Transcriptome-wide analysis of expressed resistance gene analogs (RGAs) in mango

Plants have developed mechanisms to recognize pathogen and insect attacks and to activate defense response against them through the action of resistance genes ( genes). Hence, gene analogs (RGAs) have been widely studied and efficiently used for breeding of resistant crops. Mango is an economic fruit crop largely cultivated in the (sub)tropics and thus, is constantly challenged by a myriad of insect pests and diseases. RGAs of mango from different varieties were identified and characterized via assembly of raw transcriptome sequences currently available in biological repositories. Using bioinformatics pipelines, a core RGA database of mango with 747 protein models was established and were classified based on their conserved domains and motifs: 53 nucleotide binding site protein (NBS); 27 nucleotide binding site-leucine rich repeat proteins (NBS-LRR); 17 coiled-coil NBS-LRR (CNL); 2 toll/interleukin-1 receptor NBS-LRR (TNL); 29 coiled-coil NBS (CN); 4 toll/interleukin-1 receptor NBS (TN); 17 toll/interleukin-1 receptor with unknown domain (TX); 158 receptor-like proteins (RLP); 362 receptor-like kinases (RLK); 72 transmembrane coiled-coil domain protein (TM-CC), and 6 NBS-encoding proteins with other domains. Phylogenetic analysis broadly clustered the core RGAs into 6 major clades based on their domain classification, while TM-CC formed subclades all across the tree. The phylogenetic results suggest highly divergent functions of the RGAs which also provide insights into the mango-pest co-evolutionary arms race. The various molecular functions, biological processes, and cellular localizations of these RGAs were functionally well-annotated through gene ontology (GO) analysis, and their expression profiles across different mango varieties were also determined. From the mango RGA transcripts, 134 unique EST-SSRs loci were identified, and primers were designed targeting these potential markers. To date, this is the most comprehensive analysis of mango RGAs which offer a trove of markers for direct utilization in resistance breeding of mango.