Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 20 (20)

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

Affiliations

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

Qiang Li et al. Int J Mol Sci.

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.

Keywords: Rhizopogon; evolution; gene rearrangement; intron; mitochondrial genome; phylogenetic analysis.

Conflict of interest statement

The authors declare that they have no conflict of interest.

Figures

Figure 1
Figure 1
Circular maps of the mitogenomes of two Rhizopogon species. Genes are represented by different colored blocks. Colored blocks outside each ring indicate that the genes are on the direct strand, while colored blocks within the ring indicates that the genes are located on the reverse strand. The circle inside the GC content graph marks the 50% threshold.
Figure 2
Figure 2
Putative secondary structures of the 25 tRNA genes identified in the mitogenomes of two Rhizopogon species. Residues conserved across the two mitogenomes are shown in green, while variable sites are shown in red. All genes are shown in order of occurrence in the mitogenome of R. salebrosus, starting from trnM.
Figure 3
Figure 3
The protein-coding, intronic, intergenic, and RNA gene region proportions of the entire mitogenomes of the two Rhizopogon species. The bottom panel shows the contribution of different gene regions to the expansion of the R. vinicolor mitogenome.
Figure 4
Figure 4
Codon usage in the mitogenomes of two Rhizopogon species. Frequency of codon usage is plotted on the y-axis. (a) R. salebrosus; (b) R. vinicolor.
Figure 5
Figure 5
Variation in the length and base composition of each of 15 protein-coding genes (PCGs) and 25 tRNA genes between two Rhizopogon mitogenomes. R. salebrosus is represented in blue and R. vinicolor is represented in red. (a) PCG length variation; (b) GC content of the PCGs; (c) AT skew; (d) GC skew; (e) lengths of shared tRNA genes; (f) GC content of shared tRNA genes.
Figure 6
Figure 6
Genetic analysis of 15 protein coding genes conserved in two Rhizopogon mitogenomes. K2P — the Kimura−2-parameter distance; Ka — the mean number of nonsynonymous substitutions per nonsynonymous site; Ks — the mean number of synonymous substitutions per synonymous site.
Figure 7
Figure 7
Molecular phylogeny of 41 Agaricomycotina species based on Bayesian inference (BI) and Maximum likelihood (ML) analysis of 15 protein coding genes and two rRNA genes. Support values are Bayesian posterior probabilities (before slash) and bootstrap (BS) values (after slash). Species and NCBI accession numbers for genomes used in the phylogenetic analysis are provided in Supplementary Table S9.

Similar articles

See all similar articles

References

    1. Franco A.R., Sousa N.R., Ramos M.A., Oliveira R.S., Castro P.M. Diversity and persistence of ectomycorrhizal fungi and their effect on nursery-inoculated Pinus pinaster in a post-fire plantation in Northern Portugal. Microb. Ecol. 2014;68:761–772. doi: 10.1007/s00248-014-0447-9. - DOI - PubMed
    1. Sulzbacher M.A., Grebenc T., Garcia M.A., Silva B.D., Silveira A., Antoniolli Z.I., Marinho P., Munzenberger B., Telleria M.T., Baseia I.G., et al. Molecular and morphological analyses confirm Rhizopogon verii as a widely distributed ectomycorrhizal false truffle in Europe, and its presence in South America. Mycorrhiza. 2016;26:377–388. doi: 10.1007/s00572-015-0678-8. - DOI - PMC - PubMed
    1. Dowie N.J., Grubisha L.C., Burton B.A., Klooster M.R., Miller S.L. Increased phylogenetic resolution within the ecologically important Rhizopogon subgenus Amylopogon using 10 anonymous nuclear loci. Mycologia. 2017;109:35–45. doi: 10.1080/00275514.2017.1285165. - DOI - PubMed
    1. Grubisha L.C., Bergemann S.E., Bruns T.D. Host islands within the California Northern Channel Islands create fine-scale genetic structure in two sympatric species of the symbiotic ectomycorrhizal fungus Rhizopogon. Mol. Ecol. 2007;16:1811–1822. doi: 10.1111/j.1365-294X.2007.03264.x. - DOI - PubMed
    1. Grubisha L.C., Trappe J.M., Molina R., Spatafora J.W. Biology of the ectomycorrhizal genus Rhizopogon. VI. Re-examination of infrageneric relationships inferred from phylogenetic analyses of ITS sequences. Mycologia. 2002;94:607–619. doi: 10.1080/15572536.2003.11833189. - DOI - PubMed
Feedback