Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses

eLife

Volumn 2015, Issue 4, 2015, Pages

  Li, Ci Xiu ^a   Shi, Mang ^a,b   Tian, Jun Hua ^c   Lin, Xian Dan ^d   Kang, Yan Jun ^a   Chen, Liang Jun ^a   Qin, Xin Cheng ^a   Xu, Jianguo ^a   Holmes, Edward C ^a,b   Zhang, Yong Zhen ^a  

^a CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION   (China)

^b University of Sydney   (Australia)

^c Wuhan Centers for Disease Prevention and Control   (China)

^d Wenzhou Center for Disease Control and Prevention   (China)

Author keywords

Arthropods; Evolution; Negative sense; Phylogeny; Segmentation; Virus

Indexed keywords

COMPLEMENTARY DNA; RIBOSOME RNA;

ARTHROPOD; ARTICLE; DNA EXTRACTION; EVOLUTION; GENETIC VARIABILITY; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; RNA VIRUS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SPECIES IDENTIFICATION; VIRUS GENOME; VIRUS PARTICLE; ANIMAL; BIODIVERSITY; CLASSIFICATION; GENETICS; GENOME; MOLECULAR EVOLUTION; VIROLOGY;

ARTHROPODA; ORTHOMYXOVIRIDAE; RNA VIRUSES; VERTEBRATA;

ANIMALS; ARTHROPODS; BIODIVERSITY; EVOLUTION, MOLECULAR; GENOME; PHYLOGENY; RNA VIRUSES;

EID: 84964694285     PISSN: None     EISSN: 2050084X     Source Type: Journal    
DOI: 10.7554/eLife.05378     Document Type: Article

References (25)

1. Ballinger MJ, Bruenn JA, Hay J, Czechowski D, Taylor DJ. 2014. Discovery and evolution of bunyavirids in arctic phantom midges and ancient bunyavirid-like sequences in insect genomes. Journal of virology 88:8783-8794. doi: 10.1128/JVI.00531-14.
2. Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T. 2009. trimAl: a tool for automated alignmenttrimming in large-scale phylogenetic analyses. Bioinformatics 25:1972-1973. doi: 10.1093/bioinformatics/btp348.
3. Cook S, Chung BY, Bass D, Moureau G, Tang S, McAlister E, Culverwell CL, Glucksman E, Wang H, Brown TD, Gould EA, Harbach RE, de Lamballerie X, Firth AE. 2013. Novel virus discovery and genome reconstruction from field RNA samples reveals highly divergent viruses in dipteran hosts. PloS one 8:e80720. doi: 10.1371/journal.pone.0080720.
4. Cui J, Holmes EC. 2012. Endogenous RNA viruses of plants in insect genomes. Virology 427:77-79. doi: 10.1016/j.virol.2012.02.014.
5. Falk BW, Tsai JH. 1998. Biology and molecular biology of viruses in the genus Tenuivirus. Annual review of phytopathology 36:139-163. doi: 10.1146/annurev.phyto.36.1.139.
6. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular marine biology and biotechnology 3:294-299. doi:
7. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A.2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature biotechnology 29:644-652. doi: 10.1038/nbt.l883.
8. Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phytogenies by maximum likelihood. Systematic biology 52:696-704. doi:
9. Junglen S, Drosten C. 2013. Virus discovery and recent insights into virus diversity in arthropods. Current opinion in microbiology 16:507-513. doi: 10.1016/j.mib.2013.06.005.
10. Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular biology and evolution 30:772-780. doi: 10.1093/molbev/mstOlO.
11. Katzourakis A, Gifford RJ. 2010. Endogenous viral elements in animal genomes. PLoS genetics 6:el001191. doi: 10.1371/journal.pgen.l001191.
12. King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ. 2012. Virus Taxonomy: 9th Report of the International Committee on Taxonomy ofViruses: Elsevier Academic Press.
13. Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nature methods 9:357-359. doi: 10.1038/nmeth.l923.
14. Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN. 2010. RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics 26:493-500. doi: DOI 10.1093/bioinformatics/btp692.
15. Machida RJ, Knowlton N. 2012. PCR primers for metazoan nuclear 18S and 28S ribosomal DNA sequences. PloS one 7:e46180. doi: 10.1371/journal.pone.0046180.
16. Marklewitz M, Handrick S, Grasse W, Kurth A, Lukashev A, Drosten C, Ellerbrok H, Leendertz FH, Pauli G, Junglen S. 2011. Gouleako virus isolated from West African mosquitoes constitutes a proposed novel genus in the family Bunyaviridae. Journal of virology 85:9227-9234. doi: 10.1128/JVI.00230-11.
17. Marklewitz M, Zirkel F, Rwego IB, Heidemann H, Trippner P, Kurth A, Rallies R, Briese T, Lipkin WI, Drosten C, Gillespie TR, Junglen S. 2013. Discovery of a unique novel clade of mosquito-associated bunyaviruses. Journal of virology 87:12850-12865. doi: 10.1128/JVI.01862-13.
18. Qin XC, Shi M, Tian JH, Lin XD, Gao DY, He JR, Wang JB, Li CX, Kang YJ, Yu B, Zhou DJ, Xu J, Plyusnin A, Holmes EC, Zhang YZ. 2014. A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors. Proceedings of the National Academy of Sciences of the United States of America 111:6744-6749. doi: 10.1073/pnas.l324194111.
19. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic acids research 41:D590-596. doi: 10.1093/nar/gksl219.
20. Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
21. Salehi-Ashtiani K, Luptak A, Litovchick A, Szostak JW. 2006. A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene. Science 313:1788-1792. doi: 10.1126/science.ll29308.
22. Tokarz R, Sameroff S, Leon MS, Jain K, Lipkin WI. 2014a. Genome characterization ofLong Island tick rhabdovirus, a new virus identified in Amblyomma americanum ticks. Virology journal 11:26. doi: 10.1186/1743-422X-11-26.
23. Tokarz R, Williams SH, Sameroff S, Sanchez Leon M, Jain K, Lipkin WI. 2014b. Virome Analysis of Amblyomma americanum, Dermacentor variabilis, and Ixodes scapularis Ticks Reveals Novel Highly Divergent Vertebrate and Invertebrate Viruses. Journal of virology 88:11480-11492. doi: 10.1128/JVI.01858-14.
24. Zhang YZ, Zhou DJ, Qin XC, Tian JH, Xiong Y, Wang JB, Chen XP, Gao DY, He YW, Jin D, Sun Q, Guo WP, Wang W, Yu B, Li J, Dai YA, Li W, Peng JS, Zhang GB, Zhang S, Chen XM, Wang Y, Li MH, Lu X, Ye C, de Jong MD, Xu J. 2012. The ecology, genetic diversity, and phylogeny ofHuaiyangshan virus in China. Journal of virology 86:2864-2868. doi: 10.1128/JVI.06192-11.
25. Zhang YZ, Zhou DJ, Xiong Y, Chen XP, He YW, Sun Q, Yu B, Li J, Dai YA, Tian JH, Qin XC, Jin D, Cui Z, Luo XL, Li W, Lu S, Wang W, Peng JS, Guo WP, Li MH, Li ZJ, Zhang S, Chen C, Wang Y, de Jong MD, Xu J. 2011. Hemorrhagic fever caused by a novel tick-borne Bunyavirus in Huaiyangshan, China. Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi 32:209-220.