Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China.
Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot, China.
BMC Plant Biol. 2024 Sep 4;24(1):830. doi: 10.1186/s12870-024-05558-8.
As an important forage in arid and semi-arid regions, Agropyron cristatum provides livestock with exceptionally high nutritional value. Additionally, A. cristatum exhibits outstanding genetic characteristics to endure drought and disease. Therefore, rich genetic diversity serves as a cornerstone for the improvement of major food crops. The purposes of this study were to systematically describe mitogenome of A.cristatum and preliminarily analyze its internal variations.
The A. cristatum mitogenome was a single-ring molecular structure of 381,065 bp that comprised 52 genes, including 35 protein-coding, 3 rRNA and 14 tRNA genes. Among these, two pseudoprotein-coding genes and multiple copies of tRNA genes were observed. A total of 320 repetitive sequences was found to cover more than 10% of the mitogenome (105 simple sequences, 185 dispersed and 30 tandem repeats), which led to a large number of fragment rearrangements in the mitogenome of A. cristatum. Leucine was the most frequent amino acid (n = 1087,10.8%) in the protein-coding genes of A. cristatum mitogenome, and the highest usage codon was ATG (initiation codon). The number of A/T changes at the third base of the codon was much higher than that of G/C. Among 23 PCGs, the range of Pi values is from 0.0021 to 0.0539, with an average of 0.013. Additionally, 81 RNA editing sites were predicted, which were considerably fewer than those reported in other plant mitogenomes. Most of the RNA editing site base positions were concentrated at the first and second codon bases, which were C to T transitions. Moreover, we identified 95 sequence fragments (total length of 34, 343 bp) that were transferred from the chloroplast to mitochondria genes, introns, and intergenic regions. The stability of the tRNA genes was maintained during this process. Selection pressure analysis of 23 protein-coding genes shared by 15 Poaceae plants, showed that most genes were subjected to purifying selection during evolution, whereas rps4, cob, mttB, and ccmB underwent positive selection in different plants. Finally, a phylogenetic tree was constructed based on 22 plant mitogenomes, which showed that Agropyron plants have a high degree of independent heritability in Triticeae.
The findings of this study provide new data for a better understanding of A. cristatum genes, and demonstrate that mitogenomes are suitable for the study of plant classifications, such as those of Agropyron. Moreover, it provides a reference for further exploration of the phylogenetic relationships within Agropyron species, and establishes a theoretical basis for the subsequent development and utilization of A. cristatum plant germplasm resources.
冰草是干旱半干旱地区重要的饲用植物，具有极高的营养价值，同时具有抗旱、抗寒、抗盐碱等优良的遗传特性。丰富的遗传多样性是改良主要粮食作物的基石。本研究旨在系统描述冰草的线粒体基因组结构，并初步分析其内部变异。
冰草的线粒体基因组是一个 381065bp 的单环分子结构，包含 52 个基因，包括 35 个蛋白编码基因、3 个 rRNA 和 14 个 tRNA 基因。其中观察到两个假蛋白编码基因和多个 tRNA 基因的拷贝。共发现 320 个重复序列，占线粒体基因组的 10%以上（105 个简单序列、185 个分散序列和 30 个串联重复序列），导致冰草线粒体基因组发生了大量的片段重排。亮氨酸是冰草线粒体基因组蛋白编码基因中最常见的氨基酸（n=1087，占 10.8%），最高使用密码子是 ATG（起始密码子）。密码子第三碱基的 A/T 变化数量明显高于 G/C。23 个 PCGs 中，Pi 值范围为 0.0021-0.0539，平均值为 0.013。此外，预测到 81 个 RNA 编辑位点，明显少于其他植物线粒体基因组报道的数量。大多数 RNA 编辑位点碱基位置集中在第一和第二密码子碱基，即 C 到 T 的转换。此外，我们鉴定了 95 个序列片段（总长 34343bp），它们从叶绿体转移到线粒体基因、内含子和基因间区。在此过程中，tRNA 基因的稳定性得以维持。对 15 种禾本科植物共有的 23 个蛋白编码基因进行选择压力分析表明，大多数基因在进化过程中受到纯化选择，而 rps4、 cob、 mttB 和 ccmB 在不同植物中经历了正选择。最后，基于 22 种植物的线粒体基因组构建了系统发育树，表明冰草在小麦族中具有高度的遗传独立性。
本研究为进一步了解冰草基因提供了新的数据，并证明线粒体基因组适合研究植物分类，如冰草属。此外，它为进一步探讨冰草属种内的系统发育关系提供了参考，并为后续开发利用冰草植物种质资源奠定了理论基础。
