Three distinct modes of intron dynamics in the evolution of eukaryotes
Three distinct modes of intron dynamics in the evolution of eukaryotes
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DOI：
10.1101/gr.6438607
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发表时间：
2007-07-01
期刊：
影响因子：
7
通讯作者：
Koonin, Eugene V.
中科院分区：
文献类型：
--
作者：
Carmel, Liran;Wolf, Yuri I.;Koonin, Eugene V.
剪接体内含子是真核生物基因的标志，其起源和进化有几种截然不同的观点。一个全面的概率模型，以获得一个明确的重建内含子进化的开发和应用于391套保守基因从19个真核生物物种。据推断，相对高的内含子密度较早达到，即，真核生物的最后共同祖先含有> 2.15个内含子/内切酶，而多细胞生命形式的最后共同祖先含有类似于3.4个内含子/内切酶的内含子密度，这比大多数现存真菌和某些动物中的内含子密度更大。在过去的13亿年里，内含子增加和丢失的速率似乎一直在下降，增加速率的下降幅度要大得多。真核细胞谱系表现出内含子-外显子结构的三种不同的进化模式。显然，主要的平衡模式在所有血统中都起作用。在这种模式下，内含子的增益和损失是强烈的，正相关的，在这些过程之间的逆相关性与以前的报告相反。第二种模式涉及内含子丢失率的升高，并且在几个谱系中普遍存在，例如真菌和昆虫。第三种模式，其特征是内含子获得速率升高，仅在树的深分支中可见，表明内含子入侵的爆发发生在真核生物进化的关键点，例如动物的起源。内含子动态可能依赖于多种机制，在平衡模式下，内含子的获得和丢失可能具有共同的机制特征。
Several contrasting scenarios have been proposed for the origin and evolution of spliceosomal introns, a hallmark of eukaryotic genes. A comprehensive probabilistic model to obtain a definitive reconstruction of intron evolution was developed and applied to 391 sets of conserved genes from 19 eukaryotic species. It is inferred that a relatively high intron density was reached early, i.e., the last common ancestor of eukaryotes contained > 2.15 introns/kilobase, and the last common ancestor of multicellular life forms harbored similar to 3.4 introns/kilobase, a greater intron density than in most of the extant fungi and in some animals. The rates of intron gain and intron loss appear to have been dropping during the last similar to 1.3 billion years, with the decline in the gain rate being much steeper. Eukaryotic lineages exhibit three distinct modes of evolution of the intron-exon structure. The primary, balanced mode, apparently, operates in all lineages. In this mode, intron gain and loss are strongly and positively correlated, in contrast to previous reports on inverse correlation between these processes. The second mode involves an elevated rate of intron loss and is prevalent in several lineages, such as fungi and insects. The third mode, characterized by elevated rate of intron gain, is seen only in deep branches of the tree, indicating that bursts of intron invasion occurred at key points in eukaryotic evolution, such as the origin of animals. Intron dynamics could depend on multiple mechanisms, and in the balanced mode, gain and loss of introns might share common mechanistic features.