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ARS Home » Southeast Area » Stoneville, Mississippi » Crop Genetics Research » Research » Publications at this Location » Publication #342750

Research Project: Development and Characterization of Soybean Germplasm, Curation of Stored Accessions, and Regional Evaluations of New Genotypes

Location: Crop Genetics Research

Title: Analysis of the genome sequence of Phomopsis longicolla: A fungal pathogen causing Phomopsis seed decay in soybean

item Li, Shuxian
item DARWISH, OMAR - Towson University
item ALKHAROUF, NADIM - Towson University
item Musungu, Bryan
item Matthews, Benjamin - Ben

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/16/2017
Publication Date: 9/5/2017
Citation: Li, S., Darwish, O., Alkharouf, N., Musungu, B.M., Matthews, B.F. 2017. Analysis of the genome sequence of Phomopsis longicolla: A fungal pathogen causing Phomopsis seed decay in soybean. BMC Genomics. 18:688.

Interpretive Summary: Phomopsis seed decay of soybean is caused primarily by a seed-borne fungus. This disease causes poor soybean seed quality, reduces seedling vigor and stand establishment, and suppresses yield. It is one of the most economically important soybean diseases worldwide, but information on how the fungus causes the disease is lacking. In the study, we used a molecular approach to analyze the DNA sequences of the fungus. This research will help identify genes associated with fungal growth and genes involved in disease development. Improved strategies for efficient management of Phomopsis seed decay in soybean could be developed based on this knowledge.

Technical Abstract: Phomopsis longicolla T. W. Hobbs (syn. Diaporthe longicolla) is a seed-borne fungus causing Phomopsis seed decay in soybean. This disease is one of the most devastating diseases reducing soybean seed quality worldwide. To facilitate investigation of the genomic basis of pathogenicity and to understand the mechanism of the disease development, the genome of an isolate MSPL10-6 from Mississippi, USA was sequenced, de novo assembled, and analyzed. Results showed that the genome of MSPL 10-6 was estimated to be approximately 62 Mb in size with an overall G+C content of 48.6 %. Of 16,597 predicted genes, 9,866 genes (59.45%) had significant matches to genes in the NCBI nr database, while 18.01% of them did not link to any gene ontology classification, and 9.64% of genes did not significantly match any known genes. Analysis of the 1,221 putative genes that encoded carbohydrate-activated enzymes (CAZys) indicated that 715 genes belong to three classes of CAZy that have a direct role in degrading plant cell walls. A novel fungal ulvan lyase (PL24; EC 4.2.2.-) was identified. Approximately 12.7% of the P. longicolla genome consists of repetitive elements. A total of 510 potentially horizontally transferred genes were identified. They appeared to originate from 22 other fungi, 26 eubacteria and 5 archaebacteria. The genome of the P. longicolla isolate MSPL10-6 represented the first reported genome sequence in the fungal Diaphothe-Phomopsis complex causing soybean diseases. The genome contains a number of unique genomic novelties. Information obtained from this study enhances our knowledge about this seed-borne pathogen and will facilitate further research on the genomic basis and pathogenicity mechanism of P. longicolla and aids in development of improved strategies for efficient management of Phomopsis seed decay in soybean.