Comparative genomic analysis of fungal genomes reveals intron-rich ancestors.
Comparative genomic analysis of fungal genomes reveals intron-rich ancestors.
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DOI：
10.1186/gb-2007-8-10-r223
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发表时间：
2007
期刊：
影响因子：
12.3
通讯作者：
Roy SW
中科院分区：
文献类型：
--
作者：
Stajich JE;Dietrich FS;Roy SW
对真菌基因组内含子得失的分析为富含内含子的真菌-动物祖先提供了支持。真核蛋白质编码基因被剪接体内含子打断，这些内含子在蛋白质翻译前从转录本中移除。剪接体内含子进化的许多方面，包括年龄、起源机制、自然选择的作用以及真核物种之间内含子数量巨大差异的原因，仍然存在争议。基因组测序和比较分析使内含子进化的全基因组分析成为可能，以解决这些问题。我们分析了25个真核物种1161组同源基因的内含子位置。我们发现了一个富含内含子的真菌-动物祖先的强有力支持，每千个碱基有超过4个内含子，可与已知的现代最高内含子密度相媲美。事实上，据估计，真菌-动物祖先比这项研究中现存的任何真菌都有更多的内含子。因此，随后的真菌进化的特征是在所有真菌分支中发生广泛和反复的内含子丢失。这些结果与先前提出的三种估计祖先内含子数量的方法相一致，这三种方法以前对8个真核物种的祖先内含子数量给出了截然不同的估计，以及第四种更新的方法。我们没有发现内含子损失率和增益率之间明显的负对应关系，这与基于选择的内含子数量种间差异的预测相反。我们的结果强调了真核生物祖先的高内含子密度以及真核生物进化过程中内含子丢失的广泛重要性。
Analysis of intron gain and loss in fungal genomes provides support for an intron-rich fungus-animal ancestor. Eukaryotic protein-coding genes are interrupted by spliceosomal introns, which are removed from transcripts before protein translation. Many facets of spliceosomal intron evolution, including age, mechanisms of origins, the role of natural selection, and the causes of the vast differences in intron number between eukaryotic species, remain debated. Genome sequencing and comparative analysis has made possible whole genome analysis of intron evolution to address these questions. We analyzed intron positions in 1,161 sets of orthologous genes across 25 eukaryotic species. We find strong support for an intron-rich fungus-animal ancestor, with more than four introns per kilobase, comparable to the highest known modern intron densities. Indeed, the fungus-animal ancestor is estimated to have had more introns than any of the extant fungi in this study. Thus, subsequent fungal evolution has been characterized by widespread and recurrent intron loss occurring in all fungal clades. These results reconcile three previously proposed methods for estimation of ancestral intron number, which previously gave very different estimates of ancestral intron number for eight eukaryotic species, as well as a fourth more recent method. We do not find a clear inverse correspondence between rates of intron loss and gain, contrary to the predictions of selection-based proposals for interspecific differences in intron number. Our results underscore the high intron density of eukaryotic ancestors and the widespread importance of intron loss through eukaryotic evolution.
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