CitrusKB

CitrusKB provides an integrated knowledge base of transcriptome and in vivo interactome data for Citrus spp. infected by Xanthomonas citri subsp. citri to support analysis of molecular and genetic mechanisms underlying early citrus canker development.

Key Features:

• In vivo interactome database: Contains in vivo interactome data describing molecular interactions between Citrus spp. and Xanthomonas citri subsp. citri across infection stages.
• Multi-cultivar infection datasets: Includes data from eight citrus cultivars with varying susceptibility, comprising control and infected samples across multiple infection stages.
• Reference genome and transcriptome annotations: Integrates a reference citrus genome and transcriptome annotations, including expressed transcripts and pseudogenes.
• Predicted genomic variation annotations: Provides predicted single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) associated with the reference genome and transcriptome data.
• Generated sequencing datasets: Contains raw sequencing reads and derived datasets from the transcriptome and interactome experiments.
• Dynamic integration of annotations and tools: Supports ongoing incorporation of novel annotations and analysis tools to expand and update the knowledge base.

Scientific Applications:

• Genetic research: Enables identification of genetic variations associated with citrus canker susceptibility to inform breeding of resistant citrus varieties.
• Molecular mechanism studies: Facilitates exploration of molecular interactions and pathways between citrus plants and Xanthomonas citri subsp. citri, particularly during early stages of infection.

Methodology:

Integration of in vivo interactome data with reference citrus genome and transcriptome annotations, including expressed transcripts, pseudogenes, predicted SNPs and SSRs, with ongoing incorporation of novel annotations and analysis tools.