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The complete chloroplast genome of Agropyron pectinatum (M. Bieb.) P. Beauv.

ABSTRACT: Agropyron pectinatum is a perennial forage widely cultivated in China, and it belongs to the Gramineous family. In this study, we assembled the complete chloroplast genome of A. pectinatum. The whole chloroplast genome of A. pectinatum is 135,041 bp in length, comprising a pair of inverted repeat (IR) regions (20,821 bp) that are separated by a large single copy (LSC) region (80,632 bp) and a small single copy (SSC) region (12,767 bp). The chloroplast genome of A. pectinatum contains 133 genes, and 87 of them are protein-coding genes, 38 are tRNA, and eight are rRNA genes. The chloroplast genome of A. pectinatum could provide valuable information for varieties identification and evolution of the Agropyron Gaertn.

SUBMITTER: Luo Y

PROVIDER: S-EPMC8330747 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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The complete chloroplast genome of Agropyron pectinatum (M. Bieb.) P. Beauv.

Luo Yijing Y Yang Junfeng J Du Wenxuan W Pang Yongzhen Y

Mitochondrial DNA. Part B, Resources 20210728 9

Agropyron pectinatum is a perennial forage widely cultivated in China, and it belongs to the Gramineous family. In this study, we assembled the complete chloroplast genome of A. pectinatum. The whole chloroplast genome of A. pectinatum is 135,041 bp in length, comprising a pair of inverted repeat (IR) regions (20,821 bp) that are separated by a large single copy (LSC) region (80,632 bp) and a small single copy (SSC) region (12,767 bp). The chloroplast genome of A. pectina ...[more]

PMID: 34377811

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Project description:BackgroundAs 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.ResultThe 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.ConclusionThe 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.

Dataset Information

The complete chloroplast genome of Agropyron pectinatum (M. Bieb.) P. Beauv.

Publications

The complete chloroplast genome of <i>Agropyron pectinatum</i> (M. Bieb.) P. Beauv.

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