Annotation and analysis of the mitochondrial genome of Coniothyrium glycines, causal agent of red leaf blotch of soybean, reveals an abundance of homing endonucleases

Abstract

Coniothyrium glycines, the causal agent of soybean red leaf blotch, is a USDA APHIS-listed Plant Pathogen Select Agent and potential threat to US agriculture. Sequencing of the C. glycines mt genome revealed a circular 98,533-bp molecule with a mean GC content of 29.01%. It contains twelve of the mitochondrial genes typically involved in oxidative phosphorylation (atp6, cob, cox1-3, nad1-6, and nad4L), one for a ribosomal protein (rps3), four for hypothetical proteins, one for each of the small and large subunit ribosomal RNAs (rns and rnl) and a set of 30 tRNAs. Genes were encoded on both DNA strands with cox1 and cox2 occurring as adjacent genes having no intergenic spacers. Likewise, nad2 and nad3 are adjacent with no intergenic spacers and nad5 is immediately followed by nad4L with an overlap of one base. Thirty-two introns, comprising 54.1% of the total mt genome, were identified within eight protein-coding genes and the rnl. Eighteen of the introns contained putative intronic ORFs with either LAGLIDADG or GIY-YIG homing endonuclease motifs, and an additional eleven introns showed evidence of truncated or degenerate endonuclease motifs. One intron possessed a degenerate N-acetyl-transferase domain. C. glycines shares some conservation of gene order with other members of the Pleosporales, most notably nad6-rnl-atp6 and associated conserved tRNA clusters. Phylogenetic analysis of the twelve shared protein coding genes agrees with commonly accepted fungal taxonomy. C. glycines represents the second largest mt genome from a member of the Pleosporales sequenced to date. This research provides the first genomic information on C. glycines, which may provide targets for rapid diagnostic assays and population studies.

The Mitogenomes of Ophiostoma minus and Ophiostoma piliferum and Comparisons With Other Members of the Ophiostomatales

“…Linear versions have also been observed and some circular version could actually exist as linear concatemers generated by a rolling circle type DNA replication mechanism ( Bendich, 1993 ; Hausner, 2003 , 2012 ; Bullerwell and Lang, 2005 ; Baidyaroy et al, 2011 ; Valach et al, 2011 ; Chen and Clark-Walker, 2018 ). Mitochondrial genome architecture and size are highly variable among the fungi due to recombination events promoted by repeats and by the presence and activities of mobile elements such group I and group II introns and intron-encoded proteins (IEPs) ( Aguileta et al, 2014 ; Wu and Hao, 2014 , 2019 ; Franco et al, 2017 ; Repar and Warnecke, 2017 ; Deng et al, 2018 ; Stone et al, 2018 ; Zubaer et al, 2018 ; Kolesnikova et al, 2019 ; Kulik et al, 2020 ; Liu et al, 2020b ). Like other fungi, most of the mitogenome variation observed among the examined members of the Ophiostomatales is due to the absence and presence of introns.…”

Fungal Mitogenomes: Relevant Features to Planning Plant Disease Management

“…The mt-genome of another member of the Pleosporales, Coniothyrium glycines, the causal agent of soybean red leaf blotch, contains 12 mt-genes and 32 introns with a high number of homing endonucleases that represent approximately 54.1% of the mt-genome. However, the gene order of nad6-rnl-atp6, is conserved among members of Pleosporales (Stone et al, 2018). Kolesnikova et al (2019) analyzed species of the genus Armillaria (Agaricales) and found that the mt-genome varied in size (98,896-122,167 bp) and arrangement.…”

The insertion of a mitochondrial selfish element into the nuclear genome and its consequences

“…Blast searches of the corresponding sequences, however, provided evidence for homology with a GIY‐YIG HE (Table ) and a LAGLIDADG HE, respectively (Table ). Like many other species of fungi (Jalalzadeh et al., 2015; Pogoda et al., 2019; Stone et al., 2018), plants (Cho, Qiu, Kuhlman, & Palmer, 1998), and even animals (Fukami, Chen, Chiou, & Knowlton, 2007; Schuster et al., 2017), the cox1 gene seems to be a hotspot of HEG‐encoding introns in smut fungi.…”