Complete mitochondrial genome of Agropyron cristatum reveals gene transfer and RNA editing events

• Published in: BMC plant biology Vol. 24; no. 1; pp. 1 - 17
• Main Authors: Ou, Taiyou, Wu, Zinian, Tian, Chunyu, Yang, Yanting, Li, Zhiyong
• Format: Journal Article
• Language: English
• Published: London BioMed Central Ltd 04.09.2024; BioMed Central; BMC
• Subjects: Agropyron; Agropyron cristatum; Amino acids; Analysis; Arid regions; Arid zones; Biological diversity; Botanical research; Chloroplasts; Classification; Codon; Drought; Editing; Evolution & development; Evolutionary genetics; Gene transfer; Genes; Genetic aspects; Genetic diversity; Genetic transformation; Genomes; Genomics; Germplasm; Heritability; Introns; Leucine; Livestock; Mitochondria; Mitogenome; Molecular structure; Nucleotide sequence; Nutritive value; Phylogenetics; Phylogeny; Physiological aspects; Plant genetics; Plant mitochondria; Plants (botany); Positive selection; Proteins; Ribonucleic acid; RNA; RNA editing; RNA processing; rRNA; Semi arid areas; Semiarid lands; Software; Transfer RNA; Triticeae; tRNA; Wheatgrasses; China
• ISSN: 1471-2229; 1471-2229
• 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.