College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
Genes (Basel). 2022 Sep 9;13(9):1621. doi: 10.3390/genes13091621.
Orchardgrass ( L.) is a species in the Gramineae family that is highly important economically and valued for its role in ecology. However, the phylogeny and taxonomy of are still controversial based on current morphological and molecular evidence. The study of chloroplast (cp) genomes has developed into a powerful tool to develop molecular markers for related species and reveal the relationships between plant evolution and phylogenetics. In this study, we conducted comparative genomic analyses and phylogenetic inferences on 14 cp genomes of originating from the Mediterranean and Eurasia. The genome size ranged from 134,375 bp to 134,993 bp and exhibited synteny of gene organization and order. A total of 129-131 genes were identified, including 85-87 protein coding genes, 38 tRNA genes and 8 rRNA genes. The cp sequences were highly conserved, and key sequence variations were detected at the junctions of inverted repeats (IRs)/small single-copy (SSC) regions. Moreover, nine highly variable regions were identified among the subspecies based on a sequence divergence analysis. A total of 285 RNA editing sites were detected that were relevant to 52 genes, where exhibited the most abundant RNA editing sites. The phylogenetic analysis revealed that all subspecies clustered into a monophyletic group and most branches provided a high support bootstrap. The main divergence time of was dated to the Miocene era, and this could have been due to changes in the climate. These findings will provide useful insights for further studies on phylogeny, the identification of subspecies and the development of hypotheses for the evolutionary history of the genus and of the Gramineae family.
杂交狗牙根（L.）是禾本科植物的一个物种，在经济上非常重要，其生态作用也很有价值。然而，基于当前的形态学和分子证据，其系统发育和分类仍然存在争议。叶绿体（cp）基因组的研究已经发展成为开发相关物种分子标记和揭示植物进化和系统发育关系的有力工具。在这项研究中，我们对来自地中海和欧亚大陆的 14 个杂交狗牙根 cp 基因组进行了比较基因组分析和系统发育推断。基因组大小范围为 134375 bp 至 134993 bp，表现出基因组织和顺序的同线性。总共鉴定出 129-131 个基因，包括 85-87 个蛋白编码基因、38 个 tRNA 基因和 8 个 rRNA 基因。cp 序列高度保守，在反向重复（IR）/小单拷贝（SSC）区域的交界处检测到关键的序列变异。此外，基于序列分歧分析，在亚种间鉴定出了 9 个高度可变区。总共检测到 285 个与 52 个基因相关的 RNA 编辑位点，其中 表现出最丰富的 RNA 编辑位点。系统发育分析表明，所有 亚种都聚类成一个单系群，大多数分支提供了高支持bootstrap 值。 的主要分歧时间可追溯到中新世，这可能是由于气候的变化。这些发现将为进一步研究系统发育、亚种鉴定以及建立禾本科属和属的进化历史假说提供有用的见解。
