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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #332000

Research Project: Enhancing Breeding of Small Grains through Improved Bioinformatics

Location: Plant, Soil and Nutrition Research

Title: Identification and distribution of the NBS-LRR gene family in the cassava genome

Author
item LOZANO, ROBERTO - CORNELL UNIVERSITY - NEW YORK
item HAMBLIN, MARTHA - CORNELL UNIVERSITY - NEW YORK
item PROCHNIK, SIMON - JOINT GENOME INSTITUTE
item JANNINK, JEAN-LUC

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/20/2015
Publication Date: 5/7/2015
Citation: Lozano, R., Hamblin, M., Prochnik, S., Jannink, J. 2015. Identification and distribution of the NBS-LRR gene family in the cassava genome. BMC Genomics. 16:360. doi: 10.1186/s12864-015-1554-9.

Interpretive Summary: Plant resistance genes (R genes) exist in large families and usually contain both a nucleotide-binding site domain and a leucine-rich repeat domain, so that these genes are called NBS-LRR genes. The genome sequence of cassava (Manihot esculenta) is a valuable resource for analyzing the genomic organization of resistance genes in this crop. With searches for protein family 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 all the genes predicted to be in the cassava genome. The genes show high sequence similarity to proteins from other plant species. 63% of the 327 R genes occurred in 39 mostly homogeneous clusters, containing NBS-LRRs derived from a recent common ancestor. This study provides insight into the evolution of NBS-LRR genes in the cassava genome that may aid efforts to further characterize the function of these predicted R genes.

Technical Abstract: Plant 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 analyzing the genomic organization of resistance genes in this crop. With 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. This 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.