Genome-wide identification and tissue-specific expression analysis of nucleotide binding site-leucine rich repeat gene family in Cicer arietinum (kabuli chickpea)

Sharma, Ranu; Rawat, Vimal; Suresh, C.G.

doi:10.1016/j.gdata.2017.08.004

Cited by 17 publications

(12 citation statements)

References 63 publications

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“…2). These results suggested that the number of introns may have increased and decreased during the structural evolution of the two types of NBS-LRR resistance genes in cabbage (Sharma et al 2017).…”

Section: Gene Characteristics and Structurementioning

confidence: 90%

Identification and expression profiling analysis of NBS–LRR genes involved in Fusarium oxysporum f.sp. conglutinans resistance in cabbage

et al. 2019

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As one of the most important resistance (R) gene families in plants, the NBS-LRR genes, encoding proteins with nucleotidebinding site (NBS) and leucine-rich repeat (LRR) domains, play significant roles in resisting pathogens. The published genomic data for cabbage (Brassica oleracea L.) provide valuable data to identify and characterize the genomic organization of cabbage NBS-LRR genes. Ultimately, we identified 105 TIR (N-terminal Toll/interleukin-1 receptor)-NBS-LRR (TNL) genes and 33 CC (coiled-coil)-NBS-LRR (CNL) genes. Further research indicated that 50.7% of the 138 NBS-LRR genes exist in 27 clusters and there are large differences among the gene structures and protein characteristics. Conserved motif and phylogenetic analysis showed that the structures of TNLs and CNLs were similar, with some differences. These NBS-LRRs are evolved under negative selection and mostly arose from whole-genome duplication events during evolution. Tissue-expression profiling of NBS-LRR genes revealed that 37.1% of the TNL genes are highly or specifically expressed in roots, especially the genes on chromosome 7 (76.5%). Digital gene expression and reverse transcription PCR analyses revealed the expression patterns of the NBS-LRR genes upon challenge by Fusarium oxysporum f.sp. conglutinans: nine genes were upregulated, and five were downregulated. The major resistance gene Foc1 probably works together with the other four genes in the same cluster to resist F. oxysporum infection.

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Section: Gene Characteristics and Structurementioning

confidence: 90%

Identification and expression profiling analysis of NBS–LRR genes involved in Fusarium oxysporum f.sp. conglutinans resistance in cabbage

et al. 2019

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“…The CNL:TNL ratio in the current study is not consistent with the findings observed in some other dicot species such as A. thaliana (1:2), A. lyrata (1:2), B. rapa (1:2), Eucalyptus grandis (1:1.25), and Thellungiella salsuginea (1:1.5) as numbers of TNLs were higher than CNLs in these species [ 14 , 30 , 65 , 66 , 67 ]. However, grapevine, chickpea, and potato genomes constituted CNL:TNL in a ratio of 4:1 [ 20 , 28 , 57 ]. The higher number of CNLs in sunflower might suggest the higher contribution of these genes providing resistance against pest or pathogen attack, which warrants future investigation.…”

Section: Discussionmentioning

confidence: 99%

“… Note: Ha: Helianthus annuus ; At: Arabidopsis thaliana ; Gm: Glycine max ; Mt: Medicago truncatula ; Bo: Brassica oleracea ; Br: Brassica rapa ; Tc: Theobroma cacao ; Pt: Populus trichocarpa ; Vv: Vitis vinifera ; Ca: Cicer arietinum ; Cs: Cucumus sativus ; Pv: Phaseolus vulgaris ; Lj: Lotus japonicas ; Cc: Cajanus cajan ; Gs: Glycine soja ; Ga: Gossypium arboretum (* = this study, a = [ 5 ], b = [ 23 ], c = [ 24 ], d = [ 20 ], e = [ 33 ], f = [ 16 ], g = [ 34 ]). …”

Section: Figurementioning

confidence: 99%

“…With the increasing availability of plant genome sequences, R gene proteins have been identified in many plant species, such as A. thaliana [ 5 , 14 ]; Vaccinium spp. [ 19 ]; Amborella trichopoda , Musa acuminata , Phyllostachys heterocycla , Capsicum annuum , and Sesamum indicum by Shao et al 2016 [ 13 ]; Cicer arietinum [ 20 ]; Glycine max [ 21 , 22 , 23 , 24 ]; Oryza sativa [ 25 , 26 ]; Medicago truncatula [ 27 ]; Vitis vinifera and Populus trichocarpa by Yang et al 2008 [ 28 ]; Solanum tuberosum [ 29 ]; Brassica rapa and Brassica oleracea by Zhang et al 2016 [ 30 ]; Hordeum vulgare [ 31 ]; Setaria italica [ 32 ]; Theobroma cacao [ 5 ]; Populus trichocarpa [ 5 ]; V. vinifera [ 5 ]; Cucumis sativus [ 33 ]; Phaseolus vulgaris [ 16 , 24 ], Lotus japonicas , Cajanus cajan , Glycine soja by Zheng et al 2016 [ 16 ], Gossypium arboretum [ 34 ], etc. A recent study by Li et al 2016 [ 35 ] has identified NBS-encoding genes as well as receptor-like protein kinases (RLKs) and receptor-like proteins (RLPs), collectively called as Resistance Gene Analogs (RGAs), for 50 plant genomes using a RGAugury pipeline.…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Identification of NBS-Encoding Resistance Genes in Sunflower (Helianthus annuus L.)

Neupane

Andersen

Neupane

et al. 2018

Genes

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Nucleotide Binding Site—Leucine-Rich Repeat (NBS-LRR) genes encode disease resistance proteins involved in plants’ defense against their pathogens. Although sunflower is affected by many diseases, only a few molecular details have been uncovered regarding pathogenesis and resistance mechanisms. Recent availability of sunflower whole genome sequences in publicly accessible databases allowed us to accomplish a genome-wide identification of Toll-interleukin-1 receptor-like Nucleotide-binding site Leucine-rich repeat (TNL), Coiled Coil (CC)-NBS-LRR (CNL), Resistance to powdery mildew8 (RPW8)-NBS-LRR (RNL) and NBS-LRR (NL) protein encoding genes. Hidden Markov Model (HMM) profiling of 52,243 putative protein sequences from sunflower resulted in 352 NBS-encoding genes, among which 100 genes belong to CNL group including 64 genes with RX_CC like domain, 77 to TNL, 13 to RNL, and 162 belong to NL group. We also identified signal peptides and nuclear localization signals present in the identified genes and their homologs. We found that NBS genes were located on all chromosomes and formed 75 gene clusters, one-third of which were located on chromosome 13. Phylogenetic analyses between sunflower and Arabidopsis NBS genes revealed a clade-specific nesting pattern in CNLs, with RNLs nested in the CNL-A clade, and species-specific nesting pattern for TNLs. Surprisingly, we found a moderate bootstrap support (BS = 50%) for CNL-A clade being nested within TNL clade making both the CNL and TNL clades paraphyletic. Arabidopsis and sunflower showed 87 syntenic blocks with 1049 high synteny hits between chromosome 5 of Arabidopsis and chromosome 6 of sunflower. Expression data revealed functional divergence of the NBS genes with basal level tissue-specific expression. This study represents the first genome-wide identification of NBS genes in sunflower paving avenues for functional characterization and potential crop improvement.

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“…Besides, some of the elements were found to be related to stress conditions. Beyond that, the cis -regulatory elements in the NBS-LRR resistance genes have four elements consisting of WBOX [ 13 ], DRE [ 14 ], CBF [ 15 ] and GCC box that highly related to stress [ 16 ]. Wu et al [ 10 ] deemed that the ZmPEAMT1 promoter contains the putative stress-responsive cis -acting elements, whose function have not been confirmed yet.…”

Section: Introductionmentioning

confidence: 99%

Cloning and Functional Analysis of Phosphoethanolamine Methyltransferase Promoter from Maize (Zea mays L.)

Niu

Gou

Han

et al. 2018

IJMS

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Betaine, a non-toxic osmoprotectant, is believed to accumulate considerably in plants under stress conditions to maintain the osmotic pressure and promote a variety of processes involved in growth and development. Phosphoethanolamine N-methyltransferase (PEAMT), a key enzyme for betaine synthesis, is reported to be regulated by its upstream promoter. In the present investigation, by using the transgenic approach, a 1048 bp long promoter region of ZmPEAMT gene from Zea mays was cloned and functionally characterized in tobacco. Computational analysis affirmed the existence of abiotic stress responsive cis-elements like ABRE, MYC, HST, LST etc., as well as pathogen, wound and phytohormone responsive motifs. For transformation in tobacco, four 5′-deletion constructs of 826 bp (P2), 642 bp (P3), 428 bp (P4) and 245 bp (P5) were constructed from the 1048 bp (P1) promoter fragment. The transgenic plants generated through a single event exhibited a promising expression of GUS reporter protein in the leaf tissues of treated with salt, drought, oxidative and cold stress as well as control plants. The GUS expression level progressively reduced from P1 to P5 in the leaf tissues, whereas a maximal expression was observed with the P3 construct in the leaves of control plants. The expression of GUS was noted to be higher in the leaves of osmotically- or salt-treated transgenic plants than that in the untreated (control) plants. An effective expression of GUS in the transgenic plants manifests that this promoter can be employed for both stress-inducible and constitutive expression of gene(s). Due to this characteristic, this potential promoter can be effectively used for genetic engineering of several crops.

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Genome-wide identification and tissue-specific expression analysis of nucleotide binding site-leucine rich repeat gene family in Cicer arietinum (kabuli chickpea)

Cited by 17 publications

References 63 publications

Identification and expression profiling analysis of NBS–LRR genes involved in Fusarium oxysporum f.sp. conglutinans resistance in cabbage

Identification and expression profiling analysis of NBS–LRR genes involved in Fusarium oxysporum f.sp. conglutinans resistance in cabbage

Genome-Wide Identification of NBS-Encoding Resistance Genes in Sunflower (Helianthus annuus L.)

Cloning and Functional Analysis of Phosphoethanolamine Methyltransferase Promoter from Maize (Zea mays L.)

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