Use of endogenous retroviral sequences (ERVs) and structural markers for retroviral phylogenetic inference and taxonomy.
Use of endogenous retroviral sequences (ERVs) and structural markers for retroviral phylogenetic inference and taxonomy.
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DOI：
10.1186/1742-4690-2-50
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发表时间：
2005-08-10
期刊：
影响因子：
3.3
通讯作者：
Blomberg J
中科院分区：
文献类型：
--
作者：
Jern P;Sperber GO;Blomberg J
内源性逆转录病毒序列（ERV）是大多数真核生物基因组的组成部分，其数量远远超过外源性逆转录病毒（XRV）。从人和鸡的遗传档案中检索具有相对完整结构的ERV，其是脊椎动物逆转录病毒的截然相反的代表（超过3300种前病毒），并使用我们开发的生物信息学程序RetroTector©进行分析。这种丰富的原病毒信息来源，积累在当地的数据库，和XRV序列的文献收集，允许重建的Pol为基础的系统发育树，比以前可能的更广泛。其目的是找到对逆转录病毒的分类和进化研究有用的特征。其中一些特征已被其他人使用，但在这里它们在比以前更广泛的背景下进行了测试。在ERV集合中，我们发现了与基于XRV的属相似的序列：α-，β-，γ-，β-和β-逆转录病毒。然而，它们之间的中间体的出现表明了一个进化的连续性，并建议分类的变化最终将是必要的。在ERV中未发现δ病毒或慢病毒代表。基于Pol相似性的分类与许多结构性状一致。在逆转录病毒进化中，dUTR的获得发生了三次。一个或两个NC锌指的损失似乎已经发生了几次在进化过程中。核苷酸偏好性在之前已经描述过慢病毒、δ病毒和β逆转录病毒，并且在这里在更大的背景下得到了证实。Pol相似性和其他结构特征有助于更好地理解逆转录病毒的遗传学。可用于基因组学的“全局”基因组特性是i.）翻译策略，ii.）Gag NC锌指基序的数目，iii.）存在Pro N-末端dUTR（dUTPasePro），iv.）Pro C-末端G-补丁的存在和v.）在Pol整合酶（IN）C-末端结构域中存在GPY/F基序。可用于描绘较低水平分类群的“局部”逆转录病毒基因组特性是i.）宿主物种范围，ii.）核苷酸组成偏差和iii.）LTR长度。
Endogenous retroviral sequences (ERVs) are integral parts of most eukaryotic genomes and vastly outnumber exogenous retroviruses (XRVs). ERVs with a relatively complete structure were retrieved from the genetic archives of humans and chickens, diametrically opposite representatives of vertebrate retroviruses (over 3300 proviruses), and analyzed, using a bioinformatic program, RetroTector©, developed by us. This rich source of proviral information, accumulated in a local database, and a collection of XRV sequences from the literature, allowed the reconstruction of a Pol based phylogenetic tree, more extensive than previously possible. The aim was to find traits useful for classification and evolutionary studies of retroviruses. Some of these traits have been used by others, but they are here tested in a wider context than before. In the ERV collection we found sequences similar to the XRV-based genera: alpha-, beta-, gamma-, epsilon- and spumaretroviruses. However, the occurrence of intermediates between them indicated an evolutionary continuum and suggested that taxonomic changes eventually will be necessary. No delta or lentivirus representatives were found among ERVs. Classification based on Pol similarity is congruent with a number of structural traits. Acquisition of dUTPase occurred three times in retroviral evolution. Loss of one or two NC zinc fingers appears to have occurred several times during evolution. Nucleotide biases have been described earlier for lenti-, delta- and betaretroviruses and were here confirmed in a larger context. Pol similarities and other structural traits contribute to a better understanding of retroviral phylogeny. "Global" genomic properties useful in phylogenies are i.) translational strategy, ii.) number of Gag NC zinc finger motifs, iii.) presence of Pro N-terminal dUTPase (dUTPasePro), iv.) presence of Pro C-terminal G-patch and v.) presence of a GPY/F motif in the Pol integrase (IN) C-terminal domain. "Local" retroviral genomic properties useful for delineation of lower level taxa are i.) host species range, ii.) nucleotide compositional bias and iii.) LTR lengths.
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影响因子：
5.4
作者：
Jern, P;Sperber, GO;Blomberg, J
通讯作者：
Blomberg, J
影响因子：
5.4
作者：
Huder, JB;Böni, J;Schüpbach, J
通讯作者：
Schüpbach, J
影响因子：
64.5
作者：
CAPPELLO, J;HANDELSMAN, K;LODISH, HF
通讯作者：
LODISH, HF
影响因子：
5.3
作者：
Ernst, RK;Bray, M;Hammarskjold, ML
通讯作者：
Hammarskjold, ML
影响因子：
64.8
作者：
Gao, F;Bailes, E;Hahn, BH
通讯作者：
Hahn, BH