Molecular Genetic Analysis and Evolution of Segment 7 in Rice Black-Streaked Dwarf Virus in China

doi:10.1371/journal.pone.0131410

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	Molecular Genetic Analysis and Evolution of Segment 7 in Rice Black-Streaked Dwarf Virus in China
	Zhou, Yu 1; Weng, Jianfeng 1; Chen, Yanping 2,3; Wu, Jirong 2,3; Meng, Qingchang 2,3; Han, Xiaohua 4; Hao, Zhuanfang 1; Li, Mingshun 1; Yong, Hongjun 1; Zhang, Degui 1
刊名	PLOS ONE
	2015
卷号	10 期号:6 页码:-
ISSN号	1932-6203
DOI	10.1371/journal.pone.0131410
通讯作者	Zhou, Yu
英文摘要	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 (p) of S7 sequences in 2013 isolates (0.0307) was significantly higher than in 2014 isolates (0.0244, P = 0.0226). The nucleotide diversity (p) 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.
学科主题	Multidisciplinary Sciences
语种	英语
出版者	PUBLIC LIBRARY SCIENCE
WOS记录号	WOS:000358150400105
内容类型	期刊论文
源URL	[http://111.203.20.206/handle/2HMLN22E/4699]
专题	作物科学研究所_职能部门
作者单位	1.Chinese Acad Agr Sci, Inst Crop Sci, Beijing 100193, Peoples R China 2.Jiangsu Acad Agr Sci, Inst Food Crops, Nanjing, Jiangsu, Peoples R China 3.Jiangsu Acad Agr Sci, Inst Food Safety & Detect, Nanjing, Jiangsu, Peoples R China 4.Henan Acad Agr Sci, Inst Food Crops, Zhengzhou, Henan Province, Peoples R China
推荐引用方式 GB/T 7714	Zhou, Yu,Weng, Jianfeng,Chen, Yanping,et al. Molecular Genetic Analysis and Evolution of Segment 7 in Rice Black-Streaked Dwarf Virus in China[J]. PLOS ONE,2015,10(6):-.
APA	Zhou, Yu.,Weng, Jianfeng.,Chen, Yanping.,Wu, Jirong.,Meng, Qingchang.,...&Li, Xinhai.(2015).Molecular Genetic Analysis and Evolution of Segment 7 in Rice Black-Streaked Dwarf Virus in China.PLOS ONE,10(6),-.
MLA	Zhou, Yu,et al."Molecular Genetic Analysis and Evolution of Segment 7 in Rice Black-Streaked Dwarf Virus in China".PLOS ONE 10.6(2015):-.