College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
Grassland Research Institute, Chongqing Academy of Animal Science, Chongqing, 402460, China.
BMC Genomics. 2024 Mar 4;25(1):235. doi: 10.1186/s12864-024-10145-0.
Orchardgrass (Dactylis glomerata L.), a perennial forage, has the advantages of rich leaves, high yield, and good quality and is one of the most significant forage for grassland animal husbandry and ecological management in southwest China. Mitochondrial (mt) genome is one of the major genetic systems in plants. Studying the mt genome of the genus Dactylis could provide more genetic information in addition to the nuclear genome project of the genus.
In this study, we sequenced and assembled two mitochondrial genomes of Dactylis species of D. glomerata (597, 281 bp) and D. aschersoniana (613, 769 bp), based on a combination of PacBio and Illumina. The gene content in the mitochondrial genome of D. aschersoniana is almost identical to the mitochondrial genome of D. glomerata, which contains 22-23 protein-coding genes (PCGs), 8 ribosomal RNAs (rRNAs) and 30 transfer RNAs (tRNAs), while D. glomerata lacks the gene encoding the Ribosomal protein (rps1) and D. aschersoniana contains one pseudo gene (atp8). Twenty-three introns were found among eight of the 30 protein-coding genes, and introns of three genes (nad 1, nad2, and nad5) were trans-spliced in Dactylis aschersoniana. Further, our mitochondrial genome characteristics investigation of the genus Dactylis included codon usage, sequences repeats, RNA editing and selective pressure. The results showed that a large number of short repetitive sequences existed in the mitochondrial genome of D. aschersoniana, the size variation of two mitochondrial genomes is due largely to the presence of a large number of short repetitive sequences. We also identified 52-53 large fragments that were transferred from the chloroplast genome to the mitochondrial genome, and found that the similarity was more than 70%. ML and BI methods used in phylogenetic analysis revealed that the evolutionary status of the genus Dactylis.
Thus, this study reveals the significant rearrangements in the mt genomes of Pooideae species. The sequenced Dactylis mt genome can provide more genetic information and improve our evolutionary understanding of the mt genomes of gramineous plants.
鸭茅（Dactylis glomerata L.）是一种多年生牧草，具有叶片丰富、产量高、品质好的优点，是中国西南地区草地畜牧业和生态管理中最重要的牧草之一。线粒体（mt）基因组是植物主要遗传系统之一。研究鸭茅属的 mt 基因组除了核基因组项目外，还可以提供更多的遗传信息。
本研究基于 PacBio 和 Illumina 测序技术，对鸭茅属的两个物种（鸭茅 D. glomerata 和鸭茅 D. aschersoniana）的线粒体基因组进行了测序和组装，分别得到了 597,281 bp 和 613,769 bp 的序列。鸭茅属线粒体基因组的基因组成几乎与鸭茅属线粒体基因组相同，包含 22-23 个蛋白编码基因（PCGs）、8 个核糖体 RNA（rRNAs）和 30 个转移 RNA（tRNAs），而鸭茅属缺少编码核糖体蛋白（rps1）的基因，鸭茅属则含有一个假基因（atp8）。在 30 个蛋白编码基因中，有 23 个基因存在内含子，其中 3 个基因（nad 1、nad2 和 nad5）的内含子在鸭茅属中发生了反式拼接。此外，我们对鸭茅属线粒体基因组特征的研究包括密码子使用、序列重复、RNA 编辑和选择压力。结果表明，鸭茅属线粒体基因组中存在大量的短重复序列，两个线粒体基因组的大小变化主要是由于大量短重复序列的存在。我们还鉴定了 52-53 个从叶绿体基因组转移到线粒体基因组的大片段，发现它们的相似度超过 70%。基于最大似然法（ML）和贝叶斯推断法（BI）的系统发育分析揭示了鸭茅属的进化地位。
因此，本研究揭示了禾本科植物 mt 基因组的显著重排。所测序的鸭茅 mt 基因组可以提供更多的遗传信息，提高我们对禾本科植物 mt 基因组进化的认识。
