Identification and characterization of genome-wide resistance gene analogs (RGAs) of durian (Durio zibethinus L.)

Cris Q Cortaga,Romnick A Latina,Rosteo R Habunal,Darlon V Lantican

doi:10.1186/s43141-022-00313-8

Abstract

BackgroundDurian (Durio zibethinus L.) is a tropical fruit crop which is popular in Southeast Asia but recently gaining popularity in other parts of the world. In this study, we analyzed the resistance gene analogs (RGAs) of durian through mining of the currently available reference genome of its ‘Musang King’ cultivar (PRJNA400310). ResultsA total of 2586 RGAs were identified in the durian genome consisting of 47 nucleotide binding site proteins (NBS), 158 NBS-leucine rich repeat proteins (NL), 400 coiled-coil NBS-LRR (CNL), 72 toll/interleukin-1 receptor NBS-LRR (TNL), 54 coiled-coil NBS (CN), 10 toll/interleukin-1 receptor NBS (TN), 19 toll/interleukin-1 receptor with unknown domain (TX), 246 receptor-like proteins (RLP), 1,377 receptor-like kinases (RLK), 185 TM-CC, and 18 other NBS-containing proteins with other domains. These RGAs were functionally annotated and characterized via gene ontology (GO) analysis. Among the RGAs with the highest copies in durian genome include the putative disease resistance RPP13-like protein 1, disease resistance protein At4g27190, disease resistance protein RPS6, Probable disease resistance protein At4g27220, and putative disease resistance protein RGA3, while 35 RGAs were found to be novel. Phylogenetic analyses revealed that the genome-wide RGAs were broadly clustered into four major clades based on their domain classification. ConclusionTo our knowledge, this is the most comprehensive analysis of durian RGAs which provides a valuable resource for genetic, agronomic, and other biological research of this important tropical fruit crop.

Highlights

Plants sense insect pests and pathogen invasion via pathogen recognition receptors (PRRs) in the cell, whereas attacker-specific effectors are identified via a gene-forgene interaction through resistance (R) proteins [1–3].The PRRs and R genes are referred to as resistance gene analogs (RGAs) which share conserved domains and motifs [4]
Using the automated RGA prediction pipeline RGAugury [4], the genome-wide RGA of durian belonging to membrane associated receptor-like kinases (RLK) and receptor-like proteins (RLP) families, and nucleotide binding site proteins (NBS) and TM-CC containing proteins were identified in the gene models from the annotated durian genome
RGAs of durian were compared to the predicted RGAs reported from other plant species [13], it was revealed that it has the most RGAs (2586), followed by peach

Summary

Introduction

Plants sense insect pests and pathogen invasion via pathogen recognition receptors (PRRs) in the cell, whereas attacker-specific effectors are identified via a gene-forgene interaction through resistance (R) proteins [1–3]. The PRRs and R genes are referred to as resistance gene analogs (RGAs) which share conserved domains and motifs [4]. They are in charge of intracellular signaling and turning on plant defense genes. We analyzed the resistance gene analogs (RGAs) of durian through mining of the currently available reference genome of its ‘Musang King’ cultivar (PRJNA400310)

Methods

Results

Conclusion