Frequent Gene Duplication/Loss Shapes Distinct Evolutionary Patterns of NLR Genes in Arecaceae Species

Xiao-Tong Li,Guang-Can Zhou,Yang Liu,Zhu-Qing Shao,Xing-Yu Feng,Zhen Zeng

doi:10.3390/horticulturae7120539

Xiao-Tong Li, Guang-Can Zhou + Show 4 more

Open Access

https://doi.org/10.3390/horticulturae7120539

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Journal: Horticulturae	Publication Date: Dec 2, 2021
Citations: 5	License type: CC BY 4.0

Affiliation: Heze University, Nanjing University

Abstract

Nucleotide-binding leucine-rich repeat (NLR) genes play a key role in plant immune responses and have co-evolved with pathogens since the origin of green plants. Comparative genomic studies on the evolution of NLR genes have been carried out in several angiosperm lineages. However, most of these lineages come from the dicot clade. In this study, comparative analysis was performed on NLR genes from five Arecaceae species to trace the dynamic evolutionary pattern of the gene family during species speciation in this monocot lineage. The results showed that NLR genes from the genomes of Elaeis guineensis (262), Phoenix dactylifera (85), Daemonorops jenkinsiana (536), Cocos nucifera (135) and Calamus simplicifolius (399) are highly variable. Frequent domain loss and alien domain integration have occurred to shape the NLR protein structures. Phylogenetic analysis revealed that NLR genes from the five genomes were derived from dozens of ancestral genes. D. jenkinsiana and E. guineensis genomes have experienced “consistent expansion” of the ancestral NLR lineages, whereas a pattern of “first expansion and then contraction” of NLR genes was observed for P. dactylifera, C. nucifera and C. simplicifolius. The results suggest that rapid and dynamic gene content and structure variation have shaped the NLR profiles of Arecaceae species.

Highlights

The innate immune system can protect plants from the threats of foreign pathogens [1].One of the core parts of the plant immune system is a set of genes, termed plant disease resistance genes (R genes), which recognize pathogen-derived virulence proteins to activate downstream defense responses [1]
All Nucleotide-binding leucine-rich repeat (NLR) genes were divided into the CNL and RNL subclasses based on the classification provided in ANNA, with no TNL
Our results show that the majority of NLR genes were organized into clusters rather than singletons in C. nucifera, D. jenkinsiana, and E. guineensis genomes, with 54.8%, 70.7% and 77.7% NLR genes detected in clusters, respectively (Table 2)

Summary

Introduction

One of the core parts of the plant immune system is a set of genes, termed plant disease resistance genes (R genes), which recognize pathogen-derived virulence proteins (called “effectors”) to activate downstream defense responses [1]. A typical NLR protein contains a variable domain at the N-terminus, a highly conserved NBS domain in the middle, and a diverse leucine-rich repeat (LRR) domain at the C-terminus [3]. CNL and TNL proteins act as “sensor NLRs” that recognize specific pathogen effectors to trigger downstream immune responses, while RNL proteins serve as downstream signal transduction molecules (“helper NLR”) of CNL and TNL proteins [6,7]

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