Nguyen Hung D, Yoshihama Maki, Kenmochi Naoya
Frontier Science Research Center, University of Miyazaki 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan.
BMC Evol Biol. 2006 Sep 8;6:69. doi: 10.1186/1471-2148-6-69.
The origin of spliceosomal introns is the central subject of the introns-early versus introns-late debate. The distribution of intron phases is non-uniform, with an excess of phase-0 introns. Introns-early explains this by speculating that a fraction of present-day introns were present between minigenes in the progenote and therefore must lie in phase-0. In contrast, introns-late predicts that the nonuniformity of intron phase distribution reflects the nonrandomness of intron insertions.
In this paper, we tested the two theories using analyses of intron phase distribution. We inferred the evolution of intron phase distribution from a dataset of 684 gene orthologs from seven eukaryotes using a maximum likelihood method. We also tested whether the observed intron phase distributions from 10 eukaryotes can be explained by intron insertions on a genome-wide scale. In contrast to the prediction of introns-early, the inferred evolution of intron phase distribution showed that the proportion of phase-0 introns increased over evolution. Consistent with introns-late, the observed intron phase distributions matched those predicted by an intron insertion model quite well.
Our results strongly support the introns-late hypothesis of the origin of spliceosomal introns.
剪接体内含子的起源是内含子早现与内含子晚现之争的核心议题。内含子相位的分布并不均匀，0相内含子过多。内含子早现假说对此的解释是，推测现今的一部分内含子存在于原始生物的小基因之间，因此必定处于0相。相比之下，内含子晚现假说预测内含子相位分布的不均匀性反映了内含子插入的非随机性。
在本文中，我们通过分析内含子相位分布对这两种理论进行了检验。我们使用最大似然法从七个真核生物的684个基因直系同源数据集推断内含子相位分布的进化情况。我们还检验了来自10个真核生物的观察到的内含子相位分布是否可以用全基因组范围内的内含子插入来解释。与内含子早现假说的预测相反，推断出的内含子相位分布进化表明，0相内含子的比例在进化过程中增加。与内含子晚现假说一致，观察到的内含子相位分布与内含子插入模型预测的结果相当吻合。
我们的结果有力地支持了剪接体内含子起源的内含子晚现假说。
