背景:作为干旱和半干旱地区的重要牧草,Agropyroncristatum为牲畜提供了非常高的营养价值。此外,A.cristatum表现出出色的遗传特征,可以忍受干旱和疾病。因此,丰富的遗传多样性是主要粮食作物改良的基石。本研究的目的是系统地描述A的有丝分裂基因组,并初步分析其内部变异。
结果:A.cristatum有丝分裂基因组是381,065bp的单环分子结构,包含52个基因,包括35个蛋白质编码,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拷贝的tRNA基因。发现总共320个重复序列覆盖了10%以上的有丝分裂基因组(105个简单序列,185个分散和30个串联重复),这导致了A的有丝分裂基因组中的大量片段重排。亮氨酸是最常见的氨基酸(n=1087,10.8%)的蛋白编码基因。并且最高使用密码子是ATG(起始密码子)。密码子第3个碱基的A/T变化数远高于G/C。在23个PCG中,Pi值范围为0.0021~0.0539,平均值为0.013。此外,预测了81个RNA编辑位点,比其他植物有丝分裂基因组报道的要少得多。大多数RNA编辑位点碱基位置集中在第一个和第二个密码子碱基,这是C到T的过渡。此外,我们确定了95个序列片段(总长度为34,343bp),从叶绿体转移到线粒体基因,内含子,和基因间区域。在此过程中保持了tRNA基因的稳定性。15种禾本科植物共有23个蛋白质编码基因的选择压力分析,表明大多数基因在进化过程中都经过纯化选择,而rps4,cob,mttB,ccmB在不同植物中进行了阳性选择。最后,基于22个植物有丝分裂基因组构建了一个系统发育树,这表明Agropyron植物在小麦中具有高度的独立遗传力。
结论:这项研究的发现为更好地理解A.cristatum基因提供了新的数据,并证明有丝分裂基因组适用于植物分类的研究,比如Agropyron.此外,它为进一步探索Agropyron物种内部的系统发育关系提供了参考,并为后续开发和利用凤梨属植物种质资源奠定了理论基础。
BACKGROUND: 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.
RESULTS: 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.
CONCLUSIONS: 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.