conversed motifs, may play essential roles in keeping the kinase functions of CDK proteins.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec12\" class=\"Section2\"\u003e \u003ch2\u003ePhylogenetic relationship of CDK family proteins\u003c/h2\u003e \u003cp\u003eThe phylogenetic analysis of CDK family proteins in ten species provided an in-deep insight for their evolutionary relationships[\u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e]. The results revealed that CDK family proteins were classified into eight major clades and the same member from different species first clustered in one branch, indicating that they were conserved in sequences among the 10 species. Clade Ⅰ was separated out initially while Clade Ⅱ, Ⅲ and Ⅳ clustered into a subfamily and the others clustered into another subfamily, manifesting that they have been evolved asymmetrically and the evolutionary relationship between this three subfamilies may be relatively far. Notably, Clade Ⅶ includes all the \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eCyclin Dependent Kinases Like proteins (\u003c/span\u003eCDKL1, CDKL2, CDKL3, CDKL4 and CDKL5), which is consistant with the study in human that divided the CDKs into CDK and CDKL[\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e]. As expected, members of the CDK proteins with a closer relationship tend to have a nearer evolutionary distance, which means that they may cluster together first. For example, \u003cem\u003eBos Indicus\u003c/em\u003e CDK1 first clustered with that of \u003cem\u003eBubalus bubalis\u003c/em\u003e, and then get together with \u003cem\u003eHybrid-Bos taurus\u003c/em\u003e, \u003cem\u003eBos taurus, Bos mutus, Hybrid-Bos Indicus\u003c/em\u003e, \u003cem\u003eBos grunniens, Bison\u003c/em\u003e, human and mouse in turn.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec13\" class=\"Section2\"\u003e \u003ch2\u003eCollinearity analysis of CDKs in bovidae\u003c/h2\u003e \u003cp\u003eThe family genes may distribute on different chromosomes or co-locate on the same chromosome, which are generally defined as segmental duplication events in the former and tandem duplication events in the latter[\u003cspan additionalcitationids=\"CR24\" citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e]. Chromosomal distributions of the CDK family genes showed that they located on 13 to 16 chromosomes in six species of bovidae, indicating both segmental and tandem duplication events have occurred for the expansion of CDK genes. The genomes of \u003cem\u003eBos taurus\u003c/em\u003e, \u003cem\u003eBos grunniens\u003c/em\u003e, \u003cem\u003eHybrid-Bos Indicus\u003c/em\u003e, \u003cem\u003eHybrid-Bos taurus\u003c/em\u003e, and \u003cem\u003eBos indicus\u003c/em\u003e consist of 29 autosomes and a pair sex chromosomes(XX/XY)[\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e, \u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e], while \u003cem\u003eBubalus bubalis\u003c/em\u003e has 24 autosomes plus a pair sex chromosomes(XX/XY). The collinearity results showed a one-to-one correspondence between chromosomes of \u003cem\u003eBos taurus\u003c/em\u003e and \u003cem\u003eHybrid-Bos Indicus\u003c/em\u003e, \u003cem\u003eHybrid-Bos taurus\u003c/em\u003e, \u003cem\u003eBos indicus\u003c/em\u003e and \u003cem\u003eBos grunniens\u003c/em\u003e, and large homologous chromosomal regions between \u003cem\u003eBos taurus\u003c/em\u003e and \u003cem\u003eBubalus\u003c/em\u003e. The arrangement of genes in some syntenic chromosomes may be totally reversed between two species, such as Chr 1, Chr 2, Chr 4, etc. between \u003cem\u003ebos taurus\u003c/em\u003e and Hybrid\u003cem\u003e-Bos taurus\u003c/em\u003e, Chr 4, Chr 5, Chr 7, etc. between \u003cem\u003eBos taurus\u003c/em\u003e and Hybrid\u003cem\u003e-Bos taurus\u003c/em\u003e, Chr 2, Chr 4, Chr 6, etc. between \u003cem\u003eBos taurus\u003c/em\u003e and \u003cem\u003eBos grunniens\u003c/em\u003e, and Chr 9, Chr 10, Chr 11, etc. between \u003cem\u003eBos taurus\u003c/em\u003e and \u003cem\u003eBubalus bubalis.\u003c/em\u003e The discrepancies may due to the opposite starting point for chromosome annotation. Since all the chromosomes were homologous in bovidae, the positions where \u003cem\u003eCDKs\u003c/em\u003e located were either collinear (conserved in the same order) or syntenic (not necessarily in the same order) between each two species except for only a few gene pairs[\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e]. For example, \u003cem\u003eCDK7\u003c/em\u003e in Chr 20 and \u003cem\u003eCDK11B\u003c/em\u003e in Chr 16 didn\u0026rsquo;t show synteny between \u003cem\u003eBos taurus\u003c/em\u003e and \u003cem\u003eBos indicus.\u003c/em\u003eThe positions of \u003cem\u003eCDKL4\u003c/em\u003e and \u003cem\u003eCDK9\u003c/em\u003e are opposite between \u003cem\u003eBos taurus\u003c/em\u003e and \u003cem\u003eBos grunniens\u003c/em\u003e, which locate at 21.50-21.55\u0026nbsp;Mb and 98.46\u0026ndash;98.47\u0026nbsp;Mb in Chr 11 of \u003cem\u003eBos taurus\u003c/em\u003e and 41.02\u0026ndash;41.08\u0026nbsp;Mb and 7.13\u0026ndash;7.14\u0026nbsp;Mb in Chr 9 of \u003cem\u003eBos grunniens.\u003c/em\u003e The deficiency and discrepancies of CDK genes might be caused by the sequence variation and chromosome rearrangement in the process of evolution[\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e]. In addition, Chr16 of \u003cem\u003eBos taurus\u003c/em\u003e showed syntenic relationship with Chr5 and scaffold NW_020228957.1 of \u003cem\u003eBubalus bubalis\u003c/em\u003e (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003ee), suggesting that NW_020228957.1, which hasn't been assembled yet, may be a part of \u003cem\u003eBubalus\u003c/em\u003e Chr5. Meanwhile, it was syntenic between CDK18 of \u003cem\u003eBos taurus\u003c/em\u003e Chr16 and that in scaffold NW_020228957.1 of \u003cem\u003eBubalus.\u003c/em\u003e In a word, the extensive homology provided rich perspectives for studying the function and evolution of CDK family genes in bovidae.\u003c/p\u003e \u003cdiv id=\"Sec14\" class=\"Section3\"\u003e \u003ch2\u003e\u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eCDK genes affecting adipocyte differentiation\u003c/span\u003e\u003c/h2\u003e \u003cp\u003eCDK family proteins, as a kind of phosphorylases, could regulate \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eadipocytes differentiation\u003c/span\u003e by \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003ephosphorylating a series of transcription-related factors or adipocyte-specific genes\u003c/span\u003e[\u003cspan additionalcitationids=\"CR13 CR14 CR15\" citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e, \u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e]. To dissect the expression pattern of CDK family genes, we analyzed the expression values of the 25 members in 60 tissue types. As a results, \u003cem\u003eCDK4\u003c/em\u003e, \u003cem\u003eCDK9\u003c/em\u003e and \u003cem\u003eCDK11B\u003c/em\u003e showed the highest expression in four types of fat tissues (omental fat, intramuscular fat, subcutaneous fat and mammary gland fat) in relative with other tissues. So we suspected the three genes may play more important and wide-ranging roles in adipose tissue compared with other members of CDK family. Previous studies have revealed that CDK4 could phosphorylate IRS2 and Rb to promote adipogenesis[\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e, \u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]. CDK9, a component of positive transcription elongation factor b (P-TEFb), could phosphorylate the C-terminal domain of RNA polymerase II and regulate the transcription of target genes by facilitating transcriptional elongation[\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e]. In 3T3-L1 cells, CDK9 increased the adipogenic potential by phosphorylating PPARγ directly and inducing its transcriptional activity[\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e]. \u003cem\u003eCDK11B\u003c/em\u003e had similar expression patterns with \u003cem\u003eCDK4\u003c/em\u003e and \u003cem\u003eCDK9\u003c/em\u003e by tissue expression analysis, while it has not been reported to be involved in adipogenic differentiation by now. It would be valuable to further explore the function of \u003cem\u003eCDK11B\u003c/em\u003e in the regulation of adipocytes differentiation.\u003c/p\u003e \u003cp\u003eAdipogenic differentiation is a complicated and well-organized process regulated by multiple genes. Analyzing the expression patterns of CDK family genes during adipocytes differentiation is the basis of exploring their functions. Results of transcriptome analysis and qPCR validation both revealed that CDK4, CDK7, CDK8 and CDK9 showed significant high expression in preadipocytes. It is speculated that the four members may have important functions in targeting newly generated lipid droplets. The expression of CDK1, CDKL3 and CDKL5 reached the highest in the second day, while CDK15 and CDK18 reached the peak in the fourth day indicating that they may play regulatory roles during adipocyte differentiation in turn. The functions of CDK1, CDK4, CDK7, CDK8 and CDK9 in adipocytes differentiation have been preliminarily studied and need to be further explored[\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e, \u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e, \u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e, \u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e, \u003cspan additionalcitationids=\"CR32 CR33 CR34\" citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e]. Expression analysis revealed that CDK15, CDK18, CDKL3 and CDKL5, whose functions has not been studied, may also play significant roles. In addition, the expression trends of some members were inconsistent between RNA-seq and qPCR validation. For instance, there was no significant differences in the expression of CDK2, CDK6, CDK10, CDK11B, CDK12, CDK16, CDK17, CDK19 and CDKL1 by RNA-seq analysis, but they showed a significant down-regulation in qPCR detection. This discrepancy may caused by different sample sources. The samples for RNA-seq were separated from inguinal subcutaneous fat of two 1\u0026nbsp;year old male Qinchuan cattle, while samples for qPCR were from perirenal fat of a premature female Holstein calf. In summary, the functions of \u003cem\u003eCDKs\u003c/em\u003e during adipocytes differentiation is complicated and need to be studied in depth and analyzed comprehensively.\u003c/p\u003e \u003cp\u003eThe CDK family genes and the interacted genes constructed an integrative network by literature mining using Agilent Literature Search plug-in of Cytoscape (Additional file 7)[\u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e]. For example, \u003cem\u003eCDK7\u003c/em\u003e could directly activate \u003cem\u003eCDK9\u003c/em\u003e to maintain the high expression of \u003cem\u003eMDM4\u003c/em\u003e and \u003cem\u003eMDM2\u003c/em\u003e[\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e, \u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e]. \u003cem\u003eMDM2\u003c/em\u003e facilitates adipocyte differentiation through CRTC-mediated activation of \u003cem\u003eSTAT3\u003c/em\u003e[\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e]. Overall, the results revealed that CDK family genes encoding the enzymes directly or indirectly interact with each other or some other genes, playing non-redundant roles, collectively regulating the life activity including cell cycle, adipocyte differentiation, lipid metabolism etc.\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e "},{"header":"Conclusions","content":" \u003cp\u003eThis study conducted a comprehensive genome-wide analysis of CDK family genes in bovidae. A total of 185 CDK genes were identified and grouped into eight distinct clades. Collinearity analysis revealed that CDK family genes were homologous between cattle and other species in bovinae. The \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eexpression analysi\u003c/span\u003e\u003cspan type=\"BoldSmallCaps\" class=\"BoldSmallCaps\" name=\"Emphasis\"\u003es\u003c/span\u003e and functional prediction indicated that \u003cem\u003eCDKs\u003c/em\u003e may play an significant and complicated role in regulating bovine \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eadipocyte differentiation\u003c/span\u003e. The results provided an essential reference for further studies of CDK family genes in the regulation of \u003cspan type=\"SmallCaps\" class=\"SmallCaps\" name=\"Emphasis\"\u003eadipocyte differentiation\u003c/span\u003e in cattle.\u003c/p\u003e "},{"header":"Methods","content":" \u003cdiv id=\"Sec17\" class=\"Section2\"\u003e \u003ch2\u003eEthics statement\u003c/h2\u003e \u003cp\u003eAnimal experiments were conducted according to the guidelines of the Regulations for the Administration of Affairs Concerning Experimental Animals (Ministry of Science and Technology, China, 2004). All animal protocols were approved by Animal Ethics Committee of Ningxia University. A premature female calf of a Holstein pregnant cow used in the experiment was released and the primary adipocyte were isolated immediately. We made all efforts to minimize the calf\u0026rsquo;s suffering.The pregnant cow are not sampled and are still being raised in Zerui ecological breeding farm (yinchuan, China) after a period of recuperation.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec18\" class=\"Section2\"\u003e \u003ch2\u003eGenome-wide identification of CDK genes\u003c/h2\u003e \u003cp\u003eThe genome and annotation of \u003cem\u003eBos taurus\u003c/em\u003e (ARS-UCD1.2.101 assembly), \u003cem\u003eBos grunniens\u003c/em\u003e (LU_Bosgru_v3.0.101 assembly), \u003cem\u003eHybrid-Bos Indicus\u003c/em\u003e (\u003cem\u003eBos indicus\u003c/em\u003e\u0026thinsp;\u0026times;\u0026thinsp;\u003cem\u003eBos taurus\u003c/em\u003e, UOA_Brahman_1.101 assembly), \u003cem\u003eHybrid-Bos taurus\u003c/em\u003e (\u003cem\u003eBos indicus\u003c/em\u003e\u0026thinsp;\u0026times;\u0026thinsp;\u003cem\u003eBos taurus\u003c/em\u003e, UOA_Angus_1.101 assembly), \u003cem\u003eBos mutus\u003c/em\u003e (BosGru_v2.0.101 assembly), \u003cem\u003eBison bison bison\u003c/em\u003e (Bison_UMD1.0.101 assembly), \u003cem\u003eHomo sapiens\u003c/em\u003e (GRCh38.101 assembly) and \u003cem\u003eMus musculus\u003c/em\u003e (GRCm38.101 assembly) are from Ensembl database (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttp://asia.ensembl.org/index.html\u003c/span\u003e\u003c/span\u003e); \u003cem\u003eBos indicus\u003c/em\u003e (GCF_000247795.1 assembly) and \u003cem\u003eBubalus bubalis\u003c/em\u003e (ASM312139v1 assembly) are from NCBI database (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://www.ncbi.nlm.nih.gov/\u003c/span\u003e\u003c/span\u003e). In order to identify all the possible CDKs in bovine, both Hidden Markov Model (HMM) search and Basic Local Alignment Search Tool (BLAST) were performed[\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e]. The number of 59 reviewed CDKs sequences of bovine \u003cem\u003e(Bos taurus)\u003c/em\u003e, human (\u003cem\u003eHomo sapiens\u003c/em\u003e) and mouse (\u003cem\u003eMus musculus\u003c/em\u003e) were obtained from UniProt database (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://www.uniprot.org/\u003c/span\u003e\u003c/span\u003e). These protein sequences were taken as seeds to query the potential candidates of CDK gene family via BLASTP with a threshold of e-value\u0026thinsp;=\u0026thinsp;10\u003csup\u003e\u003cb\u003e\u0026minus;\u003c/b\u003e\u0026thinsp;5\u003c/sup\u003e. Besides, the HMM of CDKs (Pkinase) was downloaded from Pfam (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://pfam.xfam.org/\u003c/span\u003e\u003c/span\u003e)[\u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e] and HMMER 3.3.1 (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttp://hmmer.org/\u003c/span\u003e\u003c/span\u003e)[\u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e] was used to constructe HMM profiles in bovidae for detection of CDK family genes with the default setting. The candidate sequences obtained from two methods were further manual checked to confirm the CDK homolog sequences. Subsequently, the non-redundant CDK homologs were submitted to NCBI CD-search [\u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e41\u003c/span\u003e] to verify the presence of the conserved protein domain. The molecular weight and isoelectric point of bovine CDK proteins were calculated by ExPASy (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://web.expasy.org/protparam/\u003c/span\u003e\u003c/span\u003e)[\u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e].\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec19\" class=\"Section2\"\u003e \u003ch2\u003ePhylogenetic analysis\u003c/h2\u003e \u003cp\u003eThe known CDK amino acid sequences in the \u003cem\u003eHomo sapiens\u003c/em\u003e and \u003cem\u003eMus musculus\u003c/em\u003e were downloaded from UniProt database (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://www.uniprot.org/\u003c/span\u003e\u003c/span\u003e) (Additional file 2). The identified and known amino acid sequences of CDK in \u003cem\u003eBos taurus\u003c/em\u003e, \u003cem\u003eBos grunniens\u003c/em\u003e, \u003cem\u003eHybrid-Bos Indicus\u003c/em\u003e, \u003cem\u003eHybrid-Bos taurus\u003c/em\u003e, \u003cem\u003eBos mutus\u003c/em\u003e ,\u003cem\u003eBison bison bison\u003c/em\u003e, \u003cem\u003eBos indicus\u003c/em\u003e and \u003cem\u003eBubalus bubalis\u003c/em\u003e, as well as the known CDKs from \u003cem\u003eHomo sapiens\u003c/em\u003e and \u003cem\u003eMus musculus\u003c/em\u003e were aligned by ClusalW and constructed a Neighbor-Joining tree in MEGA 7.0[\u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e43\u003c/span\u003e]. The bootstrap was set as 1000 replication. FigTree software (version 1.4.3) was used to adjust and beautify the evolutionary tree.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec20\" class=\"Section2\"\u003e \u003ch2\u003eStructural features analysis\u003c/h2\u003e \u003cp\u003eTo further evaluate the structural diversity of cattle CDK genes and proteins, a phylogenetic Neighbor-Joining tree was constructed and the conserved motifs were detected in MEME 5.0[\u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e] and visualized in TBtools[\u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e45\u003c/span\u003e]. The minimum and maximum number of amino acids in each motif were 6 and 50. The motif number of each CDK protein was limited to 10. Also, coding sequences and corresponding genomic sequences of bovine CDKs were loaded into the TBtools to portray the numbers and positions of CDSs and introns graphically.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec21\" class=\"Section2\"\u003e \u003ch2\u003eChromosomal distribution and collinearity analysis\u003c/h2\u003e \u003cp\u003ePositional information of predicted CDK genes of \u003cem\u003eBos taurus\u003c/em\u003e, \u003cem\u003eBos grunniens\u003c/em\u003e, \u003cem\u003eHybrid-Bos Indicus\u003c/em\u003e, \u003cem\u003eHybrid-Bos taurus\u003c/em\u003e, \u003cem\u003eBos indicus\u003c/em\u003e and \u003cem\u003eBubalus bubalis\u003c/em\u003e were extracted from the genomic sequence and annotation files and then were visualized in TBtools[\u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e45\u003c/span\u003e]. The identified CDKs of each species were mapping on chromosomes. Comparisons between each two genomes were determined by all-against-all BLASTP searches (e-value\u0026thinsp;=\u0026thinsp;10\u003csup\u003e\u003cb\u003e\u0026minus;\u003c/b\u003e\u0026thinsp;5\u003c/sup\u003e) using the proteome sequences of \u003cem\u003eBos taurus\u003c/em\u003e as queries against those of other five bovine species above. The collinearity analysis between \u003cem\u003eBos taurus\u003c/em\u003e and other five species for orthologous genes was conducted using MCScanX toolkit[\u003cspan citationid=\"CR46\" class=\"CitationRef\"\u003e46\u003c/span\u003e]. The results of collinearity analysis and orthologous CDKs were visualized by TBtools[\u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e45\u003c/span\u003e].\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec22\" class=\"Section2\"\u003e \u003ch2\u003eGene expression analysis by transcriptom\u003c/h2\u003e \u003cp\u003eThe RNA-Seq data of preadipocytes and differentiated adipocytes was downloaded from the National Center for Biotechnology Information (NCBI) Sequence Read Archive(SRR3056892, SRR3064490, SRR3064491, SRR3064492)[\u003cspan citationid=\"CR47\" class=\"CitationRef\"\u003e47\u003c/span\u003e] and transformed into fastaq format by Fastq-dump.The sequencing quality was checked using FastQC[\u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e48\u003c/span\u003e]. Quality control of raw sequence data, including removal of the adapter sequences and low-quality sequences were performed using the Trim_galore. Clean reads were then mapped to the Bos taurus genome(ARS-UCD1.2.101) using STAR. The RSEM and FeatureCounts was used to calculate the expression of transcripts. Data was normalized by calculating the RPKM for each gene. These results were used to analyze the expression of \u003cem\u003eCDKs\u003c/em\u003e between preadipocytes and differentiated adipocytes in cattle. The RNA-Seq data of 163 bovine tissue samples were downloaded from Ruminant Genome Database (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttp://animal.nwsuaf.edu.cn/code/index.php/RGD\u003c/span\u003e\u003c/span\u003e)[\u003cspan citationid=\"CR49\" class=\"CitationRef\"\u003e49\u003c/span\u003e]. The SRR number and adjusted RPKM values of 163 tissue samples were provided in Additional file 8. The heatmap was performed in R software.\u003c/p\u003e \u003cp\u003e \u003cb\u003eIsolation, culture and induction differentiation of bovine primary adipocytes\u003c/b\u003e \u003c/p\u003e \u003cp\u003ePrimary adipocyte was isolated and cultured from the perirenal adipose tissue of premature calf in Zerui ecological breeding farm. Type Ⅰ collagenase digestion method was used for the isolation and cultivation of calf preadipocytes. The method described by Huang et al.[\u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e50\u003c/span\u003e] was adopted in the induction of preadipocytes differentiation, and the method described by Wang et al.[\u003cspan citationid=\"CR51\" class=\"CitationRef\"\u003e51\u003c/span\u003e] was applied for oil red O staining.\u003c/p\u003e \u003c/div\u003e \n\u003ch2\u003eRna Extraction And Quantitative Rt-pcr (qrt-pcr)\u003c/h2\u003e\n \u003cdiv class=\"Heading\"\u003eRNA extraction and quantitative RT-PCR (qRT-PCR)\u003c/div\u003e \u003cp\u003eAccording to reference sequence from NCBI, quantitative primers of \u003cem\u003eCDK\u003c/em\u003e family genes were designed used Primer Premier 5.0 software and the primer sequences were provided in Additional file 9. Total RNA were extracted at 0d, 2d, 4d, 6d and 10d during the differentiation of bovine preadipocytes by phenol-chloroform method using the TRIzol reagent (9109, Takara). RNA samples were measured for absorbance at 260\u0026nbsp;nm and 280\u0026nbsp;nm in the multifunctional full-wavelength Multiskan and the samples with an OD260/OD280 ratio between 1.8 and 2.0 was used in the subsequent experiment. Then, 1000\u0026nbsp;ng total RNA was reverse transcribed using random primers with Moloney murine leukemia virus reverse transcriptase (Takara Bio, Kyoto, Japan). Realtime PCR was carried out in a CFX96 Touch Real-Time PCR Detection System (Bio-Rad, Hercules, CA, USA) with SYBR Green Master Mix (Takara Bio, Kyoto, Japan).\u003c/p\u003e \u003cdiv id=\"Sec24\" class=\"Section2\"\u003e \u003ch2\u003eStatistical Analysis\u003c/h2\u003e \u003cp\u003eAll qRT-PCR results were calculated using a 2\u003csup\u003e\u0026minus;∆∆Ct\u003c/sup\u003e method. Three independent technical repetitions were processed for each test. Statistical significance was examined using Graphpad Prism 7.0 software.\u003c/p\u003e \u003c/div\u003e "},{"header":"Abbreviations","content":"\u003cp\u003eCDK: cyclin dependent kinases; CDS: coding sequences; HMM: Hidden Markov Model; Chr: Chromosome; IMF: intramuscular\u0026nbsp;fat; pI: isoelectric points; Mw: molecular weight\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eAcknowledgments\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe would like to thank all the participants in our study. We would also like to thank Li Qingfeng and Chen Chengjie for providing valuable advices in the research.\u003c/p\u003e\n\u003cp\u003eAuthors' contributions\u003c/p\u003e\n\u003cp\u003eCLP and ZXL made the same contribution to the paper. Conceived and designed the research:YM and CLP; Analyzed the data and conducted the experiment: CLP and ZXL; Wrote the paper: CLP; Modified manuscript: YM, LW, ZXL, SZW, XPW, DWW, XYC, ZMLR. All authors read and approved the final manuscript.\u003c/p\u003e\n\u003cp\u003eFunding\u003c/p\u003e\n\u003cp\u003eThis study was funded by the National Natural Science Foundation of China (32072720 and 31672403), the Leading Talents Fund in Science and Technology Innovation in Henan Province(No. 194200510022), the Key Research and Talent Introduction Project of Ningxia Hui Autonomous Region(2019YCZX0068) and the Science and Technology Innovation Team Projects of Ningxia Hui Autonomous Region(03010360052). The funding bodies played no role in the design of the study, collection, analysis, and interpretation of data and writing the manuscript.\u003c/p\u003e\n\u003cp\u003eAvailability of data and materials\u003c/p\u003e\n\u003cp\u003eAll data generated or analyzed during this study are included in this published article and its supplementary information files.\u003c/p\u003e\n\u003cp\u003eEthics approval and consent to participate\u003c/p\u003e\n\u003cp\u003eThe Animal Ethics Committees of Ningxia University approved the experimental design and animal sample collection for the present study (permit number NXUC20200618).We obtained the verbal informed consent to participate from the owners and the Ethics Committees of Zerui ecological breeding farm, because our laboratory has a long-term cooperation agreement with the farm about the experiment animals used in experimental research. And animal experiments were conducted strictly followed the guidelines of the Regulations for the Administration of Affairs Concerning Experimental Animals (Ministry of Science and Technology, China, 2004).\u003c/p\u003e\n\u003cp\u003eConsent for publication\u003c/p\u003e\n\u003cp\u003eNot applicable.\u003c/p\u003e\n\u003cp\u003eCompeting interests\u003c/p\u003e\n\u003cp\u003eThe authors declare that we have no competing interests.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eFox KE, Fankell DM, Erickson PF, Majka SM, Crossno JJ, Klemm DJ. Depletion of cAMP-response element-binding protein/ATF1 inhibits adipogenic conversion of 3T3-L1 cells ectopically expressing CCAAT/enhancer-binding protein (C/EBP) alpha, C/EBP beta, or PPAR gamma. J BIOL CHEM. 2006;281(52):40341\u0026ndash;53.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eGuo L, Li X, Tang QQ. Transcriptional regulation of adipocyte differentiation: a central role for CCAAT/enhancer-binding protein (C/EBP) beta. J BIOL CHEM. 2015;290(2):755\u0026ndash;61.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eCristancho AG, Lazar MA. Forming functional fat: a growing understanding of adipocyte differentiation. Nat Rev Mol Cell Biol. 2011;12(11):722\u0026ndash;34.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eChung SS, Lee JS, Kim M, Ahn BY, Jung HS, Lee HM, Kim JW, Park KS. Regulation of Wnt/beta-catenin signaling by CCAAT/enhancer binding protein beta during adipogenesis. Obesity (Silver Spring). 2012;20(3):482\u0026ndash;7.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eRahman N, Jeon M, Kim YS. Delphinidin, a major anthocyanin, inhibits 3T3-L1 pre-adipocyte differentiation through activation of Wnt/beta-catenin signaling. BIOFACTORS. 2016;42(1):49\u0026ndash;59.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eHorton JD, Shah NA, Warrington JA, Anderson NN, Park SW, Brown MS, Goldstein JL. Combined analysis of oligonucleotide microarray data from transgenic and knockout mice identifies direct SREBP target genes. Proc Natl Acad Sci U S A. 2003;100(21):12027\u0026ndash;32.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLiu S, Huang J, Wang X, Ma Y. Transcription factors regulate adipocyte differentiation in beef cattle. ANIM GENET. 2020;51(3):351\u0026ndash;7.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eMalumbres M. Cyclin-dependent kinases. GENOME BIOL. 2014;15(6):122.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eHochegger H, Takeda S, Hunt T. Cyclin-dependent kinases and cell-cycle transitions: does one fit all? Nat Rev Mol Cell Biol. 2008;9(11):910\u0026ndash;6.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eMalumbres M, Harlow E, Hunt T, Hunter T, Lahti JM, Manning G, Morgan DO, Tsai LH, Wolgemuth DJ. Cyclin-dependent kinases: a family portrait. NAT CELL BIOL. 2009;11(11):1275\u0026ndash;6.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eMalumbres M, Barbacid M. Mammalian cyclin-dependent kinases. TRENDS BIOCHEM SCI. 2005;30(11):630\u0026ndash;41.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eAhonen MA, Haridas P, Mysore R, Wabitsch M, Fischer-Posovszky P, Olkkonen VM. miR-107 inhibits CDK6 expression, differentiation, and lipid storage in human adipocytes. MOL CELL ENDOCRINOL. 2019;479:110\u0026ndash;6.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLi X, Kim JW, Gronborg M, Urlaub H, Lane MD, Tang QQ. Role of cdk2 in the sequential phosphorylation/activation of C/EBPbeta during adipocyte differentiation. Proc Natl Acad Sci U S A. 2007;104(28):11597\u0026ndash;602.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLagarrigue S, Lopez-Mejia IC, Denechaud PD, Escote X, Castillo-Armengol J, Jimenez V, Chavey C, Giralt A, Lai Q, Zhang L et al: \u003cb\u003eCDK4 is an essential insulin effector in adipocytes\u003c/b\u003e. \u003cem\u003eJ CLIN INVEST\u003c/em\u003e 2016, \u003cb\u003e126\u003c/b\u003e(\u003cb\u003e1\u003c/b\u003e):\u003cb\u003e335\u0026ndash;348\u003c/b\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eAbella A, Dubus P, Malumbres M, Rane SG, Kiyokawa H, Sicard A, Vignon F, Langin D, Barbacid M, Fajas L. Cdk4 promotes adipogenesis through PPARgamma activation. CELL METAB. 2005;2(4):239\u0026ndash;49.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eWang H, Liu L, Lin JZ, Aprahamian TR, Farmer SR. Browning of White Adipose Tissue with Roscovitine Induces a Distinct Population of UCP1(+) Adipocytes. CELL METAB. 2016;24(6):835\u0026ndash;47.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eHelenius K, Yang Y, Alasaari J, Makela TP. Mat1 inhibits peroxisome proliferator-activated receptor gamma-mediated adipocyte differentiation. MOL CELL BIOL. 2009;29(2):315\u0026ndash;23.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eZhao X, Feng D, Wang Q, Abdulla A, Xie XJ, Zhou J, Sun Y, Yang ES, Liu LP, Vaitheesvaran B et al: \u003cb\u003eRegulation of lipogenesis by cyclin-dependent kinase 8-mediated control of SREBP-1\u003c/b\u003e. \u003cem\u003eJ CLIN INVEST\u003c/em\u003e 2012, \u003cb\u003e122\u003c/b\u003e(\u003cb\u003e7\u003c/b\u003e):\u003cb\u003e2417\u0026ndash;2427\u003c/b\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eVallbracht M, Fuchs W, Klupp BG, Mettenleiter TC. \u003cb\u003eFunctional Relevance of the Transmembrane Domain and Cytoplasmic Tail of the Pseudorabies Virus Glycoprotein H for Membrane Fusion\u003c/b\u003e. \u003cem\u003eJ VIROL\u003c/em\u003e 2018, 92(\u003cb\u003e12\u003c/b\u003e).\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eOta M, Kinoshita K, Nishikawa K. Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation. J MOL BIOL. 2003;327(5):1053\u0026ndash;64.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003e\u003cb\u003evan\u003c/b\u003e Montfort RL, Pijning T, Kalk KH, Hangyi I, Kouwijzer ML, Robillard GT, Dijkstra BW: The structure of the Escherichia coli phosphotransferase IIAmannitol reveals a novel fold with two conformations of the active site. STRUCTURE 1998, 6(3):377\u0026ndash;88.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eSong L, Wu S, Tsang A. Phylogenetic Analysis of Protein Family. Methods Mol Biol. 2018;1775:267\u0026ndash;75.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eXie T, Chen C, Li C, Liu J, Liu C, He Y. Genome-wide investigation of WRKY gene family in pineapple: evolution and expression profiles during development and stress. BMC GENOMICS. 2018;19(1):490.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eGerdol M, Greco S, Pallavicini A. \u003cb\u003eExtensive Tandem Duplication Events Drive the Expansion of the C1q-Domain-Containing Gene Family in Bivalves\u003c/b\u003e. \u003cem\u003eMAR DRUGS\u003c/em\u003e 2019, 17(\u003cb\u003e10\u003c/b\u003e).\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eKrsticevic FJ, Arce DP, Ezpeleta J, Tapia E: \u003cb\u003eTandem Duplication Events in the Expansion of the Small Heat Shock Protein Gene Family in Solanum lycopersicum\u003c/b\u003e (\u003cb\u003ecv\u003c/b\u003e. \u003cb\u003eHeinz 1706\u003c/b\u003e). G3 (Bethesda) 2016, \u003cb\u003e6\u003c/b\u003e(\u003cb\u003e10\u003c/b\u003e):\u003cb\u003e3027\u003c/b\u003e\u0026ndash;\u003cb\u003e3034\u003c/b\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eZimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, Hanrahan F, Pertea G, \u003cb\u003eVan\u003c/b\u003e Tassell CP, Sonstegard TS et al: \u003cb\u003eA whole-genome assembly of the domestic cow, Bos taurus\u003c/b\u003e. \u003cem\u003eGENOME BIOL\u003c/em\u003e 2009, \u003cb\u003e10\u003c/b\u003e(\u003cb\u003e4\u003c/b\u003e):\u003cb\u003eR42\u003c/b\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eHu Q, Ma T, Wang K, Xu T, Liu J, Qiu Q. The Yak genome database: an integrative database for studying yak biology and high-altitude adaption. BMC GENOMICS. 2012;13:600.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLiu J, Wang Z, Li J, Li H, Yang L. Genome-wide identification of Diacylglycerol Acyltransferases (DGAT) family genes influencing Milk production in Buffalo. BMC GENET. 2020;21(1):26.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eWeckselblatt B, Rudd MK. Human Structural Variation: Mechanisms of Chromosome Rearrangements. TRENDS GENET. 2015;31(10):587\u0026ndash;99.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eParua PK, Kalan S, Benjamin B, Sanso M, Fisher RP. Distinct Cdk9-phosphatase switches act at the beginning and end of elongation by RNA polymerase II. NAT COMMUN. 2020;11(1):4338.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eIankova I, Petersen RK, Annicotte JS, Chavey C, Hansen JB, Kratchmarova I, Sarruf D, Benkirane M, Kristiansen K, Fajas L. Peroxisome proliferator-activated receptor gamma recruits the positive transcription elongation factor b complex to activate transcription and promote adipogenesis. MOL ENDOCRINOL. 2006;20(7):1494\u0026ndash;505.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eMu RF, Niu YF, Wang Q, Zhou HM, Hu J, Qin WY, Xiong WY. Eriocalyxin B Inhibits Adipogenesis in 3T3-L1 Adipocytes by Cell Cycle Arrest. Nat Prod Bioprospect. 2020;10(3):131\u0026ndash;40.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eMarquez MP, Alencastro F, Madrigal A, Jimenez JL, Blanco G, Gureghian A, Keagy L, Lee C, Liu R, Tan L et al: \u003cb\u003eThe Role of Cellular Proliferation in Adipogenic Differentiation of Human Adipose Tissue-Derived Mesenchymal Stem Cells\u003c/b\u003e. \u003cem\u003eSTEM CELLS DEV\u003c/em\u003e 2017, \u003cb\u003e26\u003c/b\u003e(\u003cb\u003e21\u003c/b\u003e):\u003cb\u003e1578\u0026ndash;1595\u003c/b\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eStetkova M, Growkova K, Fojtik P, Valcikova B, Palusova V, Verlande A, Jorda R, Krystof V, Hejret V, Alexiou P et al: \u003cb\u003eCDK9 activity is critical for maintaining MDM4 overexpression in tumor cells\u003c/b\u003e. \u003cem\u003eCELL DEATH DIS\u003c/em\u003e 2020, \u003cb\u003e11\u003c/b\u003e(\u003cb\u003e9\u003c/b\u003e):\u003cb\u003e754\u003c/b\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eMbonye U, Wang B, Gokulrangan G, Shi W, Yang S, Karn J. Cyclin-dependent kinase 7 (CDK7)-mediated phosphorylation of the CDK9 activation loop promotes P-TEFb assembly with Tat and proviral HIV reactivation. J BIOL CHEM. 2018;293(26):10009\u0026ndash;25.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eShannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. GENOME RES. 2003;13(11):2498\u0026ndash;504.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eHallenborg P, Siersbaek M, Barrio-Hernandez I, Nielsen R, Kristiansen K, Mandrup S, Grontved L, Blagoev B. MDM2 facilitates adipocyte differentiation through CRTC-mediated activation of STAT3. CELL DEATH DIS. 2016;7(6):e2289.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLi Y, He L, Li J, Chen J, Liu C. Genome-Wide Identification, Characterization, and Expression Profiling of the Legume BZR Transcription Factor Gene Family. FRONT PLANT SCI. 2018;9:1332.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eEl-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, Qureshi M, Richardson LJ, Salazar GA, Smart A et al: \u003cb\u003eThe Pfam protein families database in 2019\u003c/b\u003e. \u003cem\u003eNUCLEIC ACIDS RES\u003c/em\u003e 2019, \u003cb\u003e47\u003c/b\u003e(\u003cb\u003eD1\u003c/b\u003e):\u003cb\u003eD427-D432\u003c/b\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003ePotter SC, Luciani A, Eddy SR, Park Y, Lopez R, Finn RD. HMMER web server: 2018 update. NUCLEIC ACIDS RES. 2018;46(W1):W200\u0026ndash;4.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLu S, Wang J, Chitsaz F, Derbyshire MK, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Marchler GH, Song JS et al: \u003cb\u003eCDD/SPARCLE: the conserved domain database in 2020\u003c/b\u003e. \u003cem\u003eNUCLEIC ACIDS RES\u003c/em\u003e 2020, \u003cb\u003e48\u003c/b\u003e(\u003cb\u003eD1\u003c/b\u003e):\u003cb\u003eD265-D268\u003c/b\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eArtimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, \u003cb\u003ede\u003c/b\u003e Castro E, Duvaud S, Flegel V, Fortier A, Gasteiger E et al: \u003cb\u003eExPASy: SIB bioinformatics resource portal\u003c/b\u003e. \u003cem\u003eNUCLEIC ACIDS RES\u003c/em\u003e 2012, \u003cb\u003e40(Web Server issue)\u003c/b\u003e:\u003cb\u003eW597-W603\u003c/b\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eKumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. MOL BIOL EVOL. 2016;33(7):1870\u0026ndash;4.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eBailey TL, Johnson J, Grant CE, Noble WS. The MEME Suite. NUCLEIC ACIDS RES. 2015;43(W1):W39\u0026ndash;49.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eChen C, Chen H, Zhang Y, Thomas HR, Frank MH, He Y, Xia R. TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data. MOL PLANT. 2020;13(8):1194\u0026ndash;202.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eWang Y, Tang H, Debarry JD, Tan X, Li J, Wang X, Lee TH, Jin H, Marler B, Guo H et al: \u003cb\u003eMCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity\u003c/b\u003e. \u003cem\u003eNUCLEIC ACIDS RES\u003c/em\u003e 2012, \u003cb\u003e40\u003c/b\u003e(\u003cb\u003e7\u003c/b\u003e):\u003cb\u003ee49\u003c/b\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eCai H, Li M, Sun X, Plath M, Li C, Lan X, Lei C, Huang Y, Bai Y, Qi X et al: \u003cb\u003eGlobal Transcriptome Analysis During Adipogenic Differentiation and Involvement of Transthyretin Gene in Adipogenesis in Cattle\u003c/b\u003e. \u003cem\u003eFRONT GENET\u003c/em\u003e 2018, \u003cb\u003e9\u003c/b\u003e:\u003cb\u003e463\u003c/b\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eWingett SW, Andrews S: \u003cb\u003eFastQ Screen\u003c/b\u003e: \u003cb\u003eA tool for multi\u003c/b\u003e-\u003cb\u003egenome mapping and quality control\u003c/b\u003e. F1000Res 2018, \u003cb\u003e7\u003c/b\u003e:\u003cb\u003e1338\u003c/b\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eChen L, Qiu Q, Jiang Y, Wang K, Lin Z, Li Z, Bibi F, Yang Y, Wang J, Nie W et al: \u003cb\u003eLarge\u003c/b\u003e-\u003cb\u003escale ruminant genome sequencing provides insights into their evolution and distinct traits\u003c/b\u003e. SCIENCE 2019, \u003cb\u003e364\u003c/b\u003e(\u003cb\u003e6446\u003c/b\u003e).\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eHuang J, Zheng Q, Wang S, Wei X, Li F, Ma Y. \u003cb\u003eHigh-Throughput RNA Sequencing Reveals NDUFC2-AS lncRNA Promotes Adipogenic Differentiation in Chinese Buffalo (Bubalus bubalis L)\u003c/b\u003e. \u003cem\u003eGenes (Basel)\u003c/em\u003e 2019, 10(\u003cb\u003e9\u003c/b\u003e).\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eWang Y, Goulart RA, Pantanowitz L. Oil red O staining in cytopathology. DIAGN CYTOPATHOL. 2011;39(4):272\u0026ndash;3.\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"bmc-genomics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gics","sideBox":"Learn more about [BMC Genomics](http://bmcgenomics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gics","title":"BMC Genomics","twitterHandle":"#BMCGenomics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"CDK gene family, Bovine, Adipocytes differentiation, Collinearity analysis, Gene expression pattern","lastPublishedDoi":"10.21203/rs.3.rs-133585/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-133585/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eBackground\u003c/strong\u003e: The cyclin dependent kinases (CDKs) are protein kinases regulating important cellular processes such as cell cycle and transcription. A variety of studies have shown that many CDK genes also played a critical role during adipogenic differentiation. However, there is a lack of systematic research on the CDK gene family regulating bovine adipocyte differentiation.Therefore, this study aimed to characterize CDK family genes in bovine and study the expression pattern during adipocyte differentiation.\u003c/p\u003e\u003cp\u003e\u003cstrong\u003eResults\u003c/strong\u003e: We performed a genome-wide analysis and identified 25, 25, 22, 21, 22, 24, 22 and 24 CDK genes in \u003cem\u003eBos taurus\u003c/em\u003e, \u003cem\u003eBos indicus\u003c/em\u003e, \u003cem\u003eHybrid-Bos taurus\u003c/em\u003e, \u003cem\u003eHybrid bos indicus\u003c/em\u003e, \u003cem\u003eBos grunniens\u003c/em\u003e, \u003cem\u003eBos mutus, Bison \u003c/em\u003eand \u003cem\u003eBubalus bubalis\u003c/em\u003e, respectively. All the CDK genes classified into 8 subfamilies through phylogenetic analysis. Chromosome localization displayed 25 bovine CDK genes distributed on 16 chromosomes. Collinearity analysis revealed that CDK family genes of \u003cem\u003eBos taurus \u003c/em\u003ewere extensively homologous with \u003cem\u003eBos indicus\u003c/em\u003e, \u003cem\u003eHybrid-Bos taurus\u003c/em\u003e, \u003cem\u003eHybrid bos indicus\u003c/em\u003e, \u003cem\u003eBos grunniens\u003c/em\u003e and \u003cem\u003eBubalus bubalis\u003c/em\u003e. Tanscriptome analysis showed that several of the CDK family genes had relatively high expression levels in preadipocytes compared with differentiated adipocytes, which is generally\u0026nbsp;similar\u0026nbsp;to qPCR, indicating that it could have a significant function in the\u0026nbsp;growth of the emerging lipid droplets.\u003c/p\u003e\u003cp\u003e\u003cstrong\u003eConclusion:\u003c/strong\u003e We performed a comprehensive analysis for the CDK family genes including identification, phylogenetic classification, structural characterization, chromosomal distribution, collinearity analysis and expression profile analysis by tanscriptome sequencing and qPCR. The results provide a basis for further study to determine the roles of CDK family genes in regulating adipocyte differentiation, which is beneficial for beef quality improvement.\u003c/p\u003e","manuscriptTitle":"Genome-Wide\u0026nbsp;Identification of Cyclin Dependent Kinase (CDK) Family Genes Influencing Adipocyte Differentiation in\u0026nbsp;Cattle","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2020-12-28 19:19:27","doi":"10.21203/rs.3.rs-133585/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"editorInvitedReview","content":"","date":"2021-01-24T00:00:00+00:00","index":2,"fulltext":"Recommendation: Reviewer's comments unavailable due to the journal's policy.\n"},{"type":"decision","content":"Major revision","date":"2021-01-24T00:00:00+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2021-01-19T00:00:00+00:00","index":1,"fulltext":"Recommendation: Reviewer's comments unavailable due to the journal's policy.\n"},{"type":"reviewerAgreed","content":"","date":"2021-01-04T00:00:00+00:00","index":2,"fulltext":""},{"type":"reviewerAgreed","content":"","date":"2020-12-29T00:00:00+00:00","index":1,"fulltext":""},{"type":"editorAssigned","content":"","date":"2020-12-27T00:00:00+00:00","index":"","fulltext":""},{"type":"reviewersInvited","content":"","date":"2020-12-27T00:00:00+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2020-12-21T21:13:06+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2020-12-21T00:00:00+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-genomics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gics","sideBox":"Learn more about [BMC Genomics](http://bmcgenomics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gics","title":"BMC Genomics","twitterHandle":"#BMCGenomics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"80ad736d-6bdb-419a-bb6d-6dc6d2545ec7","owner":[],"postedDate":"December 28th, 2020","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[{"id":1603827,"name":"Epigenetics \u0026 Genomics"}],"tags":[],"updatedAt":"2021-08-22T15:27:20+00:00","versionOfRecord":{"articleIdentity":"rs-133585","link":"https://doi.org/10.1186/s12864-021-07653-8","journal":{"identity":"bmc-genomics","isVorOnly":false,"title":"BMC Genomics"},"publishedOn":"2021-07-12 15:02:35","publishedOnDateReadable":"July 12th, 2021"},"versionCreatedAt":"2020-12-28 19:19:27","video":"","vorDoi":"10.1186/s12864-021-07653-8","vorDoiUrl":"https://doi.org/10.1186/s12864-021-07653-8","workflowStages":[]},"version":"v1","identity":"rs-133585","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-133585","identity":"rs-133585","version":["v1"]},"buildId":"_2-kVJe1T_tPrBINL-cwx","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}