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Characterization of Complete Mitochondrial Genomes of the Five Peltigera and Comparative Analysis with Relative Species.

ABSTRACT: In the present study, the complete mitochondrial genomes of five Peltigera species (Peltigera elisabethae, Peltigera neocanina, Peltigera canina, Peltigera ponojensis, Peltigera neckeri) were sequenced, assembled and compared with relative species. The five mitogenomes were all composed of circular DNA molecules, and their ranged from 58,132 bp to 69,325 bp. The mitochondrial genomes of the five Peltigera species contain 15 protein-coding genes (PCGs), 2 rRNAs, 26-27 tRNAs and an unidentified open reading frame (ORF). The PCG length, AT skew and GC skew varied among the 15 PCGs in the five mitogenomes. Among the 15 PCGs, cox2 had the least K2P genetic distance, indicating that the gene was highly conserved. The synteny analysis revealed that the coding regions were highly conserved in the Peltigera mitochondrial genomes, but gene rearrangement occurred in the intergenic regions. The phylogenetic analysis based on the 14 PCGs showed that the 11 Peltigera species formed well-supported topologies, indicating that the protein-coding genes in the mitochondrial genome may be used as a reliable molecular tool in the study of the phylogenetic relationship of Peltigera.

SUBMITTER: Anwar G

PROVIDER: S-EPMC10607270 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature

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Characterization of Complete Mitochondrial Genomes of the Five Peltigera and Comparative Analysis with Relative Species.

Anwar Gulmira G Mamut Reyim R Wang Jiaqi J

Journal of fungi (Basel, Switzerland) 20230926 10

In the present study, the complete mitochondrial genomes of five Peltigera species (Peltigera elisabethae, Peltigera neocanina, Peltigera canina, Peltigera ponojensis, Peltigera neckeri) were sequenced, assembled and compared with relative species. The five mitogenomes were all composed of circular DNA molecules, and their ranged from 58,132 bp to 69,325 bp. The mitochondrial genomes of the five Peltigera species contain 15 protein-coding genes (P ...[more]

PMID: 37888225

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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

Characterization of Complete Mitochondrial Genomes of the Five Peltigera and Comparative Analysis with Relative Species.

Publications

Characterization of Complete Mitochondrial Genomes of the Five <i>Peltigera</i> and Comparative Analysis with Relative Species.

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