Large-scale identification and comparative characterization of date palm (Phoenix dactylifera L.) nucleotide-binding site (NBS) resistance genes provide insight into their structure, evolution and function

• Published in: Trees (Berlin, West) West), 2022-12, Vol.36 (6), p.1777-1796
• Main Authors: Chatti, Khaled, Rhouma, Soumaya, Bouktila, Dhia
• Format: Article
• Language: English
• Subjects: Agriculture; Binding sites; Biomedical and Life Sciences; Crop yield; Disease resistance; Divergence; Evolutionary genetics; Expressed sequence tags; Forestry; Genes; Genomes; Life Sciences; Molecular modelling; NBS-LRR gene; Nucleotides; Original Article; Phoenix dactylifera; Phylogeny; Phytopathology; Plant Anatomy/Development; Plant Pathology; Plant Physiology; Plant Sciences; Plant species; Proteins; Reproduction (copying); Structure-function relationships
• ISSN: 0931-1890; 1432-2285
• DOI: 10.1007/s00468-022-02327-8

Key message The date palm NBS-encoding family of resistance genes has a wide set of structural features and distinct domains. Recent duplication and relaxed selection have both played major roles in biotic stress adaptation. Several genes that we discussed will aid in genetic improvement. Date palm, Phoenix dactylifera L., is one of the crucial socio-economic plants in the irrigable deserts of South West Asia and North Africa and its sweet edible fruits are traded globally. Crop yield is still vulnerable to a variety of biotic stressors. The largest class of disease resistance ( R ) genes in plants involves genes encoding nucleotide-binding site (NBS) domains. In the current study, we performed a genome-wide investigation of the structural diversity, phylogenetic relationships and functional attributes of the NBS-encoding R gene family in P. dactylifera , using comparison with banana, Musa acuminata . In date palm and banana, 123 and 85 regular NBS-encoding protein sequences, respectively, were identified. All proteins in both species lacked the TIR domain, while proteins with the LRR domain (NBS-LRR subfamily) represented one-third of the NBS protein complement. In addition to the NBS, LRR, and TIR, other atypical domains were discovered and their probable roles in the molecular mechanisms of host-pathogen recognition were widely discussed, providing insight into the functional flexibility of the NBS gene family in date palm. Motif discovery in the full NBS complement from date palm and banana revealed matches to the eight primary motifs of the NB-ARC domain, with slight variation in motif frequencies among both species. Thirty eight (38) date palm NBS (PdNBS) gene paralogous pairs were identified, accounting for almost two-thirds (61.7%) of the total PdNBS genes, demonstrating the relevance of duplication in the expansion of this gene family in date palm. The majority of these duplication pairings (73.68%) had a Ka/Ks greater than 0.3, implying that selection was relaxed, allowing for some functional divergence following duplication. Seven pairs of orthologs were identified between PdNBSs and known disease resistance genes from several plant species, shedding light on the function of date palm R genes. Finally, we found that 23 PdNBSs were supported by expression evidence from expressed sequence tags (ESTs). The findings of this study generate a detailed overview of date palm NBS genes and offer potential functional candidates for disease resistance.