An online database for einkorn wheat to aid in gene discovery and functional genomics studies

Authors: SHARMA, PARVA - University Of Maryland; AHMED, HANIN IBRAHIM - University Of Zurich; HEUBERGER, MATTIAS - King Abdullah University Of Science And Technology; KOO, DAL-HOE - Kansas State University; QUIROZ-CHAVEZ, JESUS - John Innes Center; ADHIKARI, LAXMAN - King Abdullah University Of Science And Technology; RAUPP, JOHN - Kansas State University; CAUET, STEPHANE - Inrae; RODDE, NATHALIE - Inrae; CRAVERO, CHARLOTTE - Inrae; CALLOT, CAROLINE - Inrae; KATHIRESAN, NAGARAJAN - King Abdullah University Of Science And Technology; ATHIYANNAN, NAVEENKUMAR - King Abdullah University Of Science And Technology; RAMIREZ GONZALEZ, RICARDO - John Innes Center; UAUY, CRISTOBAL - John Innes Center; WICKER, THOMAS - University Of Zurich; ABROUK, MICHAEL - King Abdullah University Of Science And Technology; Gu, Yong; KRATTINGER, SIMON - King Abdullah University Of Science And Technology; Lazo, Gerard; TIWARI, VIJAY - University Of Maryland

Submitted to: Database: The Journal of Biological Databases and Curation
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/26/2023
Publication Date: 11/16/2023
Citation: Sharma, P.K., Ahmed, H., Heuberger, M., Koo, D., Quiroz-Chavez, J., Adhikari, L., Raupp, J., Cauet, S., Rodde, N., Cravero, C., Callot, C., Kathiresan, N., Athiyannan, N., Ramirez Gonzalez, R.H., Uauy, C., Wicker, T., Abrouk, M., Gu, Y.Q., Krattinger, S.G., Lazo, G.R., Tiwari, V.K. 2023. An online database for einkorn wheat to aid in gene discovery and functional genomics studies . Database: The Journal of Biological Databases and Curation. 00. Article baad079. https://doi.org/10.1093/database/baad079.
DOI: https://doi.org/10.1093/database/baad079

Interpretive Summary: Diploid A-genome wheat (einkorn wheat) presents a nutrition-rich option as an ancient grain crop and a resource for the improvement of bread wheat against abiotic and biotic stresses. Realizing the importance of this wheat species, reference-level assemblies of two einkorn wheat accessions were generated (wild type and domesticated). This work reports an einkorn genome database that provides an interface to the cereals research community to perform comparative genomics, applied breeding, and genetics research. It features queries for annotated genes, the use of a recent genome browser release, and the ability to search for sequence alignments using a modern BLAST interface. Other features include a comparison of reference einkorn assemblies with other wheat cultivars through genomic synteny visualization and an alignment visualization tool for BLAST results. Altogether, this resource will help in the quality improvement of modern-day wheat. The database can be accessed at avena.pw.usda.gov/genomes/mono.

Technical Abstract: Diploid A-genome wheat (einkorn wheat) presents a nutrition-rich option as an ancient grain crop and a resource for the improvement of bread wheat against abiotic and biotic stresses. Realizing the importance of this wheat species, reference-level assemblies of two einkorn wheat accessions were generated (wild type and domesticated). This work reports an einkorn genome database that provides an interface to the cereals research community to perform comparative genomics, applied breeding, and genetics research. It features queries for annotated genes, the use of a recent genome browser release, and the ability to search for sequence alignments using a modern BLAST interface. Other features include a comparison of reference einkorn assemblies with other wheat cultivars through genomic synteny visualization and an alignment visualization tool for BLAST results. Altogether, this resource will help in the quality improvement of modern-day wheat. The database can be accessed at avena.pw.usda.gov/genomes/mono.