Complete mitochondrial genome of the endophytic fungus Pestalotiopsis fici: features and evolution

Abstract

Endophytic fungi (EF) live within plants and have profound impacts on plant communities. They are astonishingly diverse but poorly studied at the genome level. Herein, we assembled the mitochondrial genome (mitogenome) of the EF Pestalotiopsis fici, annotated and compared it with those of other relatives to better understand the evolution of the EF lineage. Except for standard fungal mitochondrial genes, the 69,529-bp circular mitogenome of P. fici harbors 18 introns acquired possibly through lateral transfer from other fungi and nine free-standing open reading frames with some scarcely seen in fungal mitogenomes. BLAST analysis detected no obvious duplication events of large fragments between mitochondrial and nuclear genomes of the fungus. Transcription analyses validated the expression of all mitochondrial genes, while most genes showed higher expression on rice than in two other media. The mitogenome of P. fici is highly syntenic with the Xylariales species Annulohypoxylon stygium and the endophyte Epichloe festucae var. lolii, but lacks synteny with another endophyte Penicillium polonicum. This study reports the first mitogenome of Pestalotiopsis and the third published mitogenome from an EF and provides insights into the evolution of the EF lineage.

The complete mitochondrial genome of the Chan‐hua fungus Isaria cicadae: a tale of intron evolution in Cordycipitaceae

“…These introns were most likely obtained by horizontal transfer from related fungal species (Supporting Information Table S6), while evidence of degeneration was also obvious for several introns. Similar results were also documented in many other fungi (Zhang et al ., ; Wang et al ., ). Mitochondrial introns are sometimes referred to as selfish genetic elements since they seem not to benefit host genomes and thus tend to degenerate rapidly due to a lack of natural selection (Edgell, ).…”

“…It possessed the largest mitogenome known in Cordycipitaceae due to the presence of 25 introns interrupting nine mitochondrial genes. In accordance with previous reports (Lang et al ., ; Zhang et al ., ), subgroup IB is more frequent than other subgroups of group I introns (Supporting Information Table S2). These introns were most likely obtained by horizontal transfer from related fungal species (Supporting Information Table S6), while evidence of degeneration was also obvious for several introns.…”

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

“…Similarly, in a study of the mitochondrial genome for Hypomyces aurantius (Hypocreales, Sordariomycetes), Hypocreaceae was clustered as [(Hypocreaceae + Clavicipitaceae: BS = 40) + Cordycipitaceae: BS = 52] in ML analysis (Deng et al, 2016). Meanwhile, as clustered in the Cordycipitaceae clade on the ML-and BI tree (Figure 2 and Supplementary Figure S2), a study of the mitochondrial genome for the endophytic fungus Pestalotiopsis fici (Xylariales, Sordariomycetes) showed a ML based phylogenetic tree in which some of the internal nodes could not be fully supported (BS = 59-72), though they were well supported in a BI tree (BPP = 1.00) (Zhang et al, 2017). Although differences in the analysis conditions (e.g., variations in the concatenated sequences and differences between the tree algorithms) need to be considered when comparing these previous studies, it is clear that informative datasets of the mitochondrial genomes from closely related family species are still necessary to improve the resolution of the Hypocreales phylogeny.…”

Characterization and phylogenetic analysis of the complete mitochondrial genome of the medicinal fungus Laetiporus sulphureus

“…Mitochondria are important in the growth and development of fungi; they are critically involved in fungal senescence, quiescence, virulence, pathogenicity, and drug resistance 28 , 29 . The mitochondrial genomes of fungal species vary remarkably in size, gene order, and number of repeats, intergenic regions, introns, and open reading frames (ORFs) 30 – 32 .…”