Streamlining and large ancestral genomes in Archaea inferred with a phylogenetic birth-and-death model.
Streamlining and large ancestral genomes in Archaea inferred with a phylogenetic birth-and-death model.
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通过系统发育的出生和死亡模型推断出古细菌中的流线和大型祖传基因组。
DOI：
10.1093/molbev/msp123
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发表时间：
2009-09
影响因子：
10.7
通讯作者：
Miklós I
中科院分区：
文献类型：
--
作者：
Csurös M;Miklós I
同源基因通过垂直遗传、复制或水平基因转移起源于共同的祖先。基于蛋白质序列相似性，可以在多个基因组中鉴定由单个祖先基因产生的整个同源家族。然而，这些序列并不总是能决定性地揭示大家族的历史。为了研究完整基因库的进化，我们在这里提出了一个数学框架，不依赖于解决基因家族史。我们表明，所谓的系统发育概况，形成的家庭大小在多个基因组，足以推断主要的进化趋势。在我们的方法中的主要新奇是一个有效的算法来计算的可能性的一个系统发育概况的出生和死亡的过程作用于一个系统发育模型。我们研究了已知的基因家族在28个古细菌基因组中使用的概率模型，涉及血统和家庭特定的基因获取，复制和丢失的组件。该模型使我们能够考虑所有可能的历史时，推断有关古细菌进化的统计数据。根据我们的重建，大多数谱系的特点是基因家族的净损失。基因库的主要增加只发生过几次。我们的重建强调了持续的精简过程在塑造基因组组成的重要性。它还表明，早期古细菌的基因组与典型的现代基因组一样复杂，甚至在产甲烷祖先的情况下显示出极其庞大的基因库的迹象。
Homologous genes originate from a common ancestor through vertical inheritance, duplication, or horizontal gene transfer. Entire homolog families spawned by a single ancestral gene can be identified across multiple genomes based on protein sequence similarity. The sequences, however, do not always reveal conclusively the history of large families. To study the evolution of complete gene repertoires, we propose here a mathematical framework that does not rely on resolved gene family histories. We show that so-called phylogenetic profiles, formed by family sizes across multiple genomes, are sufficient to infer principal evolutionary trends. The main novelty in our approach is an efficient algorithm to compute the likelihood of a phylogenetic profile in a model of birth-and-death processes acting on a phylogeny. We examine known gene families in 28 archaeal genomes using a probabilistic model that involves lineage- and family-specific components of gene acquisition, duplication, and loss. The model enables us to consider all possible histories when inferring statistics about archaeal evolution. According to our reconstruction, most lineages are characterized by a net loss of gene families. Major increases in gene repertoire have occurred only a few times. Our reconstruction underlines the importance of persistent streamlining processes in shaping genome composition in Archaea. It also suggests that early archaeal genomes were as complex as typical modern ones, and even show signs, in the case of the methanogenic ancestor, of an extremely large gene repertoire.
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影响因子：
12.3
作者：
Brochier C;Forterre P;Gribaldo S
通讯作者：
Gribaldo S
DOI：
10.1098/rstb.2006.1841
发表时间：
2006-06-29
影响因子：
6.3
作者：
Gribaldo, Simonetta;Brochier-Armanet, Celine
通讯作者：
Brochier-Armanet, Celine
影响因子：
10.7
作者：
Escobar-Páramo, P;Ghosh, S;DiRuggiero, J
通讯作者：
DiRuggiero, J
影响因子：
2.4
作者：
Bapteste, Eric;Brochier, Celine;Boucher, Yan
通讯作者：
Boucher, Yan
影响因子：
5.8
作者：
Iwasaki, Wataru;Takagi, Toshihisa
通讯作者：
Takagi, Toshihisa