Phylogenetic Relationships of Three Ramaria Species Based on Mitochondrial Genome Analysis

Ramaria has been a remarkable genus throughout the history of macrofungi. However, there is a lack of information on this genus of macrofungi. This study determined the order of nucleotides in the mitochondrial genomes (mitogenomes) of three Ramaria species, followed by a detailed investigation of the obtained genetic information. Circular mitogenomes of Ramaria brunnecliacina, R. ichnusensis, and R. flavescens had sizes of 78,960, 61,851, and 81,282 bp, respectively. The genomes exhibited variations in genetic content, gene length, tRNA, and codon usage. Ramaria mitogenomes demonstrated variable evolutionary rates across several protein-coding genes. The results revealed significant gene rearrangements in Ramaria mitogenomes, including gene displacement and tRNA duplication. Utilizing Bayesian inference and maximum likelihood methods on a comprehensive set of conserved mitochondrial proteins, we generated a well-supported phylogenetic tree for Basidiomycota. This analysis revealed that R. brunneciacina and R. flavescens are closely related, while confirming the paraphyletic nature of the Ramaria genus and its genetic affinity with other species of the subclass Phallomycetidae. This study presents a basic structure for understanding the evolutionary dynamics, genetic makeup, and taxonomy categorization of this significant fungal community.