The Dynamic Evolution Of NBS Genes In Angiosperm Plants

NBS-LRR genes, also termed as NBS genes, are the most frequently isolated type of plant disease resistance genes. To understand their evolution patterns and to facilitate the molecular cloning of these genes, collective studies have devoted to investigate NBS gene profiles in angiosperms, especially in species with genome sequence available. Genome-wide analysis of NBS genes has been carried out in more than twenty angiosperms in the past ten years. All of these genome-wide investigations provided a wealth of information on NBS gene profiles in angiosperms.However, very fewer efforts were paid on comparative analyses of NBS genes among species at long time-scales, which impedes their proper identification and utilization.In this study, we identified NBS genes from 14 angiosperm genomes, and perfomed comparative-genomics and phylogenetic analysis to understand their dynamic evolutionary pattarn.Firstly, bioinformatic analysis was performed to identify NBS genes from the nine genomes of brassicaceae and legume families. Our data revealed that the numbers of NBS genes within and among brassicaceae and legume species are highly variable, rangeing from 88 to 571. Howevr, legume species geneally possess more NBS genes (287 to 571) than those of brassicaceae species (88 to 204). Furthermore,the classes composion of NBS genes also exhibits family-specific pattern. The identified NBS genes belonging to TNL subclass are more than those in nTNL subclass in four out five brassicaceae genome. To the contrary, the identified NBS genes belonging to nTNL subclass are more than those in TNL subclass in each legume genome. In addition, the uneven distribution of NBS-encoding genes on different chromosomes was observed in brassicaceae and legume genomes surveyed in this study. Most NBS genes are present in clusters of at least two genes, while few singleton loci were identified. Synteny analyses were performed to explore the conservation pattern of these loci across legume or brassicaceae genomes, and frequent presence/absence polymorphisms were found. For example, among the 298 integrated NBS gene loci in legume, only 13 were shared by all of the four species. In contrast, 105,nine, 28 and 83 species-specific NBS gene loci were detected in M.truncatula, C. cajan, P. vulgaris and G. max, respectively, suggesting that either new NBS gene loci are rapidly produced in a species, or common NBS gene loci are lost convergently from different species.Secondly, to trace the ancient state of NBS genes prior the separation of legume and brassicaceae families, and also to explore the variation of main NBS gene lineages during species-speciation, we reconstructed phylogenetic trees for nTNL and TNL genes based on conserved NBS domain sequences. Both phylogenies were then reconciled with the real species tree to restore the NBS gene duplication and loss events that occurred at different stages of legume and brassicaceae evolution. Our data revealed that 31 ancient rosid NBS genes (23 nTNL and 8 TNL) were present in the common ancestor of legumes and brassicaceae.These genes experienced various losses and independent duplications during the diverging lineages, resulting in a variable number of NBS genes in different genomes. Notably, several ancient NBS genes were maintained as single copy genes, suggesting that an NBS gene guarding a target protein in function could be maintained for an extremely long period.Comparing the evolutionary patterns of NBS gene at different time-scales revealed that NBS genes experienced "expansion to contraction" process before and after the divergence of brassicaceae, gene loss plays major role in the recent evolution of NBS gene in brassicaceae genomes. On the contrary, NBS genes were constantly expanded during the legume species evolution since their common ancestor separated from the rosid-lineage, with local tandem duplication as the major driving force of species-specific NBS expansion, while ectopic duplication also occurs at certain frequency. The discrepant evolution pattern of NBS gene in brassicaceae and legume should be the major driving force of NBS gene number varation between the two families.Finaly, we expanded our analysis on NBS evolution to angiosperm-scale by selecting seven representative species from key angiosperm lineages. Our data demonstrated that there are at least 29 ancient NBS genes in the common ancestor of angiosperm plants, including 18 nTNL and 11 TNL genes. Similar to the results observed from brassicaceae and legume, all of these genes were differentially inherited during species-speciation, with gene loss and gain frequently occured. Our data also showed that TNL genes lost are more frequently than nTNL genes in angiosperm divergence. In addition, by looking into the angiosperm nTNL tree, we found that a group of conserved nTNL gene that characterized with RPW8 domain(termed as RNL gene) is not derived from an angiosperm CNL lineage, but is sister to all CNL genes on phylogeny. This indicates that nTNL gene is composed of two ancient originated NBS classes, RNL and CNL.