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Biol Direct. 2012 Apr 16;7:11. doi: 10.1186/1745-6150-7-11.
Evolution of exon-intron structure of eukaryotic genes has been a matter of long-standing, intensive debate. The introns-early concept, later rebranded 'introns first' held that protein-coding genes were interrupted by numerous introns even at the earliest stages of life's evolution and that introns played a major role in the origin of proteins by facilitating recombination of sequences coding for small protein/peptide modules. The introns-late concept held that introns emerged only in eukaryotes and new introns have been accumulating continuously throughout eukaryotic evolution. Analysis of orthologous genes from completely sequenced eukaryotic genomes revealed numerous shared intron positions in orthologous genes from animals and plants and even between animals, plants and protists, suggesting that many ancestral introns have persisted since the last eukaryotic common ancestor (LECA). Reconstructions of intron gain and loss using the growing collection of genomes of diverse eukaryotes and increasingly advanced probabilistic models convincingly show that the LECA and the ancestors of each eukaryotic supergroup had intron-rich genes, with intron densities comparable to those in the most intron-rich modern genomes such as those of vertebrates. The subsequent evolution in most lineages of eukaryotes involved primarily loss of introns, with only a few episodes of substantial intron gain that might have accompanied major evolutionary innovations such as the origin of metazoa. The original invasion of self-splicing Group II introns, presumably originating from the mitochondrial endosymbiont, into the genome of the emerging eukaryote might have been a key factor of eukaryogenesis that in particular triggered the origin of endomembranes and the nucleus. Conversely, splicing errors gave rise to alternative splicing, a major contribution to the biological complexity of multicellular eukaryotes. There is no indication that any prokaryote has ever possessed a spliceosome or introns in protein-coding genes, other than relatively rare mobile self-splicing introns. Thus, the introns-first scenario is not supported by any evidence but exon-intron structure of protein-coding genes appears to have evolved concomitantly with the eukaryotic cell, and introns were a major factor of evolution throughout the history of eukaryotes.
真核生物基因中外显子-内含子结构的演化一直是一个长期以来备受关注的话题。内含子早期假说，后来又被重新命名为“内含子优先”，认为蛋白质编码基因在生命演化的早期就被大量的内含子所打断，而且内含子通过促进编码小蛋白/肽模块的序列重组，在蛋白质的起源中发挥了重要作用。内含子晚期假说则认为内含子仅在真核生物中出现，并且新的内含子在真核生物的演化过程中一直在不断积累。对来自完全测序的真核生物基因组的直系同源基因的分析表明，动物和植物的直系同源基因甚至在动物、植物和原生生物之间都存在许多共同的内含子位置，这表明许多祖先内含子自最后一个真核生物共同祖先（LECA）以来一直存在。利用不断增加的不同真核生物基因组的集合以及日益先进的概率模型，对内含子获得和丢失的重建令人信服地表明，LECA 和每个真核超群的祖先都具有内含子丰富的基因，其内含子密度与最富含内含子的现代基因组（如脊椎动物的基因组）相当。随后，在大多数真核生物谱系的演化过程中，主要涉及内含子的丢失，只有少数情况下会发生大量的内含子获得，而这些获得可能伴随着重大的进化创新，如后生动物的起源。原始的自我剪接的 II 组内含子（可能来源于线粒体内共生体）对新兴真核生物基因组的最初入侵，可能是真核生物起源的一个关键因素，特别是触发了内膜系统和核的起源。相反，剪接错误导致了选择性剪接，这是多细胞真核生物生物学复杂性的主要贡献。没有迹象表明任何原核生物在蛋白质编码基因中拥有剪接体或内含子，除了相对罕见的可移动的自我剪接内含子。因此，内含子优先的情景没有任何证据支持，但是蛋白质编码基因的外显子-内含子结构似乎与真核细胞一起演化，并且内含子在真核生物的整个演化历史中都是一个重要的演化因素。
