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Genomic analysis of Sweet potato feathery mottle virus from East Africa
Physiological and Molecular Plant Pathology ( IF 2.7 ) Pub Date : 2020-04-01 , DOI: 10.1016/j.pmpp.2020.101473
Godfrey Wokorach 1 , Geoffrey Otim 1, 2 , Joyce Njuguna 3 , Hilary Edema 1 , Vincent Njung'e 3 , Eunice M Machuka 3 , Nasser Yao 3 , Francesca Stomeo 3 , Richard Echodu 1, 2, 4
Affiliation  

Sweet potato feathery mottle virus is a potyvirus that infect sweet potato. The genome of the virus was analysed to understand genetic diversity, evolution and gene flow. Motifs, nucleotide identity and a phylogenetic tree were used to determine phylogroup of the isolates. Gene flow and genetic diversity were tested using DnaSP v.5. Codons evolution were tested using three methods embedded in Datamonkey. The results indicate occurrence of an isolate of phylogroup B within East Africa. Low genetic differentiation was observed between isolates from Kenya and Uganda indicating evidence of gene flow between the two countries. Four genes were found to have positively selected codons bordering or occurring within functional motifs. A motif within P1 gene evolved differently between phylogroup A and B. The evidence of gene flow indicates frequent exchange of the virus between the two countries and P1 gene motif provide a possible marker that can be used for mapping the distribution of the phylogroups.

中文翻译:

东非甘薯羽状斑驳病毒基因组分析

甘薯羽状斑驳病毒是一种感染甘薯的病毒。分析了病毒的基因组以了解遗传多样性、进化和基因流。使用基序、核苷酸同一性和系统发育树来确定分离株的系统群。使用 DnaSP v.5 测试基因流和遗传多样性。使用 Datamonkey 中嵌入的三种方法测试密码子进化。结果表明在东非出现了系统群 B 的分离株。在来自肯尼亚和乌干达的分离株之间观察到低遗传分化,表明两国之间有基因流动的证据。发现四个基因具有与功能基序接壤或出现在功能基序内的积极选择的密码子。P1 基因中的一个基序在系统群 A 和 B 之间进化不同。
更新日期:2020-04-01
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