摘要
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-coiI-N BS-LRR.
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-coiI-N BS-LRR.
基金
supported by the National Natural Science Foundation of China(30930008,31170210,31200177,91231102,31300190,31400201 and 31470327)
China Postdoctoral Science Foundation(2013M540435 and 2014T70503)
Postdoctoral Science Foundation of Jiangsu Province(1302131C)
Fundamental Research Funds for the Central Universities(20620140546 and 20620140558)
Natural Science Founding of Jiangsu Province(BK20130565)
Qing Lan Project of Jiangsu Province
