Comparative Mitochondrial Genome Analysis of Two Ectomycorrhizal Fungi (Rhizopogon) Reveals Dynamic Changes of Intron and Phylogenetic Relationships of the Subphylum Agaricomycotina

Abstract

In the present study, we assembled and compared two mitogenomes from the Rhizopogon genus. The two mitogenomes of R. salebrosus and R. vinicolor comprised circular DNA molecules, with the sizes of 66,704 bp and 77,109 bp, respectively. Comparative mitogenome analysis indicated that the length and base composition of protein coding genes (PCGs), rRNA genes and tRNA genes varied between the two species. Large fragments aligned between the mitochondrial and nuclear genomes of both R. salebrosus (43.41 kb) and R. vinicolor (12.83 kb) indicated that genetic transfer between mitochondrial and nuclear genomes has occurred over evolutionary time of Rhizopogon species. Intronic regions were found to be the main factors contributing to mitogenome expansion in R. vinicolor. Variations in the number and type of introns in the two mitogenomes indicated that frequent intron loss/gain events occurred during the evolution of Rhizopogon species. Phylogenetic analyses based on Bayesian inference (BI) and Maximum likelihood (ML) methods using a combined mitochondrial gene set yielded identical and well-supported tree topologies, wherein Rhizopogon species showed close relationships with Agaricales species. This is the first study of mitogenomes within the genus Rhizopogon, and it provides a basis for understanding the evolution and differentiation of mitogenomes from the ectomycorrhizal fungal genus.

Exploring the Relationship Among Divergence Time and Coding and Non-coding Elements in the Shaping of Fungal Mitochondrial Genomes

“…The authors reported the presence of 19 introns in A. bisporus and 23 introns in E. resinifera, which was considered the fungal species with the largest number of introns in this gene. Introns have also been identified in other genes, such as cox2, cob, and rrnl in two species of Rhizopogon (Agaricomycotina) (Li et al, 2019). In the fungus O. sinensis (Hypocreales), the genes cox1 and rrnl were reported as the main reservoir of introns (Li et al, 2015).…”

“…The presence of fungal mitochondrial genes in the nuclear genome was assessed by sequence similarity searches using Blast software according to Li et al (2019) with some modifications. For this analysis, 18 nuclear fungal genomes publicly available to date (out of the 35 evaluated in this study) were used ( Supplementary Table S1).…”

Comparative mitogenome analysis of two ectomycorrhizal fungi (Paxillus) reveals gene rearrangement, intron dynamics, and phylogeny of basidiomycetes

“…Up to now, only two mitogenomes from Boletales have been published (Li et al 2019a). We compared the genome sizes, base compositions, gene numbers, intron numbers, and gene arrangements among different Boletales species to assess variations and conservativeness among the mitogenomes.…”

Characterization of the complete mitochondrial genome of biocontrol yeast Sporobolomyces sp. (Sporidiobolales: Sporidiobolaceae) with phylogenetic analysis

“…To investigate the phylogenetic positions of Sporobolomyces sp., we constructed a phylogenetic tree for 18 Basidiomycota species. Rhizopogon salebrosus from the Boletales order was set as the outgroup (Li, Ren, et al 2019). The phylogenetic tree was constructed using the Bayesian analysis (BI) method based on the combined 14 core proteincoding genes according to previously described methods (Li, Wang, Jin, Chen, Xiong, Li, Liu, et al 2019;Li, Wang, Jin, Chen, Xiong, Li, Zhao, et al 2019;Li, Yang, et al 2020).…”