The Mitochondrial Genome of the Phytopathogenic Fungus Bipolaris sorokiniana and the Utility of Mitochondrial Genome to Infer Phylogeny of Dothideomycetes

Abstract

A number of species in Bipolaris are important plant pathogens. Due to a limited number of synapomorphic characters, it is difficult to perform species identification and to estimate phylogeny of Bipolaris based solely on morphology. In this study, we sequenced the complete mitochondrial genome of Bipolaris sorokiniana, and presented the detailed annotation of the genome. The B. sorokiniana mitochondrial genome is 137,775 bp long, and contains two ribosomal RNA genes, 12 core proteincoding genes, 38 tRNA genes. In addition, two ribosomal protein genes (rps3 gene and rps5 gene) and the fungal mitochondrial RNase P gene (rnpB) are identified. The large genome size is mostly determined by the presence of numerous intronic and intergenic regions. A total of 28 introns are inserted in eight core proteincoding genes. Together with the published mitochondrial genome sequences, we conducted a preliminary phylogenetic inference of Dothideomycetes under various datasets and substitution models. The monophyly of Capnodiales, Botryosphaeriales and Pleosporales are consistently supported in all analyses. The Venturiaceae forms an independent lineage, with a distant phylogenetic relationship to Pleosporales. At the family level, the Mycosphaerellaceae, Botryosphaeriaceae. Phaeosphaeriaceae, and Pleosporaceae are recognized in the majority of trees.

Mitogenomes of Two Phallus Mushroom Species Reveal Gene Rearrangement, Intron Dynamics, and Basidiomycete Phylogeny

“…The mitogenome is often used in phylogenetic and evolutionary studies of eukaryotes due to its small genome size, conserved gene sequence, low level of recombination, and numerous molecular markers (Zhang et al, 2017;Ramos et al, 2018). Compared to animals, research on the mitogenomes of fungi is infrequent (Song et al, 2020). The development of nextgeneration sequencing technology has enabled research on fungal mitogenomes (Li et al, 2019c).…”

“…Stinkhorn mushrooms have unique characteristics but few morphological characteristics useful for classification. In contrast, the mitogenome is a reliable tool for eukaryotic phylogenetic analysis, and it has been previously used in taxonomic and evolutionary studies of the Basidiomycetes (Li et al, 2019d, 2020. The mitogenomes of Phallus, Phallaceae, and Phallales, have not been reported, and this has limited understanding of stinkhorn fungi evolution.…”

Revealing the high variability on nonconserved core and mobile elements of Austropuccinia psidii and other rust mitochondrial genomes

“…It is often useful as a valuable source of information to study systematics and evolutionary biology in eukaryotes where insufficient phylogenetic signals have accumulated in nuclear genes [17,25]. For instance, Song et al [26] resolved some incongruences of Dothideomycetes phylogeny using the mitochondrial genome of many phytopathogens belonging to this Class [26]. The availability of mitochondrial genome sequences provides valuable information about genome organization and enables evaluating structural rearrangements using comparative studies [27].…”

“…For instance, Song et al . [ 26 ] resolved some incongruences of Dothideomycetes phylogeny using the mitochondrial genome of many phytopathogens belonging to this Class [ 26 ]. The availability of mitochondrial genome sequences provides valuable information about genome organization and enables evaluating structural rearrangements using comparative studies [ 27 ].…”

Trichoderma Koningiopsis (Hypocreaceae) has the Smallest Mitogenome of the Genus Trichoderma

“…Recently, development of high-throughput sequencing technologies and related bioinformatics tools have allowed considerably greater numbers of nucleotides to be characterized and the genome-scale data to be more easily assembled. Compared to the whole-genome data, mitogenomes are more readily sequenced with broader taxon sampling and a reasonable cost (Song et al 2020). The number of complete lamentous fungal mitogenome sequences has signi cantly increased facilitating evolutionary and systematic studies (Mardanov et al 2014).…”