Avena sativa cultivars
Overview
PanOat is an international pan-genome project for oat where scientists across the world constructed and analysed annotated chromosome-scale reference genome sequences of diverse oat genotypes. The PanOat panel comprises 33 diverse oat lines including 24 cultivars of Avena sativa. The analysis goals include characterization of core gene sets, identifying lineage-specific genes, cataloguing structural variation in wild and domesticated oats, accumulating comparative sequence information for use in agronomic and quality trait mapping, and evolutionary genomic analyses to understand the origin and evolution of oat.
Assemblies
Out of 24 Avena sativa cultivars, two assemblies were published previously: A. sativa Sang and A. sativa OT3098. The genomes of two lines — A. sativa Gehl and A. sativa Nicolas — were sequenced with Illumina short reads. Genome assemblies for Gehl and Nicolas were scaffolded using TRITEX and Hi-C to guide pseudomolecule assembly as described here and remaining genome sequences were assembled from accurate long reads generated on the PacBio HiFi platform. All contig-level assemblies were scaffolded with chromosome conformation capture (Hi-C) sequencing data.
Links
Annotation
The genes were annotated using a multi-tiered approach. For the 18 oat cultivars represented here, de novo structural gene prediction, confidence classification and functional annotation were done following a protocol described here, although differs in the use of TE soft-masked genome sequences instead of TE hints. Gene predictions for the lines A. sativa OT380 (which had no native transcriptome data) was done using a gene consolidation approach that has been described previously. The gene predictions for all the given 19 oat lines were cross-mapped with the genome sequences of one another to identify and correct for missed gene models and to annotate genomes without native transcriptome data. For the remaining three lines A. sativa Leggett, A. sativa Williams and A. sativa AC Morgan, the gene content were predicted using the projection method as described here.
Gene annotation provided for Avena sativa OT3098 has previously been done as mentioned here whereas annotation for Avena sativa Sang was derived from here.
References
- Avni et al., "A pangenome and pantranscriptome of hexaploid oat", Nature, 2025
- Bekele et al. "Global genomic population structure of wild and cultivated oat reveals signatures of chromosome rearrangements", Nature Communications, 2025
- Kamal, N., Tsardakas Renhuldt, N., Bentzer, J. et al. The mosaic oat genome gives insights into a uniquely healthy cereal crop. Nature 606, 113–119 (2022)
| Cultivar | Scientific name | Ensembl Assembly | Accession | More information |
|---|---|---|---|---|
 Avena sativa AslakView example location | Karyotype and statistics | Avena sativa | Asativa_cv_Aslak_v1.0 | GCA_947310285.1 | |
 Avena sativa BannisterView example location | Karyotype and statistics | Avena sativa | Asativa_cv_Bannister_v1.0 | GCA_947310875.1 | |
 Avena sativa Clintland60View example location | Karyotype and statistics | Avena sativa | Asativa_cv_Clintland60_v1.0 | GCA_947311085.1 | |
 Avena sativa NicolasView example location | Karyotype and statistics | Avena sativa | Asativa_cv_Nicolas_v1.0 | GCA_947311135.1 | |
 Avena sativa LionView example location | Karyotype and statistics | Avena sativa | Asativa_cv_Lion_v1.0 | GCA_947311155.1 | |
 Avena sativa HifiView example location | Karyotype and statistics | Avena sativa | Asativa_cv_HiFi_v1.0 | GCA_947311165.1 | |
 Avena sativa HativesdesAlpesView example location | Karyotype and statistics | Avena sativa | Asativa_cv_Hatives_des_Alpes_v1.0 | GCA_947311225.1 | |
 Avena sativa Gmi423View example location | Karyotype and statistics | Avena sativa | Asativa_cv_GMI423_v1.0 | GCA_947311235.1 | |
 Avena sativa RhapsodyView example location | Karyotype and statistics | Avena sativa | Asativa_cv_Rhapsody_v1.0 | GCA_947311295.1 | |
 Avena sativa ParkView example location | Karyotype and statistics | Avena sativa | Asativa_cv_Park_v1.0 | GCA_947311345.1 | |
 Avena sativa Fm13View example location | Karyotype and statistics | Avena sativa | Asativa_FM13_v1.0 | GCA_947311355.1 | |
 Avena sativa GehlView example location | Karyotype and statistics | Avena sativa | Asativa_cv_Gehl_v1.0 | GCA_947311365.1 | |
 Avena sativa BingoView example location | Karyotype and statistics | Avena sativa | Asativa_cv_Bingo_v1.0 | GCA_947311525.1 | |
 Avena sativa DelfinView example location | Karyotype and statistics | Avena sativa | Asativa_cv_Delfin_v1.0 | GCA_947311555.1 | |
 Avena sativa VictoriaView example location | Karyotype and statistics | Avena sativa | Asativa_cv_Victoria_v1.0 | GCA_947311595.1 | |
 Avena sativa BilbyView example location | Karyotype and statistics | Avena sativa | Asativa_cv_Bilby_v1.0 | GCA_947311775.1 | |
 Avena sativa Gs7View example location | Karyotype and statistics | Avena sativa | Asativa_GS7_v1.0 | GCA_947311915.1 | |
 Avena sativa Ot380View example location | Karyotype and statistics | Avena sativa | Asativa_OT380_v1.0 | GCA_947311925.1 | |
 Avena sativa Pi182478View example location | Karyotype and statistics | Avena sativa | Asativa_PI182478_v1.0 | GCA_947312425.1 | |
 Avena sativa WilliamsView example location | Karyotype and statistics | Avena sativa | Asativa_cv_Williams_v1.0 | GCA_951802345.1 | |
 Avena sativa LeggettView example location | Karyotype and statistics | Avena sativa | Asativa_cv_Legett_v1.0 | GCA_951802355.1 | |
 Avena sativa MorganView example location | Karyotype and statistics | Avena sativa | Asativa_cv_Morgan_v1.0 | GCA_951802365.1 | |
 Avena sativa SangView example location | Karyotype and statistics | Avena sativa | Asativa_sang.v1.1 | GCA_910574605.1 |
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