Mitochondrial DNA of Vitis vinifera and the Issue of Rampant Horizontal Gene Transfer
Mitochondrial DNA of Vitis vinifera and the Issue of Rampant Horizontal Gene Transfer
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DOI：
10.1093/molbev/msn226
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发表时间：
2009-01-01
影响因子：
10.7
通讯作者：
Viola, Roberto
中科院分区：
文献类型：
--
作者：
Goremykin, Vadim V.;Salamini, Francesco;Viola, Roberto
介绍了葡萄(Vitis Vinifera)的线粒体基因组，这是迄今为止测得的最大的细胞器基因组。该基因组全长773,279个核苷酸，是已知被子植物线粒体DNA(MtDNA)中编码能力最高的。无论是绝对的还是相对的，来自叶绿体的混杂DNA在基因组中的比例也是被子植物mtDNA中所报道的最大的。总体而言，葡萄属植物叶绿体基因组的42.4%已整合到其线粒体基因组中。为了验证水平基因转移(HGT)是否也对葡萄mtDNA的基因含量有贡献，我们用葡萄及其同源植物线粒体基因组的线粒体基因编码序列构建了系统发育树。得到了许多不一致的基因树拓扑结构。然而，这些基因树之间的不一致程度并不明显大于叶绿体基因最优树中观察到的程度，叶绿体基因的共同祖先从来没有被怀疑过。在这两种情况下，我们将这种不一致归因于树重建的人工制品、字符数量不足和基因同源。这一发现使我们对Bergthorsson等人最近的系统发育解释提出了质疑。(2003,2004)和Richardson和Palmer(2007)，HGT在Amborella的mtDNA中的猖獗，最好地解释了被子植物线粒体基因树之间的系统发育不一致。发现HGT进入葡萄mtDNA的唯一证据是两个编码序列的片段，这两个编码序列来自两种引起这种植物卷叶病的冠状病毒。我们还报道，对叶绿体和线粒体基因组共有序列的分析为先前未知的从线粒体到叶绿体的基因转移途径提供了证据。
The mitochondrial genome of grape (Vitis vinifera), the largest organelle genome sequenced so far, is presented. The genome is 773,279 nt long and has the highest coding capacity among known angiosperm mitochondrial DNAs (mtDNAs). The proportion of promiscuous DNA of plastid origin in the genome is also the largest ever reported for an angiosperm mtDNA, both in absolute and relative terms. In all, 42.4% of chloroplast genome of Vitis has been incorporated into its mitochondrial genome. In order to test if horizontal gene transfer (HGT) has also contributed to the gene content of the grape mtDNA, we built phylogenetic trees with the coding sequences of mitochondrial genes of grape and their homologs from plant mitochondrial genomes. Many incongruent gene tree topologies were obtained. However, the extent of incongruence between these gene trees is not significantly greater than that observed among optimal trees for chloroplast genes, the common ancestry of which has never been in doubt. In both cases, we attribute this incongruence to artifacts of tree reconstruction, insufficient numbers of characters, and gene paralogy. This finding leads us to question the recent phylogenetic interpretation of Bergthorsson et al. (2003, 2004) and Richardson and Palmer (2007) that rampant HGT into the mtDNA of Amborella best explains phylogenetic incongruence between mitochondrial gene trees for angiosperms. The only evidence for HGT into the Vitis mtDNA found involves fragments of two coding sequences stemming from two closteroviruses that cause the leaf roll disease of this plant. We also report that analysis of sequences shared by both chloroplast and mitochondrial genomes provides evidence for a previously unknown gene transfer route from the mitochondrion to the chloroplast.