Abstract
Effective crop improvement, whether through selective breeding or biotech strategies, is largely dependent on the cumulative knowledge of a species’ pangenome and its containing genes. Acquiring this knowledge is specially challenging in grapevine, one of the oldest fruit crops grown worldwide, which is known to have more than 30,000 genes. Well-established research communities studying model organisms have created and maintained, through public and private funds, a diverse range of online tools and databases serving as repositories of genomes and gene function data. The lack of such resources for the non-model, but economically important, Vitis vinifera species has driven the need for a standardised collection of genes within the grapevine community. In an effort led by the Integrape COST Action CA17111, we have recently developed the first grape gene reference catalogue, where genes are ascribed to functional data, including their accession identifiers from different genome-annotation versions (https://integrape.eu/resources/genes-genomes/). We present and discuss this gene repository together with a validation-level scheme based on varied supporting evidence found in current literature. The catalogue structure and online submission form provided permits community curation. Finally, we present the Gene Cards tool, developed within the Vitis Visualization (VitViz) platform, to visualize the data collected in the catalogue and link gene function with tissue-specific expression derived from public transcriptomic data. This perspective article aims to present these resources to the community as well as highlight their potential use, in particular for plant-breeding applications.
Highlights
David Navarro-Payá1*, Antonio Santiago1, Luis Orduña1, Chen Zhang1, Alessandra Amato2, Erica D’Inca2, Chiara Fattorini2, Mario Pezzotti2, Giovanni Battista Tornielli2, Sara Zenoni2, Camille Rustenholz3 and José Tomás Matus1*
Whether through selective breeding or biotech strategies, is largely dependent on the cumulative knowledge of a species’ pangenome and its containing genes. Acquiring this knowledge is specially challenging in grapevine, one of the oldest fruit crops grown worldwide, which is known to have more than 30,000 genes
We present the Gene Cards tool, developed within the Vitis Visualization (VitViz) platform, to visualize the data collected in the catalogue and link gene function with tissue-specific expression derived from public transcriptomic data
Summary
Online tools and databases are key to harness the potential offered by genomic advances to both research and industry. The Arabidopsis Information Resource (TAIR) for the A. thaliana community represents the most successful example in the plant field (Berardini et al, 2015), providing up-to-date biological information on individual genes as well as related resources such as single-gene mutant collections. Other examples of equivalent resources are the Sol Genomics Network (SGN) for Solanacea family members such as tomato, potato, and tobacco (FernandezPozo et al, 2015), the Rice Annotation Project Database (RAP-DB) (Sakai et al, 2013), and the
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