Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea.
Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea.
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DOI：
10.1186/1745-6150-2-33
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发表时间：
2007-11-27
期刊：
影响因子：
5.5
通讯作者：
Koonin EV
中科院分区：
文献类型：
--
作者：
Makarova KS;Sorokin AV;Novichkov PS;Wolf YI;Koonin EV
从测序的基因组中区分直系同源物和旁系同源物的基因的进化分类对于基因组注释和进化重建是必不可少的。在细菌、古生菌和单细胞真核生物的多个基因组序列可用后不久，在蛋白质的正交群（COG）中实施了对这种分类的尝试。基因组序列的快速积累为改进COG创造了机会，但由于错误扩增也代表了挑战。其中一个实用的策略涉及构建基因组遗传紧凑子集的精细COG。构建了41个古细菌基因组（13 Crenarchaeota，27 Euryarchaeota和一个Nanoarchaeon）的新的同源基因簇（arCOG），使用改进的程序，该程序采用较小的组特异性簇之间的相似性树，半自动分区多结构域蛋白质中的同源结构域，并使用配置文件搜索识别远程同源。arCOGs的注释是基于COGs、CDD数据库和NR数据库中同源物注释的三个分配之间的共识。7538个arCOG平均覆盖基因组中约88%的基因，而COG的覆盖率为约76%。从4538个arCOG对应于2362个COG的事实可以看出，arCOG中直系同源物识别的粒度更细;约40%的arCOG是新的。古细菌基因核心（在所有41个基因组中发现的蛋白质编码基因）由166个arCOG组成。arCOGs被用来重建古细菌进化过程中的基因丢失和基因获得事件以及祖先形式的基因集。保守估计，最后的共同祖先（LACA）拥有996个基因，而泉古菌和广古菌的最后共同祖先分别拥有1245和1335个基因。据推断，LACA是一种化能自养的超嗜热菌，除了核心的古细菌功能外，还编码更多的特异质系统，例如，抗病毒防御的卡斯系统和一些毒素-抗毒素系统。arCOGs为古细菌基因组的功能注释、比较基因组学和进化重建提供了一个方便、灵活的框架。基因组重建表明，古生菌最后的共同祖先可能（几乎）与现代古生菌超嗜热菌一样先进。ArcOG和相关信息可在以下网址获得：。本文由Peer博尔克、帕特里克福特尔和Purificacion Lopez-Garcia审阅。
An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on such a classification was implemented in Clusters of Orthologous Groups of proteins (COGs). Rapid accumulation of genome sequences creates opportunities for refining COGs but also represents a challenge because of error amplification. One of the practical strategies involves construction of refined COGs for phylogenetically compact subsets of genomes. New Archaeal Clusters of Orthologous Genes (arCOGs) were constructed for 41 archaeal genomes (13 Crenarchaeota, 27 Euryarchaeota and one Nanoarchaeon) using an improved procedure that employs a similarity tree between smaller, group-specific clusters, semi-automatically partitions orthology domains in multidomain proteins, and uses profile searches for identification of remote orthologs. The annotation of arCOGs is a consensus between three assignments based on the COGs, the CDD database, and the annotations of homologs in the NR database. The 7538 arCOGs, on average, cover ~88% of the genes in a genome compared to a ~76% coverage in COGs. The finer granularity of ortholog identification in the arCOGs is apparent from the fact that 4538 arCOGs correspond to 2362 COGs; ~40% of the arCOGs are new. The archaeal gene core (protein-coding genes found in all 41 genome) consists of 166 arCOGs. The arCOGs were used to reconstruct gene loss and gene gain events during archaeal evolution and gene sets of ancestral forms. The Last Archaeal Common Ancestor (LACA) is conservatively estimated to possess 996 genes compared to 1245 and 1335 genes for the last common ancestors of Crenarchaeota and Euryarchaeota, respectively. It is inferred that LACA was a chemoautotrophic hyperthermophile that, in addition to the core archaeal functions, encoded more idiosyncratic systems, e.g., the CASS systems of antivirus defense and some toxin-antitoxin systems. The arCOGs provide a convenient, flexible framework for functional annotation of archaeal genomes, comparative genomics and evolutionary reconstructions. Genomic reconstructions suggest that the last common ancestor of archaea might have been (nearly) as advanced as the modern archaeal hyperthermophiles. ArCOGs and related information are available at: . This article was reviewed by Peer Bork, Patrick Forterre, and Purificacion Lopez-Garcia.
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影响因子：
12.3
作者：
Brochier C;Forterre P;Gribaldo S
通讯作者：
Gribaldo S
影响因子：
12.3
作者：
Dagan, Tal;Martin, William
通讯作者：
Martin, William
DOI：
10.2307/2412448
发表时间：
1970-01-01
期刊：
SYSTEMATIC ZOOLOGY
影响因子：
--
作者：
FITCH, WM
通讯作者：
FITCH, WM
影响因子：
7
作者：
Falb, M;Pfeiffer, F;Oesterhelt, D
通讯作者：
Oesterhelt, D
影响因子：
7
作者：
Baliga, NS;Bonneau, R;Ng, WV
通讯作者：
Ng, WV