DIVERSIFICATION INTO THE GENUS Badnavirus: PHYLOGENY AND POPULATION GENETIC VARIABILITY

C. H. Ferreira, Lucas Jordao, R. Ramos-Sobrinho, M. Ferro, S. J. D. Silva, I. Assunção, G. S. Lima
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引用次数: 4

Abstract

Badnaviruses (family Caulimoviridae) have semicircular dsDNA genomes encapsidated into bacilliform particles. The genus Badnavirus is the most important due to its high number of species reported infecting cultivated plants worldwide. This study aimed to evaluate the phylogenetic positioning and population genetic variability into Badnavirus. Data sets comprising the badnavirus complete genome and partial sequences of the RT and RNaseH genes were obtained from the GenBank database. Multiple nucleotide sequence alignments from complete genome, ORFIII, complete genomic domain RT/RNaseH (1020pb) and partial (579pb) were performed. A total of 127 genomes were obtained, representing 53 species of badnavirus. Nucleotide sequence comparisons for the RT/RNaseH domain showed only a few isolates reported as distinct species shared ≥80% identity, the current threshold used for species demarcation into this genus. Phylogenetic trees for the complete genome and for ORFIII showed four well supported clusters (badnavirus groups 1-4), with clusters 1 and 3 being sister groups comprising predominantly sugarcane- and banana-infecting species. Non-tree-like evolution analysis evidenced putative recombination events among badnaviruses, and at least 23 independent events were detected. High levels of nucleotide diversity were observed for the partial RT/RNaseH region in isolates of 11 badnavirus species. These results showed that mutation and recombination are important mechanisms that acting on badnavirus diversification.
向坏病毒属的分化:系统发育和群体遗传变异
坏病毒(Caulimoviridae)具有半圆形的dsDNA基因组,被封装到杆菌状颗粒中。由于其在世界范围内感染栽培植物的物种数量众多,Badnavirus属是最重要的。本研究旨在评价恶性病毒的系统发育定位和群体遗传变异性。从GenBank数据库中获得了包括坏病毒全基因组和RT和RNaseH基因部分序列的数据集。从全基因组、ORFIII、全基因组区域RT/RNaseH (1020pb)和部分(579pb)进行多个核苷酸序列比对。共获得127个基因组,代表53种坏病毒。RT/RNaseH结构域的核苷酸序列比较显示,只有少数被报道为不同物种的分离株具有≥80%的一致性,这是目前用于物种划分为该属的阈值。完整基因组和ORFIII的系统发育树显示了4个支持良好的集群(坏病毒群1-4),集群1和3是姐妹群,主要由甘蔗和香蕉感染物种组成。非树状进化分析证实了坏病毒之间可能的重组事件,并且至少检测到23个独立事件。在11种恶性病毒的分离株中,观察到部分RT/RNaseH区域具有高水平的核苷酸多样性。这些结果表明,突变和重组是影响坏病毒多样化的重要机制。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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