Genome Survey of Sphallerocarpus gracilis Based on High-throughput Sequencing

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The analysis of the genomic characteristic information of S. gracilis can lay a theoretical foundation for whole genome sequencing and molecular mechanism research of the biosynthesis of bioactive active ingredients. In this study, survey genome sequencing technology was employed to evaluate the genomic characteristics of S. gracilis using K-mer analysis, and smudgeplot analysis was used to evaluate its chromosome ploidy. The K-mer analysis results showed that the genome size of the sample was approximately 1,071 Mb, and the corrected genome size was 1,063 Mb. The heterozygosity rate, the proportion of repeat sequences, and GC content were determined 1.22%, 76.33%, and 35.70%, respectively. Based on the smudgeplot analysis, the maximum possible ploidy of the analyzed species was AB type, corresponding to a diploid plant. Blast analysis revealed S. gracilis to have a close relative relationship with Daucus carota (4.78%). In summary, the results indicate that the genome of S.gracilis is a complex and large genome with high heterozygosity and repetition and a large genome. This study provides a theoretical basis for future whole genome sequencing and related research. Biological sciences/Biological techniques/Genomic analysis/Genome wide analysis of gene expression Biological sciences/Biotechnology/Genomics Biological sciences/Plant sciences/Plant genetics Biological sciences/Plant sciences/Plant molecular biology Sphallerocarpus gracilis High-thoughput Squencing Genome size K-mer analysis Ploidy Heterozygosity Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Introduction Sphallerocarpus gracilis , commonly known as Xiaoyeshan Red Radish and Huangfeng, is a single plant of Sphallerocarpus , belonging to the family Apiaceae 1 . It is scattered in the northwest, northeast, and north of China, particularly in Qilian Mountain and Yanzhi Mountain (Zhangye City, Gansu Province). It is rare to form a large regional population advantage in the growth of wild S. gracilis in Shandan County, Zhangye City 2 . The fleshy roots of S. gracilis are large and conical, and are used to cook porridge and various other dishes. S. gracilis grows in alpine humid grasslands and semi-steppe and mountain beaches at an altitude of 1700–3000 m. It is a non-polluting and non-toxic green food. S. gracilis is rich in more than 10 types of beneficial amino acids, vitamins A and vitamin C, Ca, P, Fe, Zn, and other minerals and trace elements 3 . It is known as “small ginseng’’ and is a natural and important medicinal and edible resource. S. gracilis and its products are favored by consumers, yet its market supply is limited. This has led to excessive excavation by local farmers in spring and autumn, causing serious damage to wild resources. These actions, combined with the deterioration of the ecological environment and the predatory management of the local people, have resulted in a decline in the number of wild S. gracilis populations. At present, the functional genome, gene sequence information, and genetic background of endangered wild S. gracilis germplasm are scarce. Thus, research that adopts genomic resources is required for the protection of S. gracilis and to determine its genetic structure. For non-model organisms, genome investigation and analysis are essential for functional gene mining and molecular mechanism research in the absence of genome data 4 . With the continuous development of sequencing technology, the K-monomeric unit (K-mer) method has become important in studying characteristics such as genome size, repeatability and heterozygosity 5-7 , and has been applied to species such as Euphrasia 8 , Aspalathus linearis 9 , Reseda pentagyna and Reseda lutea 10 , and Platostoma palustre A.J.Paton 11 . The current research on S. gracilis focuses on polysaccharides function 12-14 , biological activity composition 15 , hepatoprotective effects 16,17 , transcriptome sequencing analysis 18,19 , etc., while studies on the genome of S. gracilis are lacking. In this study, K-mer analysis was performed to evaluate the genome size, heterozygosity, repeatability, GC content, chromosome ploidy, and related species relationship with wild S. gracilis by genome survey sequencing technology. The results provide theoretical reference for genome assembly, molecular mechanism research of pharmacodynamic component synthesis, functional gene resource mining, and new drug development and innovation of S. gracilis . Results Morphological characteristics of S. gracilis To investigate the genomic characteristics of wild S. gracilis , we collected plant samples from the nature reserve near Shandan Horse Farm three, Shandan County, Zhangye City, Gansu Province, China (Fig. 1 A). Wild S. gracilis is a perennial herb with a plant height of 50–120 cm (Fig. 1 B). The root is large and conical, the stem is round and multi-branched, the cauline leaves are 2–3 pinnately divided, and the umbellate inflorescence is small (Fig. 1 B). Genome sequencing and quality control of S. gracilis Based on the second-generation Illumina NovaSeq sequencing platform, the genomic DNA of S. gracilis was sequenced to obtain 109.64 Gb raw sequencing data, resulting in 96.16 Gb quality sequencing data after filtering (Table 1 ). The distribution of each read sequence length over all sequences was 150 bp (Fig. 2 ), indicating that the sequencing quality was stable and accurate. An evaluation of the sequencing quality showed that the Q20 and Q30 values of S. gracilis were 98.09% and 94.74% (Table 1 ), respectively, revealing that the genomic data were reliable and could be used for the subsequent analysis. Most of the quality values of the sequencing data in the S. gracilis genome were greater than 35 (Fig. 3 ), indicating that read quality of the genome sequencing and the reliability of the sequencing results were high. The complementary bases of A and T, and C and G in the genome sequencing data S. gracilis were essentially the same, and the position base N was 0. The GC content of the genome was approximately 35.70% (Table 1 ). The GC distribution map showed that the GC content of the sequencing results followed a normal distribution (Fig. 4 ), indicating that there was no bias and that the data was not contaminated by exogenous species. In addition, the proportion of A, G, C, and T in each base position in the sequencing results was balanced (Fig. 4 ), further confirming the high reliability of the sequencing results. The GC content distribution exhibited a single peak, demonstrating normally (Fig. 5 ). The sequencing results were consistent with the GC content of all the genes expressed in the species. However, due to the low sequencing quality of the first few bases and the deviation of the DNA template amplification, these bases exhibited large fluctuations, which is expected. In summary, the results prove that the genome survey of S. gracilis has obtained high-quality sequencing data. Table 1 Survey sequencing data of the Sphallerocarpus_gracilis genome Type ReadNum BaseCount (Gb) ReadLength (bp) Q20 (%) Q30 (%) GC Content (%) raw 730,929,594 109.64 150 97.11 93.44 36.18 dedup 651,373,830 96.16 147 98.09 94.74 35.70 Evaluation of the genome size and heterozygosity of S. gracilis K-mer analysis was employed to estimate the genome size, heterozygosity, and repeatability of the species, with a Kvalue of 17. The results of the K-mer analysis showed that the size of the S. gracilis genome was about 1,071 Mb, with a corrected genome size of 1,063 Mb (Table 2 , Fig. 5 ). The heterozygosity rate was 1.22%, and the proportion of repeat sequences was 76.33% (Table 2 , Fig. 6 ). The K-mer depth distribution revealed the presence of a peak at 1/2 of the main peak position (Fig. 6 ). This indicates that the heterozygosity of S. gracilis genome was high. Moreover, the K-mer curve showed obvious tailing (Fig. 6 ), suggesting that the content of repetitive sequences in S. gracilis genome was high. These results indicate that the S. gracilis genome belongs to a species with a large genome, high heterozygosity, and numerous repeat sequences. Table 2 Genomic characteristics of Sphallerocarpus_gracilis (K = 17) K-mer number K-mer Depth Genome Size (bp) Revised Genome Size (bp) Heterozygous Ratio (%) Repeat (%) 85,719,933,597 80 1,071,499,170 1,063,284,596 1.22 76.33 Determination of the S. gracilis ploidy using smudgeplots The genomic structure and ploidy of S. gracilis were analyzed using smudgeplots. The peak value of the AB ploidy of the S. gracilis genome was determined as 0.63 (Table 3 ) and followed a single peak curve (Fig. 7 ), it to be a heterozygous diploid. This is consistent with the reported genome ploidy of carrot ( Daucus carota ). Table 3 Smudgeplot analysis results of the Sphallerocarpus_gracilis genome peak kmers kmers (%) summit B / (A + B) summit A + B AB 16,443,246 0.63 0.48 78.73 AABB 4,361,639 0.17 0.49 162.2 AAB 3,437,341 0.13 0.32 114.51 AAAABB 980,872 0.04 0.32 233.75 AAAAB 706,114 0.03 0.19 209.9 Relative species of S. gracilis The NCBI database was used to compare with the nucleic acid sequence of S. gracilis . The read matching rates of Daucus carota (4.78%), Anthriscus Hoffm (1.16%), Hedera helix (1.10%), Ostericum sieboldii (1.00%), and Apium graveolens (0.97%) were relatively high (Table 4 ). This suggests that Daucus carota is a relative species of S. gracilis . No abnormal results were observed with other species such as animals in the comparison data. Table 4 Comparison of high-quality data NT library of Sphallerocarpus gracilis plants Genus Kingdom Blast number Hit number Percentage of hits (%) Percentage of extraction (%) Median identity (%) Daucus Viridiplantae 956 3,659 26.13 4.78 91.25 Anthriscus Viridiplantae 232 3,659 6.34 1.16 99.31 Hedera Viridiplantae 220 3,659 6.01 1.10 84.91 Ostericum Viridiplantae 199 3,659 5.44 1.00 99.33 Apium Viridiplantae 194 3,659 5.30 0.97 100.00 Ferula Viridiplantae 152 3,659 4.15 0.76 99.16 Pulicaria Viridiplantae 80 3,659 2.19 0.40 83.99 Heracleum Viridiplantae 69 3,659 1.89 0.34 100.00 Torilis Viridiplantae 63 3,659 1.72 0.32 98.67 Pternopetalum Viridiplantae 52 3,659 1.42 0.26 98.67 Solanum Viridiplantae 46 3,659 1.26 0.23 84.62 Sphallerocarpus Viridiplantae 41 3,659 1.12 0.21 99.33 Zizia Viridiplantae 40 3,659 1.09 0.20 100.00 Saposhnikovia Viridiplantae 38 3,659 1.04 0.19 99.33 Panax Viridiplantae 32 3,659 0.87 0.16 100.00 Gossypium Viridiplantae 32 3,659 0.87 0.16 86.07 Chenopodium Viridiplantae 29 3,659 0.79 0.14 88.36 Angelica Viridiplantae 28 3,659 0.77 0.14 99.33 Vigna Viridiplantae 27 3,659 0.74 0.14 83.19 Ipomoea Viridiplantae 27 3,659 0.74 0.14 84.21 Medicago Viridiplantae 26 3,659 0.71 0.13 85.83 Cuminum Viridiplantae 26 3,659 0.71 0.13 98.67 Impatiens Viridiplantae 24 3,659 0.66 0.12 84.92 Geum Viridiplantae 21 3,659 0.57 0.10 90.20 Scutellaria Viridiplantae 21 3,659 0.57 0.10 84.93 Peucedanum Viridiplantae 20 3,659 0.55 0.10 99.67 Musa Viridiplantae 18 3,659 0.49 0.09 90.34 Hansenia Viridiplantae 18 3,659 0.49 0.09 98.67 Ballota Viridiplantae 18 3,659 0.49 0.09 83.21 Osmorhiza Viridiplantae 17 3,659 0.46 0.08 98.67 Clematis Viridiplantae 17 3,659 0.46 0.08 100.00 Hymenidium Viridiplantae 16 3,659 0.44 0.08 99.33 Cicer Viridiplantae 16 3,659 0.44 0.08 88.83 Fraxinus Viridiplantae 16 3,659 0.44 0.08 83.72 Physospermopsis Viridiplantae 16 3,659 0.44 0.08 99.67 Bupleurum Viridiplantae 16 3,659 0.44 0.08 99.33 Ligusticum Viridiplantae 15 3,659 0.41 0.07 98.01 Sinocarum Viridiplantae 15 3,659 0.41 0.07 98.66 Arachis Viridiplantae 15 3,659 0.41 0.07 96.00 Meeboldia Viridiplantae 14 3,659 0.38 0.07 98.01 Theobroma Viridiplantae 14 3,659 0.38 0.07 86.15 Discussion The analysis of whole genome information based on sequencing technology lays a foundation for the study of plant origin, evolution, reproduction, development, resistance and sex regulation. Considering the large differences in the heterozygosity and repeat content of the genomes of different species, it is important to determine the genome characteristics before whole genome sequencing. A genome survey is a low-depth sequencing method based on small fragment libraries that can quickly obtain the genome size, heterozygosity, and weight by K-mer analysis 7,20 . The analysis of filtered high-quality data revealed that the heterozygosity of the S. gracilis genome was 1.22% and the proportion of repetitive sequences was 76.33% (Table 2 ). This indicates that the S. gracilis genome is complex with high repetition and high heterozygosity. A heterozygosity exceeding 0.8% is typically considered to be high 21 . A heterozygosity increases the difficulty of genome-wide assembly and interferes with the estimation progress of K-mer, making the estimation result deviate from the actual size 22 . The GC content of the S. gracilis genome was 35.70% (Table 1 ), which is within the acceptable range of 25–65%, indicating the feasibility of the genome assembly 23 . Based on the K-mer and smudgeplot analysis, the genome size of S. gracilis was estimated to be 1,063 Mb, indicating that it is an AB-type diploid plant (Tables 2 and 3 , Fig. 7 ). This is consistent with previous research that reported the karyotype of S. gracilis to be 2n = 20 24 . Moreover, most Apiaceae plants are diploid 25,26 , such as Daucus carota (2n = 18) 27,28 , Coriandrum sativum (2n = 22) 29 , and Apium graveolens (2n = 22) 30 , with genome sizes of 421 Mb, 2130 Mb, and 2.21 Gb, respectively. Our results suggest that S. gracilis is a species with high repetition, high heterozygosity, and a large genome. The genomic characteristic data of S. gracilis obtained in this study lay a foundation for subsequent genome sequencing. The study of genomics can reveal the genetic diversity, genome evolution, and gene function of species. The phylogenetic tree can directly show the genetic relationship and evolution process 31 . We used high-quality reads to compare NCBI nucleic acid data. The similarity of plants included in the NT library did not exceed 10%, only Daucus carota was 4.78% (Table 4 ). This may be attributed to the limited sequence information of S. gracilis and its approximate species included in the NT library. The morphological characteristics of S. gracilis are similar to those of carrot ( Daucus carota ) plants (Fig. 1 B), and S. gracilis is also known as the “small red carrot”. Moreover, the genomes of S. gracilis and carrot are different by a factor of just 2.5. Thus, the advanced research results of carrot 28,32,33 can provide a reference for further research on S. gracilis . With the rapid development of sequencing and analysis techniques, the genomes of large, highly repeated, and highly heterozygous species have been sequenced at the fine chromosome level 34–38 . The publication of these high-quality reference genomes provides a basis for the study of the origin and evolution of important economic plants, the protection and utilization of germplasm resources, the molecular mechanism of important component anabolism, and the breeding of new varieties. It also provides a reference for whole genome sequencing and assembly strategies of complex genome species. In this study, the genome size, chromosome ploidy and related species of S. gracilis were estimated by K-mer analysis. This provides a basis for the subsequent development of the fine mapping of the whole genome of S. gracilis . Materials and methods Plant materials and genome DNA extraction In January 2024, wild S. gracilis was collected with soil from three fields of Junmachang, Shandan County, Zhangye City, Gansu Province (101.05° N, 38.32° W) and brought back to the laboratory of Hexi University (Fig. 1 A). According to the conventional cultivation method, the root segment of S. gracilis was planted in a flowerpot with a diameter of the bottom of 18 cm, a diameter of the upper of 30 cm, and a depth of 38 cm. The potted soil comprised equal amounts of sterilized nutrient soil with a volume of 2/3 of the flowerpot. After one month of plant growth, young leaves were selected, frozen in liquid nitrogen, and stored in a refrigerator at − 80°C. According to the manufacturer’s instructions, total genomic DNA was extracted from the young leaf tissues using the SteadyPure Plant Genomic DNA Extraction Kit (Accurate Biotechnology, Co., Ltd). The quality, purity and concentration of DNA samples were detected by 1% agarose electrophoresis and a Nanodrop2000 Spectrophotometer (Thermo Scientific, USA). Library preparation and sequencing The genome survey was completed by Wuhan OneMore Technology Co., Ltd. A library of 300–400 bp fragments was constructed from the DNA sample. The DNA fragments were subjected to end repair, 3' A tailing and ligation with adaptors 39 . Double-end (PE, paired-end, 150) sequencing was then performed on the constructed library based on the DNBseq sequencing platform. Quality control of sequencing data The raw data obtained by sequencing were filtered by FASTQC v0.12.0 40 to obtain high-quality data (clean data) for the analysis of the GC content, heterozygosity, and genome size. For the analysis, the adaptor sequences of reads were removed 41 , the inaccurate bases at both ends of the reads were cut off, and five bases at the left and right ends were cut off. Moreover, reads containing more than 10% N were removed and read pairs with more than 20% of the base mass fraction less than 20 in a read were discarded. Estimation of the S. gracilis genome size using K-mer analysis Based on the clean data, the K-mer method 20 was employed to estimate the genome size of S. gracilis . The K value was set as 17 and the K-mer of the four bases in A, T, C, and G was counted. The Lander–Waterman algorithm was used to calculate the K-mer total and depth. The K-mer curve frequency distribution was drawn based on the calculated K-mer. The K-mer depth C value was obtained using the curve and the genome size was estimated. Ploidy estimation of S. gracilis Smudgeplot v0.4.0 6 was used to estimate ploidy levels of S. gracilis from modified reads generated by the default settings of MECAT v2.0 42 . Smudgeplot extracts heterozygous K-mer pairs from the K-mer database of sequencing data and trains heterozygous K-mer pairs. By comparing the total number and relative coverage of K-mer pairs, the number of heterozygous K-mers pairs was counted to analyze the genome structure. Comparative analysis of near-source species of S. gracilis To study the similarity between S. gracilis and its related species, we randomly selected 10,000 single-end reads data from the filtered high-quality data, and compared them with the NCBI nucleotide database (NT library, July 4, 2024) using Blast. Declarations Competing interests The authors have no conflict of interest declaring. Permissions Statement We have obtained permission or authority for the collection, sequencing and related research work of S. gracilis plant materials. The wild S. gracilis has been deposited in the Herbarium of Agricultural and Ecological Engineering College of Hexi University. The wild S. gracilis materials were identified by Dr. C.Z. and Dr. S.Q. Author Contribution S.Q. and C.Z. planned and designed the research. Y.C. and R.Z. collected plant materials. S.Q., C.Z., F.Y., Z.X., G.Z., and H.S. performed the experiments. S.Q. and C.Z. drafed and revised the manuscript. All the authors reviewed and approved the manuscript. Acknowledgements We are grateful to the professional editors of Charlesworth Author Services for critical reading and revision of the manuscript. This work was supported by National Natural Science Foundation of China (No. 32160745); Natural Science Foundation of Gansu Province (No.22JR5RG566). Data Availability Sequence data that support the findings of this study have been deposited in the NCBI Sequence Read Archive (SRA) on January 17,2025 with the primary accession code PRJNA1211825, entitled Sphallerocarpus gracilis Genome sequencing and assembly. References ZY, W., AM, L., YC, T., ZD, C. & DZ, L. The families and genera of Angiosperms in China a comprehensive analysis. (Beijing: Science Press, 2003). Huixian, J., Qing, Z., Xiangqing, Y., Zhenxia, Z. & Mingyan, Z. 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The chromosome-scale high-quality genome assembly of Panax notoginseng provides insight into dencichine biosynthesis. Plant Biotechnol. J. 19 , 869–871, doi:https://doi.org/10.1111/pbi.13558 (2021). Han, X. et al. The chromosome-level genome of female ginseng ( Angelica sinensis ) provides insights into molecular mechanisms and evolution of coumarin biosynthesis. Plant J. 112 , 1224–1237, doi:https://doi.org/10.1111/tpj.16007 (2022). Niu, S. et al. The Chinese pine genome and methylome unveil key features of conifer evolution. Cell 185 , 204–217.e214, doi:https://doi.org/10.1016/j.cell.2021.12.006 (2022). Wang, Z. et al. Chromosome-level genome assembly of Cnidium monnieri , a highly demanded traditional Chinese medicine. Sci. Data. 11 , 667, doi:https://doi.org/10.1038/s41597-024-03523-6 (2024). Khan, M. W., Habibi, N., Shaheed, F. & Mustafa, A. S. Draft genome sequences of five clinical strains of Brucella melitensis isolated from patients residing in Kuwait. 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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-5782050","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":405592499,"identity":"eeb4dee9-501f-4c57-8290-7e9c4f0b8870","order_by":0,"name":"Shiming Qi","email":"","orcid":"","institution":"College of Agriculture and Ecological Engineering","correspondingAuthor":false,"prefix":"","firstName":"Shiming","middleName":"","lastName":"Qi","suffix":""},{"id":405592500,"identity":"de90d67a-3a3d-475e-a646-e5dc50e9c9d7","order_by":1,"name":"Chunmei Zhang","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA0UlEQVRIiWNgGAWjYDACCQglZwCm2EjQYky6lsQNRGuRn9387OGXmm3p2yVyDBg+lB1m4J/dgF8L45xj5sYyx27n7uw5Y8A449xhBok7B/BrYZZIMJOWbLidu+F4jwEzb9thBgOJBPxa2CTSv4G0pBsc5jFg/kuMFh6JHDPJjw23EwxAtjASo0VCIqdMmuHYbcMNZ44VHOw5l84jcYOAFvkZ6dskf9Tclje4kbzxwY8yazn+GQS0gAAzD5RxAORSwuqBgPEHUcpGwSgYBaNgxAIAPi1Br6Pl+ooAAAAASUVORK5CYII=","orcid":"","institution":"College of Agriculture and Ecological Engineering","correspondingAuthor":true,"prefix":"","firstName":"Chunmei","middleName":"","lastName":"Zhang","suffix":""},{"id":405592501,"identity":"5e82e0a6-6646-46be-9de2-0c0daef75c73","order_by":2,"name":"Fang Yan","email":"","orcid":"","institution":"Key Laboratory of Hexi Corridor Resources Utilization of GanSu","correspondingAuthor":false,"prefix":"","firstName":"Fang","middleName":"","lastName":"Yan","suffix":""},{"id":405592502,"identity":"6782440c-0322-41ff-8591-3fda0a66d04d","order_by":3,"name":"Xifeng Zhang","email":"","orcid":"","institution":"College of Agriculture and Ecological Engineering","correspondingAuthor":false,"prefix":"","firstName":"Xifeng","middleName":"","lastName":"Zhang","suffix":""},{"id":405592503,"identity":"1e42b1d4-aac6-46df-a103-ae56e411008b","order_by":4,"name":"Gang Zhao","email":"","orcid":"","institution":"College of Agriculture and Ecological Engineering","correspondingAuthor":false,"prefix":"","firstName":"Gang","middleName":"","lastName":"Zhao","suffix":""},{"id":405592504,"identity":"5dbc4314-ed58-42f6-989a-b2389995337f","order_by":5,"name":"Hai Song","email":"","orcid":"","institution":"Key Laboratory of Hexi Corridor Resources Utilization of GanSu","correspondingAuthor":false,"prefix":"","firstName":"Hai","middleName":"","lastName":"Song","suffix":""},{"id":405592505,"identity":"fe0b2de0-4084-4221-912b-49c00835ca78","order_by":6,"name":"Ye Chen","email":"","orcid":"","institution":"College of Agriculture and Ecological Engineering","correspondingAuthor":false,"prefix":"","firstName":"Ye","middleName":"","lastName":"Chen","suffix":""},{"id":405592506,"identity":"92b42ba0-1834-4786-a427-dd455e5bfeeb","order_by":7,"name":"Zhenrong Liu","email":"","orcid":"","institution":"College of Agriculture and Ecological Engineering","correspondingAuthor":false,"prefix":"","firstName":"Zhenrong","middleName":"","lastName":"Liu","suffix":""}],"badges":[],"createdAt":"2025-01-07 14:08:26","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-5782050/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-5782050/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":74695954,"identity":"92a854c2-7cbd-4dcb-869c-886f225eecea","added_by":"auto","created_at":"2025-01-24 20:16:56","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":4052144,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eLocation and plant morphological characteristics of \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eSphallerocarpus gracilis\u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003e. \u003c/strong\u003e(A) Location of \u003cem\u003eS. gracilis\u003c/em\u003e in the nature reserve of Shandan County, Zhangye City. (B) Morphological characteristics of a single \u003cem\u003eS. gracilis\u003c/em\u003e plant growing in Shandan County Nature Reserve. The white and yellow scales denote 20 mm and 5 mm, respectively.\u003c/p\u003e","description":"","filename":"Fig.1.png","url":"https://assets-eu.researchsquare.com/files/rs-5782050/v1/7f9a58193d7f32388acc8352.png"},{"id":74695979,"identity":"9aeaafeb-01fb-4ed1-8b4b-cbe96ea7e645","added_by":"auto","created_at":"2025-01-24 20:16:58","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":3650030,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eSequence length distribution of all \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eSphallerocarpus gracilis \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003esequences. \u003c/strong\u003eSequence length distribution of the first-end (A) and other-end (B) sequencing reads of the double-end sequencing sequence.\u003c/p\u003e","description":"","filename":"Fig.2.png","url":"https://assets-eu.researchsquare.com/files/rs-5782050/v1/6ed89046c13b6a8fdf6ffa2f.png"},{"id":74695980,"identity":"4bd0f0f1-fd5a-4aa5-8066-01eb9dc595b9","added_by":"auto","created_at":"2025-01-24 20:16:58","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":5304445,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eProportion of bases T, C, A, and G in the \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eSphallerocarpus gracilis \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003egenome. \u003c/strong\u003eA. Proportion of bases T, C, A, and G at each base position in the first read; B: Proportion of bases T, C, A, and G at each base position in the second read.\u003c/p\u003e","description":"","filename":"Fig.3.png","url":"https://assets-eu.researchsquare.com/files/rs-5782050/v1/ecc6dc3712aca4df47c6c1b9.png"},{"id":74695957,"identity":"fe993def-ce2b-4eda-81cf-5c2ad35ef57f","added_by":"auto","created_at":"2025-01-24 20:16:57","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":5116371,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eProportion of bases T, C, A, and G in the \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eSphallerocarpus gracilis \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003egenome. \u003c/strong\u003eA. Proportion of bases T, C, A, and G at each base position in the first read; B: Proportion of bases T, C, A, and G at each base position in the second read.\u003c/p\u003e","description":"","filename":"Fig.4.png","url":"https://assets-eu.researchsquare.com/files/rs-5782050/v1/45af9483b42583d57785dc8e.png"},{"id":74695969,"identity":"b2bc0f86-d90b-47cb-9f80-4159d7acc9fb","added_by":"auto","created_at":"2025-01-24 20:16:58","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":8339660,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eDistribution structure of the GC content in the \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eSphallerocarpus gracilis\u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003e genome. \u003c/strong\u003eDistribution structure of the GC content of the first-end (A) and other-end (B) sequencing reads of the double-end sequencing sequence.\u003c/p\u003e","description":"","filename":"Fig.5.png","url":"https://assets-eu.researchsquare.com/files/rs-5782050/v1/9cd89702cb4f1ae088aa3305.png"},{"id":74695967,"identity":"a09d51c0-d476-4290-9373-c7c7bf988611","added_by":"auto","created_at":"2025-01-24 20:16:58","extension":"png","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":444863,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eK-mer species frequency and depth distribution of \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eSphallerocarpus gracilis.\u003c/strong\u003e\u003c/em\u003e x- and y-axis represent the coverage and frequency of the K-mer species, respectively.\u003c/p\u003e","description":"","filename":"Fig.6.png","url":"https://assets-eu.researchsquare.com/files/rs-5782050/v1/939c08faaa28fcc7fe5ff5ba.png"},{"id":74695955,"identity":"032e8a7e-c14b-4cb8-83d8-47484ab2e7a5","added_by":"auto","created_at":"2025-01-24 20:16:57","extension":"png","order_by":7,"title":"Figure 7","display":"","copyAsset":false,"role":"figure","size":758795,"visible":true,"origin":"","legend":"\u003cp\u003eSmudgeplots for the diploid \u003cem\u003eSphallerocarpus gracilis\u003c/em\u003e based on real datasets.\u003c/p\u003e","description":"","filename":"Fig.7.png","url":"https://assets-eu.researchsquare.com/files/rs-5782050/v1/8c3674b356e30379512ee468.png"},{"id":80886644,"identity":"4566a505-b407-425b-acd3-24ebb470ea13","added_by":"auto","created_at":"2025-04-18 09:02:33","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":17190492,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5782050/v1/20029139-662e-48be-b8e1-e7d403e941cd.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Genome Survey of Sphallerocarpus gracilis Based on High-throughput Sequencing","fulltext":[{"header":"Introduction","content":"\u003cp\u003e\u003cem\u003eSphallerocarpus gracilis\u003c/em\u003e, commonly known as Xiaoyeshan Red Radish and Huangfeng, is a single plant of\u0026nbsp;\u003cem\u003eSphallerocarpus\u003c/em\u003e, belonging to the family \u003cem\u003eApiaceae\u003c/em\u003e \u003csup\u003e1\u003c/sup\u003e. It is scattered in the northwest, northeast, and north of China, particularly in Qilian Mountain and Yanzhi Mountain (Zhangye City, Gansu Province). It is rare to form a large regional population advantage in the growth of wild\u0026nbsp;\u003cem\u003eS. gracilis\u003c/em\u003e in Shandan County, Zhangye City\u0026nbsp;\u003csup\u003e2\u003c/sup\u003e. The fleshy roots of\u0026nbsp;\u003cem\u003eS. gracilis\u003c/em\u003e are large and conical, and are used to cook porridge and various other dishes.\u0026nbsp;\u003cem\u003eS. gracilis\u003c/em\u003e grows in alpine humid grasslands and semi-steppe and mountain beaches at an altitude of 1700\u0026ndash;3000 m. It is a non-polluting and non-toxic green food.\u0026nbsp;\u003cem\u003eS. gracilis\u003c/em\u003e is rich in more than 10 types of beneficial amino acids, vitamins A and vitamin C, Ca, P, Fe, Zn, and other minerals and trace elements \u003csup\u003e3\u003c/sup\u003e. It is known as \u0026ldquo;small ginseng\u0026rsquo;\u0026rsquo; and is a natural and important medicinal and edible resource.\u003c/p\u003e\n\u003cp\u003e\u003cem\u003eS.\u003c/em\u003e\u003cem\u003e\u0026nbsp;gracilis\u003c/em\u003e and its products are favored by consumers, yet its market supply is limited. This has led to excessive excavation by local farmers in spring and autumn, causing serious damage to wild resources. These actions, combined with the deterioration of the ecological environment and the predatory management of the local people, have resulted in a decline in the number of wild\u0026nbsp;\u003cem\u003eS.\u003c/em\u003e\u003cem\u003e\u0026nbsp;gracilis\u003c/em\u003e populations. At present, the functional genome, gene sequence information, and genetic background of endangered wild\u0026nbsp;\u003cem\u003eS.\u003c/em\u003e\u003cem\u003e\u0026nbsp;gracilis\u003c/em\u003e germplasm are scarce. Thus, research that adopts genomic resources is required for the protection of\u0026nbsp;\u003cem\u003eS.\u003c/em\u003e\u003cem\u003e\u0026nbsp;gracilis\u003c/em\u003e and to determine its genetic structure.\u003c/p\u003e\n\u003cp\u003eFor non-model organisms, genome investigation and analysis are essential for functional gene mining and molecular mechanism research in the absence of genome data \u003csup\u003e4\u003c/sup\u003e.\u0026nbsp;With the continuous development of sequencing technology, the K-monomeric unit (K-mer) method has become important in studying characteristics such as genome size, repeatability and heterozygosity \u003csup\u003e5-7\u003c/sup\u003e, and has been applied to species such as\u003cem\u003e\u0026nbsp;Euphrasia\u003c/em\u003e \u003csup\u003e8\u003c/sup\u003e, \u003cem\u003eAspalathus linearis\u003c/em\u003e \u003csup\u003e9\u003c/sup\u003e, \u003cem\u003eReseda pentagyna\u003c/em\u003e and \u003cem\u003eReseda lutea\u003c/em\u003e \u003csup\u003e10\u003c/sup\u003e, and \u003cem\u003ePlatostoma palustre\u003c/em\u003e A.J.Paton \u003csup\u003e11\u003c/sup\u003e. The current research on\u0026nbsp;\u003cem\u003eS.\u003c/em\u003e\u003cem\u003e\u0026nbsp;gracilis\u003c/em\u003e focuses on polysaccharides function \u003csup\u003e12-14\u003c/sup\u003e, biological activity composition \u003csup\u003e15\u003c/sup\u003e, hepatoprotective effects \u003csup\u003e16,17\u003c/sup\u003e, transcriptome sequencing analysis \u003csup\u003e18,19\u003c/sup\u003e, etc., while studies on the genome of\u0026nbsp;\u003cem\u003eS.\u003c/em\u003e\u003cem\u003e\u0026nbsp;gracilis\u003c/em\u003e are lacking.\u003c/p\u003e\n\u003cp\u003eIn this study, K-mer analysis was performed to evaluate the genome size, heterozygosity, repeatability, GC content, chromosome ploidy, and related species relationship with wild\u0026nbsp;\u003cem\u003eS.\u003c/em\u003e\u003cem\u003e\u0026nbsp;gracilis\u0026nbsp;\u003c/em\u003eby genome survey sequencing technology. The results provide theoretical reference for genome assembly, molecular mechanism research of pharmacodynamic component synthesis, functional gene resource mining, and new drug development and innovation of\u0026nbsp;\u003cem\u003eS.\u003c/em\u003e\u003cem\u003e\u0026nbsp;gracilis\u003c/em\u003e.\u003c/p\u003e"},{"header":"Results","content":"\u003cp\u003e\u003cstrong\u003eMorphological characteristics of\u003c/strong\u003e \u003cstrong\u003eS. gracilis\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eTo investigate the genomic characteristics of wild \u003cem\u003eS. gracilis\u003c/em\u003e, we collected plant samples from the nature reserve near Shandan Horse Farm three, Shandan County, Zhangye City, Gansu Province, China (Fig. \u003cspan class=\"InternalRef\"\u003e1\u003c/span\u003eA). Wild \u003cem\u003eS. gracilis\u003c/em\u003e is a perennial herb with a plant height of 50\u0026ndash;120 cm (Fig. \u003cspan class=\"InternalRef\"\u003e1\u003c/span\u003eB). The root is large and conical, the stem is round and multi-branched, the cauline leaves are 2\u0026ndash;3 pinnately divided, and the umbellate inflorescence is small (Fig. \u003cspan class=\"InternalRef\"\u003e1\u003c/span\u003eB).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eGenome sequencing and quality control of\u003c/strong\u003e \u003cstrong\u003eS. gracilis\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eBased on the second-generation Illumina NovaSeq sequencing platform, the genomic DNA of \u003cem\u003eS. gracilis\u003c/em\u003e was sequenced to obtain 109.64 Gb raw sequencing data, resulting in 96.16 Gb quality sequencing data after filtering (Table \u003cspan class=\"InternalRef\"\u003e1\u003c/span\u003e). The distribution of each read sequence length over all sequences was 150 bp (Fig. \u003cspan class=\"InternalRef\"\u003e2\u003c/span\u003e), indicating that the sequencing quality was stable and accurate. An evaluation of the sequencing quality showed that the Q20 and Q30 values of \u003cem\u003eS. gracilis\u003c/em\u003e were 98.09% and 94.74% (Table \u003cspan class=\"InternalRef\"\u003e1\u003c/span\u003e), respectively, revealing that the genomic data were reliable and could be used for the subsequent analysis. Most of the quality values of the sequencing data in the \u003cem\u003eS. gracilis\u003c/em\u003e genome were greater than 35 (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003e), indicating that read quality of the genome sequencing and the reliability of the sequencing results were high. The complementary bases of A and T, and C and G in the genome sequencing data \u003cem\u003eS. gracilis\u003c/em\u003e were essentially the same, and the position base N was 0. The GC content of the genome was approximately 35.70% (Table \u003cspan class=\"InternalRef\"\u003e1\u003c/span\u003e). The GC distribution map showed that the GC content of the sequencing results followed a normal distribution (Fig. \u003cspan class=\"InternalRef\"\u003e4\u003c/span\u003e), indicating that there was no bias and that the data was not contaminated by exogenous species. In addition, the proportion of A, G, C, and T in each base position in the sequencing results was balanced (Fig. \u003cspan class=\"InternalRef\"\u003e4\u003c/span\u003e), further confirming the high reliability of the sequencing results. The GC content distribution exhibited a single peak, demonstrating normally (Fig. \u003cspan class=\"InternalRef\"\u003e5\u003c/span\u003e). The sequencing results were consistent with the GC content of all the genes expressed in the species. However, due to the low sequencing quality of the first few bases and the deviation of the DNA template amplification, these bases exhibited large fluctuations, which is expected. In summary, the results prove that the genome survey of\u0026nbsp;\u003cem\u003eS. gracilis\u003c/em\u003e has obtained high-quality sequencing data.\u003c/p\u003e\n\u003cdiv class=\"gridtable\"\u003e\u0026nbsp;\u003ctable id=\"Tab1\" border=\"1\"\u003e\n \u003ccaption language=\"En\"\u003e\n \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e\n \u003cdiv class=\"CaptionContent\"\u003e\n \u003cp\u003eSurvey sequencing data of the \u003cem\u003eSphallerocarpus_gracilis\u003c/em\u003e genome\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003ccolgroup cols=\"7\"\u003e\u003c/colgroup\u003e\n \u003cthead\u003e\n \u003ctr\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eType\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eReadNum\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eBaseCount (Gb)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eReadLength (bp)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eQ20 (%)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eQ30 (%)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eGC Content (%)\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003c/thead\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eraw\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e730,929,594\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e109.64\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e150\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e97.11\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e93.44\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e36.18\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003ededup\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e651,373,830\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e96.16\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e147\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e98.09\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e94.74\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e35.70\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n \u003c/table\u003e\n\u003c/div\u003e\n\u003cp\u003e\u003cstrong\u003eEvaluation of the genome size and heterozygosity of\u003c/strong\u003e \u003cstrong\u003eS. gracilis\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eK-mer analysis was employed to estimate the genome size, heterozygosity, and repeatability of the species, with a Kvalue of 17. The results of the K-mer analysis showed that the size of the \u003cem\u003eS. gracilis\u003c/em\u003e genome was about 1,071 Mb, with a corrected genome size of 1,063 Mb (Table \u003cspan class=\"InternalRef\"\u003e2\u003c/span\u003e, Fig. \u003cspan class=\"InternalRef\"\u003e5\u003c/span\u003e). The heterozygosity rate was 1.22%, and the proportion of repeat sequences was 76.33% (Table \u003cspan class=\"InternalRef\"\u003e2\u003c/span\u003e, Fig. \u003cspan class=\"InternalRef\"\u003e6\u003c/span\u003e). The K-mer depth distribution revealed the presence of a peak at 1/2 of the main peak position (Fig. \u003cspan class=\"InternalRef\"\u003e6\u003c/span\u003e). This indicates that the heterozygosity of \u003cem\u003eS. gracilis\u003c/em\u003e genome was high. Moreover, the K-mer curve showed obvious tailing (Fig. \u003cspan class=\"InternalRef\"\u003e6\u003c/span\u003e), suggesting that the content of repetitive sequences in \u003cem\u003eS. gracilis\u003c/em\u003e genome was high. These results indicate that the\u0026nbsp;\u003cem\u003eS. gracilis\u003c/em\u003e genome belongs to a species with a large genome, high heterozygosity, and numerous repeat sequences.\u003c/p\u003e\n\u003cdiv class=\"gridtable\"\u003e\u0026nbsp;\u003ctable id=\"Tab2\" border=\"1\"\u003e\n \u003ccaption language=\"En\"\u003e\n \u003cdiv class=\"CaptionNumber\"\u003eTable 2\u003c/div\u003e\n \u003cdiv class=\"CaptionContent\"\u003e\n \u003cp\u003eGenomic characteristics of \u003cem\u003eSphallerocarpus_gracilis\u003c/em\u003e (K\u0026thinsp;=\u0026thinsp;17)\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003ccolgroup cols=\"6\"\u003e\u003c/colgroup\u003e\n \u003cthead\u003e\n \u003ctr\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eK-mer number\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eK-mer Depth\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eGenome Size (bp)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eRevised Genome Size (bp)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eHeterozygous Ratio (%)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eRepeat (%)\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003c/thead\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e85,719,933,597\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e80\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e1,071,499,170\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e1,063,284,596\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e1.22\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e76.33\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n \u003c/table\u003e\n\u003c/div\u003e\n\u003cp\u003e\u003cstrong\u003eDetermination of the\u003c/strong\u003e \u003cstrong\u003eS. gracilis\u003c/strong\u003e \u003cstrong\u003eploidy using smudgeplots\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe genomic structure and ploidy of \u003cem\u003eS. gracilis\u003c/em\u003e were analyzed using smudgeplots. The peak value of the AB ploidy of the \u003cem\u003eS. gracilis\u003c/em\u003e genome was determined as 0.63 (Table \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003e) and followed a single peak curve (Fig. \u003cspan class=\"InternalRef\"\u003e7\u003c/span\u003e), it to be a heterozygous diploid. This is consistent with the reported genome ploidy of carrot (\u003cem\u003eDaucus carota\u003c/em\u003e).\u003c/p\u003e\n\u003cdiv class=\"gridtable\"\u003e\u0026nbsp;\u003ctable id=\"Tab3\" border=\"1\"\u003e\n \u003ccaption language=\"En\"\u003e\n \u003cdiv class=\"CaptionNumber\"\u003eTable 3\u003c/div\u003e\n \u003cdiv class=\"CaptionContent\"\u003e\n \u003cp\u003eSmudgeplot analysis results of the \u003cem\u003eSphallerocarpus_gracilis\u003c/em\u003e genome\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003ccolgroup cols=\"5\"\u003e\u003c/colgroup\u003e\n \u003cthead\u003e\n \u003ctr\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003epeak\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003ekmers\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003ekmers (%)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003esummit B / (A\u0026thinsp;+\u0026thinsp;B)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003esummit A\u0026thinsp;+\u0026thinsp;B\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003c/thead\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAB\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e16,443,246\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.63\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.48\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e78.73\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAABB\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e4,361,639\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.17\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.49\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e162.2\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAAB\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,437,341\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.13\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.32\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e114.51\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAAAABB\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e980,872\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.04\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.32\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e233.75\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAAAAB\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e706,114\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.03\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.19\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e209.9\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n \u003c/table\u003e\n\u003c/div\u003e\n\u003cp\u003e\u003cstrong\u003eRelative species of\u003c/strong\u003e \u003cstrong\u003eS. gracilis\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe NCBI database was used to compare with the nucleic acid sequence of \u003cem\u003eS. gracilis\u003c/em\u003e. The read matching rates of \u003cem\u003eDaucus carota\u003c/em\u003e (4.78%), \u003cem\u003eAnthriscus Hoffm\u003c/em\u003e (1.16%), \u003cem\u003eHedera helix\u003c/em\u003e (1.10%), \u003cem\u003eOstericum sieboldii\u003c/em\u003e (1.00%), and \u003cem\u003eApium graveolens\u003c/em\u003e (0.97%) were relatively high (Table \u003cspan class=\"InternalRef\"\u003e4\u003c/span\u003e). This suggests that \u003cem\u003eDaucus carota\u003c/em\u003e is a relative species of \u003cem\u003eS. gracilis\u003c/em\u003e. No abnormal results were observed with other species such as animals in the comparison data.\u003c/p\u003e\n\u003cdiv class=\"gridtable\"\u003e\u0026nbsp;\u003ctable id=\"Tab4\" border=\"1\"\u003e\n \u003ccaption language=\"En\"\u003e\n \u003cdiv class=\"CaptionNumber\"\u003eTable 4\u003c/div\u003e\n \u003cdiv class=\"CaptionContent\"\u003e\n \u003cp\u003eComparison of high-quality data NT library of \u003cem\u003eSphallerocarpus gracilis\u003c/em\u003e plants\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003ccolgroup cols=\"7\"\u003e\u003c/colgroup\u003e\n \u003cthead\u003e\n \u003ctr\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eGenus\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eKingdom\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eBlast number\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eHit number\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003ePercentage of hits (%)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003ePercentage of extraction (%)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eMedian identity (%)\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003c/thead\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eDaucus\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e956\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e26.13\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e4.78\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e91.25\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eAnthriscus\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e232\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e6.34\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1.16\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.31\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eHedera\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e220\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e6.01\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1.10\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e84.91\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eOstericum\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e199\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e5.44\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1.00\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.33\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eApium\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e194\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e5.30\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.97\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e100.00\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eFerula\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e152\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e4.15\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.76\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.16\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003ePulicaria\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e80\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e2.19\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.40\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e83.99\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eHeracleum\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e69\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1.89\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.34\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e100.00\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eTorilis\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e63\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1.72\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.32\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e98.67\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003ePternopetalum\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e52\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1.42\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.26\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e98.67\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eSolanum\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e46\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1.26\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.23\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e84.62\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eSphallerocarpus\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e41\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1.12\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.21\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.33\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eZizia\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e40\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1.09\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.20\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e100.00\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eSaposhnikovia\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e38\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1.04\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.19\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.33\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003ePanax\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e32\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.87\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.16\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e100.00\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eGossypium\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e32\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.87\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.16\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e86.07\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eChenopodium\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e29\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.79\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.14\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e88.36\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eAngelica\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e28\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.77\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.14\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.33\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eVigna\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e27\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.74\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.14\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e83.19\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eIpomoea\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e27\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.74\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.14\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e84.21\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eMedicago\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e26\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.71\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.13\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e85.83\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eCuminum\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e26\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.71\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.13\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e98.67\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eImpatiens\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e24\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.66\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.12\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e84.92\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eGeum\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e21\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.57\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.10\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e90.20\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eScutellaria\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e21\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.57\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.10\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e84.93\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003ePeucedanum\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e20\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.55\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.10\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.67\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eMusa\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e18\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.49\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.09\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e90.34\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eHansenia\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e18\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.49\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.09\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e98.67\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eBallota\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e18\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.49\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.09\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e83.21\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eOsmorhiza\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e17\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.46\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.08\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e98.67\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eClematis\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e17\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.46\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.08\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e100.00\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eHymenidium\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e16\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.44\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.08\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.33\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eCicer\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e16\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.44\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.08\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e88.83\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eFraxinus\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e16\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.44\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.08\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e83.72\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003ePhysospermopsis\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e16\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.44\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.08\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.67\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eBupleurum\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e16\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.44\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.08\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e99.33\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eLigusticum\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e15\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.41\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.07\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e98.01\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eSinocarum\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e15\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.41\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.07\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e98.66\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eArachis\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e15\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.41\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.07\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e96.00\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eMeeboldia\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e14\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.38\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.07\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e98.01\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eTheobroma\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eViridiplantae\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e14\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e3,659\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.38\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e0.07\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e86.15\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n \u003c/table\u003e\n\u003c/div\u003e"},{"header":"Discussion","content":"\u003cp\u003eThe analysis of whole genome information based on sequencing technology lays a foundation for the study of plant origin, evolution, reproduction, development, resistance and sex regulation. Considering the large differences in the heterozygosity and repeat content of the genomes of different species, it is important to determine the genome characteristics before whole genome sequencing. A genome survey is a low-depth sequencing method based on small fragment libraries that can quickly obtain the genome size, heterozygosity, and weight by K-mer analysis \u003csup\u003e7,20\u003c/sup\u003e. The analysis of filtered high-quality data revealed that the heterozygosity of the \u003cem\u003eS. gracilis\u003c/em\u003e genome was 1.22% and the proportion of repetitive sequences was 76.33% (Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e). This indicates that the \u003cem\u003eS. gracilis\u003c/em\u003e genome is complex with high repetition and high heterozygosity. A heterozygosity exceeding 0.8% is typically considered to be high \u003csup\u003e21\u003c/sup\u003e. A heterozygosity increases the difficulty of genome-wide assembly and interferes with the estimation progress of K-mer, making the estimation result deviate from the actual size \u003csup\u003e22\u003c/sup\u003e. The GC content of the \u003cem\u003eS. gracilis\u003c/em\u003e genome was 35.70% (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e), which is within the acceptable range of 25\u0026ndash;65%, indicating the feasibility of the genome assembly \u003csup\u003e23\u003c/sup\u003e. Based on the K-mer and smudgeplot analysis, the genome size of \u003cem\u003eS. gracilis\u003c/em\u003e was estimated to be 1,063 Mb, indicating that it is an AB-type diploid plant (Tables\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e and \u003cspan refid=\"Tab3\" class=\"InternalRef\"\u003e3\u003c/span\u003e, Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003e). This is consistent with previous research that reported the karyotype of \u003cem\u003eS. gracilis\u003c/em\u003e to be 2n\u0026thinsp;=\u0026thinsp;20 \u003csup\u003e24\u003c/sup\u003e. Moreover, most \u003cem\u003eApiaceae\u003c/em\u003e plants are diploid \u003csup\u003e25,26\u003c/sup\u003e, such as \u003cem\u003eDaucus carota\u003c/em\u003e (2n\u0026thinsp;=\u0026thinsp;18) \u003csup\u003e\u003cem\u003e27,28\u003c/em\u003e\u003c/sup\u003e, \u003cem\u003eCoriandrum sativum\u003c/em\u003e (2n\u0026thinsp;=\u0026thinsp;22)\u003csup\u003e\u003cem\u003e29\u003c/em\u003e\u003c/sup\u003e, and \u003cem\u003eApium graveolens\u003c/em\u003e (2n\u0026thinsp;=\u0026thinsp;22) \u003csup\u003e\u003cem\u003e30\u003c/em\u003e\u003c/sup\u003e, with genome sizes of 421 Mb, 2130 Mb, and 2.21 Gb, respectively. Our results suggest that \u003cem\u003eS. gracilis\u003c/em\u003e is a species with high repetition, high heterozygosity, and a large genome. The genomic characteristic data of \u003cem\u003eS. gracilis\u003c/em\u003e obtained in this study lay a foundation for subsequent genome sequencing.\u003c/p\u003e \u003cp\u003eThe study of genomics can reveal the genetic diversity, genome evolution, and gene function of species. The phylogenetic tree can directly show the genetic relationship and evolution process \u003csup\u003e31\u003c/sup\u003e. We used high-quality reads to compare NCBI nucleic acid data. The similarity of plants included in the NT library did not exceed 10%, only \u003cem\u003eDaucus carota\u003c/em\u003e was 4.78% (Table\u0026nbsp;\u003cspan refid=\"Tab4\" class=\"InternalRef\"\u003e4\u003c/span\u003e). This may be attributed to the limited sequence information of \u003cem\u003eS. gracilis\u003c/em\u003e and its approximate species included in the NT library. The morphological characteristics of \u003cem\u003eS. gracilis\u003c/em\u003e are similar to those of carrot (\u003cem\u003eDaucus carota\u003c/em\u003e) plants (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eB), and \u003cem\u003eS. gracilis\u003c/em\u003e is also known as the \u0026ldquo;small red carrot\u0026rdquo;. Moreover, the genomes of \u003cem\u003eS. gracilis\u003c/em\u003e and carrot are different by a factor of just 2.5. Thus, the advanced research results of carrot \u003csup\u003e28,32,33\u003c/sup\u003e can provide a reference for further research on \u003cem\u003eS. gracilis\u003c/em\u003e.\u003c/p\u003e \u003cp\u003eWith the rapid development of sequencing and analysis techniques, the genomes of large, highly repeated, and highly heterozygous species have been sequenced at the fine chromosome level \u003csup\u003e34\u0026ndash;38\u003c/sup\u003e. The publication of these high-quality reference genomes provides a basis for the study of the origin and evolution of important economic plants, the protection and utilization of germplasm resources, the molecular mechanism of important component anabolism, and the breeding of new varieties. It also provides a reference for whole genome sequencing and assembly strategies of complex genome species. In this study, the genome size, chromosome ploidy and related species of \u003cem\u003eS. gracilis\u003c/em\u003e were estimated by K-mer analysis. This provides a basis for the subsequent development of the fine mapping of the whole genome of \u003cem\u003eS. gracilis\u003c/em\u003e.\u003c/p\u003e"},{"header":"Materials and methods","content":"\u003cdiv id=\"Sec4\" class=\"Section2\"\u003e \u003ch2\u003ePlant materials and genome DNA extraction\u003c/h2\u003e \u003cp\u003eIn January 2024, wild \u003cem\u003eS. gracilis\u003c/em\u003e was collected with soil from three fields of Junmachang, Shandan County, Zhangye City, Gansu Province (101.05\u0026deg; N, 38.32\u0026deg; W) and brought back to the laboratory of Hexi University (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eA). According to the conventional cultivation method, the root segment of \u003cem\u003eS. gracilis\u003c/em\u003e was planted in a flowerpot with a diameter of the bottom of 18 cm, a diameter of the upper of 30 cm, and a depth of 38 cm. The potted soil comprised equal amounts of sterilized nutrient soil with a volume of 2/3 of the flowerpot. After one month of plant growth, young leaves were selected, frozen in liquid nitrogen, and stored in a refrigerator at \u0026minus;\u0026thinsp;80\u0026deg;C. According to the manufacturer\u0026rsquo;s instructions, total genomic DNA was extracted from the young leaf tissues using the SteadyPure Plant Genomic DNA Extraction Kit (Accurate Biotechnology, Co., Ltd). The quality, purity and concentration of DNA samples were detected by 1% agarose electrophoresis and a Nanodrop2000 Spectrophotometer (Thermo Scientific, USA).\u003c/p\u003e \u003c/div\u003e\n\u003ch3\u003eLibrary preparation and sequencing\u003c/h3\u003e\n\u003cp\u003eThe genome survey was completed by Wuhan OneMore Technology Co., Ltd. A library of 300\u0026ndash;400 bp fragments was constructed from the DNA sample. The DNA fragments were subjected to end repair, 3' A tailing and ligation with adaptors \u003csup\u003e39\u003c/sup\u003e. Double-end (PE, paired-end, 150) sequencing was then performed on the constructed library based on the DNBseq sequencing platform.\u003c/p\u003e\n\u003ch3\u003eQuality control of sequencing data\u003c/h3\u003e\n\u003cp\u003eThe raw data obtained by sequencing were filtered by FASTQC v0.12.0 \u003csup\u003e40\u003c/sup\u003e to obtain high-quality data (clean data) for the analysis of the GC content, heterozygosity, and genome size. For the analysis, the adaptor sequences of reads were removed \u003csup\u003e41\u003c/sup\u003e, the inaccurate bases at both ends of the reads were cut off, and five bases at the left and right ends were cut off. Moreover, reads containing more than 10% N were removed and read pairs with more than 20% of the base mass fraction less than 20 in a read were discarded.\u003c/p\u003e \u003cp\u003e \u003cb\u003eEstimation of the\u003c/b\u003e \u003cb\u003eS. gracilis\u003c/b\u003e \u003cb\u003egenome size using K-mer analysis\u003c/b\u003e\u003c/p\u003e \u003cp\u003eBased on the clean data, the K-mer method \u003csup\u003e20\u003c/sup\u003e was employed to estimate the genome size of \u003cem\u003eS. gracilis\u003c/em\u003e. The K value was set as 17 and the K-mer of the four bases in A, T, C, and G was counted. The Lander\u0026ndash;Waterman algorithm was used to calculate the K-mer total and depth. The K-mer curve frequency distribution was drawn based on the calculated K-mer. The K-mer depth C value was obtained using the curve and the genome size was estimated.\u003c/p\u003e \u003cp\u003e \u003cb\u003ePloidy estimation of\u003c/b\u003e \u003cb\u003eS. gracilis\u003c/b\u003e\u003c/p\u003e \u003cp\u003eSmudgeplot v0.4.0 \u003csup\u003e6\u003c/sup\u003e was used to estimate ploidy levels of \u003cem\u003eS. gracilis\u003c/em\u003e from modified reads generated by the default settings of MECAT v2.0 \u003csup\u003e42\u003c/sup\u003e. Smudgeplot extracts heterozygous K-mer pairs from the K-mer database of sequencing data and trains heterozygous K-mer pairs. By comparing the total number and relative coverage of K-mer pairs, the number of heterozygous K-mers pairs was counted to analyze the genome structure.\u003c/p\u003e \u003cp\u003e \u003cb\u003eComparative analysis of near-source species of\u003c/b\u003e \u003cb\u003eS. gracilis\u003c/b\u003e\u003c/p\u003e \u003cp\u003eTo study the similarity between \u003cem\u003eS. gracilis\u003c/em\u003e and its related species, we randomly selected 10,000 single-end reads data from the filtered high-quality data, and compared them with the NCBI nucleotide database (NT library, July 4, 2024) using Blast.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e \u003ch2\u003eCompeting interests\u003c/h2\u003e \u003cp\u003eThe authors have no conflict of interest declaring.\u003c/p\u003e \u003c/p\u003e\u003cp\u003e \u003ch2\u003ePermissions Statement\u003c/h2\u003e \u003cp\u003eWe have obtained permission or authority for the collection, sequencing and related research work of \u003cem\u003eS. gracilis\u003c/em\u003e plant materials. The wild \u003cem\u003eS. gracilis\u003c/em\u003e has been deposited in the Herbarium of Agricultural and Ecological Engineering College of Hexi University. The wild \u003cem\u003eS. gracilis\u003c/em\u003e materials were identified by Dr. C.Z. and Dr. S.Q.\u003c/p\u003e \u003c/p\u003e\u003ch2\u003eAuthor Contribution\u003c/h2\u003e\u003cp\u003eS.Q. and C.Z. planned and designed the research. Y.C. and R.Z. collected plant materials. S.Q., C.Z., F.Y., Z.X., G.Z., and H.S. performed the experiments. S.Q. and C.Z. drafed and revised the manuscript. All the authors reviewed and approved the manuscript.\u003c/p\u003e\u003ch2\u003eAcknowledgements\u003c/h2\u003e \u003cp\u003eWe are grateful to the professional editors of Charlesworth Author Services for critical reading and revision of the manuscript. This work was supported by National Natural Science Foundation of China (No. 32160745); Natural Science Foundation of Gansu Province (No.22JR5RG566).\u003c/p\u003e\u003ch2\u003eData Availability\u003c/h2\u003e\u003cp\u003eSequence data that support the findings of this study have been deposited in the NCBI Sequence Read Archive (SRA) on January 17,2025 with the primary accession code PRJNA1211825, entitled Sphallerocarpus gracilis Genome sequencing and assembly.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003eZY, W., AM, L., YC, T., ZD, C. \u0026amp; DZ, L. The families and genera of Angiosperms in China a comprehensive analysis. (Beijing: Science Press, 2003).\u003c/li\u003e\n\u003cli\u003eHuixian, J., Qing, Z., Xiangqing, Y., Zhenxia, Z. \u0026amp; Mingyan, Z. Studies on distribution and content of trace elements of Shandan Huangshen. \u003cem\u003eActa Botanica Boreali-Occidentalia Sinica\u003c/em\u003e\u003cstrong\u003e21\u003c/strong\u003e, 188\u0026ndash;190, doi:https://doi.org/1000-4025-(2001)01-0188-03 (2001).\u003c/li\u003e\n\u003cli\u003eYe, C., Tianren, C. \u0026amp; Guanghong, L. 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The analysis of the genomic characteristic information of \u003cem\u003eS. gracilis\u003c/em\u003e can lay a theoretical foundation for whole genome sequencing and molecular mechanism research of the biosynthesis of bioactive active ingredients. In this study, survey genome sequencing technology was employed to evaluate the genomic characteristics of \u003cem\u003eS. gracilis\u003c/em\u003e using K-mer analysis, and smudgeplot analysis was used to evaluate its chromosome ploidy. The K-mer analysis results showed that the genome size of the sample was approximately 1,071 Mb, and the corrected genome size was 1,063 Mb. The heterozygosity rate, the proportion of repeat sequences, and GC content were determined 1.22%, 76.33%, and 35.70%, respectively. Based on the smudgeplot analysis, the maximum possible ploidy of the analyzed species was AB type, corresponding to a diploid plant. Blast analysis revealed \u003cem\u003eS. gracilis\u003c/em\u003e to have a close relative relationship with Daucus carota (4.78%). In summary, the results indicate that the genome of \u003cem\u003eS.gracilis\u003c/em\u003e is a complex and large genome with high heterozygosity and repetition and a large genome. This study provides a theoretical basis for future whole genome sequencing and related research.\u003c/p\u003e","manuscriptTitle":"Genome Survey of Sphallerocarpus gracilis Based on High-throughput Sequencing","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-01-24 20:16:50","doi":"10.21203/rs.3.rs-5782050/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"a56083c2-118e-4fad-8cde-9c644677c4c5","owner":[],"postedDate":"January 24th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":43246511,"name":"Biological sciences/Biological techniques/Genomic analysis/Genome wide analysis of gene expression"},{"id":43246512,"name":"Biological sciences/Biotechnology/Genomics"},{"id":43246513,"name":"Biological sciences/Plant sciences/Plant genetics"},{"id":43246514,"name":"Biological sciences/Plant sciences/Plant molecular biology"}],"tags":[],"updatedAt":"2025-04-18T08:54:11+00:00","versionOfRecord":[],"versionCreatedAt":"2025-01-24 20:16:50","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-5782050","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-5782050","identity":"rs-5782050","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}