Dataset Information

Comparative analysis of the complete mitochondrial genomes of related species Chrysolophus amherstiae and Chrysolophus pictus.

ABSTRACT: Chrysolophus amherstiae and Chrysolophus pictus are two related species of Chrysolophus. Understanding the differences in their mitochondrial genome structure is of great significance for studying their phylogenetic relationship. In this study, the full mitochondrial genome of C. amherstiae was sequenced and annotated and analyzed with C. pictus to reveal their structural differences. At the same time, the phylogenetic trees were constructed based on the BI and ML methods with other species of the same family to analyze the phylogenetic relationship of Phasianidae. The results showed that the basic characteristics of mitochondrial genomes of C. amherstiae and C. pictus were similar. By comparing the secondary structures of rRNA and the relative synonymous codon usage of protein-coding genes, the subtle differences of mitochondrial structures between the two were further demonstrated.

SUBMITTER: Zhou T

PROVIDER: S-EPMC8741247 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Comparative analysis of the complete mitochondrial genomes of related species Chrysolophus amherstiae and Chrysolophus pictus.

Zhou Tong T Zhou Fei F Yao Yongfang Y Xie Meng M Ni Qingyong Q Zhang Mingwang M Xu Huailiang H

Mitochondrial DNA. Part B, Resources 20220105 1

Chrysolophus amherstiae and Chrysolophus pictus are two related species of Chrysolophus. Understanding the differences in their mitochondrial genome structure is of great significance for studying their phylogenetic relationship. In this study, the full mitochondrial genome of C. amherstiae was sequenced and annotated and analyzed with C. pictus to reveal their structural differences. At the same time, the phylogenetic trees were constructed based on the BI and ...[more]

PMID: 35005229

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Project description:In this study, we assembled and annotated the chloroplast (cp) genomes of four Ligustrum species, L. sinense, L. obtusifolium, L. vicaryi, and L. ovalifolium 'Aureum'. Including six other published Ligustrum species, we compared various characteristics such as gene structure, sequence alignment, codon preference, and nucleic acid diversity, and performed positive-selection genes screening and phylogenetic analysis. The results showed that the cp genome of Ligustrum was 162,185-166,800 bp in length, with a circular tetrad structure, including a large single-copy region (86,885-90,106 bp), a small single-copy region (11,446-11,499 bp), and a pair of IRa and IRb sequences with the same coding but in opposite directions (31,608-32,624 bp). This structure is similar to the cp genomes of most angiosperms. We found 132-137 genes in the cp genome of Ligustrum, including 89-90 protein-coding genes, 35-39 tRNAs, and 8 rRNAs. The GC content was 37.93-38.06% and varied among regions, with the IR region having the highest content. The single-nucleotide (A/T)n was dominant in simple-sequence repeats of the Ligustrum cp genome, with an obvious A/T preference. Six hotspot regions were identified from multiple sequence alignment of Ligustrum; the ycf1 gene region and the clpP1 exon region can be used as potential DNA barcodes for the identification and phylogeny of the genus Ligustrum. Branch-site model and Bayes empirical Bayes (BEB) analysis showed that four protein-coding genes (accD, clpP, ycf1, and ycf2) were positively selected, and BEB analysis showed that accD and rpl20 had positively selected sites. A phylogenetic tree of Oleaceae species was constructed based on the whole cp genomes, and the results were consistent with the traditional taxonomic results. The phylogenetic results showed that genus Ligustrum is most closely related to genus Syringa. Our study provides important genetic information to support further investigations of the phylogenetic development and adaptive evolution of Ligustrum species.

Dataset Information

Comparative analysis of the complete mitochondrial genomes of related species Chrysolophus amherstiae and Chrysolophus pictus.

Publications

Comparative analysis of the complete mitochondrial genomes of related species <i>Chrysolophus amherstiae</i> and <i>Chrysolophus pictus</i>.

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