Resistance Gene Analogs of Mango: Insights on Molecular Defenses and Evolutionary Dynamics

Abstract

Mango is an economically important fruit crop largely cultivated in the tropics and, thus, is constantly challenged by a myriad of insect pests and diseases. However, no detailed analysis of its resistance gene analogs (RGAs) has been performed, which is a vital resource for plant breeding. Here, we analyzed the RGAs of mango via de novo assembly of transcriptomic sequences and mining of the recently published whole genome sequence (WGS). From the transcriptomic assembly, a core mango RGA database with 747 protein models was established. Meanwhile, 1,775 RGAs were identified in the mango WGS and classified based on conserved domains and motifs: 54 nucleotide binding site proteins (NBS), 107 NBS – leucine rich repeat proteins (NBSLRR), 242 coiled-coil NBS-LRR (CNL), 79 toll/interleukin-1 receptor NBS-LRR (TNL), 78 coiled-coil NBS (CN), 30 toll/interleukin-1 receptor NBS (TN), 45 toll/interleukin-1 receptor with unknown domain (TX), 133 receptor-like proteins (RLP), 917 receptor-like kinases (RLK), 83 transmembrane coiled-coil domain protein (TM-CC), and seven NBS-encoding proteins with other domains. The transcriptome- and genome-wide RGAs have been functionally wellannotated through gene ontology (GO) analysis, and their expression profiles across different mango varieties were also examined. Phylogenetic analyses of expressed and genome-wide RGAs suggest highly divergent functions of the RGAs, which were broadly clustered into 6 and 8 major clades, respectively, based on their domain classification. From the mango RGA transcripts, 134 unique EST-SSR (expressed sequence tags – simple sequence repeat) loci were identified and primers were designed targeting these potential markers. Moreover, comparative analysis of mango with other plant species revealed 65 species-specific RGA families (396 orthologous genes) and detected 1,005 RGA gene duplication events. To date, this is the most comprehensive analysis of mango RGAs, which also provide insights into the dynamic mangopest co-evolutionary arms race and offer a trove of markers for utilization in resistance breeding.