Hordeum vulgare subsp. vulgare cultivars

Hordeum vulgare Cultivars

Overview

The barley pangenome comprises 76 wild and domesticated barley accessions, including diverse domesticated germplasm with a focus on genebank accessions from barley’s center of diversity in the Middle East; accessions of barley’s wild progenitor H. vulgare subsp. spontaneum from across that taxon’s geographic range, and cultivars of agronomic or scientific relevance such as Bonus, Foma, and Bowman, three parents of classical mutants.

The pangenome contains >16,000 core pangenes (at least one homologous gene in all 76 genotypes), ~78,000 shell pangenes (absent from at least one genotype but present in at least two), and ~800 genes on average unique to each accession. It has been used to explore allelic diversity at structurally complex loci linked to traits of interest for barley growing and malting.

Assemblies

Genome sequences of each accession were assembled to contig-level from PacBio HiFi accurate long reads and scaffolded with conformation capture sequencing (Hi-C) data to chromosome-scale pseudomolecules.

Annotation

Gene models were annotated using transcriptional evidence and homology. Illumina RNA sequencing (RNA-seq) and PacBio isoform sequencing of five different tissues (embryo, root, shoot, inflorescence, and caryopsis) were generated for 20 accessions. Gene models predicted in these genomes were projected onto the remaining 56 sequence assemblies.

Other Accessions

Golden Promise is a 2-row spring-type historical variety extensively used for malting and whisky production. Recently, its main research interest lies in being the most efficient genotype for genetic transformation in barley. A contiguous reference assembly was produced by integrating Illumina paired-end reads, long mate-pair reads, Dovetail Chicago in vitro proximity ligation libraries, and chromosome conformation capture sequencing (Hi-C), as described in http://dx.doi.org/10.1534/g3.119.401010. Tritex gene annotation was generated by association, as described in https://doi.org/10.6084/m9.figshare.9705125.v3.

TRITEX is actually the reference cultivar Morex with an updated assembly, as described at https://doi.org/10.1186/s13059-019-1899-5. Gene annotation was taken from https://doi.org/10.5447/ipk/2019/8. For clarity, it is shown as a separate strain until the Morex V3 assembly is not published.

References

• Jayakodi, M. et al. (2024). Structural variation in the pangenome of wild and domesticated barley. Nature. [online] DOI: https://doi.org/10.1038/s41586-024-08187-1.
• Schreiber, M. et al. (2020).A genome assembly of the barley “transformation reference” cultivar Golden Promise. G3 Genes|Genomes|Genetics, 10(6), pp. 1823–1827. DOI: https://doi.org/10.1534/g3.119.401010
• Monat, C. et al. (2019). TRITEX: Chromosome-scale sequence assembly of Triticeae genomes with open-source tools. Genome Biology, 20(1). DOI: https://doi.org/10.1186/s13059-019-1899-5
  Mascher, M. (2019-05-09). Pseudomolecules and annotation of the second version of the reference genome sequence assembly of barley cv. Morex [Morex V2].
  DOI: https://doi.org/10.5447/ipk/2019/8.