scholarly journals Genome-wide identification and comparative analysis of NBS-LRR resistance genes in Brassica napus

2018 ◽  
Vol 69 (1) ◽  
pp. 72 ◽  
Author(s):  
Salman Alamery ◽  
Soodeh Tirnaz ◽  
Philipp Bayer ◽  
Reece Tollenaere ◽  
Boulos Chaloub ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Brassica Napus ◽  
Resistance Genes ◽  
Plant Disease Resistance ◽  
Interleukin 1 ◽  
Critical Role ◽  
Coiled Coil ◽  
Genome Wide ◽  
High Level ◽  
Plant Disease Resistance Genes

Plant disease-resistance genes play a critical role in providing resistance against pathogens. The largest family of resistance genes are the nucleotide-binding site (NBS) and leucine-rich repeat (LRR) genes. They are classified into two major subfamilies, toll/interleukin-1 receptor (TIR)-NBS-LRR (TNL) and coiled-coil (CC)-NBS-LRR (CNL) proteins. We have identified and characterised 641 NBS-LRR genes in Brassica napus, 249 in B. rapa and 443 in B. oleracea. A ratio of 1 : 2 of CNL : TNL genes was found in the three species. Domain structure analysis revealed that 57% of the NBS-LRR genes are typical resistance genes and contain all three domains (TIR/CC, NBS, LRR), whereas the remaining genes are partially deleted or truncated. Of the NBS-LRR genes, 59% were found to be physically clustered, and individual genes involved in clusters were more polymorphic than those not clustered. Of the NBS-LRR genes in B. napus, 50% were identified as duplicates, reflecting a high level of genomic duplication and rearrangement. Comparative analysis between B. napus and its progenitor species indicated that >60% of NBS-LRR genes are conserved in B. napus. This study provides a valuable resource for the identification and characterisation of candidate NBS-LRR genes.

scholarly journals Coiled-coil networking shapes cell molecular machinery

2012 ◽  
Vol 23 (19) ◽  
pp. 3911-3922 ◽  
Author(s):  
Yongqiang Wang ◽  
Xinlei Zhang ◽  
Hong Zhang ◽  
Yi Lu ◽  
Haolong Huang ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Critical Role ◽  
Coiled Coil ◽  
Coiled Coils ◽  
Protein Protein Interactions ◽  
Full Spectrum ◽  
Kinetochore Assembly ◽  
Genome Wide ◽  
Molecular Machinery ◽  
Systematic Understanding

The highly abundant α-helical coiled-coil motif not only mediates crucial protein–protein interactions in the cell but is also an attractive scaffold in synthetic biology and material science and a potential target for disease intervention. Therefore a systematic understanding of the coiled-coil interactions (CCIs) at the organismal level would help unravel the full spectrum of the biological function of this interaction motif and facilitate its application in therapeutics. We report the first identified genome-wide CCI network in Saccharomyces cerevisiae, which consists of 3495 pair-wise interactions among 598 predicted coiled-coil regions. Computational analysis revealed that the CCI network is specifically and functionally organized and extensively involved in the organization of cell machinery. We further show that CCIs play a critical role in the assembly of the kinetochore, and disruption of the CCI network leads to defects in kinetochore assembly and cell division. The CCI network identified in this study is a valuable resource for systematic characterization of coiled coils in the shaping and regulation of a host of cellular machineries and provides a basis for the utilization of coiled coils as domain-based probes for network perturbation and pharmacological applications.

scholarly journals Identification of Immune Related LRR-Containing Genes in Maize (Zea maysL.) by Genome-Wide Sequence Analysis

2015 ◽  
Vol 2015 ◽  
pp. 1-11 ◽  
Author(s):  
Wei Song ◽  
Baoqiang Wang ◽  
Xinghua Li ◽  
Jianfen Wei ◽  
Ling Chen ◽  
...  
Keyword(s):  
Zea Mays ◽  
Plant Disease Resistance ◽  
Interleukin 1 ◽  
Protein Structures ◽  
Gene Clusters ◽  
Amino Acid Sequences ◽  
Leucine Rich Repeat ◽  
Immune Receptors ◽  
Genome Wide ◽  
First Time

A large number of immune receptors consist of nucleotide binding site-leucine rich repeat (NBS-LRR) proteins and leucine rich repeat-receptor-like kinases (LRR-RLK) that play a crucial role in plant disease resistance. Although many NBS-LRR genes have been previously identified inZea mays, there are no reports on identifying NBS-LRR genes encoded in the N-terminal Toll/interleukin-1 receptor (TIR) motif and identifying genome-wide LRR-RLK genes. In the present study, 151 NBS-LRR genes and 226 LRR-RLK genes were identified after performing bioinformatics analysis of the entire maize genome. Of these identified genes, 64 NBS-LRR genes and four TIR-NBS-LRR genes were identified for the first time. The NBS-LRR genes are unevenly distributed on each chromosome with gene clusters located at the distal end of each chromosome, while LRR-RLK genes have a random chromosomal distribution with more paired genes. Additionally, six LRR-RLK/RLPs including FLS2, PSY1R, PSKR1, BIR1, SERK3, and Cf5 were characterized inZea maysfor the first time. Their predicted amino acid sequences have similar protein structures with their respective homologues in other plants, indicating that these maize LRR-RLK/RLPs have the same functions as their homologues act as immune receptors. The identified gene sequences would assist in the study of their functions in maize.

Genome-wide mining and comparative analysis of fatty acid elongase gene family in Brassica napus and its progenitors

Gene ◽  
2020 ◽  
Vol 747 ◽  
pp. 144674
Author(s):  
Yufei Xue ◽  
Jiayi Jiang ◽  
Xia Yang ◽  
Huanhuan Jiang ◽  
Youjie Du ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Comparative Analysis ◽  
Brassica Napus ◽  
Gene Family ◽  
Fatty Acid Elongase ◽  
Genome Wide

Arabidopsis thaliana: A source of candidate disease-resistance genes for Brassica napus

Genome ◽  
2000 ◽  
Vol 43 (3) ◽  
pp. 452-460 ◽  
Author(s):  
D Sillito ◽  
I AP Parkin ◽  
R Mayerhofer ◽  
D J Lydiate ◽  
A G Good
Keyword(s):  
Arabidopsis Thaliana ◽  
Disease Resistance ◽  
Brassica Napus ◽  
Resistance Genes ◽  
Plant Disease Resistance ◽  
Disease Resistance Genes ◽  
R Gene ◽  
R Genes ◽  
Rapid Divergence ◽  
Genomic Regions

Common structural and amino acid motifs among cloned plant disease-resistance genes (R genes), have made it possible to identify putative disease-resistance sequences based on DNA sequence identity. Mapping of such R-gene homologues will identify candidate disease-resistance loci to expedite map-based cloning strategies in complex crop genomes. Arabidopsis thaliana expressed sequence tags (ESTs) with homology to cloned plant R genes (R-ESTs), were mapped in both A. thaliana and Brassica napus to identify candidate R-gene loci and investigate intergenomic collinearity. Brassica R-gene homologous sequences were also mapped in B. napus. In total, 103 R-EST loci and 36 Brassica R-gene homologous loci were positioned on the N-fo-61-9 B. napus genetic map, and 48 R-EST loci positioned on the Columbia × Landsberg A. thaliana map. The mapped loci identified collinear regions between Arabidopsis and Brassica which had been observed in previous comparative mapping studies; the detection of syntenic genomic regions indicated that there was no apparent rapid divergence of the identified genomic regions housing the R-EST loci.Key words: RFLP mapping, candidate R genes, R-gene homologues, genomic collinearity, Arabidopsis ESTs.

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