Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution.
Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution.
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DOI：
10.1186/1743-422x-6-223
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发表时间：
2009-12-17
期刊：
影响因子：
4.8
通讯作者：
Koonin EV
中科院分区：
文献类型：
--
作者：
Yutin N;Wolf YI;Raoult D;Koonin EV
核质大DNA病毒（NCLDV）包括一类明显单系的病毒，其感染多种真核宿主。最近在分离新病毒和基因组测序方面的进展导致NCLDV多样性的大幅扩展，从而为比较基因组分析提供了额外的机会，并需要对病毒基因进行全面分类。对6个科45株NCLDV的基因组编码蛋白序列进行了比较分析，以确定其基因簇。使用先前开发的计算方法进行同源性鉴定，鉴定了1445个核质病毒同源群（NCVOG），其中177个代表一个以上的NCLDV家族。NCVOG是人工策划和注释的，可以用作新NCLDV基因组的功能注释和进化分析的计算平台。NCLDV进化的最大似然重建产生了一组47个保守基因，这些基因可能存在于这类真核病毒的共同祖先的基因组中。该重建的祖先基因组对重建过程的参数是稳健的，因此可能准确地反映祖先NCLDV的基因核心，表明该病毒编码复杂的复制、表达和形态发生机制，使其相对独立于宿主细胞功能。NCVOG是一个灵活和可扩展的平台，用于新表征的NCLDV的基因组分析和功能注释。采用NCVOG的进化重建指向复杂的祖先病毒。
The Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) comprise an apparently monophyletic class of viruses that infect a broad variety of eukaryotic hosts. Recent progress in isolation of new viruses and genome sequencing resulted in a substantial expansion of the NCLDV diversity, resulting in additional opportunities for comparative genomic analysis, and a demand for a comprehensive classification of viral genes. A comprehensive comparison of the protein sequences encoded in the genomes of 45 NCLDV belonging to 6 families was performed in order to delineate cluster of orthologous viral genes. Using previously developed computational methods for orthology identification, 1445 Nucleo-Cytoplasmic Virus Orthologous Groups (NCVOGs) were identified of which 177 are represented in more than one NCLDV family. The NCVOGs were manually curated and annotated and can be used as a computational platform for functional annotation and evolutionary analysis of new NCLDV genomes. A maximum-likelihood reconstruction of the NCLDV evolution yielded a set of 47 conserved genes that were probably present in the genome of the common ancestor of this class of eukaryotic viruses. This reconstructed ancestral gene set is robust to the parameters of the reconstruction procedure and so is likely to accurately reflect the gene core of the ancestral NCLDV, indicating that this virus encoded a complex machinery of replication, expression and morphogenesis that made it relatively independent from host cell functions. The NCVOGs are a flexible and expandable platform for genome analysis and functional annotation of newly characterized NCLDV. Evolutionary reconstructions employing NCVOGs point to complex ancestral viruses.