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

Authors: Stone, Christine; Frederick, Reid; Tooley, Paul; Luster, Douglas - Doug; CAMPOS, BRITTANY - Mri Global; WINEGAR, RICHARD - Mri Global; MELCHER, ULRICH - Oklahoma State University; FLETCHER, JACQUE - Oklahoma State University; BLAGDEN, TRENNA - Oklahoma State University

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/24/2018
Publication Date: 11/7/2018
Citation: Stone, C.L., Frederick, R.D., Tooley, P.W., Luster, D.G., Campos, B., Winegar, R.A., Melcher, U., Fletcher, J., Blagden, T. 2018. Annotation and analysis of the mitochondrial genome of Coniothyrium glycines, causal agent of red leaf blotch of soybean, reveals an abundance of homing endonucleases. PLoS One. 13(11):e0207062.

Interpretive Summary: Soybean red leaf blotch is a serious foliar disease of soybeans in sub-Sahara Africa caused by the fungal pathogen Coniothyrium glycines. The pathogen produces a resting spore that can survive for many years in the soil and infect soybeans. If the pathogen were introduced and became established in the U.S., there is the potential for significant yield losses to occur. The mitochondrial genome of the pathogen was sequenced and found to contain genes that encode 17 proteins, the small and large ribosomal RNA subunits, and 30 transfer RNAs. Gene order and phylogenetic comparisons to all available fungal mitochondrial genomes supports current fungal taxonomy. This study provides the first genomic information on this fungal pathogen that might be useful for plant pathologists to develop targets for rapid diagnostic assays or strain identification.

Technical 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 98533-base pair molecule with a mean GC content of 29.01 percent. 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 occur in two contiguous strands of opposite direction with cox1 and cox2 occurring as adjacent proteins 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. Seventeen of the introns contained putative intronic ORFs with either LAGLIDADG or GIY-YIG homing endonuclease motifs, and an additional twelve 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 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.