Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns

Abstract

Nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes make up the largest plant disease resistance gene family (R genes), with hundreds of copies occurring in individual angiosperm genomes. However, the expansion history of NBS-LRR genes during angiosperm evolution is largely unknown. By identifying more than 6,000 NBS-LRR genes in 22 representative angiosperms and reconstructing their phylogenies, we present a potential framework of NBS-LRR gene evolution in the angiosperm. Three anciently diverged NBS-LRR classes (TNLs, CNLs, and RNLs) were distinguished with unique exon-intron structures and DNA motif sequences. A total of seven ancient TNL, 14 CNL, and two RNL lineages were discovered in the ancestral angiosperm, from which all current NBS-LRR gene repertoires were evolved. A pattern of gradual expansion during the first 100 million years of evolution of the angiosperm clade was observed for CNLs. TNL numbers remained stable during this period but were eventually deleted in three divergent angiosperm lineages. We inferred that an intense expansion of both TNL and CNL genes started from the Cretaceous-Paleogene boundary. Because dramatic environmental changes and an explosion in fungal diversity occurred during this period, the observed expansions of R genes probably reflect convergent adaptive responses of various angiosperm families. An ancient whole-genome duplication event that occurred in an angiosperm ancestor resulted in two RNL lineages, which were conservatively evolved and acted as scaffold proteins for defense signal transduction. Overall, the reconstructed framework of angiosperm NBS-LRR gene evolution in this study may serve as a fundamental reference for better understanding angiosperm NBS-LRR genes.

Tracking ancestral lineages and recent expansions of NBS-LRR genes in angiosperms

“…In combination with motif composition analysis of the NBS domain and intron structure and phase detection, our study provides strong evidence that RNL is an ancient NBS-LRR class that has been largely ignored by most previous studies. 6 Thus our results suggest that angiosperm NBS-LRR genes are composed of 3 anciently diverged classes, namely, TNL, CNL, and RNL.…”

“…These questions were further addressed in our study by tracing the ancient state of NBS-LRR genes at key divergence nodes of angiosperms step by step. 6 A total of 23 NBS-LRR lineages were finally recovered in the common ancestor of investigated angiosperms. 6 Further comparison of ancestral NBS-LRR lineages at the internal divergence nodes of angiosperm, including mesangiospermae (Ma), eudicots (Ed), monocots (Mo), asterids (As), and rosids (Ro), revealed that 3 NBS-LRR classes underwent distinct evolutionary patterns during angiosperm radiation.…”

“…6 Further comparison of ancestral NBS-LRR lineages at the internal divergence nodes of angiosperm, including mesangiospermae (Ma), eudicots (Ed), monocots (Mo), asterids (As), and rosids (Ro), revealed that 3 NBS-LRR classes underwent distinct evolutionary patterns during angiosperm radiation. 6 The RNL gene retained a few copies during the entire evolutionary history of angiosperms, which well reflects its functional restriction for defense signal transduction. 6 In contrast, both TNL and CNL genes underwent intensive recent expansions.…”

“…Benefits from the conserved NBS domain in NBS-LRR proteins, highthroughput bioinformatics methods for genome-wide identification of NBS-LRR genes have been developed, 2,3 with which dozens to hundreds of NBS-LRR genes have been identified from various angiosperm plant genomes. [4][5][6][7][8][9] Previous studies have divided angiosperm NBS-LRR genes into 2 separate classes, TIR-NBS-LRR (TNL) and non-TIR-NBS-LRR (nTNL), based on the presence or absence of a Toll/ IL-1 receptor-like (TIR) domain at the N-terminal of translated proteins. 10,11 The nTNL genes are also called CC-NBS-LRR genes (CNL), which is based on a frequently detected coiledcoil (CC) domain at the N-terminal of nTNL proteins.…”

“…12,13 A controversy was then raised by comparing independent phylogenetic analysis, referring to whether RNL genes are derived from a CNL lineage recently or represent another ancient NBS-LRR class that sister to CNL and TNL genes. 2,5,7 To clarify this basic concept for NBS-LRR gene classification, our recent study 6 performed large-scale phylogenetic analysis of NBS-LRR genes from 22 genomes across major angiosperm lineages. In combination with motif composition analysis of the NBS domain and intron structure and phase detection, our study provides strong evidence that RNL is an ancient NBS-LRR class that has been largely ignored by most previous studies.…”