title: Global-scale computational analysis of genomic sequences reveals the recombination pattern and coevolution dynamics of cereal-infecting geminiviruses.
abstract: Genetic diversity and recombination patterns were evaluated for 229 isolates of Wheat dwarf virus (WDV), which are important cereal-infecting geminiviruses. Recombination hot spots were concentrated at the boundary of the genes encoding for the replication protein (Rep), the coat protein (cp) and the movement protein (mp), as well as inside Rep and cp and in the short intergenic regions (SIR). Phylogenomic analyses confirmed that the global population of WDV clustered into two groups according to their specific host: wheat and barley, and the crucial regions for the division of two groups were mp and the large intergenic regions (LIR). The computationally inferred pattern of coevolution between amino acid residues and the predicted 3D structure for the viral proteins provided further differences among the strains or species at the genome and protein level. Pervasive interaction between Rep and Rep A proteins in WDV-wheat-specific group reflected their important and complex function in the replication and transcription of WDV. Furthermore, significant predicted interactions between CP and Rep and CP and Rep A proteins in the WDV-wheat-specific group are thought to be crucial for successful encapsidation and movement of the virus during infection.
authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
authors: Beilei
authors: B
authors: Wu
authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
authors: Xiaonan
authors: X
authors: Shang
authors: Institute for Biosafety in Plant Biotechnology, Federal Research Institute for Cultivated Plants, Julius Kuehn Institute, Erwin-Baur-Straβe 27, 06484, Quedlinburg, Germany.
authors: Jörg
authors: J
authors: Schubert
authors: Institute for Resistance Research and Stress Tolerance, Federal Research Institute for Cultivated Plants, Julius Kuehn Institute, Erwin-Baur-Straβe 27, 06484, Quedlinburg, Germany.
authors: Antje
authors: A
authors: Habekuß
authors: 1] Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022 València, Spain [2] The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe NM87501, USA.
authors: Santiago F
authors: SF
authors: Elena
authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
authors: Xifeng
authors: X
authors: Wang
mesh_terms: D019943:Amino Acid Substitution; D003062:Codon; D019295:Computational Biology / Q000379:methods; D002523:Edible Grain / Q000821:virology; D019143:Evolution, Molecular; D017791:Geminiviridae / Q000145:classification / Q000235:genetics*; D014644:Genetic Variation; D016679:Genome, Viral; D023281:Genomics / Q000379:methods; D005838:Genotype; D054884:Host-Pathogen Interactions; D010802:Phylogeny; D010940:Plant Proteins / Q000378:metabolism; D011485:Protein Binding; D060066:Protein Interaction Maps; D011995:Recombination, Genetic; D012641:Selection, Genetic; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D003062:Codon; D010940:Plant Proteins; D014764:Viral Proteins
references: Arch Virol. 2013 Jun;158(6):1411-24
references: 23340592
references: Viruses. 2011 Sep;3(9):1699-738
references: 21994803
references: J Virol. 2009 Mar;83(6):2697-707
references: 19116260
references: EMBO J. 1989 Feb;8(2):359-64
references: 2721484
references: Arch Virol. 2009;154(3):535-40
references: 19189198
references: Plant Mol Biol. 1988 Jan;11(1):35-43
references: 24272156
references: BMC Evol Biol. 2007 Nov 08;7:214
references: 17996036
references: Virus Res. 2007 Jul;127(1):61-70
references: 17449126
references: Virology. 1991 Oct;184(2):786-90
references: 1887595
references: Virol J. 2012 Oct 20;9:241
references: 23082767
references: PLoS One. 2011 Feb 04;6(2):e16896
references: 21326861
references: Virology. 1994 May 1;200(2):677-85
references: 8178452
references: BMC Evol Biol. 2008 Dec 18;8:335
references: 19094195
references: Phytopathology. 1997 Jul;87(7):737-44
references: 18945096
references: Virus Genes. 2009 Jun;38(3):468-74
references: 19326201
references: PLoS One. 2011;6(5):e19193
references: 21603653
references: J Virol. 2003 Oct;77(20):10808-18
references: 14512531
references: Phytopathology. 2014 Aug;104(8):897-904
references: 24502202
references: J Gen Virol. 1998 Dec;79 ( Pt 12):3091-9
references: 9880027
references: Bioinformatics. 2006 Nov 15;22(22):2821-2
references: 17005535
references: J Mol Biol. 1999 Sep 17;292(2):195-202
references: 10493868
references: Virology. 2005 Jul 5;337(2):273-83
references: 15913696
references: Plant Cell Rep. 2014 Apr;33(4):633-41
references: 24384822
references: BMC Evol Biol. 2011 Dec 02;11:350
references: 22136133
references: PLoS One. 2013 Sep 09;8(9):e74165
references: 24040199
references: Nat Protoc. 2010 Apr;5(4):725-38
references: 20360767
references: J Virol. 2001 Dec;75(23):11686-99
references: 11689650
references: Mol Biol Evol. 2006 Feb;23(2):254-67
references: 16221896
references: J Gen Virol. 2008 Sep;89(Pt 9):2063-2074
references: 18753214
references: Genetics. 2006 May;173(1):9-23
references: 16547113
references: Plant Dis. 2011 Jan;95(1):76
references: 30743673
references: Plant Mol Biol. 1998 Nov;38(5):699-712
references: 9862488
references: PLoS Pathog. 2011 Sep;7(9):e1002203
references: 21949649
references: PLoS Pathog. 2007 Nov;3(11):e181
references: 18052529
references: Mol Biol Evol. 2011 Oct;28(10):2731-9
references: 21546353
references: EMBO J. 1993 Nov;12(11):4445-52
references: 8223454
references: Syst Biol. 2001 Aug;50(4):580-601
references: 12116655
references: Bioinformatics. 2010 Oct 1;26(19):2462-3
references: 20798170
references: Virus Genes. 2014 Feb;48(1):133-9
references: 24122067
references: J Gen Virol. 2007 Nov;88(Pt 11):3154-3165
references: 17947543
references: BMC Bioinformatics. 2004 Aug 19;5:113
references: 15318951
references: Virology. 2007 Aug 15;365(1):210-9
references: 17467025
references: Nucleic Acids Res. 2007;35(10):3375-82
references: 17478507
references: PLoS Pathog. 2011 May;7(5):e1002028
references: 21573141
references: FEBS Lett. 2009 Jun 18;583(12):1825-32
references: 19497325
references: Virology. 2000 Jul 20;273(1):178-88
references: 10891420
references: Virus Res. 2014 Sep 22;190:34-9
references: 25016035