Huang Ya-Yi, Cho Shu-Ting, Haryono Mindia, Kuo Chih-Horng
Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
PLoS One. 2017 Jun 15;12(6):e0179055. doi: 10.1371/journal.pone.0179055. eCollection 2017.
Common bermudagrass (Cynodon dactylon (L.) Pers.) belongs to the subfamily Chloridoideae of the Poaceae family, one of the most important plant families ecologically and economically. This grass has a long connection with human culture but its systematics is relatively understudied. In this study, we sequenced and investigated the chloroplast genome of common bermudagrass, which is 134,297 bp in length with two single copy regions (LSC: 79,732 bp; SSC: 12,521 bp) and a pair of inverted repeat (IR) regions (21,022 bp). The annotation contains a total of 128 predicted genes, including 82 protein-coding, 38 tRNA, and 8 rRNA genes. Additionally, our in silico analyses identified 10 sets of repeats longer than 20 bp and predicted the presence of 36 RNA editing sites. Overall, the chloroplast genome of common bermudagrass resembles those from other Poaceae lineages. Compared to most angiosperms, the accD gene and the introns of both clpP and rpoC1 genes are missing. Additionally, the ycf1, ycf2, ycf15, and ycf68 genes are pseudogenized and two genome rearrangements exist. Our phylogenetic analysis based on 47 chloroplast protein-coding genes supported the placement of common bermudagrass within Chloridoideae. Our phylogenetic character mapping based on the parsimony principle further indicated that the loss of the accD gene and clpP introns, the pseudogenization of four ycf genes, and the two rearrangements occurred only once after the most recent common ancestor of the Poaceae diverged from other monocots, which could explain the unusual long branch leading to the Poaceae when phylogeny is inferred based on chloroplast sequences.
普通狗牙根（Cynodon dactylon (L.) Pers.）属于禾本科虎尾草亚科，禾本科是生态和经济方面最重要的植物科之一。这种草与人类文化有着悠久的联系，但其系统发育学研究相对较少。在本研究中，我们对普通狗牙根的叶绿体基因组进行了测序和研究，其长度为134,297 bp，有两个单拷贝区域（LSC：79,732 bp；SSC：12,521 bp）和一对反向重复（IR）区域（21,022 bp）。注释共包含128个预测基因，包括82个蛋白质编码基因、38个tRNA基因和8个rRNA基因。此外，我们的电子分析确定了10组长度超过20 bp的重复序列，并预测存在36个RNA编辑位点。总体而言，普通狗牙根的叶绿体基因组与其他禾本科谱系的基因组相似。与大多数被子植物相比，accD基因以及clpP和rpoC1基因的内含子缺失。此外，ycf1、ycf2、ycf15和ycf68基因已假基因化，并且存在两个基因组重排。我们基于47个叶绿体蛋白质编码基因的系统发育分析支持普通狗牙根在虎尾草亚科中的位置。我们基于简约原则的系统发育特征图谱进一步表明，accD基因和clpP内含子的缺失、四个ycf基因的假基因化以及两个重排在禾本科最近的共同祖先与其他单子叶植物分化后仅发生了一次，这可以解释在基于叶绿体序列推断系统发育时导致禾本科的异常长分支。
