Comparative Mitogenomic Analysis Reveals Dynamics of Intron Within and Between Tricholoma Species and Phylogeny of Basidiomycota.

Wenli Huang,Xin Jin,Huiyu Feng,Qiang Li,Ping Li,Wenying Tu,Chuan Xiong,Xu Wang

doi:10.3389/fgene.2021.534871

Abstract

The genus of Tricholoma is a group of important ectomycorrhizal fungi. The overlapping of morphological characteristics often leads to the confusion of Tricholoma species classification. In this study, the mitogenomes of five Tricholoma species were sequenced based on the next-generation sequencing technology, including T. matsutake SCYJ1, T. bakamatsutake, T. terreum, T. flavovirens, and T. saponaceum. These five mitogenomes were all composed of circular DNA molecules, with sizes ranging from 49,480 to 103,090 bp. Intergenic sequences were considered to be the main factor contributing to size variations of Tricholoma mitogenomes. Comparative mitogenomic analysis showed that the introns of the Agaricales mitogenome experienced frequent loss/gain events. In addition, potential gene transfer was detected between the mitochondrial and nuclear genomes of the five species of Tricholoma. Evolutionary analysis showed that the rps3 gene of the Tricholoma species was under positive selection or relaxed selection in the evolutionary process. In addition, large-scale gene rearrangements were detected between some Tricholoma species. Phylogenetic analysis using the Bayesian inference and maximum likelihood methods based on a combined mitochondrial gene set yielded identical and well-supported tree topologies. This study promoted the understanding of the genetics, evolution, and phylogeny of the Tricholoma genus and related species.

Highlights

As the “second genome” of eukaryotes, the mitochondrial genome plays an important role in eukaryotic growth and development, stress resistance, energy metabolism, aging, and death (Lang et al, 1999; Latorre-Pellicer et al, 2016)
Comparing them with two published T. matsutake strains from Korea (Yoon et al, 2016) and Japan (LC385608), we revealed the features of Tricholoma mitogenomes and the variations or similarities in genome size, gene content, gene arrangement, and repeat sequences within and among Tricholoma species
Comparative mitogenomic analyses indicated that intron was one of the main factors contributing to size variations of Tricholoma mitogenomes, even within species

Summary

Introduction

As the “second genome” of eukaryotes, the mitochondrial genome plays an important role in eukaryotic growth and development, stress resistance, energy metabolism, aging, and death (Lang et al, 1999; Latorre-Pellicer et al, 2016). The variation of the genome size, structure, gene content, gene arrangement, repeat sequences, and introns of the mitochondrial genome provides abundant information about the evolution and phylogeny of animals and fungi (Basse, 2010; Cameron, 2014; Li et al, 2020a). As of December 24, 2019, only 654 fungal mitochondrial genomes had been deposited in the National Center for Biotechnology Information (NCBI) database, of which

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