Positive selection, molecular recombination structure and phylogenetic reconstruction of members of the family Tombusviridae: Implication in virus taxonomy.
Positive selection, molecular recombination structure and phylogenetic reconstruction of members of the family Tombusviridae: Implication in virus taxonomy.
复制标题
DOI：
10.1590/s1415-47572011005000046
复制
发表时间：
2011-10
影响因子：
2.1
通讯作者：
Boulila M
中科院分区：
文献类型：
--
作者：
Boulila M
利用RECCO和RDP版本3.31β算法，对目前已知的Tombusviridae家族成员全基因组的重组事件及其进化频率进行了详细的研究，其中包括从国际数据库检索的79个片段。第一个程序可以检测到8个病毒属中的7个（金黄色病毒、Avenavirus、Carmovirus、Dianthovirus、坏死病毒、panicvirus和Tombusvirus）的潜在重组位点，第二个程序提供了除Dianthovirus属外的相同结果。另一方面，这两种方法都未能检测到Machlomovirus属成员基因组中的重组断点。此外，基于Fisher 's精确中性检验，在涉及15个不同谱系的17个接入对中检测到蛋白质编码基因的正选择。除大瘤病毒属、panicvirus属和未分类的tombusvirus科外，其余分类属和未分类的tombusvirus科均有阳性选择代表。所有Tombusviridae成员的进化历史表明，它们分为8个不同的类群，对应于构成该科的8个属。推断出的系统发育改变了国际病毒分类学委员会目前采用的分类。有人提议重新分类。
A detailed study of putative recombination events and their evolution frequency in the whole genome of the currently known members of the family Tombusviridae, comprising 79 accessions retrieved from the international databases, was carried out by using the RECCO and RDP version 3.31β algorithms. The first program allowed the detection of potential recombination sites in seven out of eight virus genera (Aureusvirus, Avenavirus, Carmovirus, Dianthovirus, Necrovirus, Panicovirus, and Tombusvirus), the second program provided the same results except for genus Dianthovirus. On the other hand, both methods failed to detect recombination breakpoints in the genome of members of genus Machlomovirus. Furthermore, based on Fisher’s Exact Test of Neutrality, positive selection exerted on protein-coding genes was detected in 17 accession pairs involving 15 different lineages. Except genera Machlomovirus, and Panicovirus along with unclassified Tombusviridae, all the other taxonomical genera and the unassigned Tombusviridae encompassed representatives under positive selection. The evolutionary history of all members of the Tombusviridae family showed that they segregated into eight distinct groups corresponding to the eight genera which constitute this family. The inferred phylogeny reshuffled the classification currently adopted by the International Committee on Taxonomy of Viruses. A reclassification was proposed.