Recent duplications dominate NBS-encoding gene expansion in two woody species

Most disease resistance genes in plants encode NBS-LRR proteins. However, in woody species, little is known about the evolutionary history of these genes. Here, we identified 459 and 330 respective NBS-LRRs in grapevine and poplar genomes. We subsequently investigated protein motif composition, phylogenetic relationships and physical locations. We found significant excesses of recent duplications in perennial species, compared with those of annuals, represented by rice and Arabidopsis. Consequently, we observed higher nucleotide identity among paralogs and a higher percentage of NBS-encoding genes positioned in numerous clusters in the grapevine and poplar. These results suggested that recent tandem duplication played a major role in NBS-encoding gene expansion in perennial species. These duplication events, together with a higher probability of recombination revealed in this study, could compensate for the longer generation time in woody perennial species e.g. duplication and recombination could serve to generate novel resistance specificities. In addition, we observed extensive species-specific expansion in TIR-NBS-encoding genes. Non-TIR-NBS-encoding genes were poly- or paraphyletic, i.e. genes from three or more plant species were nested in different clades, suggesting different evolutionary patterns between these two gene types.

植物中的大多数抗病基因编码NBS - LRR蛋白。然而，在木本植物中，人们对这些基因的进化历史知之甚少。在此，我们在葡萄和杨树基因组中分别鉴定出459个和330个NBS - LRR基因。随后我们研究了蛋白质基序组成、系统发育关系以及基因的物理位置。我们发现，与以水稻和拟南芥为代表的一年生植物相比，多年生植物中近期基因重复的情况明显过多。因此，我们观察到葡萄和杨树中旁系同源基因间的核苷酸一致性更高，并且位于众多基因簇中的NBS编码基因的百分比也更高。这些结果表明，近期的串联重复在多年生植物的NBS编码基因扩增中起主要作用。这些重复事件，以及本研究中揭示的更高的重组概率，可以弥补木本多年生植物较长的世代时间，例如重复和重组有助于产生新的抗性特异性。此外，我们观察到TIR - NBS编码基因存在大量的物种特异性扩增。非TIR - NBS编码基因是多系或并系的，即来自三个或更多植物物种的基因嵌套在不同的分支中，这表明这两种基因类型之间存在不同的进化模式。