Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.
Plant Cell. 2011 Jul;23(7):2499-513. doi: 10.1105/tpc.111.087189. Epub 2011 Jul 8.
Members of the flowering plant family Cucurbitaceae harbor the largest known mitochondrial genomes. Here, we report the 1685-kb mitochondrial genome of cucumber (Cucumis sativus). We help solve a 30-year mystery about the origins of its large size by showing that it mainly reflects the proliferation of dispersed repeats, expansions of existing introns, and the acquisition of sequences from diverse sources, including the cucumber nuclear and chloroplast genomes, viruses, and bacteria. The cucumber genome has a novel structure for plant mitochondria, mapping as three entirely or largely autonomous circular chromosomes (lengths 1556, 84, and 45 kb) that vary in relative abundance over a twofold range. These properties suggest that the three chromosomes replicate independently of one another. The two smaller chromosomes are devoid of known functional genes but nonetheless contain diagnostic mitochondrial features. Paired-end sequencing conflicts reveal differences in recombination dynamics among chromosomes, for which an explanatory model is developed, as well as a large pool of low-frequency genome conformations, many of which may result from asymmetric recombination across intermediate-sized and sometimes highly divergent repeats. These findings highlight the promise of genome sequencing for elucidating the recombinational dynamics of plant mitochondrial genomes.
葫芦科植物家族的成员拥有已知最大的线粒体基因组。在这里，我们报告了黄瓜（Cucumis sativus）的 1685kb 线粒体基因组。我们通过展示其主要反映了分散重复序列的增殖、现有内含子的扩张以及来自多种来源的序列的获取，包括黄瓜核和叶绿体基因组、病毒和细菌，解决了一个关于其大尺寸起源的 30 年谜团。黄瓜基因组具有植物线粒体的新型结构，映射为三个完全或主要自主的圆形染色体（长度为 1556、84 和 45kb），其相对丰度在两倍范围内变化。这些特性表明这三个染色体彼此独立复制。这两个较小的染色体没有已知的功能基因，但仍然包含诊断线粒体特征。配对末端测序冲突揭示了染色体之间重组动力学的差异，为此提出了一个解释模型，以及一个大型低频基因组构象库，其中许多可能是由中间大小且有时高度分化的重复之间的不对称重组产生的。这些发现强调了基因组测序在阐明植物线粒体基因组重组动力学方面的潜力。
