Gramene 2021: harnessing the power of comparative genomics and pathways for plant research.

Gramene (http://www.gramene.org), a knowledgebase founded on comparative functional analyses of genomic and pathway data for model plants and major crops, supports agricultural researchers worldwide. The resource is committed to open access and reproducible science based on the FAIR data principles. Since the last NAR update, we made nine releases; doubled the genome portal's content; expanded curated genes, pathways and expression sets; and implemented the Domain Informational Vocabulary Extraction (DIVE) algorithm for extracting gene function information from publications. The current release, #63 (October 2020), hosts 93 reference genomes-over 3.9 million genes in 122 947 families with orthologous and paralogous classifications. Plant Reactome portrays pathway networks using a combination of manual biocuration in rice (320 reference pathways) and orthology-based projections to 106 species. The Reactome platform facilitates comparison between reference and projected pathways, gene expression analyses and overlays of gene-gene interactions. Gramene integrates ontology-based protein structure-function annotation; information on genetic, epigenetic, expression, and phenotypic diversity; and gene functional annotations extracted from plant-focused journals using DIVE. We train plant researchers in biocuration of genes and pathways; host curated maize gene structures as tracks in the maize genome browser; and integrate curated rice genes and pathways in the Plant Reactome.

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations.

Advances in genome sequencing and assembly technologies are generating many high-quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimized data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents >78% of the genome with a scaffold N50 of 88.8 kb that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNA-seq and Pacific Biosciences (PacBio) full-length cDNAs to identify 104,091 high-confidence protein-coding genes and 10,156 noncoding RNA genes. We confirmed three known and identified one novel genome rearrangements. Our approach enables the rapid and scalable assembly of wheat genomes, the identification of structural variants, and the definition of complete gene models, all powerful resources for trait analysis and breeding of this key global crop.

transPLANT Resources for Triticeae Genomic Data.

The genome sequences of many important Triticeae species, including bread wheat ( L.) and barley ( L.), remained uncharacterized for a long time because their high repeat content, large sizes, and polyploidy. As a result of improvements in sequencing technologies and novel analyses strategies, several of these have recently been deciphered. These efforts have generated new insights into Triticeae biology and genome organization and have important implications for downstream usage by breeders, experimental biologists, and comparative genomicists. transPLANT () is an EU-funded project aimed at constructing hardware, software, and data infrastructure for genome-scale research in the life sciences. Since the Triticeae data are intrinsically complex, heterogenous, and distributed, the transPLANT consortium has undertaken efforts to develop common data formats and tools that enable the exchange and integration of data from distributed resources. Here we present an overview of the individual Triticeae genome resources hosted by transPLANT partners, introduce the objectives of transPLANT, and outline common developments and interfaces supporting integrated data access.