Complete genome sequence of a Chinese isolate of pepper vein yellows virus and evolutionary analysis based on the CP, MP and RdRp coding regions

详细信息    查看全文

• 作者：Maoyan Liu ; Xiangning Liu ; Xun Li ; Deyong Zhang ; Liangyin Dai…
• 关键词：Pepper vein yellows virus ; Deep sequencing ; Complete genome ; Molecular evolution
• 刊名：Archives of Virology
• 出版年：2016
• 出版时间：March 2016
• 年：2016
• 卷：161
• 期：3
• 页码：677-683
• 全文大小：479 KB
• 参考文献：1.Murakami R, Nakashima N, Hinomoto N, Kawano S, Toyosato T (2011) The genome sequence of pepper vein yellows virus (family Luteoviridae, genus Polerovirus). Arch Virol 156:921–923PubMedCentral CrossRef PubMed
  2.Alfaro-Fernández A, ElShafie EE, Ali MA, El Bashir OOA, Córdoba-Sellés MC, Font San Ambrosio MI (2014) First report of Pepper vein yellows virus infecting hot pepper in Sudan. Plant Dis 98(10):1446–1446CrossRef
  3.Knierim D, Tsai WS, Kenyon L (2013) Analysis of sequences from field samples reveals the presence of the recently described pepper vein yellows virus (genus Polerovirus) in six additional countries. Arch Virol 158:1337–1341CrossRef PubMed
  4.Tiendrébéogo F, Lefeuvre P, Hoareau M, Traoré VS, Barro N, Péréfarres F, Reynaud B, Traoré AS, Konaté G, Lett JM, Traoré O (2011) Molecular and biological characterization of Pepper yellow vein Mali virus (PepYVMV) isolates associated with pepper yellow vein disease in Burkina Faso. Arch Virol 156:483–487CrossRef PubMed
  5.Yonaha T, Toyosato T, Kawano S, Osaki T (1995) Pepper vein yellows virus, a novel luteovirus from bell pepper plants in Japan. Ann Phytopathol Soc Jpn 61:178–184CrossRef
  6.Knierim D, Deng TC, Tsai WS, Green SK, Kenyon L (2010) Molecular identification of three distinct Polerovirus species and a recombinant Cucurbit aphid-borne yellows virus strain infecting cucurbit crops in Taiwan. Plant Pathol 59:991–1002CrossRef
  7.Shang QV, Xiang HY, Han CG, Li DW, Yu JL (2009) Distribution and molecular diversity of three cucurbit-infecting poleroviruses in China. Virus Res 145:341–346CrossRef PubMed
  8.Xiang HY, Shang QX, Han CG, Li DW, Yu JL (2008) Complete sequence analysis reveals two distinct poleroviruses infecting cucurbits in China. Arch Virol 153:1155–1160CrossRef PubMed
  9.Villanueva F, Castillo P, Font MI, Alfaro-Fernández A, Moriones E, Navas-Castillo J (2013) First report of Pepper vein yellows virus infecting sweet pepper in Spain. Plant Dis 97:1261CrossRef
  10.Gibbs AJ, Ohshima K (2010) Potyviruses and the digital revolution. Ann Rev Phytopathol 48:205–223CrossRef
  11.Mohapatra SS, Poole RJ, Dhindsa RS (1987) Changes in protein patterns and translatable messenger RNA populations during cold acclimation of alfalfa. Plant Physiol 84:1172–1176PubMedCentral CrossRef PubMed
  12.Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829PubMedCentral CrossRef PubMed
  13.Wu Q, Wang Y, Cao M, Pantaleo V, Burgyan J, Li WX, Ding SW (2012) Homology-independent discovery of replicating pathogenic circular RNAs by deep sequencing and a new computational algorithm. Proc Natl Acad Sci USA 109:3938–3943PubMedCentral CrossRef PubMed
  14.Wu Q, Luo Y, Lu R, Lau N, Lai EC, Li WX, Ding SW (2010) Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs. Proc Natl Acad Sci USA 107:1606–1611PubMedCentral CrossRef PubMed
  15.Hall TA (1999) BIOEDIT: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nuc Acids Symp Ser 41:95–98
  16.Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 25:4876–4882PubMedCentral CrossRef PubMed
  17.Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) CLUSTAL W and CLUSTALX version 2.0. Bioinformatics 23:2947–2948CrossRef PubMed
  18.Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P (2010) RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26:2462–2463PubMedCentral CrossRef PubMed
  19.Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC (1999) Fulllength human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 73:152–160PubMedCentral PubMed
  20.He Z, Li W, Yasaka R, Huang Y, Zhang Z, Ohshima K, Li S (2014) Molecular variability of sugarcane streak mosaic virus in China based on an analysis of the P1 and CP protein coding regions. Arch Virol 159:1149–1154CrossRef PubMed
  21.Guindon S, Gascuel O (2003) A simple fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704CrossRef PubMed
  22.Posada D (2008) jModelTest: phylogenetic model averaging. Mol Biol Evol 25:1253–1256CrossRef PubMed
  23.Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA 5: molecular evolutionary genetics analysis using maximum-likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739PubMedCentral CrossRef PubMed
  24.Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120CrossRef PubMed
  25.Dayhoff MO, Barker WC, Hunt LT (1983) Establishing homologies in protein sequences. Methods Enzymol 91:524–545CrossRef PubMed
  26.Pamilo P, Bianchi NO (1993) Evolution of the Zfx and Zfy genes: rates and interdependence between the genes. Mol Biol Evol 10:271–281PubMed
  27.Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452CrossRef PubMed
  28.Dombrovsky A, Glanz E, Pearlsman M, Lachman O, Antignus Y (2010) Characterization of Pepper yellow leaf curl virus, a tentative new Polerovirus species causing a yellowing disease of pepper. Phytoparasitica 38:477–486CrossRef
  29.Yin X, Zheng FQ, Tang W, Zhu QQ, Li XD, Zhang GM, Liu HT, Liu BS (2013) Genetic structure of Rice black-streaked dwarf virus populations in China. Arch Virol 158:2505–2515CrossRef PubMed
  30.Wei TY, Yang JG, Liao FR, Liao FL, Gao FL, Lu LM, Zhang XT, Li F, Wu ZJ, Lin QY, Xie LH, Lin HX (2009) Genetic diversity and population structure of Rice stripe virus in China. J Gen Virol 90:1025–1034CrossRef PubMed
  31.Miller WA, Dinesh-Kumar SP, Paul CP (1995) Luteovirus gene expression. Crit Rev Plant Sci 14:179–211CrossRef
  32.Moonan F, Molina J, Mirkov TE (2000) Sugarcane yellowleaf virus:an emerging virus that has evolved by recombination between luteoviral and poleroviral ancestors. Virology 269:156–171CrossRef PubMed
  33.Knierim D, Deng TC, Tsai WS, Green SK, Kenyon L (2010) Molecular identification of three distinct Polerovirus species and a recombinant Cucurbit aphid-borne yellows virus strain infecting cucurbit crops in Taiwan. Plant Pathol 59:991–1002CrossRef
  34.Silva TF, Corrêa RL, Castilho Y, Silvie P, Belot JL, Vaslin MF (2008) Widespread distribution and a new recombinant species of Brazilian virus associated with cotton blue disease. Virol J 5:123PubMedCentral CrossRef PubMed
  35.García-Arenal F, Fraile A, Malpica JM (2001) Variability and genetic structure of plant virus populations. Ann Rev Phytopathol 39:157–186CrossRef
  
• 作者单位：Maoyan Liu (1) (2)
  Xiangning Liu (1) (2)
  Xun Li (1) (4)
  Deyong Zhang (5)
  Liangyin Dai (1) (2)
  Qianjun Tang (1) (2) (3)
  
  1. College of Plant Protection, Hunan Agricultural University, Hunan, 410128, China
  2. Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Hunan, 410128, China
  4. Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50010, USA
  5. Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Hunan, 410125, China
  3. Virus Research Institute, Hunan Agricultural University, Hunan, 410128, China
  
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Biomedicine
  Virology
  Medical Microbiology
  Infectious Diseases
  
• 出版者：Springer Wien
• ISSN：1432-8798

文摘

The genome sequence of pepper vein yellows virus (PeVYV) (PeVYV-HN, accession number KP326573), isolated from pepper plants (Capsicum annuum L.) grown at the Hunan Vegetables Institute (Changsha, Hunan, China), was determined by deep sequencing of small RNAs. The PeVYV-HN genome consists of 6244 nucleotides, contains six open reading frames (ORFs), and is similar to that of an isolate (AB594828) from Japan. Its genomic organization is similar to that of members of the genus Polerovirus. Sequence analysis revealed that PeVYV-HN shared 92 % sequence identity with the Japanese PeVYV genome at both the nucleotide and amino acid levels. Evolutionary analysis based on the coat protein (CP), movement protein (MP), and RNA-dependent RNA polymerase (RdRP) showed that PeVYV could be divided into two major lineages corresponding to their geographical origins. The Asian isolates have a higher population expansion frequency than the African isolates. Negative selection and genetic drift (founder effect) were found to be the potential drivers of the molecular evolution of PeVYV. Moreover, recombination was not the distinct cause of PeVYV evolution. This is the first report of a complete genomic sequence of PeVYV in China.