Revisiting the Origin of Plant NBS-LRR Genes

Shao, Zhu‐Qing; Xue, Jia‐Yu; Wang, Qiang; Wang, Bin; Chen, Jian-Qun

doi:10.1016/j.tplants.2018.10.015

Cited by 138 publications

(147 citation statements)

References 11 publications

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“…NBS-LRR domain-containing proteins are the largest family of R-proteins (Dangl and Jones, 2001) and can be subdivided further into the TIR-NBS-LRR (TNL) and the non-TIR-NBS-LRR (nTNL), which are distinguished by the presence of a Toll/Interleukin-1 receptor (TIR) domain in the protein amino terminus (Shao et al, 2016;Zhou et al, 2004). Because most nTNL genes encode a coiled-coil (CC) domain at the N terminus, the nTNL genes often are called CC-NBS-LRR (CNL) genes (Ameline-Torregrosa et al, 2008;Shao et al, 2019). Likewise, TM-LRRs can be subdivided into two classes: surface-localized receptor-like protein kinases (RLKs) and membrane-associated receptor-like proteins (RLPs) (Hammond-Kosack and Jones, 1997).…”

Section: Introductionmentioning

confidence: 99%

Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation

Dolatabadian

Bayer

Tirnaz

et al. 2019

Plant Biotechnology Journal

104

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Summary Methods based on single nucleotide polymorphism (SNP), copy number variation (CNV) and presence/absence variation (PAV) discovery provide a valuable resource to study gene structure and evolution. However, as a result of these structural variations, a single reference genome is unable to cover the entire gene content of a species. Therefore, pangenomics analysis is needed to ensure that the genomic diversity within a species is fully represented. Brassica napus is one of the most important oilseed crops in the world and exhibits variability in its resistance genes across different cultivars. Here, we characterized resistance gene distribution across 50 B. napus lines. We identified a total of 1749 resistance gene analogs (RGAs), of which 996 are core and 753 are variable, 368 of which are not present in the reference genome (cv. Darmor‐bzh). In addition, a total of 15 318 SNPs were predicted within 1030 of the RGAs. The results showed that core R‐genes harbour more SNPs than variable genes. More nucleotide binding site‐leucine‐rich repeat (NBS‐LRR) genes were located in clusters than as singletons, with variable genes more likely to be found in clusters. We identified 106 RGA candidates linked to blackleg resistance quantitative trait locus (QTL). This study provides a better understanding of resistance genes to target for genomics‐based improvement and improved disease resistance.

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Section: Introductionmentioning

confidence: 99%

Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation

Dolatabadian

Bayer

Tirnaz

et al. 2019

Plant Biotechnology Journal

104

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“…DNA repair and disease-resistance pathways have been found to play a crucial role in the highland adaptation of Tibetan highland plants [46,54]. In the present study, we detected significant expressions of many unigenes related to pathogen response that contained either a nucleotide binding (NB)-ARC domain or a leucine-rich repeat (LRR) domain, which were present in most resistance (R) proteins [55][56][57]. We also identified many differentially expressed unigenes that were significantly enriched in the DNA repair pathways.…”

Section: F Macclureana Has Presumably Evolved An Integrated Mechanismentioning

confidence: 55%

De novo sequencing of the transcriptome reveals regulators of the floral transition in Fargesia macclureana (Poaceae)

Zhang

Yang

et al. 2020

Preprint

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Background: Fargesia macclureana (Poaceae) is a woody bamboo species found on the Qinghai–Tibet Plateau (QTP) approximately 2,000 ~ 3,800 m above sea level. It rarely blossoms in the QTP, but it flowered 20 days after growing in our lab, which is in a low-altitude area outside the QTP. To date, little is known regarding the molecular mechanism of bamboo flowering, and no studies of flowering have been conducted on wild bamboo plants growing in extreme environments. Here, we report the first de novo transcriptome sequence for F. macclureana to investigate the putative mechanisms underlying the flowering time control used by F. macclureana to adapt to its environment. Results: Illumina deep sequencing of the F. macclureana transcriptome generated 140.94 Gb of data, assembled into 99,056 unigenes. A comprehensive analysis of the broadly, specifically and differentially expressed unigenes (BEUs, SEUs and DEUs) indicated that they were mostly involved in metabolism and signal transduction, as well as DNA repair and plant-pathogen interactions, which may be of adaptive importance. In addition, comparison analysis between non-flowering and flowering tissues revealed that expressions of FmFT and FmHd3a, two putative F. macclureana orthologs, were differently regulated in NF- vs F- leaves, and carbohydrate metabolism and signal transduction were two major KEGG pathways that DEUs were enriched in. Finally, we detected 9,296 simple sequence repeats (SSRs) that may be useful for further molecular marker-assisted breeding. Conclusions: F. macclureana may have evolved specific reproductive strategies for flowering-related pathways in response to photoperiodic cues to ensure long vegetation growing period. Our findings will provide new insights to future investigations into the mechanisms of flowering time control and adaptive evolution in plants growing at high altitudes.

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“…However, the fusion events of NBS and LRR domain was found in Chlorophyta and plants. This indicated that the origin of R protein could be traced back to Chlorophyta, such as Chromochloris zofingiensis and Botryococcus braunii [67]. In the current study, six up-regulated genes encoding NBS, LRR, or TIR containing proteins were predicted as R protein candidates in Pyr.…”

Section: The Ancient Origin Of Genes In the Innate Immune System Of Pmentioning

confidence: 57%

“…Nearly all the identified R proteins typically share commonly conversed domains of TNL (TIR-NBS-LRR) or nTNL (NBS-LRR) [17]. Recent studies analyzed the R protein in plants, Charophytes, Chlorophyta, Rhodophyta, and Glaucophyta [66,67]. Proteins containing NBS or LRR domain are found to exist in all species.…”

Section: The Ancient Origin Of Genes In the Innate Immune System Of Pmentioning

confidence: 99%

Transcriptomic insights into innate immunity responding to red rot disease in red alga Pyropia yezoensis

Tang

Qiu

Liu

et al. 2019

Preprint

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Pyropia yezoensis , one of the most economically important marine algae, suffers from the biotic stress of oomycete necrotrophic pathogen Pythium porphyrae . However, little is known about the molecular defensive mechanisms employed by Pyr. yezoensis during the infection process. In the present study, we defined three stages of infection based on the histopathological features and photosynthetic physiology. Transcriptomic analysis was carried out at different stages of infection to identify the genes related to the innate immune system in Pyr. yezoensis . In total, 2139 up-regulated genes and 1672 down-regulated genes were identified from all the infected groups. Three upregulated genes encoding extracellular lectin domains (one C-type lectin gene and two L-type lectin genes) were predicted to be p attern r ecognition r eceptors (PRRs) that activate PAMP-triggered immunity (PTI). Several defense mechanisms that were typically regarded as PTI in plants were induced during the infection. These include defensive and protective enzymes, heat shock proteins, secondary metabolites, cellulase, and protease inhibitors. Twenty-three genes that encode typical plant R protein domains (LRR, NBS, or TIR) were found to be up-regulated after infection. They were likely to be regarded as candidates of putative R proteins in Pyr. yezoensis . As a part of E ffector-t riggered i mmunity (ETI), expression of genes related to the ubiquitin-proteasome system (UPS) and hypersensitive cell death response (HR) increased significantly during the infection. The current study suggests that, similar to plants, Pyr. yezoensis possesses a relatively complete innate immune system to counter the invasion of necrotrophic pathogen Pyt. porphyrae . However, innate immunity genes of Pyr. yezoensis appear to be more ancient in origin compared to that in plants. BackgroundPlant suffer from a variety of diseases that are caused by fungi [1-3], oomycetes [4,5], bacteria [6] and viruses [7][8][9]. It is evident that plants rely on their innate immune system to resist infection by the pathogens. Jones proposed a four-phased 'zigzag' model to illustrate how the plants' innate immune system fights against the pathogen [10]. At the onset, the plant recognizes the pathogenassociated molecular patterns (PAMPs) by their transmembrane pattern recognition receptors (PRRs) to activate PAMP-triggered immunity (PTI). PTI includes callose deposition [11,12], cell-wall 3 thickening [13,14] and reactive oxygen species (ROS) production [15,16], to control the colonization of pathogen nonspecifically. Next, pathogen interferes with the PTI by its effectors, resulting in effector-triggered susceptibility (ETS) of the plant. Further, the plant specifically recognizes effectors via R proteins either directly or indirectly to activate ETI[17]. ETI can amplify PTI and enhance the resistance by activating the hypersensitive cell death in the plant. Finally, pathogen represses ETI by modifying or acquiring new effectors that prevent the recognition of R proteins, further induci...

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Revisiting the Origin of Plant NBS-LRR Genes

Cited by 138 publications

References 11 publications

Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation

Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation

De novo sequencing of the transcriptome reveals regulators of the floral transition in Fargesia macclureana (Poaceae)

Transcriptomic insights into innate immunity responding to red rot disease in red alga Pyropia yezoensis

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