A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana

Weyer, Anna-Lena Van de; Monteiro, Freddy; Furzer, Oliver J.; Nishimura, Marc T.; Çevik, Volkan; Witek, Kamil; Jones, Jonathan D. G.; Dangl, Jeffery L.; Weigel, Detlef; Bemm, Felix

doi:10.1016/j.cell.2019.07.038

Cited by 308 publications

(361 citation statements)

References 133 publications

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“…Another interesting feature of the RPW8 locus is the intraspecific gene amplification and diversity within Arabidopsis. RenSeq was conducted on 65 Arabidopsis accessions and revealed two types of sequence variation at the RPW8 locus (Barragan et al, 2019;Van de Weyer et al, 2019). Firstly, there have been a large number of recent duplication events.…”

Section: Introductionmentioning

confidence: 99%

An rpw8 quadruple mutant of Arabidopsis Col-0 is partially compromised in bacterial and fungal resistance

Castel

Xiao

et al. 2019

Preprint

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Section: Introductionmentioning

confidence: 99%

An rpw8 quadruple mutant of Arabidopsis Col-0 is partially compromised in bacterial and fungal resistance

Castel

Xiao

et al. 2019

Preprint

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“…The sites under pervasive and episodic selection pressures at the C-terminal LRRs showed high variations. Noticeably, some OGs displayed a significantly greater sites under the selection pressures as observed for the NLRs of Arabidopsis [32]. The clades in the upper half of the phylogeny, such as G4 and G10 (Main Figure 1c), appeared more frequently to have 10 or more sites detected.…”

Section: Resultsmentioning

confidence: 99%

“…However, limitations existed as short reads from the Illumina platforms could not completely resolve highly repetitive sequences and physical clusters of NLRs[31]. Combined with single-molecule real time (SMRT) sequencing of PacBio, RenSeq has enabled more accurate recovery of NLRs and been successfully applied for the discovery of new functional R genes and evolutionary study of diverse accessions of Arabidopsis species[32]. In this study, we employed SMRT RenSeq to identify NLRs from 18 Solanaceae accessions ( S. lycopersicum Heinz, 15 wild tomato accessions belonging to 5 species, Nicotiana benthamiana and Capsicum annuum ECW20R).…”

Section: Introductionmentioning

confidence: 99%

Evolution of NLR resistance genes with non-canonical N-terminal domains in wild tomato species

Seong

Seo

et al. 2019

Preprint

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AbstractBackgroundNucleotide-binding and leucine-rich repeat immune receptors (NLRs) are an important component of plant immunity that provides resistance against diverse pathogens. NLRs often exist as large gene families, the members of which display diverse multi-domain architectures (MDAs) and evolve through various mechanisms of duplications and selections.ResultsWe conducted resistance gene enrichment sequencing (RenSeq) with single-molecule real time (SMRT) sequencing of PacBio for 18 accessions in Solanaceae including 15 wild tomatoes. We demonstrate what was previously known as Solanaceae Domain (SD) not only is more diverse in structure and function but also far anciently originated from the most recent common ancestor (MRCA) between Asterids and Amaranthaceae. In tomato, NLRs with the extended N-terminus displayed distinct patterns of evolution based on phylogenetic clades by proliferation, continuous elongation and domain losses.ConclusionsOur study provides high quality gene models of NLRs that can serve as resources for future studies for crop engineering and elucidates greater evolutionary dynamics of the extended NLRs than previously assumed.

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“…Approximately half of all NLRs in a given A. thaliana accession are found in multi-gene clusters, which are unevenly distributed across the genome (Meyers et al 2003; Van de Weyer et al 2019). Tandem duplication events are common in NLR clusters, and duplicate genes are a major source of genetic variation, since they often experience relaxed selection and enable neofunctionalization (Ohno 1970;Force et al 1999;Lynch and Conery 2000;Conant and Wolfe 2008).…”

Section: Introductionmentioning

confidence: 99%

A singleton NLR of recent origin causes hybrid necrosis inArabidopsis thaliana

Barragan

Collenberg

Wang

et al. 2020

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Hybrid necrosis in plants arises from conflict between divergent alleles of immunity genes contributed by different parents, resulting in autoimmunity. We investigate a severe hybrid necrosis case in Arabidopsis thaliana, where the hybrid does not develop past the cotyledon stage and dies three weeks after sowing. Massive transcriptional changes take place in the hybrid, including the upregulation of most NLR disease resistance genes. This is due to an incompatible interaction between the singleton TIR-NLR gene DANGEROUS MIX 10 (DM10), which was recently relocated from a larger NLR cluster, and an unlinked locus, DANGEROUS MIX 11 (DM11). There are multiple DM10 allelic variants in the global A. thaliana population, several of which have premature stop codons. One of these, which has a truncated LRR domain, corresponds to the DM10 risk allele. The DM10 locus and the adjacent genomic region in the risk allele carriers are highly differentiated from those in the non-risk carriers in the global A. thaliana population, suggesting that this allele became geographically widespread only relatively recently. The DM11 risk allele is much rarer and found only in two accessions from southwestern Spain -a region from which the DM10 risk haplotype is absent -indicating that the ranges of DM10 and DM11 risk alleles may be non-overlapping.

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A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana

Cited by 308 publications

References 133 publications

An rpw8 quadruple mutant of Arabidopsis Col-0 is partially compromised in bacterial and fungal resistance

An rpw8 quadruple mutant of Arabidopsis Col-0 is partially compromised in bacterial and fungal resistance

Evolution of NLR resistance genes with non-canonical N-terminal domains in wild tomato species

A singleton NLR of recent origin causes hybrid necrosis inArabidopsis thaliana

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