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Tools to kill: Genome of one of the most destructive plant pathogenic fungi Macrophomina phaseolina

Md Shahidul Islam1, Md Samiul Haque1, Mohammad Moinul Islam1, Emdadul Mannan Emdad1, Abdul Halim1, Quazi Md Mosaddeque Hossen1, Md Zakir Hossain1, Borhan Ahmed1, Sifatur Rahim1, Md Sharifur Rahman1, Md Monjurul Alam1, Shaobin Hou2, Xuehua Wan2, Jennifer A Saito3 and Maqsudul Alam12*

Author affiliations

1 Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Manik Mia Avenue, Dhaka 1207, Bangladesh

2 Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, 2565 McCarthy Mall, Keller 319, Honolulu, Hawaii 96822, USA

3 Centre for Chemical Biology, Universiti Sains Malaysia, Penang, 11800, Malaysia

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Citation and License

BMC Genomics 2012, 13:493  doi:10.1186/1471-2164-13-493

Published: 19 September 2012



Macrophomina phaseolina is one of the most destructive necrotrophic fungal pathogens that infect more than 500 plant species throughout the world. It can grow rapidly in infected plants and subsequently produces a large amount of sclerotia that plugs the vessels, resulting in wilting of the plant.


We sequenced and assembled ~49 Mb into 15 super-scaffolds covering 92.83% of the M. phaseolina genome. We predict 14,249 open reading frames (ORFs) of which 9,934 are validated by the transcriptome. This phytopathogen has an abundance of secreted oxidases, peroxidases, and hydrolytic enzymes for degrading cell wall polysaccharides and lignocelluloses to penetrate into the host tissue. To overcome the host plant defense response, M. phaseolina encodes a significant number of P450s, MFS type membrane transporters, glycosidases, transposases, and secondary metabolites in comparison to all sequenced ascomycete species. A strikingly distinct set of carbohydrate esterases (CE) are present in M. phaseolina, with the CE9 and CE10 families remarkably higher than any other fungi. The phenotypic microarray data indicates that M. phaseolina can adapt to a wide range of osmotic and pH environments. As a broad host range pathogen, M. phaseolina possesses a large number of pathogen-host interaction genes including those for adhesion, signal transduction, cell wall breakdown, purine biosynthesis, and potent mycotoxin patulin.


The M. phaseolina genome provides a framework of the infection process at the cytological and molecular level which uses a diverse arsenal of enzymatic and toxin tools to destroy the host plants. Further understanding of the M. phaseolina genome-based plant-pathogen interactions will be instrumental in designing rational strategies for disease control, essential to ensuring global agricultural crop production and security.

Genome sequencing; Phytopathogens; Charcoal rot; Phenotypic microarray