School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China.
School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China.
Mol Phylogenet Evol. 2020 Aug;149:106848. doi: 10.1016/j.ympev.2020.106848. Epub 2020 May 5.
Sugarcane mosaic virus (SCMV), a member of the genus Potyvirus in the family Potyviridae, is an important pathogen that causes mosaic diseases in maize, sugarcane, canna and other graminaceous species worldwide. Previously, several reports have showed the genetic variation and population structure of SCMV. However, the evolutionary dynamics, synonymous codon usage pattern and adaptive evolution of the virus is unclear. In this study, we performed comprehensive analyses of phylodynamics, composition bias and codon usage of SCMV using 108 complete genomic sequences. Our phylogenetic analysis found six host- and geographically confined phylogenetic lineages within the SCMV non-recombinant isolates. We found a relatively stable and conserved genomic composition with a lower codon usage choice in the SCMV protein coding sequences. Mutation pressure and natural selection have shaped the codon usage patterns of the SCMV protein coding sequences with natural selection being the dominant factor. The codon adaptation index (CAI), relative codon deoptimization index (RCDI) and similarity index (SiD) analyses revealed a stronger correlation between SCMV and maize than between SCMV and sugarcane or canna. Our study is the first to evaluate the codon usage pattern of SCMV based on complete sequences and may provide a better understanding of the origin of SCMV and its evolutionary patterns for future research.
甘蔗花叶病毒（SCMV）是马铃薯 Y 病毒科马铃薯 Y 病毒属的成员，是一种重要的病原体，可导致玉米、甘蔗、美人蕉等禾本科植物在全球范围内发生花叶病。先前已有数份报告显示了 SCMV 的遗传变异和种群结构。然而，该病毒的进化动态、同义密码子使用模式和适应性进化尚不清楚。在这项研究中，我们使用 108 个完整基因组序列对 SCMV 的系统发育动力学、组成偏倚和密码子使用进行了综合分析。我们的系统发育分析发现，在 SCMV 非重组分离株中存在六个以宿主和地理为界限的系统发育谱系。我们发现 SCMV 蛋白编码序列具有相对稳定和保守的基因组组成，密码子使用选择较低。突变压力和自然选择塑造了 SCMV 蛋白编码序列的密码子使用模式，其中自然选择是主导因素。密码子适应指数（CAI）、相对密码子去优化指数（RCDI）和相似性指数（SiD）分析表明，SCMV 与玉米之间的相关性强于 SCMV 与甘蔗或美人蕉之间的相关性。我们的研究首次基于完整序列评估了 SCMV 的密码子使用模式，可为进一步研究 SCMV 的起源及其进化模式提供更好的理解。
