CitrusKB: A Comprehensive Knowledge Base for Transcriptome and Interactome ofCitrusspp. Infected byXanthomonas citrisubsp.citriat Different Infection Stages

Abstract

Citrus canker type A is a serious disease caused by Xanthomonas citri subsp. citri (X. citri), which is responsible for severe losses to growers and to the citrus industry worldwide. To date, no canker-resistant citrus genotypes are available, and there is limited information regarding the molecular and genetic mechanisms involved in the early stages of the citrus canker development. Here, we present the knowledge base for transcriptome of in vivo citrus interactome, the CitrusKB. This is the first in vivo interactome database for different citrus cultivars, and it was produced to provide a valuable source of information on citrus and their interaction with the citrus canker bacterium X. citri. The database provides tools for a user-friendly web interface to search and analyze a large amount of information regarding eight citrus cultivars with distinct levels of susceptibility to the disease and their interaction, at different stages of infection, with the citrus canker bacterium X. citri. Currently, CitrusKB comprises a reference citrus genome and its transcriptome, expressed transcripts, pseudogenes and predicted genomic variations (SNPs and SSRs). The updating process will continue by incorporating annotations and analysis tools. We expect that CitrusKB may substantially contribute to the area of citrus genomics. CitrusKB is accessible at http://bioinfo.deinfo.uepg.br/citrus. Users can download all the generated raw sequences and generated datasets by this study from the CitrusKB website.

A Genomic and Transcriptomic Overview of MATE, ABC, and MFS Transporters in Citrus sinensis Interaction with Xanthomonas citri subsp. citri

“…Since CitrusKB CRT was generated from eight Citrus spp. [ 9 ], this result may indicate that these transcripts are derived from other than C sinensis . Moreover, most transcripts were expressed by genes located on Chr 2, Chr 1, and Chr 4 for MATE, ABC, and MFS families, respectively ( Figure 1 , Table S4 ).…”

“…Moreover, distinct susceptibility levels to CC across Citrus spp. were observed [ 8 ], reflecting a complex array of plant-pathogen interaction and defense-response mechanisms [ 9 ].…”

“…As part of our efforts to understand the Citrus-Xac interaction, we built an in vivo database for the transcriptome of citrus and Xac interactome (CitrusKB database, ) [ 9 ]. The CitrusKB integrates gene expression data from eight Citrus spp.…”

“…The CitrusKB integrates gene expression data from eight Citrus spp. showing different CC susceptibility levels (e.g., from the less susceptible species: ‘Kumquat’ Fortunella spp., tangerine mandarin ‘Satsuma’ C. unshiu , and tangerine mandarin ‘Ponkan’ C. reticulata , to the intermediate susceptible as sweet oranges cultivars ‘Pera Rio’ and ‘Valencia’ C. sinensis , and highly susceptible as sweet oranges ‘Hamlin’ and ‘Bahia’ C. sinensis , and Acid lime ‘Galego’ C. aurantifolia ) [ 9 ]. Furthermore, the CitrusKB provides the citrus reference transcriptome (CRT), composed of non-redundant sequences derived from the eight Citrus spp.…”

“…available at CitrusKB. [ 9 ]. Using the CRT data from CitrusKB along with the public C. sinensis genome assembled at chromosome-scale (v2.0 HZAU), an in silico analysis was conducted with the aims to identify, classify, and propose potential roles for the MATE, ABC, and MFS gene families at genomic and transcriptomic contexts.…”