{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T01:52:59Z","timestamp":1778637179559,"version":"3.51.4"},"reference-count":51,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2019,11,7]],"date-time":"2019-11-07T00:00:00Z","timestamp":1573084800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["2018T110266"],"award-info":[{"award-number":["2018T110266"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["31801376"],"award-info":[{"award-number":["31801376"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["2017M611344"],"award-info":[{"award-number":["2017M611344"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0224569","type":"journal-article","created":{"date-parts":[[2019,11,7]],"date-time":"2019-11-07T13:46:43Z","timestamp":1573134403000},"page":"e0224569","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":6,"title":["Molecular characteristics of segment 5, a unique fragment encoding two partially overlapping ORFs in the genome of rice black-streaked dwarf virus"],"prefix":"10.1371","volume":"14","author":[{"given":"Hongyue","family":"Zu","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hong","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Minhao","family":"Yao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiayue","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hong","family":"Di","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lin","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ling","family":"Dong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhenhua","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9748-0914","authenticated-orcid":true,"given":"Yu","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2019,11,7]]},"reference":[{"key":"pone.0224569.ref001","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1007\/s12250-011-3170-9","article-title":"Molecular characterization of segments S7 to S10 of a southern rice black-streaked dwarf virus isolate from maize in northern China","volume":"26","author":"X Yin","year":"2011","journal-title":"Virol Sin"},{"key":"pone.0224569.ref002","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1016\/j.gene.2015.07.008","article-title":"Whole-genome expression analysis of Rice black-streaked dwarf virus in different plant hosts and small brown planthopper","volume":"572","author":"QF Xu","year":"2015","journal-title":"Gene"},{"key":"pone.0224569.ref003","doi-asserted-by":"crossref","first-page":"1588","DOI":"10.1094\/PDIS-12-16-1814-RE","article-title":"Rice black-streaked dwarf virus Genome in China: Diversification, Phylogeny, and Selection","volume":"101","author":"Y Zhou","year":"2017","journal-title":"Plant Dis"},{"key":"pone.0224569.ref004","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1007\/s00705-013-1832-2","article-title":"Rice black-streaked dwarf virus genome segment S5 is a bicistronic mRNA in infected plants","volume":"159","author":"J Yang","year":"2014","journal-title":"Arch Virol"},{"key":"pone.0224569.ref005","doi-asserted-by":"crossref","first-page":"1649","DOI":"10.1007\/s00705-013-1660-4","article-title":"Interactions between the P6 and P5-1 proteins of southern rice black-streaked dwarf fijivirus in yeast and plant cells","volume":"158","author":"J Li","year":"2013","journal-title":"Arch Virol"},{"key":"pone.0224569.ref006","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1007\/s00705-015-2382-6","article-title":"P5-2 of rice black-streaked dwarf virus is a non-structural protein targeted to chloroplasts","volume":"160","author":"XY Liu","year":"2015","journal-title":"Arch Virol"},{"key":"pone.0224569.ref007","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1146\/annurev.mi.41.100187.002205","article-title":"Rapid evolution of RNA viruses","volume":"41","author":"DA Steinhauer","year":"1987","journal-title":"Annu. Rev. Microbiol"},{"issue":"1","key":"pone.0224569.ref008","doi-asserted-by":"crossref","DOI":"10.1094\/PHYTO-05-13-0145-R","article-title":"Genetic Variation and Possible Mechanisms Driving the Evolution of Worldwide Fig mosaic virus Isolates","volume":"104","author":"JJ Walia","year":"2014","journal-title":"Phytopathology"},{"issue":"10","key":"pone.0224569.ref009","doi-asserted-by":"crossref","DOI":"10.1094\/PHYTO-01-11-0017","article-title":"Advances in Plant Virus Evolution: Translating Evolutionary Insights into Better Disease Management","volume":"101","author":"R Acosta-Leal","year":"2011","journal-title":"Phytopathology"},{"issue":"1","key":"pone.0224569.ref010","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.virusres.2003.12.002","article-title":"The dsRNA viruses","volume":"101","author":"P. Mertens","year":"2004","journal-title":"VIRUS RES"},{"key":"pone.0224569.ref011","doi-asserted-by":"crossref","first-page":"3197","DOI":"10.1007\/s00705-014-2180-6","article-title":"Genetic variation in potato virus M isolates infecting pepino (Solanum muricatum) in China","volume":"159","author":"BB Ge","year":"2014","journal-title":"Arch Virol"},{"key":"pone.0224569.ref012","doi-asserted-by":"crossref","first-page":"949","DOI":"10.1094\/PHYTO-01-13-0013-R","article-title":"Selection pressure and founder effects constrain genetic variation in differentiated populations of soilborne bymovirus Wheat yellow mosaic virus (Potyviridae) in China","volume":"103","author":"BJ Sun","year":"2013","journal-title":"Phytopathology"},{"key":"pone.0224569.ref013","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0096582","article-title":"Genetic structure and molecular variability of Cucumber mosaic virus isolates in the United States","volume":"9","author":"S Nouri","year":"2014","journal-title":"PLoS One"},{"key":"pone.0224569.ref014","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1146\/annurev.phyto.35.1.191","article-title":"Mechanisms of plant virus evolution","volume":"35","author":"MJ Roossinck","year":"1997","journal-title":"ANNU REV PHYTOPATHOL"},{"key":"pone.0224569.ref015","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1186\/1743-422X-5-156","article-title":"An overview of molecular epidemiology of hepatitis B virus (HBV) in India","volume":"5","author":"S. Datta","year":"2008","journal-title":"Virol J"},{"key":"pone.0224569.ref016","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1006\/viro.1994.1071","article-title":"New overlapping gene encoded by the cucumber mosaic virus genome","volume":"198","author":"SW Ding","year":"1994","journal-title":"Virology"},{"key":"pone.0224569.ref017","doi-asserted-by":"crossref","first-page":"740","DOI":"10.1099\/vir.0.058164-0","article-title":"Biological properties and expression strategy of rosellinia necatrix megabirnavirus 1 analysed in an experimental host, Cryphonectria parasitica","volume":"95","author":"L Salaipeth","year":"2014","journal-title":"J Gen Virol"},{"key":"pone.0224569.ref018","doi-asserted-by":"crossref","first-page":"2596","DOI":"10.1099\/vir.0.82927-0","article-title":"2b ORFs encoded by subgroup IB strains of cucumber mosaic virus induce differential virulence on Nicotiana species","volume":"88","author":"ZY Du","year":"2007","journal-title":"J Gen Virol"},{"key":"pone.0224569.ref019","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.virol.2009.07.007","article-title":"Molecular variability and genetic structure of the population of Soybean mosaic virus based on the analysis of complete genome sequences","volume":"393","author":"JK Seo","year":"2009","journal-title":"Virology"},{"issue":"2","key":"pone.0224569.ref020","doi-asserted-by":"crossref","first-page":"151","DOI":"10.2165\/00822942-200504020-00010","article-title":"JAE: Jemboss Alignment Editor","volume":"4","author":"TJ Carver","year":"2005","journal-title":"Appl Bioinformatics"},{"issue":"7","key":"pone.0224569.ref021","first-page":"1351","article-title":"Molecular variation and recombination in RNA segment 10 of rice black-streaked dwarf virus isolated from China during 2007\u20132010","volume":"2012157","author":"YQ Li","journal-title":"Arch Virol"},{"issue":"12","key":"pone.0224569.ref022","first-page":"1213","article-title":"[Genome sequences of coxsackievirus B5 isolated from viral encephalitis patients in Henan province, 2011]","volume":"34","author":"HX Ma","year":"2013","journal-title":"Zhonghua Liu Xing Bing Xue Za Zhi"},{"key":"pone.0224569.ref023","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1186\/1471-2229-13-98","article-title":"A non-synonymous SNP within theisopentenyl transferase2 locus is associated with kernel weight in Chinese maize inbreds (Zea mays L.)","volume":"13","author":"JF Weng","year":"2013","journal-title":"BMC Plant Biol"},{"issue":"1","key":"pone.0224569.ref024","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/0378-1119(90)90491-9","article-title":"The effective number of codons used in a gene","volume":"87","author":"F. Wright","year":"1990","journal-title":"Gene"},{"issue":"7","key":"pone.0224569.ref025","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1093\/molbev\/msw054","article-title":"MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets","volume":"33","author":"S Kumar","year":"2016","journal-title":"Mol Biol Evol"},{"issue":"1","key":"pone.0224569.ref026","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/ve\/vev003","article-title":"RDP4: Detection and analysis of recombination patterns in virus genomes","volume":"1","author":"DP Martin","year":"2015","journal-title":"Virus Evol"},{"issue":"11","key":"pone.0224569.ref027","doi-asserted-by":"crossref","first-page":"1451","DOI":"10.1093\/bioinformatics\/btp187","article-title":"DnaSP v5: A software for comprehensive analysis of DNA polymorphism data","volume":"25","author":"P Librado","year":"2009","journal-title":"Bioinformatics"},{"issue":"4","key":"pone.0224569.ref028","first-page":"323","article-title":"The genetical structure of populations","volume":"15","author":"S. Wright","year":"1951","journal-title":"Ann Eugen"},{"issue":"18","key":"pone.0224569.ref029","doi-asserted-by":"crossref","first-page":"2496","DOI":"10.1093\/bioinformatics\/btg359","article-title":"DnaSP, DNA polymorphism analyses by the coalescent and other methods","volume":"19","author":"J Rozas","year":"2003","journal-title":"Bioinformatics"},{"key":"pone.0224569.ref030","doi-asserted-by":"crossref","first-page":"1548","DOI":"10.1099\/vir.0.84058-0","article-title":"Genetic diversity and population structure of rice stripe virus in China","volume":"90","author":"TY Wei","year":"2009","journal-title":"J Gen Virol"},{"issue":"1","key":"pone.0224569.ref031","doi-asserted-by":"crossref","first-page":"3248","DOI":"10.1038\/s41598-018-21677-3","article-title":"Identification of a locus conferring dominant resistance to maize rough dwarf disease in maize","volume":"8","author":"RG Li","year":"2018","journal-title":"Sci Rep"},{"key":"pone.0224569.ref032","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1007\/s11032-011-9652-0","article-title":"Identification of a major quantitative trait locus for resistance to maize rough dwarf virus in a Chinese maize inbred line X178 using a linkage map based on 514 gene-derived single nucleotide polymorphisms","volume":"30","author":"LY Shi","year":"2012","journal-title":"MOL BREEDING"},{"key":"pone.0224569.ref033","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1186\/1471-2229-13-145","article-title":"Identification and fine-mapping of a QTL, qMrdd1, that confers recessive resistance to maize rough dwarf disease","volume":"13","author":"YF Tao","year":"2013","journal-title":"BMC Plant Biol"},{"issue":"12","key":"pone.0224569.ref034","doi-asserted-by":"crossref","first-page":"2505","DOI":"10.1007\/s00705-013-1766-8","article-title":"Genetic structure of rice black-streaked dwarf virus populations in China","volume":"158","author":"X Yin","year":"2013","journal-title":"Arch Virol"},{"issue":"4","key":"pone.0224569.ref035","doi-asserted-by":"crossref","first-page":"1119","DOI":"10.1007\/s00705-014-2291-0","article-title":"Phylogenetic and recombination analysis of rice black-streaked dwarf virus segment 9 in China","volume":"160","author":"Y Zhou","year":"2015","journal-title":"Arch Virol"},{"issue":"1","key":"pone.0224569.ref036","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0168-1702(02)00309-X","article-title":"The extent of codon usage bias in human RNA viruses and its evolutionary origin","volume":"92","author":"GM Jenkins","year":"2003","journal-title":"Virus Res"},{"issue":"1","key":"pone.0224569.ref037","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1016\/S0378-1119(01)00576-5","article-title":"Gene expressivity is the main factor in dictating the codon usage variation among the genes in Pseudomonas aeruginosa","volume":"273","author":"SK Gupta","year":"2001","journal-title":"Gene"},{"key":"pone.0224569.ref038","article-title":"Second codon positions of genes and the secondary structures of proteins","author":"ML Chiusano","journal-title":"Relationships and implications for the origin of the genetic code"},{"issue":"1\u20132","key":"pone.0224569.ref039","first-page":"93","article-title":"The relationship between synonymous codon usage and protein structure","volume":"434","author":"T Xie","year":"1998","journal-title":"FEBS Lett"},{"issue":"1","key":"pone.0224569.ref040","doi-asserted-by":"crossref","first-page":"162","DOI":"10.3390\/v5010162","article-title":"Base composition and translational selection are insufficient to explain codon usage bias in plant viruses","volume":"5","author":"DJ Cardinale","year":"2013","journal-title":"Viruses"},{"issue":"18","key":"pone.0224569.ref041","doi-asserted-by":"crossref","first-page":"10698","DOI":"10.1073\/pnas.95.18.10698","article-title":"Replicational and transcriptional selection on codon usage in Borrelia burgdorferi","volume":"95","author":"JO McInerney","year":"1998","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pone.0224569.ref042","doi-asserted-by":"crossref","first-page":"11334","DOI":"10.1038\/ncomms11334","article-title":"Energy efficiency trade-offs drive nucleotide usage in transcribed regions","volume":"7","author":"WH Chen","year":"2016","journal-title":"Nat Commun"},{"issue":"19","key":"pone.0224569.ref043","doi-asserted-by":"crossref","first-page":"4272","DOI":"10.1093\/nar\/gkf546","article-title":"Synonymous codon usage is subject to selection in thermophilic bacteria","volume":"30","author":"DJ Lynn","year":"2002","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"pone.0224569.ref044","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1017\/S1355838201001741","article-title":"A tertiary structure model of the internal ribosome entry site (IRES) for methionine-independent initiation of translation","volume":"7","author":"Y Kanamori","year":"2001","journal-title":"RNA"},{"issue":"5","key":"pone.0224569.ref045","doi-asserted-by":"crossref","first-page":"933","DOI":"10.1007\/s00705-005-0675-x","article-title":"A phylogenetic survey of recombination frequency in plant RNA viruses","volume":"151","author":"ER Chare","year":"2006","journal-title":"Arch Virol"},{"key":"pone.0224569.ref046","doi-asserted-by":"crossref","first-page":"1016","DOI":"10.1099\/vir.0.82402-0","article-title":"Recombination and gene duplication in the evolutionary diversification of P1 proteins in the family Potyviridae","volume":"88","author":"A Valli","year":"2007","journal-title":"J Gen Virol"},{"key":"pone.0224569.ref047","doi-asserted-by":"crossref","first-page":"2535","DOI":"10.1099\/0022-1317-80-10-2535","article-title":"Evolutionary aspects of recombination in RNA viruses","volume":"80","author":"M Worobey","year":"1999","journal-title":"J Gen Virol"},{"issue":"6","key":"pone.0224569.ref048","doi-asserted-by":"crossref","first-page":"1183","DOI":"10.1007\/s007050070118","article-title":"Genetic diversity of rice tungro spherical virus in tungro-endemic provinces of the Philippines and Indonesia","volume":"145","author":"O Azzam","year":"2000","journal-title":"Arch Virol"},{"issue":"2","key":"pone.0224569.ref049","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1007\/s00705-014-2268-z","article-title":"Characterization of homologous and heterologous interactions between viroplasm proteins P6 and P9-1 of the fijivirus southern rice black-streaked dwarf virus","volume":"160","author":"J Li","year":"2015","journal-title":"Arch Virol"},{"key":"pone.0224569.ref050","first-page":"305","article-title":"Two virus-encoded rna silencing suppressors, p14 ofbeet necrotic yellow vein virusand s6 ofrice black streak dwarf virus","volume":"50","author":"LD Zhang","year":"2005","journal-title":"CHINESE SCI BULL"},{"key":"pone.0224569.ref051","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1099\/vir.0.82318-0","article-title":"Baculovirus expression of the 11 mycoreovirus-1 genome segments and identification of the guanylyltransferase-encoding segment","volume":"88","author":"S Supyani","year":"2007","journal-title":"J Gen Virol"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0224569","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,11,7]],"date-time":"2019-11-07T13:47:11Z","timestamp":1573134431000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0224569"}},"subtitle":[],"editor":[{"given":"Ulrich","family":"Melcher","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2019,11,7]]},"references-count":51,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2019,11,7]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0224569","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,11,7]]}}}