Phylogenetic Relationships of Three <i>Ramaria</i> Species Based on Mitochondrial Genome Analysis

<i>Ramaria</i> 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 <i>Ramaria</i> species, followed by a detailed investigation of the obtained genetic information. Circular mitogenomes of <i>Ramaria brunnecliacina</i>, <i>R</i>. <i>ichnusensis</i>, and <i>R. flavescens</i> 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. <i>Ramaria</i> mitogenomes demonstrated variable evolutionary rates across several protein-coding genes. The results revealed significant gene rearrangements in <i>Ramaria</i> 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 <i>R</i>. <i>brunneciacina</i> and <i>R. flavescens</i> are closely related, while confirming the paraphyletic nature of the <i>Ramaria</i> 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.