College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang Province, China; and Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.
College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang Province, China.
Plant Dis. 2017 Sep;101(9):1588-1596. doi: 10.1094/PDIS-12-16-1814-RE. Epub 2017 Jul 12.
Rice black-streaked dwarf virus (RBSDV), a Fijivirus, causes maize rough dwarf disease and rice black-streaked dwarf disease in the summer maize-growing regions of the Yellow and Huai rivers, respectively, in 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 open reading frames (ORFs). 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 nonstructural 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.
水稻锯齿叶矮缩病毒（Rice black-streaked dwarf virus，RBSDV）是斐济病毒属的一种病毒，分别在中国的黄淮海夏玉米种植区引起玉米粗缩病和水稻锯齿叶矮缩病。然而，其 S1 到 S10 全长的多样化和选择仍未得到阐明。本研究分析了来自中国 9 个地理位置的 21 个玉米（Zea mays L.）和水稻（Oryza sativa）宿主的 RBSDV 分离物的全基因组分子变异、进化、保守区和其他基因组特性。所有 13 个 RBSDV 开放阅读框（ORF）的低密码子适应指数值（0.1878 到 0.2918）表明，所有这些 ORF 的密码子使用偏好程度较低，潜在的表达水平也较低。ORF9-2 的密码子使用偏好性比其他 ORF 更强，因为该 ORF 的大多数点都接近 Nc 图中的标准曲线（有效密码子数 [Nc] 与同义第三位置上 G+C 的频率 [GC3]）。在 RBSDV 基因组的 3'UTR 中检测到 S8 的 9 个碱基缺失突变。核苷酸多样性分析表明，RBSDV 的结构蛋白，如 S2 和 S4，比非结构蛋白，如 S9，更为保守。S9 序列的核苷酸多样性（π）最高（0.0656），明显高于 S4 序列（0.0225，P < 0.01）。10 个片段之间的保守区数量差异很大。S5 中有 5 个保守区，而 S9 中没有保守区。核苷酸多样性和保守区数量与片段长度无关。核苷酸多样性也与片段中的保守区数量无关。在 21 个分离物中发现了 7 个片段的 10 个重组事件，其断点位置在 UTR、基因间间隔区和基因编码区。重组事件的数量也与片段长度无关。无论宿主或地理位置如何，使用 10 个片段序列或 S1 到 S10 的串联序列，都可以将中国的 RBSDV 分离物分为两组。基于 S9 和 S3 等个别 RBSDV 片段的核苷酸同一性生成的系统发育树，其核苷酸同一性值分别为 93.74%和 95.86%，与基于整个 RBSDV 基因组串联序列构建的系统发育树相似。RBSDV 的 13 个 ORF 受到负向和纯化选择（Ka/Ks < 1）。ORF5-2 受到的选择压力最大；然而，ORF2，它编码 RBSDV 的核心蛋白，受到的选择压力最小。
