RGADE

RGADE (Resistance Gene Analogs Differentially Expressed) is a software tool that analyzes and compares the expression of resistance gene analogs (RGAs) in sugarcane genotypes with different resistance levels to diseases, such as smut. The tool helps identify RGAs differentially expressed between resistant and susceptible genotypes, providing insights into the genetic basis of disease resistance in sugarcane.

Key features of RGADE:

1. Predicts and identifies RGAs in sugarcane genomes and transcriptomes.

2. Investigate the genomic features and organization of RGAs, including their clustering and synteny.

3. Compares the expression of RGAs between resistant and susceptible sugarcane genotypes to identify differentially expressed RGAs (RGADEs).

4. Traces the evolutionary origin of RGADEs by identifying their orthologs in ancestral sugarcane species, such as Saccharum spontaneum.

5. Provides insights into the roles of different RGA classes, such as RLK (receptor-like kinase) and RLP (receptor-like protein), in disease resistance.

Topic

Mapping;Genotype and phenotype;Plant biology;Agricultural science;Gene expression

Detail

  • Operation: De-novo assembly;Clustering;Genotyping;Fold recognition

  • Software interface: Command-line user interface

  • Language: Python

  • License: Not stated

  • Cost: Free of charge

  • Version name: -

  • Credit: Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq).

  • Input: -

  • Output: -

  • Contact: Claudia B. Monteiro-Vitorello cbmontei@usp.br

  • Collection: -

  • Maturity: -

Publications

  • Genome survey of resistance gene analogs in sugarcane: genomic features and differential expression of the innate immune system from a smut-resistant genotype.
  • Rody HVS, et al. Genome survey of resistance gene analogs in sugarcane: genomic features and differential expression of the innate immune system from a smut-resistant genotype. Genome survey of resistance gene analogs in sugarcane: genomic features and differential expression of the innate immune system from a smut-resistant genotype. 2019; 20:809. doi: 10.1186/s12864-019-6207-y
  • https://doi.org/10.1186/S12864-019-6207-Y
  • PMID: 31694536
  • PMC: PMC6836459

Download and documentation

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