Genome-wide identification of NBS-encoding resistance genes in Brassica rapa.
Nucleotide-binding site (NBS)-encoding resistance genes are key plant disease-resistance genes and are abundant in plant genomes, comprising up to 2% of all genes. The availability of genome sequences from several plant models enables the identification and cloning of NBS-encoding genes from closely related species based on a comparative genomics approach. In this study, we used the genome sequence of Brassica rapa to identify NBS-encoding genes in the Brassica genome. We identified 92 non-redundant NBS-encoding genes [30 CC-NBS-LRR (CNL) and 62 TIR-NBS-LRR (TNL) genes] in approximately 100 Mbp of B. rapa euchromatic genome sequence. Despite the fact that B. rapa has a significantly larger genome than Arabidopsis thaliana due to a recent whole genome triplication event after speciation, B. rapa contains relatively small number of NBS-encoding genes compared to A. thaliana, presumably because of deletion of redundant genes related to genome diploidization. Phylogenetic and evolutionary analyses suggest that relatively higher relaxation of selective constraints on the TNL group after the old duplication event resulted in greater accumulation of TNLs than CNLs in both Arabidopsis and Brassica genomes. Recent tandem duplication and ectopic deletion are likely to have played a role in the generation of novel Brassica lineage-specific resistance genes.
Genomics Division, Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro, Gwonseon-gu, Suwon, 441-707, Korea. munjh@rda.go.kr
Jeong-Hwan
JH
Mun
Hee-Ju
HJ
Yu
Soomin
S
Park
Beom-Seok
BS
Park
D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D029741:Brassica rapa / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D008969:Molecular Sequence Data; D009711:Nucleotides / Q000378:metabolism*; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012641:Selection, Genetic
D009711:Nucleotides; D010940:Plant Proteins