Comparative Analysis Of Completely Sequenced Genomes

细菌、古细菌和真核生物基因组完全测序数据库的快速增长（截至2010年初，已有超过1100个基因组可用，还有更多正在进行中）为基因组研究创造了新的机遇和挑战。在过去的一年里，我们进行了几项研究，利用基因组信息建立了基因组进化和功能的基本原理。特别是，我们进行了真核核胞质大DNA病毒（NCLDV）的全面比较分析，包括同源基因簇的构建和病毒基因组进化的重建。NCLDV包括明显单系的一类病毒，可感染多种真核宿主。最近在分离新病毒和基因组测序方面取得的进展导致NCLDV多样性的大幅扩大，从而为比较基因组分析提供了更多机会，并需要对病毒基因进行全面分类。对6个科45株NCLDV基因组编码的蛋白序列进行了全面比较，以确定同源病毒基因簇。使用先前开发的同源鉴定计算方法，鉴定了1445个核细胞质病毒同源群（NCVOGs），其中177个在一个以上的NCLDV家族中有代表性。ncvogg是人工整理和注释的，可以作为新的NCLDV基因组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。这个重建的祖先基因集对重建过程的参数具有鲁棒性，因此可能准确地反映了祖先NCLDV的基因核心，这表明该病毒编码了一个复杂的复制、表达和形态发生机制，使其相对独立于宿主细胞功能。NCVOGs是一个灵活和可扩展的平台，用于新鉴定的NCLDV的基因组分析和功能注释。利用NCVOGs进行的进化重建指向复杂的祖先病毒。

The rapidly growing database of completely sequenced genomes of bacteria, archaea and eukaryotes (over 1100 genomes available by the beginning of 2010 and many more in progress) creates both new opportunities and new challenges for genome research. During the last year, we performed several studies that took advantage of the genomic information to establish fundamental principles of genome evolution and function. In particular, we performed a comprehensive comparative analysis of eukaryotic nucleo-cytoplasmic large DNA viruses (NCLDV) including the construction of clusters of orthologous genes and reconstruction of viral genome evolution. The 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. In another project, we investigated the abundance and distribution of type I toxin-antitoxin systems in bacteria with the goals of searching for new candidates and discovering novel families. Small, hydrophobic proteins whose synthesis is repressed by small RNAs (sRNAs), denoted type I toxin-antitoxin modules, were first discovered on plasmids where they regulate plasmid stability, but were subsequently found on a few bacterial chromosomes. We used exhaustive PSI-BLAST and TBLASTN searches across 774 bacterial genomes to identify homologs of known type I toxins. These searches substantially expanded the collection of predicted type I toxins, revealed homology of the Ldr and Fst toxins, and suggested that type I toxin-antitoxin loci are not spread by horizontal gene transfer. To discover novel type I toxin-antitoxin systems, we developed a set of search parameters based on characteristics of known loci including the presence of tandem repeats and clusters of charged and bulky amino acids at the C-termini of short proteins containing predicted transmembrane regions. We detected sRNAs for three predicted toxins from enterohemorrhagic Escherichia coli and Bacillus subtilis, and showed that two of the respective proteins indeed are toxic when overexpressed. We also demonstrated that the local free-energy minima of RNA folding can be used to detect the positions of the sRNA genes. Our results suggest that type I toxin-antitoxin modules are much more widely distributed among bacteria than previously appreciated. In a separate comparative genomic study we explored distinct patterns of expression and evolution of intronless and intron-containing mammalian genes. Comparison of expression levels and breadth and evolutionary rates of intronless and intron-containing mammalian genes shows that intronless genes are expressed at lower levels, tend to be tissue specific, and evolve significantly faster than spliced genes. By contrast, monomorphic spliced genes that are not subject to detectable alternative splicing and polymorphic alternatively spliced genes show similar statistically indistinguishable patterns of expression and evolution. Alternative splicing is most common in ancient genes, whereas intronless genes appear to have relatively recent origins. These results imply tight coupling between different stages of gene expression, in particular, transcription, splicing, and nucleocytosolic transport of transcripts, and suggest that formation of intronless genes is an important route of evolution of novel tissue-specific functions in animals.