Isolation, characterization and phylogenetic analysis of the resistance gene analogues (RGAs) in banana (Musa spp.)

According to the conservative regions of the nucleotide-binding site and the leucine-rich repeat (NBS-LRR) in resistance genes (R genes), the polymerase chain reaction (PCR) with degenerate primers was employed to isolate R gene analogues (RGAs) from five species of banana (Musa spp.), i.e. wild species of Gongjiao (AA) and Xinyiyejiao (BB), cultivated species of Zhongshandajiao (ABB), Fenjiao (AAB) and Williams (AAA), respectively. As a result, a total of 91 sequences with uninterrupted open reading frame (ORFs) were typical of RGAs out of 208 clones sequenced, of which 33 sequences with identity of deduced amino acid sequence below 97% were further analyzed. Based on the phylogenetic analysis by using MEGA software, the 33 sequences could be divided into 12 distinct Musa RGAs. All of them belong to the non-TIR-NBS type. No representatives of the TIR-type RGAs were detected by PCR amplification using TIR-type specific primers, suggesting the TIR-NBS-type of R genes were selectively lost in banana during evolution process. Comparison and phylogenetic analysis of the Musa RGAs with the known R genes from other plant species revealed their evolutionary relationship. Despite the high diversity of the RGAs found in banana, the 12 Musa RGAs were detected in all banana species tested, with the exception of two Musa RGAs: Musa RGA-I only presented and expressed in Zhongshandajiao (ABB) and Gongjiao (AA), while Musa RGA-K only appeared and expressed in Zhongshandajiao, suggesting there was minor differentiation between wild and cultivated forms in general. To the best of our knowledge, the isolation, characterization and phylogenetic analysis of RGAs in banana has not been reported in the literature to date.