Uncovering the dynamic evolution of nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes in Brassicaceae.
Plant genomes harbor dozens to hundreds of nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes; however, the long-term evolutionary history of these resistance genes has not been fully understood. This study focuses on five Brassicaceae genomes and the Carica papaya genome to explore changes in NBS-LRR genes that have taken place in this Rosid II lineage during the past 72 million years. Various numbers of NBS-LRR genes were identified from Arabidopsis lyrata (198), A. thaliana (165), Brassica rapa (204), Capsella rubella (127), Thellungiella salsuginea (88), and C. papaya (51). In each genome, the identified NBS-LRR genes were found to be unevenly distributed among chromosomes and most of them were clustered together. Phylogenetic analysis revealed that, before and after Brassicaceae speciation events, both toll/interleukin-1 receptor-NBS-LRR (TNL) genes and non-toll/interleukin-1 receptor-NBS-LRR (nTNL) genes exhibited a pattern of first expansion and then contraction, suggesting that both subclasses of NBS-LRR genes were responding to pathogen pressures synchronically. Further, by examining the gain/loss of TNL and nTNL genes at different evolutionary nodes, this study revealed that both events often occurred more drastically in TNL genes. Finally, the phylogeny of nTNL genes suggested that this NBS-LRR subclass is composed of two separate ancient gene types: RPW8-NBS-LRR and Coiled-coil-NBS-LRR.
State Key Laboratory of Pharmaceutical Biotechnology, Center of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China.|Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
Yan-Mei
YM
Zhang
State Key Laboratory of Pharmaceutical Biotechnology, Center of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China.
Zhu-Qing
ZQ
Shao
State Key Laboratory of Pharmaceutical Biotechnology, Center of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China.
Qiang
Q
Wang
Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
Yue-Yu
YY
Hang
Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
Jia-Yu
JY
Xue
State Key Laboratory of Pharmaceutical Biotechnology, Center of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China.
Bin
B
Wang
State Key Laboratory of Pharmaceutical Biotechnology, Center of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China.
Jian-Qun
JQ
Chen
D001665:Binding Sites; D019607:Brassicaceae / Q000235:genetics*; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D017343:Genes, Plant; D056426:Genetic Loci; D000090263:Leucine-Rich Repeat Proteins; D016013:Likelihood Functions; D005810:Multigene Family; D009711:Nucleotides / Q000378:metabolism*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D011506:Proteins / Q000235:genetics*; D013045:Species Specificity; D026801:Synteny / Q000235:genetics
D000090263:Leucine-Rich Repeat Proteins; D009711:Nucleotides; D010940:Plant Proteins; D011506:Proteins
Dynamic evolution; nucleotide-binding site-leucine-rich repeat gene; phylogenetic relationship; plant disease resistance