An angiosperm<i>NLR</i>atlas reveals that<i>NLR</i>gene reduction is associated with ecological specialization and signal transduction component deletion

Liu, Yang; Zeng, Zhen; Li, Qian; Jiang, Xing-Mei; Jiang, Zhen; Tang, Jihong; Zhang, Yanmei; Chen, Dijun; Wang, Qiang; Chen, Jian-Qun; Shao, Zhu‐Qing

doi:10.1101/2021.02.10.430603

Cited by 6 publications

(26 citation statements)

References 68 publications

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“…The remaining two A. thaliana RNL genes form a sister lineage to ADR1, corresponding to the NRG1 lineage. This topology is in accordance with the previous finding that the RNL-NRG1 lineage was lost in the common ancestor of monocots (Collier et al, 2011;Shao et al, 2016;Liu et al, 2021).…”

Section: Species-specific Preservation and Amplification Of Ancestral Nlr Lineages During The Speciation Of Barley And Wheatsupporting

confidence: 93%

“…The results showed that the 468 barley NLR genes comprise one RNL and 467 CNL genes. TNL genes were not detected in the barley genome, which is consistent with the notion that TNL genes are lost in the common ancestor of monocots (Collier et al, 2011;Shao et al, 2016;Liu et al, 2021).…”

Section: Barley Genome Contains Over 400 Nlr Genessupporting

confidence: 86%

“…Two previous studies performed genome-wide analyses of NLR genes, using earlier versions of the barley genome assemblies by short-read sequence strategy, and only 100 or so NLR genes were identified (Andersen et al, 2016;Habachi-Houimli et al, 2018). These numbers are much smaller than those in diploid wheat genomes, which have more than 500 1 https://www.croptrust.org/crop/barley/ NLR genes (Liu et al, 2021). A recent study reported a newly assembly of barley genome of the cultivar Morex by long-read sequencing technology (Mascher et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

“…Genome-wide analysis revealed that angiosperm genomes contain abundant and variable number of NLR genes. For example, the NLR gene number in Poaceae species ranges from 145 in Zea mays to 2298 in Triticum aestivum ( Liu et al, 2021 ). NLR subclasses composition is also different among angiosperm species.…”

Section: Introductionmentioning

confidence: 99%

“…NLR subclasses composition is also different among angiosperm species. Generally, all monocots and most sequenced magnoliids lack the TNL subclasses, whereas the majority of dicot species genomes have all three NLR subclasses ( Liu et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Analysis of NLR Disease Resistance Genes in an Updated Reference Genome of Barley

Jiang

Shao

2021

Front. Genet.

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Barley is one of the top 10 crop plants in the world. During its whole lifespan, barley is frequently infected by various pathogens. In this study, we performed genome-wide analysis of the largest group of plant disease resistance (R) genes, the nucleotide binding site–leucine-rich repeat receptor (NLR) gene, in an updated barley genome. A total of 468 NLR genes were identified from the improved barley genome, including one RNL subclass and 467 CNL subclass genes. Proteins of 43 barley CNL genes were shown to contain 25 different integrated domains, including WRKY and BED. The NLR gene number identified in this study is much larger than previously reported results in earlier versions of barley genomes, and only slightly fewer than that in the diploid wheat Triticum urartu. Barley Chromosome 7 contains the largest number of 112 NLR genes, which equals to seven times of the number of NLR genes on Chromosome 4. The majority of NLR genes (68%) are located in multigene clusters. Phylogenetic analysis revealed that at least 18 ancestral CNL lineages were presented in the common ancestor of barley, T. urartu and Arabidopsis thaliana. Among them fifteen lineages expanded to 533 sub-lineages prior to the divergence of barley and T. urartu. The barley genome inherited 356 of these sub-lineages and duplicated to the 467 CNL genes detected in this study. Overall, our study provides an updated profile of barley NLR genes, which should serve as a fundamental resource for functional gene mining and molecular breeding of barley.

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Section: Species-specific Preservation and Amplification Of Ancestral Nlr Lineages During The Speciation Of Barley And Wheatsupporting

confidence: 93%

Section: Barley Genome Contains Over 400 Nlr Genessupporting

confidence: 86%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Analysis of NLR Disease Resistance Genes in an Updated Reference Genome of Barley

Jiang

Shao

2021

Front. Genet.

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The genome of the rice variety LTH provides insight into its universal susceptibility mechanism to worldwide rice blast fungal strains

Yang

Zhao

Sha

et al. 2022

Computational and Structural Biotechnology Journal

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Differential EDS1 requirement for cell death activities of plant TIR-domain proteins

Lapin

Johanndrees

Baggs

et al. 2021

Preprint

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Toll/interleukin-1 Receptor (TIR) domains are integral to immune systems across all domains of life. TIRs exist as single-domain and as larger receptor or adaptor proteins. In plants, TIRs constitute N-terminal domains of nucleotide-binding leucine-rich repeat (NLR) immune receptors. Although TIR-NLR and TIR signaling requires the Enhanced disease susceptibility 1 (EDS1) protein family, TIR domains persist in species that have incomplete or no EDS1 members. To assess whether particular TIR groups appear with EDS1, we searched for TIR-EDS1 co-occurrence patterns. Using a large-scale phylogenetic analysis of TIR domains from 39 algae and land plant species, we identify four conserved TIR groups, two of which are TIR-NLRs present in eudicots and two are more widespread. Presence of one TIR-only protein group is highly correlated with EDS1 and members of this group elicit EDS1-dependent cell death. By contrast, a more widely represented TIR group of TIR-NB-WD40/TPR (TNP) proteins (formerly called XTNX) has at least one member which can induce EDS1-independent cell death. Our data provide a new phylogeny-based plant TIR classification and identify TIR groups that appear to have evolved with and are dependent on EDS1, while others have EDS1-independent activity.One sentence summaryLand plants have evolved four conserved TIR groups

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An angiospermNLRatlas reveals thatNLRgene reduction is associated with ecological specialization and signal transduction component deletion

Cited by 6 publications

References 68 publications

Genome-Wide Analysis of NLR Disease Resistance Genes in an Updated Reference Genome of Barley

Genome-Wide Analysis of NLR Disease Resistance Genes in an Updated Reference Genome of Barley

The genome of the rice variety LTH provides insight into its universal susceptibility mechanism to worldwide rice blast fungal strains

Differential EDS1 requirement for cell death activities of plant TIR-domain proteins

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