The Genome Database for Rosaceae (GDR, https://www.rosaceae.org) is an integrated web-based community database resource providing access to publicly available genomics, genetics and breeding data and data-mining tools to facilitate basic, translational and applied research in Rosaceae. The volume of data in GDR has increased greatly over the last 5 years. The GDR now houses multiple versions of whole genome assembly and annotation data from 14 species, made available by recent advances in sequencing technology. Annotated and searchable reference transcriptomes, RefTrans, combining peer-reviewed published RNA-Seq as well as EST datasets, are newly available for major crop species. Significantly more quantitative trait loci, genetic maps and markers are available in MapViewer, a new visualization tool that better integrates with other pages in GDR. Pathways can be accessed through the new GDR Cyc Pathways databases, and synteny among the newest genome assemblies from eight species can be viewed through the new synteny browser, SynView. Collated single-nucleotide polymorphism diversity data and phenotypic data from publicly available breeding datasets are integrated with other relevant data. Also, the new Breeding Information Management System allows breeders to upload, manage and analyze their private breeding data within the secure GDR server with an option to release data publicly.

We have created an open access web portal with pathosystem-wide resources and bioinformatics tools for the host citrus, the vector Asian citrus psyllid (ACP) and multiple pathogens including Ca. Liberibacter asiaticus. To the best of our knowledge, this is the first example of a database to use the pathosystem as a holistic framework to understand an insect transmitted plant disease. This endeavor integrates and enables the analysis of data sets generated by the community to study the citrus greening disease complex. Users can submit relevant data sets to enable sharing and allow the community to better analyze their data within an integrated system. The portal contains a variety of tools for omics data. Metabolic pathway databases, CitrusCyc and DiaphorinaCyc provide organism specific pathways that can be used to mine metabolomics, transcriptomics and proteomics results to identify pathways and regulatory mechanism involved in disease response. Psyllid Expression Network (PEN) contains expression profiles of ACP genes from multiple life stages, tissues, conditions and hosts. Citrus Expression Network (CEN) contains public expression data from multiple tissues and conditions for various citrus hosts. All tools like Apollo/JBrowse, Biocyc, Blast, CEN and PEN connect to a central database containing gene models for citrus, ACP and multiple Liberibacter pathogens. The portal also includes electrical penetration graph (EPG) recordings of ACP feeding on citrus, information about citrus rootstock trials and metabolomics data in addition to traditional omics data types with a goal of combining and mining all information related to a pathosystem. The portal includes user-friendly manual curation tools to allow the research community to continuously improve this knowledge base as more experimental research is published. Bulk downloads are available for all genome and annotation datasets from the FTP site (ftp://ftp.citrusgreening.org). The portal can be accessed at https://citrusgreening.org/.

The Genome Sequence Annotation Server (GenSAS, https://www.gensas.org) is a secure, web-based genome annotation platform for structural and functional annotation, as well as manual curation. Requiring no installation by users, GenSAS integrates popular command line-based, annotation tools under a single, easy-to-use, online interface. GenSAS integrates JBrowse and Apollo, so users can view annotation data and manually curate gene models. Users are guided step by step through the annotation process by embedded instructions and a more in-depth GenSAS User's Guide. In addition to a genome assembly file, users can also upload organism-specific transcript, protein, and RNA-seq read evidence for use in the annotation process. The latest versions of the NCBI RefSeq transcript and protein databases and the SwissProt and TrEMBL protein databases are provided for all users. GenSAS projects can be shared with other GenSAS users enabling collaborative annotation. Once annotation is complete, GenSAS generates the final files of the annotated gene models in common file formats for use with other annotation tools, submission to a repository, and use in publications.

The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require data management plans for publicly funded research. Furthermore, the value of data increases exponentially when they are properly stored, described, integrated and shared, so that they can be easily utilized in future analyses. AgBioData (https://www.agbiodata.org) is a consortium of people working at agricultural biological databases, data archives and knowledgbases who strive to identify common issues in database development, curation and management, with the goal of creating database products that are more Findable, Accessible, Interoperable and Reusable. We strive to promote authentic, detailed, accurate and explicit communication between all parties involved in scientific data. As a step toward this goal, we present the current state of biocuration, ontologies, metadata and persistence, database platforms, programmatic (machine) access to data, communication and sustainability with regard to data curation. Each section describes challenges and opportunities for these topics, along with recommendations and best practices.

Understanding the genomic relationship between wild and cultivated genomes would facilitate access to the untapped variability found in crop wild relatives. We developed genome assemblies of a cultivated lentil (Lens culinaris) as well as a wild relative (L. ervoides). Comparative analyses revealed large-scale structural rearrangements and additional repetitive DNA in the cultivated genome, resulting in regions of reduced recombination, segregation distortion and permanent heterozygosity in the offspring of a cross between the two species. These novel findings provide plant breeders with better insight into how best to approach accessing the novel variability available in wild relatives.