Complete Mitochondrial Genome of the Fungal Biocontrol Agent Trichoderma atroviride: Genomic Features, Comparative Analysis and Insight Into the Mitochondrial Evolution in Trichoderma

Abstract

The improvement of biopesticides for use in the agriculture industry requires an understanding of the biological-and ecological principles underlying their behavior in natural environments. The nuclear genomes of members of the genus Trichoderma, which are representative fungal biocontrol agents, have been actively studied in relation to the unique characteristics of these species as effective producers of CAZymes/secondary metabolites and biopesticides, but their mitochondrial genomes have received much less attention. In this study, the mitochondrial genome of Trichoderma atroviride (Hypocreales, Sordariomycetes), which targets wood-decaying fungal pathogens and has the ability to degrade chemical fungicides, was assembled de novo. A 32,758 bp circular DNA molecule was revealed with specific features, such as a few more protein CDS and trn genes, two homing endonucleases (LAGLIDADG-/GIY-YIG-type), and even a putative overlapping tRNA gene, on a closer phylogenetic relationship with T. gamsii among hypocrealean fungi. Particularly, introns were observed with several footprints likely to be evolutionarily associated with the intron dynamics of the Trichoderma mitochondrial genomes. This study is the first to report the complete de novo mitochondrial genome of T. atroviride, while comparative analyses of Trichoderma mitochondrial genomes were also conducted from the perspective of mitochondrial evolution for the first time.

An Update on Trichoderma Mitogenomes: Complete De Novo Mitochondrial Genome of the Fungal Biocontrol Agent Trichoderma harzianum (Hypocreales, Sordariomycetes), an Ex-Neotype Strain CBS 226.95, and Tracing the Evolutionary Divergences of Mitogenomes in Trichoderma

“…Thus far, most studies of fungal mitogenomes have focused on the (1) sequencing and characterization of individuals and (2) the elucidation of their phylogenetic positions within its relatives to support the potentials for one of the significant molecular markers identifying fungal species. Until recently, few studies have reported on comparative analyses of mitogenomes, ranging from a taxa level for specific fungal groups, under evolutionary viewpoints [ 8 , 9 , 10 , 11 ].…”

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

“…The largest intergenic region was between nad5 and cob genes. Meanwhile, in the T. reesei QM 9414 mitogenome, the species with the largest mitogenome in the genus, the intergenic regions accounted for a total of 7,405 bp (17.58% of total mitogenome), similar to the latter (Kwak 2020). So in this genus, it could be suggested that the intergenic regions were not an important force modeling mt genomic size variation.…”

“…Mitochondria (mt) use electron transport coupled with oxidative phosphorylation to generate ATP and these organelles also participate in several other cellular important functions [1]. Mitochondrial DNA or mitochondrial genome, also known as mitogenome, is made up of genes that encodes a small number of proteins whose mRNAs are translated by a distinctive mitochondrial protein-synthesizing system Burger et al 2003;Kwak 2020). Evolutionarily mitogenome exhibit remarkable variation in conformation, size, actual gene content, arrangement and expression (Gray et al 1999;Li et al 2019).…”

“…However, in spite of the extensive studies on biocontrol and nuclear genes of Trichoderma genus, information about its mitogenomes remains largely unknown. To date, even if Trichoderma genus has more than one hundred known species, only ve mitogenomes are available, including Trichoderma asperellum, Trichoderma atroviride, Trichoderma gamsii, Trichoderma hamatum, and Trichoderma reesei (Kwak 2020). The characteristics of mitogenomes belonging to different representatives of Trichoderma genus are needed to elucidate the understanding of the evolution and potential technological use of speci c isolates of this genus.…”

“…Related to the other species in the genus, T. gamsii has one intron of 1,609 bp reported in its mitogenome, T. asperellum has three introns with a total size of 2,065 bp; T. atroviride has four introns with a total size of 2,983 bp; T. hamatum with ve introns with a total size of 2,366 bp; and, T. reesei has eleven introns reported with a total size of 7,741 bp (Kwak 2020).…”