Reevaluation of the cox1 group I intron in Araceae and angiosperms indicates a history dominated by loss rather than horizontal transfer
Reevaluation of the cox1 group I intron in Araceae and angiosperms indicates a history dominated by loss rather than horizontal transfer
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DOI：
10.1093/molbev/msm241
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发表时间：
2008-02-01
影响因子：
10.7
通讯作者：
Renner, Susanne S.
中科院分区：
文献类型：
--
作者：
Cusimano, Natalie;Zhang, Li-Bing;Renner, Susanne S.
内含子的起源和传递方式仍然是一个有争议的问题。先前的研究，我组内含子在被子植物cox 1基因推断频繁被子植物到被子植物的水平传输的内含子从明显的不一致性之间的内含子coxgenies和被子植物coxgenies，被子植物之间的内含子的斑片状分布，和cox 1外显子的共转换域（第一个22 nt下游插入的内含子）之间的差异。我们分析了179种被子植物的cox 1基因，其中110种含有内含子（内含子（+）），69种缺乏内含子（内含子）。我们在天南星科的分类群取样特别密集，以测试Cho和Palmer（1999）提出的关于内含子垂直和水平传递的假设。天南星科进化过程中线粒体cox 1基因I组内含子水平转移的多重获得分子生物学评价16：1155-1165）。天南星科cox 1内含子的最大似然树，也是所有被子植物cox 1内含子，在很大程度上与已知的系统发育关系，在这些类群一致。例外情况可以解释为低信号的内含子和长分支的吸引力之间的一些类群与高线粒体取代率。对179个共转换域的分析揭示了20种类型的域（其中11种仅在单个物种中发现，所有这些域都涉及沉默取代）。这些道的被子植物染色体发生的分布显示了一个共同的祖先类型，大多数内含子+和一些内含子（-）被子植物的特点，和几个衍生道类型所产生的逐步回复突变的coconverted核苷酸。小内含子（+）和内含子（-）姐妹分支的分子时钟测年表明，在天南星科，其cox 1序列进化相对缓慢的共转换域已持续了70万年。110个内含子之间的序列相似性范围从91%到相同，而假定的同源物从真菌是高度不同的，但在真菌中的采样仍然稀少。总之，这些结果表明，cox 1内含子进入被子植物一次，已大部分或全部垂直传输，并已失去了无数次，与coconversion道足迹提供不可靠的信号前内含子的存在。
The origin and modes of transmission of introns remain matters of much debate. Previous studies of the group I intron in the angiosperm cox1 gene inferred frequent angiosperm-to-angiosperm horizontal transmission of the intron from apparent incongruence between intron phylogenies and angiosperm phylogenies, patchy distribution of the intron among angiosperms, and differences between cox1 exonic coconversion tracts (the first 22 nt downstream of where the intron inserted). We analyzed the cox1 gene in 179 angiosperms, 110 of them containing the intron (intron(+)) and 69 lacking it (intron). Our taxon sampling in Araceae is especially dense to test hypotheses about vertical and horizontal intron transmission put forward by Cho and Palmer (1999. Multiple acquisitions via horizontal transfer of a group I intron in the mitochondrial cox1 gene during evolution of the Araceae family. Mol Biol Evol. 16:1155-1165). Maximum likelihood trees of Araceae cox1 introns, and also of all angiosperm cox1 introns, are largely congruent with known phylogenetic relationships in these taxa. The exceptions can be explained by low signal in the intron and long-branch attraction among a few taxa with high mitochondrial substitution rates. Analysis of the 179 coconversion tracts reveals 20 types of tracts (11 of them only found in single species, all involving silent substitutions). The distribution of these tracts on the angiosperm phylogeny shows a common ancestral type, characterizing most intron+ and some intron(-) angiosperms, and several derivative tract types arising from gradual back mutation of the coconverted nucleotides. Molecular clock dating of small intron(+) and intron(-) sister clades suggests that coconversion tracts have persisted for 70 Myr in Araceae, whose cox1 sequences evolve comparatively slowly. Sequence similarity among the 110 introns ranges from 91% to identical, whereas putative homologs from fungi are highly different, but sampling in fungi is still sparse. Together, these results suggest that the cox1 intron entered angiosperms once, has largely or entirely been transmitted vertically, and has been lost numerous times, with coconversion tract footprints providing unreliable signal of former intron presence.