Cusimano Natalie, Zhang Li-Bing, Renner Susanne S
Department of Biology, Ludwig Maximilian University, Munich, Germany.
Mol Biol Evol. 2008 Feb;25(2):265-76. doi: 10.1093/molbev/msm241. Epub 2007 Dec 24.
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 coxl 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.
内含子的起源和传播方式仍然是备受争议的问题。先前对被子植物细胞色素氧化酶亚基1（cox1）基因中I类内含子的研究，从内含子系统发育与被子植物系统发育之间明显的不一致、该内含子在被子植物中的零散分布以及cox1外显子共转换片段（内含子插入位点下游的前22个核苷酸）之间的差异，推断出该内含子在被子植物之间频繁发生水平传播。我们分析了179种被子植物的cox1基因，其中110种含有该内含子（内含子阳性），69种不含该内含子（内含子阴性）。我们对天南星科的分类群抽样尤为密集，以检验Cho和Palmer（1999年。天南星科进化过程中线粒体cox1基因I类内含子通过水平转移的多次获得。《分子生物学与进化》。16:1155 - 1165）提出的关于内含子垂直和水平传播的假说。天南星科cox1内含子以及所有被子植物cox1内含子的最大似然树，在很大程度上与这些分类群中已知的系统发育关系一致。这些例外情况可以通过内含子信号较低以及少数线粒体替换率高的分类群之间的长枝吸引来解释。对179个共转换片段的分析揭示了20种片段类型（其中11种仅在单个物种中发现，均涉及沉默替换）。这些片段在被子植物系统发育树上的分布显示出一种共同的祖先类型，其特征是大多数内含子阳性和一些内含子阴性被子植物，以及由共转换核苷酸的逐渐反向突变产生的几种衍生片段类型。对小型内含子阳性和内含子阴性姐妹分支的分子钟定年表明，共转换片段在天南星科中已经存在了7000万年，其cox1序列进化相对缓慢。110个内含子之间的序列相似性范围从91%到完全相同，而来自真菌的假定同源物差异很大，但对真菌的抽样仍然很少。综合这些结果表明，cox1内含子曾一次进入被子植物，在很大程度上或完全通过垂直传播，并且已经多次丢失，共转换片段足迹为以前内含子的存在提供了不可靠的信号。
