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ARS Home » Southeast Area » Stoneville, Mississippi » Crop Genetics Research » Research » Publications at this Location » Publication #412651
Research Project: Breeding Stress Tolerant Soybeans, Regeneration and Evaluation of USDA Germplasm Collection,and Management of Uniform Soybean Trials

Location: Crop Genetics Research

Title: Comparative analysis of the mitochondrial genome sequences of Diaporthe longicolla (syn. Phomopsis longicolla) isolates causing Phomopsis seed decay in soybean

Author
item Li, Shuxian
item HU, XIAOJUN - Animal And Plant Health Inspection Services (APHIS), National Wildlife Center
item Song, Qijian

Submitted to: The Journal of Fungi
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/3/2024
Publication Date: 8/13/2024
Citation: Li, S., Hu, X., Song, Q. 2024. Comparative analysis of the mitochondrial genome sequences of Diaporthe longicolla (syn. Phomopsis longicolla) isolates causing Phomopsis seed decay in soybean. Journal of Fungi. 10:570. https://doi.org/10.3390/jof10080570.
DOI: https://doi.org/10.3390/jof10080570

Interpretive Summary: Phomopsis seed decay is one of the most devastating seed diseases and reduces soybean seed quality and yield worldwide. The disease is caused primarily by a seed-borne fungus, but information about the genetic variability of the fungus is lacking. In this study, we compared the DNA sequences of the fungus from different states in the U.S. Differences in the genome size, number of repetitive sequences, and other molecular elements were identified. Results from this research will be useful for scientists to further study the molecular basis of seed-borne pathogens causing seed diseases, and to develop improved control strategies for Phomopsis seed decay of soybean based on this knowledge.

Technical Abstract: Diaporthe longicolla (syn. Phomopsis longicolla) is an important seed-borne fungal pathogen and the primary cause of Phomopsis seed decay (PSD) in soybean. PSD is one of the most devastating seed diseases and reduces soybean seed quality and yield worldwide. As part of a genome sequencing project on the fungal Diaporthe-Phomopsis complex, draft genomes of eight D. longicolla isolates were sequenced and assembled. Sequences of mitochondrial genomes were extracted and analyzed. The circular mitochondrial genomes ranged from 52,534 bp to 58,280 bp long with a mean GC content of 34%. A total of 14 core protein-coding genes, 23 tRNA and two rRNA genes were identified. Introns were detected in the genes of atp6, cob, cox1, cox2, cox3, nad1, nad2, nad5, and rnl. Three isolates (PL7, PL10, and PL185E) had more introns than other isolates. Approximately 6.4% of the mitochondrial genomes consist of repetitive elements. Moreover, 48 single nucleotide polymorphisms (SNPs) and six superfamilies of transposons were identified. The mitochondrial genome sequences of D. longicolla will be useful to further study the molecular basis of seed-borne pathogens causing seed diseases, investigate genetic variation among isolates, and to develop improved control strategies for Phomopsis seed decay of soybean.