De novo mitochondrial genome sequencing of Cladonia subulata and phylogenetic analysis with other dissimilar species

In this study, the complete mitochondrial genome of Cladonia subulata (L.) FH Wigg was sequenced and assembled and then compared with those of other Cladonia species. The mitogenome of Cladonia subulata, the type species of Cladonia, consisted of a circular DNA molecule of 58,895 bp 44 genes (15 pro...

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Bibliographic Details
Published in:PloS one 2023-05, Vol.18 (5), p.e0285818-e0285818
Main Authors: Fang, Jinjin, Mamut, Reyim, Wang, Lidan, Anwar, Gulmira
Format: Article
Language:English
Subjects:
Adenosine triphosphate
Analysis
Annotations
Ascomycota
Base composition
Biology and Life Sciences
Chromosome Mapping
Circular DNA
Cladonia
Cladonia subulata
Computer and Information Sciences
Deoxyribonucleic acid
DNA
DNA sequencing
Evolution & development
Evolutionary genetics
Fungi
Gene sequencing
Genes
Genetic aspects
Genetic diversity
Genome, Mitochondrial
Genomes
Genomics
Health aspects
Introns
Lichens
Mitochondria
Morphology
Nucleotide sequence
Nucleotide sequencing
Phosphorylation
Phylogenetics
Phylogeny
Properties
rRNA
Transfer RNA
tRNA
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Summary:In this study, the complete mitochondrial genome of Cladonia subulata (L.) FH Wigg was sequenced and assembled and then compared with those of other Cladonia species. The mitogenome of Cladonia subulata, the type species of Cladonia, consisted of a circular DNA molecule of 58,895 bp 44 genes (15 protein-coding genes, 2 rRNA genes, and 27 tRNA genes). The base composition had shown an obvious AT preference, and all 27 tRNA genes formed a typical clover structure. Comparison with other 7 Cladonia species indicated that the duplication/loss of tRNAs had occurred during evolution, and introns appeared to explain the variation in cox1 genes in Cladonia, the mitochondrial genome tends to be generally conservative and local dynamic changes. Repeat sequences were mainly located in gene intervals, which were mainly distributed among intergenic spacers and may cause rearrangement of the mitogenome. The phylogenetic results showed that Cladonia subulata and C. polycarpoides were assigned to the Cladonia Subclade. The results add to the available mitochondrial genome sequence information of Cladonia subulata, provide basic data for the systematic development, resource protection, and genetic diversity research in Cladonia subulata, and also provide theoretical support for further genomic research of lichens.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0285818