The complete mitochondrial genome of the early flowering plant Nymphaea colorata is highly repetitive with low recombination.
The complete mitochondrial genome of the early flowering plant Nymphaea colorata is highly repetitive with low recombination.
复制标题
早期开花植物睡莲的完整线粒体基因组重复性高，重组率低
DOI：
10.1186/s12864-018-4991-4
复制
发表时间：
2018-08-14
期刊：
影响因子：
4.4
通讯作者：
Liu Y
中科院分区：
文献类型：
--
作者：
Dong S;Zhao C;Chen F;Liu Y;Zhang S;Wu H;Zhang L;Liu Y
背景开花植物（被子植物）的线粒体基因组在基因组结构中高度动态。最早的被子植物 Amborella 的有丝分裂基因组在携带大量外源 DNA 方面表现出色，而鹅掌楸则相反，后者是另一种唯一已知的早期被子植物有丝分裂基因组，被描述为“化石”。在两种早期开花植物线粒体基因组中观察到的独特特征增加了目前对早期开花植物的外观的困惑。扩大采样将为了解早期被子植物的线粒体基因组进化提供更多细节。在这里，我们报告了来自睡莲目（最早的被子植物三个目之一）的睡莲 Nymphaea colorata 的完整线粒体基因组。 结果Pac-Bio 长读长测序数据的组装产生了 617,195 bp 的圆形线粒体染色体，平均深度为 601×。该基因组编码 41 个蛋白质编码基因、20 个 tRNA 和 3 个 rRNA 基因，其中 25 个 II 组内含子破坏了 10 个蛋白质编码基因。近一半的基因组由重复序列组成，这对内含子大小的扩展做出了重大贡献，使得睡莲线粒体基因组的总内含子长度成为被子植物中最长的内含子之一，其中cox2中有一个11.4-Kb的内含子，这是迄今为止报道的植物中最长的细胞器内含子。然而，在睡莲属中，重复介导的同源重组出乎意料地低，从所检查的 886,982 个重复对中的 10 个重组活性重复对中检测到的 74 个重组读数证明了这一点。在三个早期被子植物有丝分裂基因组中检测到广泛的基因顺序变化，即分别需要 38 或 44 个倒位和易位事件才能使睡莲与安博拉或鹅掌楸的有丝分裂基因组协调一致。与具有六个外源线粒体 DNA 基因组等价物的 Amborella 相比，在睡莲线粒体基因组中没有观察到单个水平基因转移事件。 结论 睡莲中的低重组水平为体内具有高度亚化学计量重排分子集的主要主构象提供了证据。
BackgroundMitochondrial genomes of flowering plants (angiosperms) are highly dynamic in genome structure. The mitogenome of the earliest angiosperm Amborella is remarkable in carrying rampant foreign DNAs, in contrast to Liriodendron, the other only known early angiosperm mitogenome that is described as ‘fossilized’. The distinctive features observed in the two early flowering plant mitogenomes add to the current confusions of what early flowering plants look like. Expanded sampling would provide more details in understanding the mitogenomic evolution of early angiosperms. Here we report the complete mitochondrial genome of water lily Nymphaea colorata from Nymphaeales, one of the three orders of the earliest angiosperms.ResultsAssembly of data from Pac-Bio long-read sequencing yielded a circular mitochondria chromosome of 617,195 bp with an average depth of 601×. The genome encoded 41 protein coding genes, 20 tRNA and three rRNA genes with 25 group II introns disrupting 10 protein coding genes. Nearly half of the genome is composed of repeated sequences, which contributed substantially to the intron size expansion, making the gross intron length of the Nymphaea mitochondrial genome one of the longest among angiosperms, including an 11.4-Kb intron in cox2, which is the longest organellar intron reported to date in plants. Nevertheless, repeat mediated homologous recombination is unexpectedly low in Nymphaea evidenced by 74 recombined reads detected from ten recombinationally active repeat pairs among 886,982 repeat pairs examined. Extensive gene order changes were detected in the three early angiosperm mitogenomes, i.e. 38 or 44 events of inversions and translocations are needed to reconcile the mitogenome of Nymphaea with Amborella or Liriodendron, respectively. In contrast to Amborella with six genome equivalents of foreign mitochondrial DNA, not a single horizontal gene transfer event was observed in the Nymphaea mitogenome.Conclusions The low recombination level in Nymphaea provides evidence for the predominant master conformation in vivo with a highly substoichiometric set of rearranged molecules.
登录
查看更多内容
睡莲作为达尔文可憎之谜的新兴模型
影响因子：
8.7
作者：
Chen F;Liu X;Yu C;Chen Y;Tang H;Zhang L
通讯作者：
Zhang L
影响因子：
11.6
作者：
Alverson, Andrew J.;Rice, Danny W.;Palmer, Jeffrey D.
通讯作者：
Palmer, Jeffrey D.
影响因子：
10.7
作者：
Goremykin, Vadim V.;Salamini, Francesco;Viola, Roberto
通讯作者：
Viola, Roberto
影响因子：
10.7
作者：
Chaw, Shu-Miaw;Shih, Arthur Chun-Chieh;Chou, The-Yuan
通讯作者：
Chou, The-Yuan
影响因子：
4.6
作者：
Gui S;Wu Z;Zhang H;Zheng Y;Zhu Z;Liang D;Ding Y
通讯作者：
Ding Y