MBE Advance Access published online on June 8, 2009
Molecular Biology and Evolution, doi:10.1093/molbev/msp114
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Research Article |
Positively selected disease response orthologous gene sets in the cereals identified using Sorghum bicolor L. Moench expression profiles and comparative genomics
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* Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853
Department of Plant Breeding, Cornell University, Ithaca, NY 14853
Computational Biology Service Unit (CBSU), Cornell Theory Center, Cornell University, Ithaca, NY 14853
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
2 Corresponding author: Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, New York 14853-1801, Email: az42{at}cornell.edu
3 Corresponding author: 158 Biotechnology Building, Cornell University, Ithaca, New York, 14853., Email: sk20{at}cornell.edu
Received for publication January 28, 2009. Revision received May 6, 2009. Accepted for publication May 20, 2009.
Disease response genes diverge under recurrent positive selection as a result of a molecular arms-race between hosts and pathogens. Most of these studies were conducted in animals, and few defense genes have been shown to evolve adaptively in plants. To test for adaptation in the molecules mediating disease resistance in the cereals we first combined information from the expression pattern of Sorghum bicolor genes and from divergence to the full genome of rice to identify candidate disease response genes. We then used evolutionary analyses of orthologous gene sets from several grass species, to determine whether the disease response genes show signals of positive selection and the residues targeted. We found 140 divergent genes upregulated under biotic stress in S. bicolor by evaluating the relative abundance of ESTs in different libraries and comparing them to rice genes. For 10 of these genes, we found sets of orthologs including sequences from rice and three other cereals; 6 genes showed a pattern of substitution that was consistent with positive selection. Three of these genes, a thaumatin, a peroxidase and a barley mlo homolog, are known antifungal proteins. The other three genes with evidence of positive selection were a MADS box transcription factor, an eIF5 translation initiation factor and a gene of unknown function but with evidence of expression during stress. Permutation analyses, using different ortholog and paralog sequences, consistently identified 5 positively selected codons in the peroxidase, a member of a cluster of genes and a large gene family. We mapped the positively selected residues onto the structure of the peroxidase and thaumatin and found that all sites are on the surface of these proteins and several are close to biochemically determined active sites. Identifying new positively selected plant disease resistance genes and the critical amino acid sites provides a basis for functional studies that may increase our understanding of their underlying molecular mechanisms of action. Additionally, it may lead to the identification of individuals having variation at functionally important sites, as well as eventually using this information in the rational design and engineering of proteins involved in plant disease resistance.
Key Words: molecular evolution • positive selection • neutral evolution • comparative genomics • expression profile • disease resistance • anthracnose • Zea • Saccharum • Sorghum • Triticum • Oryza • bioinformatics
1 Current Address: Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, New York 14853-1801