title: Molecular Genetic Analysis and Evolution of Segment 7 in Rice Black-Streaked Dwarf Virus in China.
abstract: Rice black-streaked dwarf virus (RBSDV) causes maize rough dwarf disease or rice black-streaked dwarf disease and can lead to severe yield losses in maize and rice. To analyse RBSDV evolution, codon usage bias and genetic structure were investigated in 111 maize and rice RBSDV isolates from eight geographic locations in 2013 and 2014. The linear dsRNA S7 is A+U rich, with overall codon usage biased toward codons ending with A (A3s, S7-1: 32.64%, S7-2: 29.95%) or U (U3s, S7-1: 44.18%, S7-2: 46.06%). Effective number of codons (Nc) values of 45.63 in S7-1 (the first open reading frame of S7) and 39.96 in S7-2 (the second open reading frame of S7) indicate low degrees of RBSDV-S7 codon usage bias, likely driven by mutational bias regardless of year, host, or geographical origin. Twelve optimal codons were detected in S7. The nucleotide diversity (π) of S7 sequences in 2013 isolates (0.0307) was significantly higher than in 2014 isolates (0.0244, P = 0.0226). The nucleotide diversity (π) of S7 sequences in isolates from Jinan (0.0391) was higher than that from the other seven locations (P < 0.01). Only one S7 recombinant was detected in Baoding. RBSDV isolates could be phylogenetically classified into two groups according to S7 sequences, and further classified into two subgroups. S7-1 and S7-2 were under negative and purifying selection, with respective Ka/Ks ratios of 0.0179 and 0.0537. These RBSDV populations were expanding (P < 0.01) as indicated by negative values for Tajima's D, Fu and Li's D, and Fu and Li's F. Genetic differentiation was detected in six RBSDV subpopulations (P < 0.05). Absolute Fst (0.0790) and Nm (65.12) between 2013 and 2014, absolute Fst (0.1720) and Nm (38.49) between maize and rice, and absolute Fst values of 0.0085-0.3069 and Nm values of 0.56-29.61 among these eight geographic locations revealed frequent gene flow between subpopulations. Gene flow between 2013 and 2014 was the most frequent.
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, China.
authors.forename: Jianfeng
authors.initials: J
authors.lastname: Weng
authors.affiliation: Institute of Food Crops and Institute of Food Safety and Detection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province, China.
authors.forename: Yanping
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Institute of Food Crops and Institute of Food Safety and Detection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province, China.
authors.forename: Jirong
authors.initials: J
authors.lastname: Wu
authors.affiliation: Institute of Food Crops and Institute of Food Safety and Detection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province, China.
authors.forename: Qingchang
authors.initials: Q
authors.lastname: Meng
authors.affiliation: Institute of Food Crops, Henan Academy of Agricultural Sciences, Zhengzhou, Henan Province, China.
authors.forename: Xiaohua
authors.initials: X
authors.lastname: Han
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, China.
authors.forename: Zhuanfang
authors.initials: Z
authors.lastname: Hao
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, China.
authors.forename: Mingshun
authors.initials: M
authors.lastname: Li
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, China.
authors.forename: Hongjun
authors.initials: H
authors.lastname: Yong
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, China.
authors.forename: Degui
authors.initials: D
authors.lastname: Zhang
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, China.
authors.forename: Shihuang
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, China.
authors.forename: Xinhai
authors.initials: X
authors.lastname: Li
mesh_terms: D001482:Base Composition / Q000235:genetics; D001483:Base Sequence; D003062:Codon / Q000235:genetics; D019143:Evolution, Molecular; D051456:Gene Flow; D014644:Genetic Variation; D006239:Haplotypes / Q000235:genetics; D009711:Nucleotides / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics; D012275:Oryza / Q000821:virology*; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology*; D011995:Recombination, Genetic / Q000235:genetics; D012087:Reoviridae / Q000235:genetics* / Q000302:isolation & purification; D012641:Selection, Genetic
chemical_list: D003062:Codon; D009711:Nucleotides