A detailed history of intron-rich eukaryotic ancestors inferred from a global survey of 100 complete genomes.
A detailed history of intron-rich eukaryotic ancestors inferred from a global survey of 100 complete genomes.
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全球对100个完整基因组的调查推断出富含内含子的真核祖先的详细历史。
DOI：
10.1371/journal.pcbi.1002150
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发表时间：
2011-09
影响因子：
4.3
通讯作者：
Koonin EV
中科院分区：
文献类型：
--
作者：
Csuros M;Rogozin IB;Koonin EV
真核生物中的蛋白质编码基因被内含子中断，但内含子密度在真核生物谱系之间差异很大。脊椎动物、某些无脊椎动物和绿色植物具有内含子丰富的基因，每个编码序列有6-7个内含子，而大多数其他真核生物具有内含子贫乏的基因。我们重建了历史上的内含子增益和损失的概率马尔可夫模型（马尔可夫链蒙特卡罗，MCMC）的245 orthopedic基因从99个基因组，代表三个的五个超组的真核生物，多个基因组序列可用。内含子丰富的祖先被自信地重建为每个主要群体，其中53%至74%的人类内含子密度推断为最后真核共同祖先（LECA）的95%置信度。MCMC重建的结果进行了比较，使用最大似然法（ML）和Dollo简约方法获得的重建。一个很好的协议之间的MCMC和ML推断证明，而Dollo简约引入了显着的偏见的估计，通常产生较低的祖先内含子密度比MCMC和ML。真核生物基因的进化以内含子丢失为主，只有在包括植物和动物在内的几个主要分支的基础上才有实质性的增加。最高的内含子密度（人类值的120%至130%）是针对动物最后的共同祖先推断的。重建表明，从LECA到哺乳动物的整个血统都是内含子丰富的，这种状态有利于选择性剪接的进化。在真核生物中，蛋白质编码基因被非编码内含子中断。内含子密度差异很大，从脊椎动物、一些无脊椎动物和植物中每个编码序列的6-7个内含子到许多单细胞形式中整个基因组中只有几个内含子。我们应用了一个强大的统计方法，马尔可夫链蒙特卡罗，重建内含子的增益和损失的历史，在整个进化的真核生物使用一组245同源基因从99个基因组，代表真核生物的多样性。对于每个主要的真核生物组，可以确信地推断出富含内含子的祖先，包括最后一个真核生物共同祖先的人类内含子密度的53%至74%，以及动物最后一个共同祖先的人类值的120%至130%。真核基因的进化主要涉及内含子的丢失，只有在包括植物和动物在内的几个主要分支的基础上才有实质性的增加。因此，所有现存真核生物的共同祖先是一个复杂的生物体，其基因结构类似于多细胞生物体。从最后一个共同祖先到哺乳动物的血统是一个不间断的富含内含子的状态，考虑到富含内含子的生物体中容易出错的剪接，这有利于功能性选择性剪接的阐述。
Protein-coding genes in eukaryotes are interrupted by introns, but intron densities widely differ between eukaryotic lineages. Vertebrates, some invertebrates and green plants have intron-rich genes, with 6–7 introns per kilobase of coding sequence, whereas most of the other eukaryotes have intron-poor genes. We reconstructed the history of intron gain and loss using a probabilistic Markov model (Markov Chain Monte Carlo, MCMC) on 245 orthologous genes from 99 genomes representing the three of the five supergroups of eukaryotes for which multiple genome sequences are available. Intron-rich ancestors are confidently reconstructed for each major group, with 53 to 74% of the human intron density inferred with 95% confidence for the Last Eukaryotic Common Ancestor (LECA). The results of the MCMC reconstruction are compared with the reconstructions obtained using Maximum Likelihood (ML) and Dollo parsimony methods. An excellent agreement between the MCMC and ML inferences is demonstrated whereas Dollo parsimony introduces a noticeable bias in the estimations, typically yielding lower ancestral intron densities than MCMC and ML. Evolution of eukaryotic genes was dominated by intron loss, with substantial gain only at the bases of several major branches including plants and animals. The highest intron density, 120 to 130% of the human value, is inferred for the last common ancestor of animals. The reconstruction shows that the entire line of descent from LECA to mammals was intron-rich, a state conducive to the evolution of alternative splicing. In eukaryotes, protein-coding genes are interrupted by non-coding introns. The intron densities widely differ, from 6–7 introns per kilobase of coding sequence in vertebrates, some invertebrates and plants, to only a few introns across the entire genome in many unicellular forms. We applied a robust statistical methodology, Markov Chain Monte Carlo, to reconstruct the history of intron gain and loss throughout the evolution of eukaryotes using a set of 245 homologous genes from 99 genomes that represent the diversity of eukaryotes. Intron-rich ancestors were confidently inferred for each major eukaryotic group including 53% to 74% of the human intron density for the last eukaryotic common ancestor, and 120% to 130% of the human value for the last common ancestor of animals. Evolution of eukaryotic genes involved primarily intron loss, with substantial gain only at the bases of several major branches including plants and animals. Thus, the common ancestor of all extant eukaryotes was a complex organism with a gene architecture resembling those in multicellular organisms. The line of descent from the last common ancestor to mammals was an uninterrupted intron-rich state that, given the error-prone splicing in intron-rich organisms, was conducive to the elaboration of functional alternative splicing.
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