ArGD: An Integrated Database and Analysis Platform for Artocarpus Genomics and Transcriptomics

TL;DR

ArGD is a new database and analysis platform for studying the genomics and transcriptomics of the Artocarpus genus, including jackfruit and breadfruit.

Contribution

ArGD integrates genomic and transcriptomic data with advanced analysis tools for the Artocarpus genus.

Findings

ArGD combines high-quality genomic sequences and functional annotations for seven Artocarpus species.

The platform offers tools like BLAST, JBrowse, and GO/KEGG enrichment for data analysis.

ArGD includes tools for identifying gene families related to fruit aroma and secondary metabolism.

Abstract

Background:The genus Artocarpus includes about 70 species, such as the economically important jackfruit and breadfruit, which serve as vital sources of food, timber, and medicine in the tropics. However, systematic research and genetic improvement have been restricted by the scarcity and fragmentation of available genomic data. Methods: Here, we developed the Artocarpus Genome Database (ArGD), a publicly accessible, comprehensive research platform dedicated to this genus. ArGD centrally integrates high-quality genomic sequences from seven Artocarpus genomes, along with related transcriptomic data and detailed functional annotations. Results: Beyond basic data retrieval, ArGD features a suite of advanced visualization and analysis modules, including BLAST, JBrowse, expression heatmaps, volcano plots, synteny viewers, ArtocarpusCYC metabolic interface, and Gene Ontology (GO)/KEGG enrichment analyses. Additionally, ArGD provides online identification tools for gene families related to fruit aroma and secondary metabolism. Conclusions: Overall, ArGD serves as a valuable resource for functional genomics and comparative studies in Artocarpus, facilitating future research and data-driven studies of genetic improvement.

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