Whole genome sequence of mulberry crinivirus (MuCV), an uncommon crinivirus containing a tRNA-like structure at the 5'- and 3'-ends of RNA1

Whole genome sequence of mulberry crinivirus (MuCV), an uncommon crinivirus containing a tRNA-like structure at the 5'- and 3'-ends of RNA1 | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Whole genome sequence of mulberry crinivirus (MuCV), an uncommon crinivirus containing a tRNA-like structure at the 5'- and 3'-ends of RNA1 Quan-You Lu, Peng Zhang, Tao-Tao Han, Jia-Xuan Tang, Kui Zhong, and 3 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-1844912/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 07 Jan, 2023 Read the published version in Archives of Virology → Version 1 posted 5 You are reading this latest preprint version Abstract The whole genome sequence of mulberry crinivirus (MuCV), a novel member of the genus Crinivirus (family Closteroviridae ) identified from mulberry ( Morus alba L), was determined. The bipartite genome of MuCV consists of RNA1, which contains 8571 nucleotides (nt) with four putative open reading frames (ORFs), and RNA2, which contains 8082 nt with eight putative ORFs. The most striking features exhibited by MuCV are tRNA-like structures at the 5'- and 3' -ends of RNA1, which have not been reported for all known members of the family Closteroviridae . Phylogenetic analysis based on RdRp amino acid sequences of criniviruses placed MuCV in “Group 1”. Figures Figure 1 Figure 2 full text Criniviruses comprise one of 7 genera within the family Closteroviridae . Except for Potato yellow vein virus (PYVV), which possesses a tripartite genome [1], all viruses in the genus Crinivirus have bipartite, positive-sense single-stranded RNA genomes [2]. Criniviruses infect mainly herbaceous plants and are transmitted by whiteflies of the genera Trialeurodes and Bemisia [3, 4] . Based on the phylogenetic analyses of RdRp amino acid (aa) sequences, criniviruses were designed into three groups. The viruses in “Group 1” are transmitted by T. vaporariorum , viruses in “Group 2” are transmitted by B. tabaci, and viruses in “Group 3” are transmitted by either T. vaporariorum or B. tabaci [2]. Mulberry ( Morus alba L.) is a tree species with important economic and ecological benefits. Mulberry viral disease is one of the most important factors limiting the value of mulberry trees. In 2019, Mulberry crinivirus (MuCV), a novel crinivirus, was identified in a mulberry tree with symptoms including mosaic, mottling and deformation on the leaves by high-throughput sequencing (HTS). MuCV is the first crinivirus to infect woody plants [5]. However, the whole genome of MuCV is not complete. Here, using a combination of HTS and Sager sequencing, we determined the full-length sequence of MuCV, which has a bipartite genome, characterized its genomic organization and phylogeny, and analyzed the sequence features of the 5' and 3' untranslated region (UTR). Double-stranded RNA (dsRNA) was extracted from MuCV-infected mulberry leaves by CF-11-cellulose chromatography and digested with DNase I and RNase A for further enrichment of dsRNA [6]. The gaps between the MuCV RNA1 contigs obtained previously by HTS were filled by reverse transcription (RT)-polymerase chain reaction (PCR) using high-fidelity polymerase, Prime STAR G×L (TaKaRa, Beijing, China) and sequence-specific primers (Table S1), the design of which was based on these contigs sequences as previously described for RNA2 [5]. The 5' and 3' termini of RNA1 and RNA2 of MuCV were determined as previously described [7]. PCR products were ligated into the pEASY ® -Blunt Zero Cloning Vector (TransGen, Beijing, China), and at least 3 independent clones for each PCR product were sequenced (SunYa, Hangzhou, China). All sequence fragments obtained by sequencing were assembled using SeqMan in DNAStar software (DNAStar Inc.) to obtain the full-length genome of MuCV. Multiple sequence alignments were performed using Clustal W in MEGA7.1. A phylogenetic tree was constructed based on the RdRp aa sequence of MuCV and other viruses of the genus Crinivirus using the neighbor-joining method in Mega7.1 [8]. Open reading frames (ORFs) in RNA1 and RNA2 of MuCV were predicted using ORF Finder (https://www.ncbi.nlm.nih.gov/orffinder/). The RNA secondary structure was predicted using mfold (http://www.unafold.org/), and the transmembrane domains in the proteins were predicted using TMHMM (https://services.healthtech.dtu.dk/service.php?TMHMM-2.0). The full-length sequences of RNA1 and RNA2 of MuCV were deposited in GenBank under the accession numbers ON931610 and ON931611, respectively. RNA1 and RNA2 of MuCV are 8571 nt and 8082 nt in length, respectively. RNA1 contains four putative ORFs, namely, ORF1a, ORF1b, ORF2, and ORF3. RNA2 contains eight ORFs (ORF1-OFR8) (Fig. 1b). The 3'-UTRs of MuCV RNA1 and RNA2 are 204 and 188 nt in length, respectively, sharing 42.6% identity. The 5'-UTRs of MuCV RNA1 and RNA2 are 245 and 174 nt in length, respectively, sharing 32.7% identity. Secondary structure analysis of the 5'- and 3'-UTRs of MuCV indicated that the 5'- and 3'-ends of RNA1 have a tRNA-like structure lacking the CCA end, respectively (Fig. 1a), which has not been reported for all known members of the family Closteroviridae [2]. The tRNA-like structures at the 5' and 3' ends are 138 nt and 71 nt, respectively. ORF1a of RNA1 encodes a putative polyprotein of ca . 242 kDa, with papain-like protease (P-Pro), methyltransferase (MT) and RNA helicase (HEL) domains. An alignment of the P-Pro sequence of MuCV with those of other criniviruses found the two catalytic aa (Cys 502 and His 551 ) identified in the protease domain and the putative cleavage site of the protease being located between Gly 570 and Val 571 . Two transmembrane domains at residues 1400-1417 and 1503-1525 were predicted in the region between the MT and HEL motifs. ORF1a terminates with UUUGA identified in most criniviruses and overlaps ORF1b. ORF1b putatively encodes an RNA-dependent RNA polymerase (RdRp), which is probably expressed via + 1 ribosomal frameshift. P5.5 and P6a show no similarity to any proteins available in the public databases and have a transmembrane domain located at residues 21-43 and 23-45, respectively. ORF1 of RNA2 encodes a small protein (P5.6) with a transmembrane domain between residues 7 and 29. P5.6 has no similarity to any other protein available in public databases. ORF2, ORF6, and ORF7 encode a heat shock protein 70 family homolog (HSP70h), major coat protein (CP) and minor coat protein (CPm), respectively, the hallmark genes of members of the family Closteroviridae . P6b, P60, and P9 located between HSP70h and CP, together with P27 located downstream of CPm, are similar to the corresponding proteins in other criniviruses. Phylogenetic analysis of RdRp aa sequences of criniviruses placed MuCV in “Group 1” (Fig. 2). The “Group 1” criniviruses are transmitted by whiteflies of the genus Trialeurodes . However, the whitefly species infesting mulberry trees in China is Bemisia myricae Kuwana , and no species in the genus Trialeurodes have been recorded in the mulberry fields to date. Therefore, we speculate that MuCV is most likely transmitted by Bemisia myricae Kuwana rather than the species in the genus Trialeurodes , although it is placed in “Group 1”. Declarations Acknowledgements This work was partially supported by the Natural Science Foundation of the Jiangsu Higher Education Institutions of China (No.18KJA210001) and the China Agriculture Research System-Sericulture (CARS-18). Conflict of interest The authors declare that they have no conflict of interest. Ethical approval This article does not contain any studies of involving human participants or animals. References Livieratos IC et al (2004) Analysis of the RNA of Potato yellow vein virus: evidence for a tripartite genome and conserved 3'-terminal structures among members of the genus Crinivirus. J Gen Virol 85(Pt 7):2065–2075 Fuchs M et al (2020) ICTV Virus Taxonomy Profile: Closteroviridae. J Gen Virol 101(4):364–365 Kiss ZA, Medina V, Falk BW (2013) Crinivirus replication and host interactions. Front Microbiol 4:99–99 Tzanetakis IE, Martin RR, Wintermantel WM (2013) Epidemiology of criniviruses: an emerging problem in world agriculture. Front Microbiol 4:119 Zhang P et al (2022) First report of a crinivirus infecting mulberry (Morus alba L.) in China. J Plant Pathol 104:447 Lu QY (2014) Studies on a novel virus and a small circular RNA identified from mulberry trees. Fuzhou, Fujian China, Fujian Agriculture and Forestry University Xie J et al (2006) Characterization of debilitation-associated mycovirus infecting the plant-pathogenic fungus Sclerotinia sclerotiorum. J Gen Virol 87(1):241–249 Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol, 33 (7): p. 1870-4 Supplementary Files Mulberrycrinivirus.txt TableS1.docx TableS2.docx Cite Share Download PDF Status: Published Journal Publication published 07 Jan, 2023 Read the published version in Archives of Virology → Version 1 posted Editorial decision: Major Revision 06 Aug, 2022 Reviewers agreed at journal 11 Jul, 2022 Reviewers invited by journal 11 Jul, 2022 Editor assigned by journal 11 Jul, 2022 First submitted to journal 10 Jul, 2022 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. 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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-1844912","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":120101128,"identity":"5269b53f-2dee-4300-8fcf-631dd78c4ed4","order_by":0,"name":"Quan-You Lu","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAtElEQVRIiWNgGAWjYFACxsYDQFKOjb39ANFaGkBKjfl4ziQQbw9IS+I8CQcD4pTLzz7ccJin7HB6mwRDAsOPim2EtRicSwRqOXc4t0268QBjz5nbRGjhYWw4zNsG1CJzIIGZsY0ILfI9EC3pbBIJBsRpYTgD0ZJAvBYDoJaDc86lG7YBA/kgUX6R72F/+OBNmbW8fHv7wQc/KohxGBiwNYOpA8SqB2mpI0HxKBgFo2AUjDgAAB+APhFPNxOvAAAAAElFTkSuQmCC","orcid":"https://orcid.org/0000-0003-4235-1944","institution":"Sericultural Research Institute","correspondingAuthor":true,"submittingAuthor":false,"prefix":"","firstName":"Quan-You","middleName":"","lastName":"Lu","suffix":""},{"id":120101129,"identity":"04b63067-723e-4e88-83cd-2bc34ad31337","order_by":1,"name":"Peng Zhang","email":"","orcid":"","institution":"Jiangsu University of Science and Technology","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Peng","middleName":"","lastName":"Zhang","suffix":""},{"id":120101130,"identity":"ea3296ae-4014-45c9-98a0-7d36d90a1345","order_by":2,"name":"Tao-Tao Han","email":"","orcid":"","institution":"Jiangsu University of Science and Technology","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Tao-Tao","middleName":"","lastName":"Han","suffix":""},{"id":120101131,"identity":"1c7865d9-9107-47c4-9afc-c4ee20068af0","order_by":3,"name":"Jia-Xuan Tang","email":"","orcid":"","institution":"Jiangsu University of Science and Technology","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Jia-Xuan","middleName":"","lastName":"Tang","suffix":""},{"id":120101132,"identity":"8acd16cc-d9c3-4825-b634-784bf0b8330a","order_by":4,"name":"Kui Zhong","email":"","orcid":"","institution":"Jiangsu University of Science and Technology","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Kui","middleName":"","lastName":"Zhong","suffix":""},{"id":120101133,"identity":"4992e301-f4a2-4c25-8efa-f35fe2a7f0fe","order_by":5,"name":"Yu Ma","email":"","orcid":"","institution":"Jiangsu University of Science and Technology","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Yu","middleName":"","lastName":"Ma","suffix":""},{"id":120101134,"identity":"c9dcbb56-3a69-4d17-94eb-255b7066cc93","order_by":6,"name":"William-Kojo Smith","email":"","orcid":"","institution":"Jiangsu University of Science and Technology","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"William-Kojo","middleName":"","lastName":"Smith","suffix":""},{"id":120101135,"identity":"2717826d-4f95-44b2-90be-10e61998ce5f","order_by":7,"name":"Wei-Guo Zhao","email":"","orcid":"","institution":"Jiangsu University of Science and Technology","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Wei-Guo","middleName":"","lastName":"Zhao","suffix":""}],"badges":[],"createdAt":"2022-07-11 02:44:22","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-1844912/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-1844912/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1007/s00705-022-05657-7","type":"published","date":"2023-01-07T18:13:44+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":24045401,"identity":"da4a3037-1bf6-449f-8adb-31efcc7504a3","added_by":"auto","created_at":"2022-07-19 16:09:45","extension":"jpeg","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":609870,"visible":true,"origin":"","legend":"\u003cp\u003eThe tRNA-like structures at the 5'- (left) and 3'-ends (right) of RNA1 (A) and the genome organization of MuCV (B). ORFs are indicated by boxes. Abbreviations: P-Pro: papain-like protease; MT: methyltransferase; HEL: helicase; RdRp: RNA-dependent RNA polymerase; HSP70h: heat shock protein 70 homolog; CP: major coat protein; CPm: minor coat protein. nt: nucleotide; UTR: untranslated region; ORF: open reading frame; aa: deduced amino acid sequence; M.M.: molecular mass.\u003c/p\u003e","description":"","filename":"floatimage1.jpeg","url":"https://assets-eu.researchsquare.com/files/rs-1844912/v1/ea7277800a0b5b3414d344f1.jpeg"},{"id":24045398,"identity":"c123885d-18f7-42ca-97bd-58239c1fffa2","added_by":"auto","created_at":"2022-07-19 16:09:45","extension":"jpeg","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":270209,"visible":true,"origin":"","legend":"\u003cp\u003ePhylogenetic tree constructed based on the RdRp amino acid sequence of MuCV and other viruses of the genus \u003cem\u003eCrinivirus\u003c/em\u003e in the family \u003cem\u003eClosteroviridae\u003c/em\u003e. The full names of the abbreviational criniviruses are listed in Table S2.\u003c/p\u003e","description":"","filename":"floatimage2.jpeg","url":"https://assets-eu.researchsquare.com/files/rs-1844912/v1/14c06d6cc4545f96ca54a1a3.jpeg"},{"id":44715979,"identity":"fd5e8b8b-baca-428e-b351-e5db229af52d","added_by":"auto","created_at":"2023-10-16 18:20:43","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":340099,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-1844912/v1/6a78ef7a-1fbf-4ede-977a-41093c918b80.pdf"},{"id":24045399,"identity":"41d2cf4b-ec19-42ef-9b97-0d69c96183ce","added_by":"auto","created_at":"2022-07-19 16:09:45","extension":"txt","order_by":4,"title":"","display":"","copyAsset":false,"role":"supplement","size":17177,"visible":true,"origin":"","legend":"","description":"","filename":"Mulberrycrinivirus.txt","url":"https://assets-eu.researchsquare.com/files/rs-1844912/v1/ef8ac15b837741bdab3d9cc7.txt"},{"id":24046278,"identity":"80648283-69b3-4873-b7c0-798d8d34074a","added_by":"auto","created_at":"2022-07-19 16:14:45","extension":"docx","order_by":5,"title":"","display":"","copyAsset":false,"role":"supplement","size":17402,"visible":true,"origin":"","legend":"","description":"","filename":"TableS1.docx","url":"https://assets-eu.researchsquare.com/files/rs-1844912/v1/94fb428f9b32624d0abc8f15.docx"},{"id":24045402,"identity":"a0d5469c-0df0-419f-98f9-3d628aa73a41","added_by":"auto","created_at":"2022-07-19 16:09:45","extension":"docx","order_by":6,"title":"","display":"","copyAsset":false,"role":"supplement","size":17575,"visible":true,"origin":"","legend":"","description":"","filename":"TableS2.docx","url":"https://assets-eu.researchsquare.com/files/rs-1844912/v1/1417ca21a60f5ba9cfda6377.docx"}],"financialInterests":"","formattedTitle":"Whole genome sequence of mulberry crinivirus (MuCV), an uncommon crinivirus containing a tRNA-like structure at the 5'- and 3'-ends of RNA1","fulltext":[{"header":"full text","content":"\u003cp\u003eCriniviruses comprise one of 7 genera within the family \u003cem\u003eClosteroviridae\u003c/em\u003e. Except for \u003cem\u003ePotato yellow vein virus\u003c/em\u003e (PYVV), which possesses a tripartite genome [1], all viruses in the genus \u003cem\u003eCrinivirus\u003c/em\u003e have bipartite, positive-sense single-stranded RNA genomes [2]. Criniviruses infect mainly herbaceous plants and are transmitted by whiteflies of the genera \u003cem\u003eTrialeurodes\u003c/em\u003e and \u003cem\u003eBemisia \u003c/em\u003e[3, 4]\u003cem\u003e.\u003c/em\u003e Based on the phylogenetic analyses of RdRp amino acid (aa) sequences, criniviruses were designed into three groups. The viruses in \u0026ldquo;Group 1\u0026rdquo; are transmitted by \u003cem\u003eT. vaporariorum\u003c/em\u003e, viruses in \u0026ldquo;Group 2\u0026rdquo; are transmitted by \u003cem\u003eB. tabaci, \u003c/em\u003e\u003cem\u003eand viruses in \u0026ldquo;Group 3\u0026rdquo; are transmitted by either T. vaporariorum \u003c/em\u003e\u003cem\u003eor B. tabaci\u003c/em\u003e\u003cem\u003e \u003c/em\u003e[2].\u003c/p\u003e\n\u003cp\u003eMulberry (\u003cem\u003eMorus alba\u003c/em\u003e L.) is a tree species with important economic and ecological benefits. Mulberry viral disease is one of the most important factors limiting the value of mulberry trees. In 2019, Mulberry crinivirus (MuCV), a novel crinivirus, was identified in a mulberry tree with symptoms including mosaic, mottling and deformation on the leaves by high-throughput sequencing (HTS). MuCV is the first crinivirus to infect woody plants [5]. However, the whole genome of MuCV is not complete. Here, using a combination of HTS and Sager sequencing, we determined the full-length sequence of MuCV, which has a bipartite genome, characterized its genomic organization and phylogeny, and analyzed the sequence features of the 5\u0026apos; and 3\u0026apos; untranslated region (UTR).\u003c/p\u003e\n\u003cp\u003eDouble-stranded RNA (dsRNA) was extracted from MuCV-infected mulberry leaves by CF-11-cellulose chromatography and digested with DNase I and RNase A for further enrichment of dsRNA [6]. The gaps between the MuCV RNA1 contigs obtained previously by HTS were filled by reverse transcription (RT)-polymerase chain reaction (PCR) using high-fidelity polymerase, Prime STAR G\u0026times;L (TaKaRa, Beijing, China) and sequence-specific primers (Table S1), the design of which was based on these contigs sequences as previously described for RNA2 [5]. The 5\u0026apos; and 3\u0026apos; termini of RNA1 and RNA2 of MuCV were determined as previously described [7]. PCR products were ligated into the \u003cem\u003epEASY\u003c/em\u003e\u003csup\u003e\u0026reg;\u003c/sup\u003e-Blunt Zero Cloning Vector (TransGen, Beijing, China), and at least 3 independent clones for each PCR product were sequenced (SunYa, Hangzhou, China).\u003c/p\u003e\n\u003cp\u003eAll sequence fragments obtained by sequencing were assembled using SeqMan in DNAStar software (DNAStar Inc.) to obtain the full-length genome of MuCV. Multiple sequence alignments were performed using Clustal W in MEGA7.1. A phylogenetic tree was constructed based on the RdRp aa sequence of MuCV and other viruses of the genus \u003cem\u003eCrinivirus\u003c/em\u003e using the neighbor-joining method in Mega7.1 [8]. Open reading frames (ORFs) in RNA1 and RNA2 of MuCV were predicted using ORF Finder (https://www.ncbi.nlm.nih.gov/orffinder/). The RNA secondary structure was predicted using mfold (http://www.unafold.org/), and the transmembrane domains in the proteins were predicted using TMHMM (https://services.healthtech.dtu.dk/service.php?TMHMM-2.0). The full-length sequences of RNA1 and RNA2 of MuCV were deposited in GenBank under the accession numbers ON931610 and ON931611, respectively.\u003c/p\u003e\n\u003cp\u003eRNA1 and RNA2 of MuCV are 8571 nt and 8082 nt in length, respectively. RNA1 contains four putative ORFs, namely, ORF1a, ORF1b, ORF2, and ORF3. RNA2 contains eight ORFs (ORF1-OFR8) (Fig. 1b). The 3\u0026apos;-UTRs of MuCV RNA1 and RNA2 are 204 and 188 nt in length, respectively, sharing 42.6% identity. The 5\u0026apos;-UTRs of MuCV RNA1 and RNA2 are 245 and 174 nt in length, respectively, sharing 32.7% identity. Secondary structure analysis of the 5\u0026apos;- and 3\u0026apos;-UTRs of MuCV indicated that the 5\u0026apos;- and 3\u0026apos;-ends of RNA1 have a tRNA-like structure lacking the CCA end, respectively (Fig. 1a), which has not been reported for all known members of the family \u003cem\u003eClosteroviridae\u003c/em\u003e [2]. The tRNA-like structures at the 5\u0026apos; and 3\u0026apos; ends are 138 nt and 71 nt, respectively.\u003c/p\u003e\n\u003cp\u003eORF1a of RNA1 encodes a putative polyprotein of \u003cem\u003eca\u003c/em\u003e. 242 kDa, with papain-like protease (P-Pro), methyltransferase (MT) and RNA helicase (HEL) domains. An alignment of the P-Pro sequence of MuCV with those of other criniviruses found the two catalytic aa (Cys\u003csub\u003e502\u003c/sub\u003e and His\u003csub\u003e551\u003c/sub\u003e) identified in the protease domain and the putative cleavage site of the protease being located between Gly\u003csub\u003e570\u003c/sub\u003e and Val\u003csub\u003e571\u003c/sub\u003e. Two transmembrane domains at residues 1400-1417 and 1503-1525 were predicted in the region between the MT and HEL motifs. ORF1a terminates with UUUGA identified in most criniviruses and overlaps ORF1b. ORF1b putatively encodes an RNA-dependent RNA polymerase (RdRp), which is probably expressed via + 1 ribosomal frameshift. P5.5 and P6a show no similarity to any proteins available in the public databases and have a transmembrane domain located at residues 21-43 and 23-45, respectively.\u003c/p\u003e\n\u003cp\u003eORF1 of RNA2 encodes a small protein (P5.6) with a transmembrane domain between residues 7 and 29. P5.6 has no similarity to any other protein available in public databases. ORF2, ORF6, and ORF7 encode a heat shock protein 70 family homolog (HSP70h), major coat protein (CP) and minor coat protein (CPm), respectively, the hallmark genes of members of the family \u003cem\u003eClosteroviridae\u003c/em\u003e. P6b, P60, and P9 located between HSP70h and CP, together with P27 located downstream of CPm, are similar to the corresponding proteins in other criniviruses.\u003c/p\u003e\n\u003cp\u003ePhylogenetic analysis of RdRp aa sequences of criniviruses placed MuCV in \u0026ldquo;Group 1\u0026rdquo; (Fig. 2). The \u0026ldquo;Group 1\u0026rdquo; criniviruses are transmitted by whiteflies of the genus \u003cem\u003eTrialeurodes\u003c/em\u003e. However, the whitefly species infesting mulberry trees in China is \u003cem\u003eBemisia myricae Kuwana\u003c/em\u003e, and no species in the genus \u003cem\u003eTrialeurodes\u003c/em\u003e have been recorded in the mulberry fields to date. Therefore, we speculate that MuCV is most likely transmitted by \u003cem\u003eBemisia myricae\u0026nbsp;\u003c/em\u003eKuwana rather than the species in the genus \u003cem\u003eTrialeurodes\u003c/em\u003e, although it is placed in \u0026ldquo;Group 1\u0026rdquo;.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eAcknowledgements\u0026nbsp;\u003c/strong\u003eThis work was partially supported by the Natural Science Foundation of the Jiangsu Higher Education Institutions of China (No.18KJA210001) and the China Agriculture Research System-Sericulture (CARS-18).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConflict of interest\u003c/strong\u003e The authors declare that they have no conflict of interest.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eEthical approval\u003c/strong\u003e This article does not contain any studies of involving human participants or animals.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eLivieratos IC et al (2004) Analysis of the RNA of Potato yellow vein virus: evidence for a tripartite genome and conserved 3'-terminal structures among members of the genus Crinivirus. J Gen Virol 85(Pt 7):2065\u0026ndash;2075\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eFuchs M et al (2020) ICTV Virus Taxonomy Profile: Closteroviridae. J Gen Virol 101(4):364\u0026ndash;365\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eKiss ZA, Medina V, Falk BW (2013) Crinivirus replication and host interactions. Front Microbiol 4:99\u0026ndash;99\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eTzanetakis IE, Martin RR, Wintermantel WM (2013) Epidemiology of criniviruses: an emerging problem in world agriculture. Front Microbiol 4:119\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eZhang P et al (2022) First report of a crinivirus infecting mulberry (Morus alba L.) in China. J Plant Pathol 104:447\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLu QY (2014) Studies on a novel virus and a small circular RNA identified from mulberry trees. Fuzhou, Fujian China, Fujian Agriculture and Forestry University\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eXie J et al (2006) Characterization of debilitation-associated mycovirus infecting the plant-pathogenic fungus Sclerotinia sclerotiorum. J Gen Virol 87(1):241\u0026ndash;249\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eKumar S, Stecher G, Tamura K (2016) \u003cem\u003eMEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.\u003c/em\u003e Mol Biol Evol, \u003cb\u003e33\u003c/b\u003e(7): p.\u0026nbsp;1870-4\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"archives-of-virology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"arvi","sideBox":"Learn more about [Archives of Virology](https://www.springer.com/journal/705)","snPcode":"705","submissionUrl":"https://submission.nature.com/new-submission/705/3","title":"Archives of Virology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-1844912/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-1844912/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eThe whole genome sequence of mulberry crinivirus (MuCV), a novel member of the genus \u003cem\u003eCrinivirus\u003c/em\u003e (family \u003cem\u003eClosteroviridae\u003c/em\u003e) identified from mulberry (\u003cem\u003eMorus alba\u003c/em\u003e L), was determined. The bipartite genome of MuCV consists of RNA1, which contains 8571 nucleotides (nt) with four putative open reading frames (ORFs), and RNA2, which contains 8082 nt with eight putative ORFs. The most striking features exhibited by MuCV are tRNA-like structures at the 5'- and 3' -ends of RNA1, which have not been reported for all known members of the family \u003cem\u003eClosteroviridae\u003c/em\u003e. Phylogenetic analysis based on RdRp amino acid sequences of criniviruses placed MuCV in “Group 1”.\u003c/p\u003e","manuscriptTitle":"Whole genome sequence of mulberry crinivirus (MuCV), an uncommon crinivirus containing a tRNA-like structure at the 5'- and 3'-ends of RNA1","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2022-07-19 16:09:43","doi":"10.21203/rs.3.rs-1844912/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Major Revision","date":"2022-08-06T15:45:43+00:00","index":"","fulltext":""},{"type":"reviewerAgreed","content":"","date":"2022-07-11T09:57:13+00:00","index":0,"fulltext":""},{"type":"reviewersInvited","content":"","date":"2022-07-11T09:08:52+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2022-07-11T07:26:33+00:00","index":"","fulltext":""},{"type":"submitted","content":"Archives of Virology","date":"2022-07-10T22:43:02+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"archives-of-virology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"arvi","sideBox":"Learn more about [Archives of Virology](https://www.springer.com/journal/705)","snPcode":"705","submissionUrl":"https://submission.nature.com/new-submission/705/3","title":"Archives of Virology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"5edb1b2e-07a8-4589-9e22-02ba07bfd8da","owner":[],"postedDate":"July 19th, 2022","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2023-10-16T18:18:08+00:00","versionOfRecord":{"articleIdentity":"rs-1844912","link":"https://doi.org/10.1007/s00705-022-05657-7","journal":{"identity":"archives-of-virology","isVorOnly":false,"title":"Archives of Virology"},"publishedOn":"2023-01-07 18:13:44","publishedOnDateReadable":"January 7th, 2023"},"versionCreatedAt":"2022-07-19 16:09:43","video":"","vorDoi":"10.1007/s00705-022-05657-7","vorDoiUrl":"https://doi.org/10.1007/s00705-022-05657-7","workflowStages":[]},"version":"v1","identity":"rs-1844912","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-1844912","identity":"rs-1844912","version":["v1"]},"buildId":"WrCJVZZCHTDjtuVLN7oU0","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}