phylogenomics

phylogenomics - Using Phylogenomics to Predict Novel Fungal...

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Using Phylogenomics to Predict Novel Fungal Pathogenicity Genes David DeCaprio, Ying Li, Hung Nguyen (sequenced Ascomycetes genomes courtesy of the Broad Institute)
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Phylogenomics Combining whole genome sequences and phylogenetic information to make inferences about gene function Phenotypic differences between related organisms can be explained in terms of genomic differences
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Plant Pathogens Magnaporthe grisea First sequenced pathogen (rice) Fusarium graminearum Wheat blight – Worst US pathogen Stagonospora nodorum Another wheat blight Other Ascomycete fungi Neurospora crassa Model organism Aspergillus nidulans Model organism Chaetomium globosum Human pathogen
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Dean analysis – Nature 2005 Identified putative pathogenicity genes in Magnaporthe grisea Found significant expansion in pth11-related gene family in M. grisea vs. N. crassa – pth11-class is required for pathogenicity (DeZwann 1999) BUT N. crassa has RIP: all families are small
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Testing the Hypothesis Examine pth11-related family in 3 pathogenic species vs. 3 non-pathogenic species If this family is pathogenicity related: – Expect to see expansion in pathogens – Expect to see no expansion in non-pathogens
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Purpose of Phylogenetic Analysis Ralph Dean’s M. grisea expansions may not actually be expansions when compared to more data sets and data sets with larger families If pth11 required for pathegenicity (appressorium development), other plant- pathogens may also contain expansions yet unidentified
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Procedure • Obtain gene families for six organisms • Pick out pth11-related family • Align all genes in family using ClustalW • Build phylogenetic tree for family • Bootstrap analysis on the tree • Examine pathogenic expansions
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Find Gene Families Obtain match score for each pair of proteins in all genes in all organisms – Obtain an all-to-all (but not identity) match of all proteins in all 6 organisms using NCBI-BLAST with default parameters and an E-value cutoff of 1e-10. – Combine all hits between a pair of proteins to
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This note was uploaded on 11/11/2011 for the course BIO 7.344 taught by Professor Bobsauer during the Spring '08 term at MIT.

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phylogenomics - Using Phylogenomics to Predict Novel Fungal...

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