The evolutionary fate of the chloroplast and nuclear rps16 genes as revealed through the sequencing and comparative analyses of four novel legume chloroplast genomes from Lupinus.
The evolutionary fate of the chloroplast and nuclear rps16 genes as revealed through the sequencing and comparative analyses of four novel legume chloroplast genomes from Lupinus.
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DOI：
10.1093/dnares/dsx006
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发表时间：
2017-08-01
期刊：
影响因子：
--
通讯作者：
Aïnouche A
中科院分区：
文献类型：
--
作者：
Keller J;Rousseau-Gueutin M;Martin GE;Morice J;Boutte J;Coissac E;Ourari M;Aïnouche M;Salmon A;Cabello-Hurtado F;Aïnouche A
由于存在广泛的结构重排、基因丢失和局部高变区域，豆科被认为是了解叶绿体基因组进化的模型系统。在这里，我们提供了羽扇豆属的四个叶绿体基因组序列，属于尚未充分研究的 Genistoid 分支。值得注意的是，我们在羽扇豆属物种中发现了必需的 rps16 基因的功能丧失，该基因很可能被编码叶绿体和线粒体靶向 RPS16 蛋白的核 rps16 基因所取代。为了研究 rps16 基因的进化命运，我们探索了所有可用的植物叶绿体、线粒体和核基因组。尽管没有植物线粒体基因组携带 rps16 基因，但许多植物仍然具有功能性核和叶绿体 rps16 基因。 Ka/Ks 比率显示叶绿体和核 rps16 拷贝都处于纯化选择之下。然而，由于核rps16基因产物的双重靶向和线粒体拷贝的缺失，叶绿体基因可能会丢失。我们还对羽扇豆质体（SNP、插入缺失和重复元件）进行了比较分析，确定了变化最大的区域并检查了它们的系统发育实用性。这里确定的标记将有助于揭示羽扇豆、Genistoids 和密切相关的分支的进化历史。
The Fabaceae family is considered as a model system for understanding chloroplast genome evolution due to the presence of extensive structural rearrangements, gene losses and localized hypermutable regions. Here, we provide sequences of four chloroplast genomes from the Lupinus genus, belonging to the underinvestigated Genistoid clade. Notably, we found in Lupinus species the functional loss of the essential rps16 gene, which was most likely replaced by the nuclear rps16 gene that encodes chloroplast and mitochondrion targeted RPS16 proteins. To study the evolutionary fate of the rps16 gene, we explored all available plant chloroplast, mitochondrial and nuclear genomes. Whereas no plant mitochondrial genomes carry an rps16 gene, many plants still have a functional nuclear and chloroplast rps16 gene. Ka/Ks ratios revealed that both chloroplast and nuclear rps16 copies were under purifying selection. However, due to the dual targeting of the nuclear rps16 gene product and the absence of a mitochondrial copy, the chloroplast gene may be lost. We also performed comparative analyses of lupine plastomes (SNPs, indels and repeat elements), identified the most variable regions and examined their phylogenetic utility. The markers identified here will help to reveal the evolutionary history of lupines, Genistoids and closely related clades.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
4.9
作者：
Coissac, Eric;Hollingsworth, Peter M.;Taberlet, Pierre
通讯作者：
Taberlet, Pierre
影响因子：
10.7
作者：
Guisinger, Mary M.;Kuehl, Jennifer V.;Jansen, Robert K.
通讯作者：
Jansen, Robert K.
影响因子：
4.1
作者：
Doyle, JJ;Doyle, JL;Palmer, JD
通讯作者：
Palmer, JD
影响因子：
7.2
作者：
Kode, V;Mudd, EA;Day, A
通讯作者：
Day, A