Fast evolution of the retroprocessed mitochondrial rps3 gene in Conifer II and further evidence for the phylogeny of gymnosperms.
Fast evolution of the retroprocessed mitochondrial rps3 gene in Conifer II and further evidence for the phylogeny of gymnosperms.
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DOI：
10.1016/j.ympev.2009.09.011
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发表时间：
2010
影响因子：
4.1
通讯作者：
Jin-Hua Ran;Hui Gao;Xiao-Quan Wang
中科院分区：
文献类型：
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作者：
Jin-Hua Ran;Hui Gao;Xiao-Quan Wang
植物线粒体基因组在序列上进化缓慢的流行观点最近受到了来自几个被子植物属的mtDNA异常高的替代率的挑战，但在植物线粒体基因中，高替代率加速伴随着巨大的长度变化的报道很少。在这里，我们研究了编码核糖体小亚基蛋白3的线粒体rps3基因的进化，发现它的一个外显子区域的长度和序列在针叶树II中都有很大的变化。与基因组DNA序列比较发现，针叶树rps3基因中不存在RNA编辑位点。对裸子植物的总DNA和mtDNA进行Southern blotting和real-time PCR分析，结果表明rps3在裸子植物中以单个线粒体位点存在。这很可能是针叶树II rps3基因经历了后处理，即其cDNA重新整合到线粒体基因组中，随后由于内含子丢失而加速了进化。此外，rps3的系统发育分析也支持了针叶树与麻属植物的亲缘关系。特别是，针叶树II的单一性受到两个rps3内含子的共同丢失的强烈支持。我们的研究结果还表明，当“编辑”的类似物与其基因组序列一起分析时，线粒体基因树的拓扑结构会受到影响。
The popular view that plant mitochondrial genome evolves slowly in sequence has been recently challenged by the extraordinarily high substitution rates of mtDNA documented mainly from several angiosperm genera, but high substitution rate acceleration accompanied with great length variation has been very rarely reported in plant mitochondrial genes. Here, we studied evolution of the mitochondrial rps3 gene that encodes the ribosomal small subunit protein 3 and found a dramatically high variation in both length and sequence of an exon region of it in Conifer II. A sequence comparison between cDNA and genomic DNA showed that there are no RNA editing sites in the Conifer II rps3 gene. Southern blotting analyses of the total DNA and mtDNA, together with the real-time PCR analysis, showed that rps3 exists as a single mitochondrial locus in gymnosperms. It is very likely that the Conifer II rps3 gene has experienced retroprocessing, i.e., the re-integration of its cDNA into the mitochondrial genome, followed by an evolutionary acceleration due to the intron loss. In addition, the phylogenetic analysis of rps3 supports the sister relationship between conifers and Gnetales. In particular, the monophyly of conifer II is strongly supported by the shared loss of two rps3 introns. Our results also indicate that the mitochondrial gene tree would be affected in topology when the “edited” paralogs are analyzed together with their genomic sequences.