Localized Retroprocessing as a Model of Intron Loss in the Plant Mitochondrial Genome.
Localized Retroprocessing as a Model of Intron Loss in the Plant Mitochondrial Genome.
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DOI：
10.1093/gbe/evw148
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发表时间：
2016-08-03
影响因子：
3.3
通讯作者：
Petersen G
中科院分区：
文献类型：
--
作者：
Cuenca A;Ross TG;Graham SW;Barrett CF;Davis JI;Seberg O;Petersen G
植物线粒体基因中内含子的丢失通常用后加工来解释。在这种模式下，mRNA被逆转录并整合回基因组，同时影响内含子和编辑位点的内容。为了评估在何种程度上逆加工解释内含子的损失，我们分析了模式的内含子内容和预测RNA编辑的30种单子叶植物泽泻目的整个线粒体基因组。在这一组中，我们发现了异常高的内含子含量的变化，甚至扩大了迄今已知的被子植物之间的变化。有些物种失去了大约三分之二的顺式剪接内含子。我们发现内含子内容和编辑频率之间存在很强的相关性，并检测到27个事件，其中内含子丢失与编辑状态下核苷酸的存在一致，支持后处理。然而，我们也发现了7例内含子丢失不容易被解释为retroprocession。我们的分析也不符合完整加工的cDNA拷贝的整个长度被整合到基因组中，而是表明逆加工通常只发生在基因的一部分。在某些情况下，几轮的逆处理可以解释完全没有内含子的基因中内含子的丢失。一些分类群的后处理似乎是非常常见的，可能是一个正在进行的过程。它会影响整个线粒体基因组。
Loss of introns in plant mitochondrial genes is commonly explained by retroprocessing. Under this model, an mRNA is reverse transcribed and integrated back into the genome, simultaneously affecting the contents of introns and edited sites. To evaluate the extent to which retroprocessing explains intron loss, we analyzed patterns of intron content and predicted RNA editing for whole mitochondrial genomes of 30 species in the monocot order Alismatales. In this group, we found an unusually high degree of variation in the intron content, even expanding the hitherto known variation among angiosperms. Some species have lost some two-third of the cis-spliced introns. We found a strong correlation between intron content and editing frequency, and detected 27 events in which intron loss is consistent with the presence of nucleotides in an edited state, supporting retroprocessing. However, we also detected seven cases of intron loss not readily being explained by retroprocession. Our analyses are also not consistent with the entire length of a fully processed cDNA copy being integrated into the genome, but instead indicate that retroprocessing usually occurs for only part of the gene. In some cases, several rounds of retroprocessing may explain intron loss in genes completely devoid of introns. A number of taxa retroprocessing seem to be very common and a possibly ongoing process. It affects the entire mitochondrial genome.