scholarly journals NLGenomeSweeper: A Tool for Genome-Wide NBS-LRR Resistance Gene Identification

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 333
Author(s):  
Nicholas Toda ◽  
Camille Rustenholz ◽  
Agnès Baud ◽  
Marie-Christine Le Paslier ◽  
Joelle Amselem ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Resistance Genes ◽  
High Specificity ◽  
Disease Resistance Genes ◽  
Gene Identification ◽  
Leucine Rich Repeat ◽  
Bioinformatic Tools ◽  
Manual Curation ◽  
Conserved Domain ◽  
Genome Wide

Although there are a number of bioinformatic tools to identify plant nucleotide-binding leucine-rich repeat (NLR) disease resistance genes based on conserved protein sequences, only a few of these tools have attempted to identify disease resistance genes that have not been annotated in the genome. The overall goal of the NLGenomeSweeper pipeline is to annotate NLR disease resistance genes, including RPW8, in the genome assembly with high specificity and a focus on complete functional genes. This is based on the identification of the complete NB-ARC domain, the most conserved domain of NLR genes, using the BLAST suite. In this way, the tool has a high specificity for complete genes and relatively intact pseudogenes. The tool returns all candidate NLR gene locations as well as InterProScan ORF and domain annotations for manual curation of the gene structure.

Genome-Wide Analysis of NBS-Encoding Disease Resistance Genes in Maize Inbred Line B73

2009 ◽  
Vol 35 (3) ◽  
pp. 566-570 ◽  
Author(s):  
Jie-Ming WANG ◽  
Hai-Yang JIANG ◽  
Yang ZHAO ◽  
Yan XIANG ◽  
Su-Wen ZHU ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Inbred Line ◽  
Resistance Genes ◽  
Disease Resistance Genes ◽  
Maize Inbred Line ◽  
Genome Wide Analysis ◽  
Genome Wide

scholarly journals Genome-Wide Architecture of Disease Resistance Genes in Lettuce

2015 ◽  
Vol 5 (12) ◽  
pp. 2655-2669 ◽  
Author(s):  
Marilena Christopoulou ◽  
Sebastian Reyes-Chin Wo ◽  
Alex Kozik ◽  
Leah K. McHale ◽  
Maria-Jose Truco ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Resistance Genes ◽  
Disease Resistance Genes ◽  
Genome Wide

scholarly journals A New ‘Comprehensive’ Annotation of Leucine-Rich Repeat-Containing Receptors in Rice

2021 ◽  
Author(s):  
Céline Gottin ◽  
Anne Dievart ◽  
Marilyne Summo ◽  
Gaëtan Droc ◽  
Christophe Périn ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Food Security ◽  
Resistance Genes ◽  
Reference Genome ◽  
Leucine Rich Repeat ◽  
Nonsense Mutations ◽  
New Approach ◽  
Manual Curation ◽  
Receptor Like Kinase ◽  
Essential Food

AbstractRice plays an essential food security role for more than half of the world’s population. Obtaining crops with high levels of disease resistance is a major challenge for breeders, especially today given the urgent need for agriculture to be more sustainable. Plant resistance genes are mainly encoded by three large Leucine-Rich Repeat (LRR)-containing receptor (LRR-CR) subfamilies: the LRR-Receptor-Like Kinase (RLK), LRR-Receptor-Like Protein (RLP) and Nucleotide-binding LRR Receptor (NLR) subfamilies. Using LRRprofiler, a pipeline we developed to annotate and classify those proteins, we compared three publicly available annotations of the rice Nipponbare reference genome. The extended discrepancies we observed for LRR-CR gene models led us to perform in-depth manual curation of their annotations while paying special attention to nonsense mutations. We then transferred this manually curated annotation to Kitaake, a Nipponbare closely related cultivar, using an optimised strategy. Here we discuss the breakthrough achieved by manual curation when comparing genomes and, in addition to ‘functional’ and ‘structural’ annotations, we propose the community to adopt this new approach, which we call ‘comprehensive’ annotation. The resulting data are crucial for further studies on the natural variability and evolution of LRR-CR in order to promote their use in breeding future resilient varieties.

scholarly journals Genome-Wide Identification of Powdery Mildew Resistance in Common Bean (Phaseolus vulgaris L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Papias H. Binagwa ◽  
Sy M. Traore ◽  
Marceline Egnin ◽  
Gregory C. Bernard ◽  
Inocent Ritte ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Powdery Mildew ◽  
Common Bean ◽  
Resistance Genes ◽  
Significant Snps ◽  
Leucine Rich Repeat ◽  
Genome Wide ◽  
Disease Resistance Protein ◽  
Resistance Protein ◽  
The Common

Genome-wide association studies (GWAS) have been utilized to detect genetic variations related to several agronomic traits and disease resistance in common bean. However, its application in the powdery mildew (PM) disease to identify candidate genes and their location in the common bean genome has not been fully addressed. Single-nucleotide polymorphism (SNP) genotyping with a BeadChip containing 5398 SNPs was used to detect genetic variations related to PM disease resistance in a panel of 211 genotypes grown under two field conditions for two consecutive years. Significant SNPs identified on chromosomes Pv04 and Pv10 were repeatable, ensuring the phenotypic data’s reliability and the causal relationship. A cluster of resistance genes was revealed on the Pv04 of the common bean genome, coiled-coil-nucleotide-binding site–leucine-rich repeat (CC-NBS-LRR, CNL), and Toll/interleukin-1 receptor-nucleotide-binding site–leucine-rich repeat type (TIR-NBS-LRR, TNL)-like resistance genes were identified. Furthermore, two resistance genes, Phavu_010G1320001g and Phavu_010G136800g, were also identified on Pv10. Further sequence analysis showed that these genes were homologs to the disease-resistance protein (RLM1A-like) and the putative disease-resistance protein (At4g11170.1) in Arabidopsis. Significant SNPs related to two LRR receptor-like kinases (RLK) were only identified on Pv11 in 2018. Many genes encoding the auxin-responsive protein, TIFY10A protein, growth-regulating factor five-like, ubiquitin-like protein, and cell wall RBR3-like protein related to PM disease resistance were identified nearby significant SNPs. These results suggested that the resistance to PM pathogen involves a network of many genes constitutively co-expressed.

Genome-wide investigation on the genetic variations of rice disease resistance genes

2006 ◽  
Vol 62 (1-2) ◽  
pp. 181-193 ◽  
Author(s):  
Sihai Yang ◽  
Zhumei Feng ◽  
Xiuyan Zhang ◽  
Ke Jiang ◽  
Xinqing Jin ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Resistance Genes ◽  
Genetic Variations ◽  
Disease Resistance Genes ◽  
Genome Wide ◽  
Rice Disease
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