Genome-wide comparative analysis of NBS-encoding genes between Brassica species and Arabidopsis thaliana

Yu, Jingyin; Tehrim, Sadia; Zhang, Fengqi; Tong, Chaobo; Huang, Junyan; Cheng, Xiaohui; Dong, Caihua; Zhou, Yanqiu; Qin, Rui; Hua, Wei; S, Liu

doi:10.1186/1471-2164-15-3

Cited by 148 publications

(190 citation statements)

References 57 publications

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“…Avr effectors are typically (but not exclusively) associated with biotrophic pathogens where R proteins conduct recognition. Plant NBS-LRR-containing R genes are involved in multiple layers of defence mechanisms as can accurately recognise and interact with corresponding pathogen avr genes (Yu et al 2014). …”

Section: Fungal Potential Against Host Immune Systemmentioning

confidence: 99%

Chitin and chitin-related compounds in plant–fungal interactions

Pusztahelyi

2018

Mycology

145

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Chitin is the second abundant polysaccharide in the world after cellulose. It is a vital structural component of the fungal cell wall but not for plants. In plants, fungi are recognised through the perception of conserved microbe-associated molecular patterns (MAMPs) to induce MAMP-triggered immunity (MTI). Chitin polymers and their modified form, chitosan, induce host defence responses in both monocotyledons and dicotyledons. The plants’ response to chitin, chitosan, and derived oligosaccharides depends on the acetylation degree of these compounds which indicates possible biocontrol regulation of plant immune system. There has also been a considerable amount of recent research aimed at elucidating the roles of chitin hydrolases in fungi and plants as chitinase production in plants is not considered solely as an antifungal resistance mechanism. We discuss the importance of chitin forms and chitinases in the plant–fungal interactions and their role in persistent and possible biocontrol.Abbreviations ET, ethylene; GAP, GTPase-activating protein; GEF, GDP/GTP exchange factor; JA, jasmonic acid; LysM, lysin motif; MAMP, microbe-associated molecular pattern; MTI, MAMP-triggered immunity; NBS, nucleotide-binding site; NBS-LRR, nucleotide-binding site leucine-rich repeats; PM, powdery mildew; PR, pathogenesis-related; RBOH, respiratory burst oxidase homolog; RLK, receptor-like kinase; RLP, receptor-like protein; SA, salicylic acid; TF, transcription factor.

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Section: Fungal Potential Against Host Immune Systemmentioning

confidence: 99%

Chitin and chitin-related compounds in plant–fungal interactions

Pusztahelyi

2018

Mycology

145

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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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“…These numbers are permanently increasing, as new genomic sequences are produced very rapidly and annotation/re-annotation efforts are continuously updated. In dicotyledons, 167 such sequences are predicted to be present in Arabidopsis thaliana (Yu et al , 2014), 333 in Medicago truncatula (Ameline-Torregrosa et al , 2008), 435 in Solanum tuberosum (Lozano et al , 2012), 459 in Vitis vinifera (Yang et al , 2008), 157 in Brassica oleracea (Yu et al , 2014), 206 in Brassica rapa (Yu et al , 2014) and 54 in Carica papaya (Porter et al , 2009). In monocotyledons, especially in cereals, 460 genes are recognized in Oryza sativa L. (Ling et al , 2013), 211 in Sorghum bicolor (Ling et al , 2013), 197 in Brachypodium distachyon (Ling et al , 2013), 106 in maize (Ling et al , 2013) and 191 in H. vulgare (International Barley Genome Sequencing Consortium, 2012).…”

Section: Introductionmentioning

confidence: 99%

Large-scale analysis of NBS domain-encoding resistance gene analogs in Triticeae

et al. 2014

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Proteins containing nucleotide binding sites (NBS) encoded by plant resistance genes play an important role in the response of plants to a wide array of pathogens. In this paper, an in silico search was conducted in order to identify and characterize members of NBS-encoding gene family in the tribe of Triticeae. A final dataset of 199 sequences was obtained by four search methods. Motif analysis confirmed the general structural organization of the NBS domain in cereals, characterized by the presence of the six commonly conserved motifs: P-loop, RNBS-A, Kinase-2, Kinase-3a, RNBS-C and GLPL. We revealed the existence of 11 distinct distribution patterns of these motifs along the NBS domain. Four additional conserved motifs were shown to be significantly present in all 199 sequences. Phylogenetic analyses, based on genetic distance and parsimony, revealed a significant overlap between Triticeae sequences and Coiled coil-Nucleotide binding site-Leucine rich repeat (CNL)-type functional genes from monocotyledons. Furthermore, several Triticeae sequences belonged to clades containing functional homologs from non Triticeae species, which has allowed for these sequences to be functionally assigned. The findings reported, in this study, will provide a strong groundwork for the isolation of candidate R-genes in Triticeae crops and the understanding of their evolution.

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Genome-wide comparative analysis of NBS-encoding genes between Brassica species and Arabidopsis thaliana

Cited by 148 publications

References 57 publications

Chitin and chitin-related compounds in plant–fungal interactions

Chitin and chitin-related compounds in plant–fungal interactions

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

Large-scale analysis of NBS domain-encoding resistance gene analogs in Triticeae

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