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

Abstract

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.

Comparative Mitogenomics Analysis Revealed Evolutionary Divergence among Neopestalotiopsis Species Complex (Fungi: Xylariales)

“…Mitogenome-related investigations across different species revealed a considerable diversity, allowing for a sturdy foundation for taxonomic clarity [ 3 ]. The high copy numbers and evolutionary rates of fungal mtDNFA make it an exceptional tool for evolutionary biology, taxonomy, and molecular phylogenetics [ 4 , 5 , 6 , 7 , 8 , 9 ]. Mitochondrial genomes possess distinct characteristics, such as a condensed size, constrained recombination rates, autonomous evolutionary path, and the abundance of analogous genes, which equip them with remarkable analytical capabilities when examining the subjects of population genetics and evolutionary biology [ 10 , 11 , 12 , 13 ].…”