The 287,403 bp Mitochondrial Genome of Ectomycorrhizal Fungus Tuber calosporum Reveals Intron Expansion, tRNA Loss, and Gene Rearrangement

Xiaolin Li; Lijiao Li; Zhijie Bao; Wenying Tu; Xiaohui He; Bo Zhang; Lei Ye; Xu Wang; Qiang Li

doi:10.3389/fmicb.2020.591453

The 287,403 bp Mitochondrial Genome of Ectomycorrhizal Fungus Tuber calosporum Reveals Intron Expansion, tRNA Loss, and Gene Rearrangement

Front Microbiol. 2020 Dec 9:11:591453. doi: 10.3389/fmicb.2020.591453. eCollection 2020.

Authors

Xiaolin Li¹, Lijiao Li², Zhijie Bao², Wenying Tu², Xiaohui He², Bo Zhang¹, Lei Ye¹, Xu Wang³, Qiang Li²

Affiliations

¹ Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China.
² School of Food and Biological Engineering, Chengdu University, Chengdu, China.
³ College of Life Sciences, Henan Agricultural University, Zhengzhou, China.

Abstract

In the present study, the mitogenome of Tuber calosporum was assembled and analyzed. The mitogenome of T. calosporum comprises 15 conserved protein-coding genes, two rRNA genes, and 14 tRNAs, with a total size of 287,403 bp. Fifty-eight introns with 170 intronic open reading frames were detected in the T. calosporum mitogenome. The intronic region occupied 69.41% of the T. calosporum mitogenome, which contributed to the T. calosporum mitogenome significantly expand relative to most fungal species. Comparative mitogenomic analysis revealed large-scale gene rearrangements occurred in the mitogenome of T. calosporum, involving gene relocations and position exchanges. The mitogenome of T. calosporum was found to have lost several tRNA genes encoding for cysteine, aspartate, histidine, etc. In addition, a pair of fragments with a total length of 32.91 kb in both the nuclear and mitochondrial genomes of T. calosporum was detected, indicating possible gene transfer events. A total of 12.83% intragenomic duplications were detected in the T. calosporum mitogenome. Phylogenetic analysis based on mitochondrial gene datasets obtained well-supported tree topologies, indicating that mitochondrial genes could be reliable molecular markers for phylogenetic analyses of Ascomycota. This study served as the first report on mitogenome in the family Tuberaceae, thereby laying the groundwork for our understanding of the evolution, phylogeny, and population genetics of these important ectomycorrhizal fungi.

Keywords: Tuber; evolution 3; gene rearrangements; mitochondria; phylogenetic analysis.