中文摘要：水稻黑条矮缩病毒（RBSDV） 可分别在黄河与淮河夏玉米种植区导致玉米粗缩病和水稻黑条矮缩病。然而，从S1到S10整个基因组的多样化与选择还没有被阐述和说明。本研究从中国9个地区采集的玉米和水稻寄主样本中获得了21个RBSDV分离株，进行基因组分子变异、进化、保守区域和其他一些基因组特性的分析。
外文摘要：Rice black-streaked dwarf virus (RBSDV), a Fijivirus, causes maize rough dwarf disease and rice black-streaked dwarf disease in the Yellow and Huai, respectively, River summer maize-growing regions of China. Nevertheless, the diversification and selection of the entire genome from S1 to S10 have not been illuminated. Molecular variation, evolution, conserved regions, and other genomic properties were analyzed in 21 RBSDV isolates from maize (Zea mays L.) and rice (Oryza sativa) hosts sampled from nine geographic locations in China. Low codon adaptation index values ranging from 0.1878 to 0.2918 indicated a low degree of codon-usage bias and low potential expression for all 13 RBSDV ORFs (open reading frames). ORF9-2 showed a stronger effect of codon usage bias than did other ORFs, as the majority of points for this ORF lay close to the standard curve in the Nc plot (the effective number of codons (Nc) versus the frequency of G+C at synonymous third-base positions (GC3)). A 9-bp deletion mutation was detected in the RBSDV genome in the 3’ UTR of S8. Nucleotide diversity analysis indicated that the structural proteins of RBSDV, such as S2 and S4, were all more conserved than non-structural proteins such as S9. Nucleotide diversity (π) was highest among S9 sequences (0.0656), and was significantly higher than among S4 sequences (0.0225, P < 0.01). The number of conserved regions among the 10 segments varied substantially. The highest number of conserved regions (5) was found in S5, whereas no conserved regions were identified in S9. Nucleotide diversity and the number of conserved regions were independent of the lengths of segments. Nucleotide diversity was also not correlated with the number of conserved regions in segments. Ten recombination events in 21 isolates were found in seven segments with breakpoint positions in UTRs, intergenic spacer regions, and gene coding regions. The number of recombination events was also independent of the lengths of segments. RBSDV isolates from China could be phylogenetically classified into two groups using either 10 segment sequences or the concatenated sequence of S1 through S10, regardless of host or geographical location. The phylogenetic tree generated from pairwise nucleotide identities of individual RBSDV segments such as S9 and S3, with nucleotide identity values of 93.74% and 95.86%, respectively, is similar to the tree constructed from the concatenated sequences of the entire RBSDV genome. The 13 RBSDV ORFs were under negative and purifying selection (Ka/Ks < 1). ORF5-2 was under the greatest selection pressure; however, ORF2, which encodes the core protein of RBSDV, was under the lowest selection pressure.
外文关键词：rice black-streaked dwarf virus; molecular diversification; conserved regions;
作者：Zhou, Yu; Zhang, Lin; Zhang, Xiaoming; Zu, Hongyue; Di, Hong; Dong, Ling; Liu, Xianjun; Zeng, Xing; Weng, Jianfeng; Wang, Zhenhua; Li, Xinhai
作者单位：中国农科院
期刊名称：PLANT DISEASE
期刊影响因子：3.173
出版年份：2017
出版刊次：9
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