Genome-wide identification and evolutionary analysis of nucleotide-binding site-encoding resistance genes in Lotus japonicus (Fabaceae)

Song, Hui; Wang, P F; Li, T T; Xia, Han; Zhao, Shuzhen; Hou, Lei; Zhao, Chuanzhi

doi:10.4238/2015.december.7.16

Cited by 10 publications

(9 citation statements)

References 39 publications

(56 reference statements)

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“…ipaënsis , respectively, were excluded in this study because these sequences contained partial NBS domains or partial sequences. Song et al [ 5 ] demonstrated that incomplete NBS–LRR sequences used in analyses can lead to incorrect results. Among the full-length sequences, two AdNBS and nine AiNBS sequences were considered potential pseudogenes because they contained either a premature stop codon or a frameshift mutation.…”

Section: Resultsmentioning

confidence: 99%

“…truncatula [ 6 ] and 71.77% NBS–LRR sequences in L . japonicas [ 5 ] had LRR domains. We found that AdNBS and AiNBS contained more LRR8 than LRR4, LRR3, LRR5, and LRR1.…”

Section: Resultsmentioning

confidence: 99%

“…NBS–LRR genes are distributed widely in plants. Researchers have studied this gene family in many plant genomes, including Arabidopsis thaliana [ 3 ], Glycine max [ 4 ], Lotus japonicus [ 5 ], Medicago truncatula [ 6 ], Oryza sativa [ 7 ], and Triticum aestivum [ 8 ]. NBS–LRR genes can be classified into two types (non-TIR and TIR) based on the N-terminal coiled-coil (CC) domain or a toll/mammalian interleukin-1 receptor (TIR) [ 3 ].…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Comparative analysis of NBS-LRR genes and their response to Aspergillus flavus in Arachis

Song

Wang

et al. 2017

PLoS ONE

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Studies have demonstrated that nucleotide-binding site–leucine-rich repeat (NBS–LRR) genes respond to pathogen attack in plants. Characterization of NBS–LRR genes in peanut is not well documented. The newly released whole genome sequences of Arachis duranensis and Arachis ipaënsis have allowed a global analysis of this important gene family in peanut to be conducted. In this study, we identified 393 (AdNBS) and 437 (AiNBS) NBS–LRR genes from A. duranensis and A. ipaënsis, respectively, using bioinformatics approaches. Full-length sequences of 278 AdNBS and 303 AiNBS were identified. Fifty-one orthologous, four AdNBS paralogous, and six AiNBS paralogous gene pairs were predicted. All paralogous gene pairs were located in the same chromosomes, indicating that tandem duplication was the most likely mechanism forming these paralogs. The paralogs mainly underwent purifying selection, but most LRR 8 domains underwent positive selection. More gene clusters were found in A. ipaënsis than in A. duranensis, possibly owing to tandem duplication events occurring more frequently in A. ipaënsis. The expression profile of NBS–LRR genes was different between A. duranensis and A. hypogaea after Aspergillus flavus infection. The up-regulated expression of NBS–LRR in A. duranensis was continuous, while these genes responded to the pathogen temporally in A. hypogaea.

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Section: Resultsmentioning

confidence: 99%

“…truncatula [ 6 ] and 71.77% NBS–LRR sequences in L . japonicas [ 5 ] had LRR domains. We found that AdNBS and AiNBS contained more LRR8 than LRR4, LRR3, LRR5, and LRR1.…”

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Comparative analysis of NBS-LRR genes and their response to Aspergillus flavus in Arachis

Song

Wang

et al. 2017

PLoS ONE

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“…We performed a stringent search against the NCBI conserved domain database CDD (MarchlerBauer et al, 2011) for identification of canonical CC and TIR domains. We did not classify as many NLRs into TNL, and especially CNL groups, as in previous studies (Supplemental Table S7; Monosi et al, 2004;Ameline-Torregrosa et al, 2008;Kim et al, 2012;Shao et al, 2014;Yu et al, 2014;Song et al, 2015;Sarris et al, 2016;Shao et al, 2016). We chose this conservative approach due to relatively poorly defined sequence composition and structure of especially the CC domains.…”

Section: The Brassicaceae Expression Shift Is Seen Across Multiple Nlmentioning

confidence: 99%

The Brassicaceae Family Displays Divergent, Shoot-Skewed NLR Resistance Gene Expression

et al. 2017

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Nucleotide-binding site leucine-rich repeat resistance genes (NLRs) allow plants to detect microbial effectors. We hypothesized that NLR expression patterns could reflect organ-specific differences in effector challenge and tested this by carrying out a metaanalysis of expression data for 1,235 NLRs from nine plant species. We found stable NLR root/shoot expression ratios within species, suggesting organ-specific hardwiring of NLR expression patterns in anticipation of distinct challenges. Most monocot and dicot plant species preferentially expressed NLRs in roots. In contrast, Brassicaceae species, including oilseed rape (Brassica napus) and the model plant Arabidopsis (Arabidopsis thaliana), were unique in showing NLR expression skewed toward the shoot across multiple phylogenetically distinct groups of NLRs. The Brassicaceae are also outliers in the sense that they have lost the common symbiosis signaling pathway, which enables intracellular infection by root symbionts. While it is unclear if these two events are related, the NLR expression shift identified here suggests that the Brassicaceae may have evolved unique patternrecognition receptors and antimicrobial root metabolites to substitute for NLR protection. Such innovations in root protection could potentially be exploited in crop rotation schemes or for enhancing root defense systems of non-Brassicaceae crops.

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“…Encoding products of most disease resistance genes in plants are nucleotide-binding site leucine-rich repeat (NBS-LRR) proteins and diverse pathogens, including bacteria, viruses, fungi, nematodes, insects and oomycetes, are detected by NBS-LRR proteins. Researchers have studied this gene family in many plant genomes, including Arabidopsis thaliana [ 8 ], Glycine max [ 9 ], Lotus japonicas [ 10 ], Helianthus annuus [ 11 ], Oryza sativa [ 12 ] and Triticum aestivum [ 13 ]. Due to the difference of the N-terminal features, the NBS-LRR proteins can be divided into two subfamilies, TIR-NBS-LRR (TNL) and non-TNL-NBS-LRR (nTNL) [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

Identification and Analysis of NBS-LRR Genes in Actinidia chinensis Genome

Wang

Jia

Zhang

et al. 2020

Plants

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Nucleotide-binding site and leucine-rich repeat (NBS-LRR) genes represent the most important disease resistance genes in plants. The genome sequence of kiwifruit (Actinidia chinensis) provides resources for the characterization of NBS-LRR genes and identification of new R-genes in kiwifruit. In the present study, we identified 100 NBS-LRR genes in the kiwifruit genome and they were grouped into six distinct classes based on their domain architecture. Of the 100 genes, 79 are truncated non-regular NBS-LRR genes. Except for 37 NBS-LRR genes with no location information, the remaining 63 genes are distributed unevenly across 18 kiwifruit chromosomes and 38.01% of them are present in clusters. Seventeen families of cis-acting elements were identified in the promoters of the NBS-LRR genes, including AP2, NAC, ERF and MYB. Pseudomonas syringae pv. actinidiae (pathogen of the kiwifruit bacterial canker) infection induced differential expressions of 16 detected NBS-LRR genes and three of them are involved in plant immunity responses. Our study provides insight of the NBS-LRR genes in kiwifruit and a resource for the identification of new R-genes in the fruit.

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Genome-wide identification and evolutionary analysis of nucleotide-binding site-encoding resistance genes in Lotus japonicus (Fabaceae)

Cited by 10 publications

References 39 publications

Comparative analysis of NBS-LRR genes and their response to Aspergillus flavus in Arachis

Comparative analysis of NBS-LRR genes and their response to Aspergillus flavus in Arachis

The Brassicaceae Family Displays Divergent, Shoot-Skewed NLR Resistance Gene Expression

Identification and Analysis of NBS-LRR Genes in Actinidia chinensis Genome

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