Identification and distribution of the NBS-LRR gene family in the Cassava genome |
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| Authors: | Roberto Lozano Martha T Hamblin Simon Prochnik Jean-Luc Jannink |
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| Institution: | .Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853 USA ;.Institute for Genomic Diversity, Biotechnology Building, Cornell University, Ithaca, NY 14853 USA ;.US Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598 USA ;.United States Department of Agriculture, Agricultural Research Service (USDA-ARS) R.W. Holley Center for Agriculture and Health, Ithaca, NY 14853 USA |
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| Abstract: | BackgroundPlant resistance genes (R genes) exist in large families and usually contain both a nucleotide-binding site domain and a leucine-rich repeat domain, denoted NBS-LRR. The genome sequence of cassava (Manihot esculenta) is a valuable resource for analysing the genomic organization of resistance genes in this crop.ResultsWith searches for Pfam domains and manual curation of the cassava gene annotations, we identified 228 NBS-LRR type genes and 99 partial NBS genes. These represent almost 1% of the total predicted genes and show high sequence similarity to proteins from other plant species. Furthermore, 34 contained an N-terminal toll/interleukin (TIR)-like domain, and 128 contained an N-terminal coiled-coil (CC) domain. 63% of the 327 R genes occurred in 39 clusters on the chromosomes. These clusters are mostly homogeneous, containing NBS-LRRs derived from a recent common ancestor.ConclusionsThis study provides insight into the evolution of NBS-LRR genes in the cassava genome; the phylogenetic and mapping information may aid efforts to further characterize the function of these predicted R genes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1554-9) contains supplementary material, which is available to authorized users. |
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