Phylogenetic Relationships of Three Ramaria Species Based on Mitochondrial Genome Analysis

Abstract

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.

Keywords: Ramaria species; clavarioid fungi; evolution; mitochondrial genome; phylogenetic analysis.

FIGURE 1

Depictions of the circular organization of the three Ramaria mitochondrial genomes. Various genes are illustrated as colored blocks. The concentric rings, moving from the innermost to the outermost, correspond to the mitogenomes of R. brunnecliacina, R. ichnusensis, and R. flavescens .

FIGURE 2

Heatmap showing the Relative Synonymous Codon Usage (RSCU) patterns across the mitogenomes of 10 Phallomycetidae species.

FIGURE 3

The RSCU in the mitochondrial genomes of three Ramaria species, presented as stacked column plots.

FIGURE 4

Differences in the length and base composition of 15 protein‐coding genes (PCGs) across five Ramaria mitochondrial genomes. (a), Variation in PCG length; (b), GC content of PCGs; (c), AT skew; (d), GC skew.

FIGURE 5

Analysis of the genetic variation in 15 PCGs among five Ramaria species. K2P, distance based on the Kimura‐2‐parameter model; Ka, rate of nonsynonymous substitutions per nonsynonymous site; Ks, rate of synonymous substitutions per synonymous site.

FIGURE 6

Analysis of mitochondrial gene arrangements across six Phallomycetidae species (with all five Ramaria species sharing the same arrangement, denoted as I). Genes highlighted in blue represent identical arrangements across all 10 species; silver blocks indicate genes that share the same arrangement in six out of nine species; red blocks signify genes that have undergone translocation; and green blocks represent genes that the genes have doubled. I: Ramaria spices, II: M. fleischeri, III: T. floccosus , IV: D. indusiate, V: P. echinovolvatus, VI: S. stellatus .

FIGURE 7

Lengths of RNA region, protein‐coding region, intronic region, and intergenic region in the 10 Phallomycetidae species. A: P. echinovolvatus, B: R. ichnusensis, C: T. floccosus , D: R. brunnecliacina, E: R. flavescens , F: D. indusiata, G: M. fleischeri, H: R. cf. rubripermanens, I: R. rubella , J: S. stellatus.

FIGURE 8

Collinearity analysis map of the 10 Phallomycetidae mitochondrial genomes. Eight homologous regions were detected across the ten mitogenomes. The sizes and positions of homologous regions varied across the mitogenomes.

FIGURE 9

Phylogenetic analysis of 77 Basidiomycota species using maximum likelihood (ML), based on 15 PCGs and 2rRNA sequences.