Intron Evolution: Testing Hypotheses of Intron Evolution Using the Phylogenomics of Tetraspanins
Intron Evolution: Testing Hypotheses of Intron Evolution Using the Phylogenomics of Tetraspanins
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DOI：
10.1371/journal.pone.0004680
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发表时间：
2009-03-05
期刊：
影响因子：
3.7
通讯作者：
DeSalle, Rob
中科院分区：
文献类型：
--
作者：
Garcia-Espana, Antonio;Mares, Roso;DeSalle, Rob
背景资料：虽然大规模的内含子信息学研究可以在广泛的推论有关模式的内含子的增益和损失，更具体的问题，在更精细的尺度上内含子的进化可以解决使用基因家族的结构和功能是众所周知的。对来自具有完全测序的基因组的广泛生物体的四跨膜蛋白进行全基因组调查是了解内含子进化细节的极好手段。我们的方法纳入了几个新的完全测序的基因组，涵盖了动物王国以及植物，原生生物和真菌的主要谱系。外显子/内含子的基因结构在这样一个进化的广泛的基因组的分析，使我们能够确定祖先的内含子结构在整个真核生命树的tetraspanins。方法/主要结果：我们进行了一个tetraspanin蛋白家族的内含子/外显子结构的tetraspanin基因组分析。此外，除了在动物中发现的编号为1至6的已被表征的四跨膜蛋白内含子之外，还发现了另外三个我们称为4a、4 b和4c的古老的0期内含子，这三个新的内含子与祖先内含子1至6结合，定义了三种基本的四跨膜蛋白基因结构，这些结构在整个动物界都是保守的。我们的tetraspanin基因组的方法也可以估计的时间，在该时间出现的33人tetraspanin旁系同源物的内含子，这在许多情况下，与伴随收购新的内含子。另一方面，我们观察到新的内含子（1-6、4a、B和c以外的内含子）不是随机插入四跨膜蛋白基因结构中。四跨膜蛋白基因的区域对应的小细胞外环（SEL）仅占总序列长度的10.5%，但有46%的新的动物内含子insertions.Conclusions/Significance：我们的研究结果表明，测试的内含子进化加强了特定的基因家族，如四跨膜蛋白基因组的方法。这些测试增加了我们对基因组创新的理解，这些创新与主要的进化分歧事件、功能约束和进化新奇性出现的时间有关。
Background: Although large scale informatics studies on introns can be useful in making broad inferences concerning patterns of intron gain and loss, more specific questions about intron evolution at a finer scale can be addressed using a gene family where structure and function are well known. Genome wide surveys of tetraspanins from a broad array of organisms with fully sequenced genomes are an excellent means to understand specifics of intron evolution. Our approach incorporated several new fully sequenced genomes that cover the major lineages of the animal kingdom as well as plants, protists and fungi. The analysis of exon/intron gene structure in such an evolutionary broad set of genomes allowed us to identify ancestral intron structure in tetraspanins throughout the eukaryotic tree of life.Methodology/Principal Findings: We performed a phylogenomic analysis of the intron/exon structure of the tetraspanin protein family. In addition, to the already characterized tetraspanin introns numbered 1 through 6 found in animals, three additional ancient, phase 0 introns we call 4a, 4b and 4c were found. These three novel introns in combination with the ancestral introns 1 to 6, define three basic tetraspanin gene structures which have been conserved throughout the animal kingdom. Our phylogenomic approach also allows the estimation of the time at which the introns of the 33 human tetraspanin paralogs appeared, which in many cases coincides with the concomitant acquisition of new introns. On the other hand, we observed that new introns (introns other than 1-6, 4a, b and c) were not randomly inserted into the tetraspanin gene structure. The region of tetraspanin genes corresponding to the small extracellular loop (SEL) accounts for only 10.5% of the total sequence length but had 46% of the new animal intron insertions.Conclusions/Significance: Our results indicate that tests of intron evolution are strengthened by the phylogenomic approach with specific gene families like tetraspanins. These tests add to our understanding of genomic innovation coupled to major evolutionary divergence events, functional constraints and the timing of the appearance of evolutionary novelty.