Abstract
BackgroundPhomopsis 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.ResultsThe 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, 9866 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 1221 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.ConclusionsThe genome of the P. longicolla isolate MSPL10–6 represented the first reported genome sequence in the fungal Diaporthe-Phomopsis complex causing soybean diseases. The genome contained a number of Pfams not described previously. 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.
Highlights
General genome features The genome of the P. longicolla isolate MSPL 10–6 was assembled from both the paired-end and mate-pair libraries with the short oligonucleotide assembler package (SOAP), a denovo assembler
Identification, and cultivation of P. longicolla isolate A P. longicolla isolate MSPL10–6 was isolated from field-grown soybean seed in Mississippi, USA in 2010 using the seed plating method
Over 100 randomly chosen soybean seeds that were harvested from the field were surface-disinfected in 0.5% sodium hypochlorite for 3 min, rinsed in sterile distilled water 3 times (3 min each time), and placed on potato dextrose agar (Difico Laboratories, Detroit, MI) that was acidified with 25% lactic acid after autoclaving (APDA)
Summary
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. Diaporthe longicolla) is a seed-borne fungus primarily causing Phomopsis seed decay (PSD) in soybean, Glycine max (L.) Merrill [1,2,3,4]. This disease decreases seed quality and has been found in most soybean production areas, worldwide [2, 4, 5]. Soybean seed infected by P. longicolla often lack of visible
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