Wainaina James M, Kubatko Laura, Harvey Jagger, Ateka Elijah, Makori Timothy, Karanja David, Boykin Laura M, Kehoe Monica A
School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, Australia.
Ohio State University, Columbus, OH, United States of America.
PeerJ. 2019 Feb 13;7:e6297. doi: 10.7717/peerj.6297. eCollection 2019.
Plant viral diseases are one of the major limitations in legume production within sub-Saharan Africa (SSA), as they account for up to 100% in production losses within smallholder farms. In this study, field surveys were conducted in the western highlands of Kenya with viral symptomatic leaf samples collected. Subsequently, next-generation sequencing was carried out to gain insights into the molecular evolution and evolutionary relationships of Bean common mosaic necrosis virus (BCMNV) and Cowpea aphid-borne mosaic virus (CABMV) present within symptomatic common bean and cowpea. Eleven near-complete genomes of BCMNV and two for CABMV were obtained from western Kenya. Bayesian phylogenomic analysis and tests for differential selection pressure within sites and across tree branches of the viral genomes were carried out. Three well-supported clades in BCMNV and one supported clade for CABMNV were resolved and in agreement with individual gene trees. Selection pressure analysis within sites and across phylogenetic branches suggested both viruses were evolving independently, but under strong purifying selection, with a slow evolutionary rate. These findings provide valuable insights on the evolution of BCMNV and CABMV genomes and their relationship to other viral genomes globally. The results will contribute greatly to the knowledge gap involving the phylogenomic relationship of these viruses, particularly for CABMV, for which there are few genome sequences available, and inform the current breeding efforts towards resistance for BCMNV and CABMV.
植物病毒病是撒哈拉以南非洲（SSA）豆类生产的主要限制因素之一，因为它们在小农户农场的生产损失中占比高达100%。在本研究中，对肯尼亚西部高地进行了实地调查，收集了有病毒症状的叶片样本。随后，进行了下一代测序，以深入了解症状明显的普通菜豆和豇豆中存在的菜豆普通花叶坏死病毒（BCMNV）和豇豆蚜传花叶病毒（CABMV）的分子进化及进化关系。从肯尼亚西部获得了11个近乎完整的BCMNV基因组和2个CABMV基因组。进行了贝叶斯系统发育基因组分析以及病毒基因组位点内和跨树枝的差异选择压力测试。BCMNV中解析出三个得到充分支持的进化枝，CABMV中解析出一个得到支持的进化枝，且与单个基因树一致。位点内和系统发育分支的选择压力分析表明，这两种病毒均独立进化，但处于强烈的纯化选择之下，进化速率缓慢。这些发现为BCMNV和CABMV基因组的进化及其与全球其他病毒基因组的关系提供了有价值的见解。研究结果将极大地填补这些病毒系统发育基因组关系方面的知识空白，特别是对于CABMV，其可用的基因组序列很少，并为目前针对BCMNV和CABMV抗性的育种工作提供参考。
