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

Parva Kumar Sharma; Hanin Ibrahim Ahmed; Matthias Heuberger; Dal Hoe Koo; Jesus Quiroz-Chavez; Laxman Adhikari; John Raupp; Stéphane Cauet; Nathalie Rodde; Charlotte Cravero; Caroline Callot; Inderjit Singh Yadav; Nagarajan Kathiresan; Naveenkumar Athiyannan; Ricardo H. Ramirez-Gonzalez; Cristobal Uauy; Thomas Wicker; Michael Abrouk; Yong Q. Gu; Jesse Poland; Simon G. Krattinger; Gerard R. Lazo; Vijay K. Tiwari

doi:10.1093/database/baad079

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

Parva Kumar Sharma, Hanin Ibrahim Ahmed, Matthias Heuberger, Dal Hoe Koo, Jesus Quiroz-Chavez, Laxman Adhikari, John Raupp, Stéphane Cauet, Nathalie Rodde, Charlotte Cravero, Caroline Callot, Inderjit Singh Yadav, Nagarajan Kathiresan, Naveenkumar Athiyannan, Ricardo H. Ramirez-Gonzalez, Cristobal Uauy, Thomas Wicker, Michael Abrouk, Yong Q. Gu, Jesse PolandSimon G. Krattinger, Gerard R. Lazo^*, Vijay K. Tiwari^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

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 and domesticated). This work reports an einkorn genome database that provides an interface to the cereals research community to perform comparative genomics, applied genetics and breeding 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 wheat research and breeding.

Original language	English (US)
Article number	baad079
Journal	Database
Volume	2023
DOIs	https://doi.org/10.1093/database/baad079
State	Published - 2023

ASJC Scopus subject areas

Information Systems
General Biochemistry, Genetics and Molecular Biology
General Agricultural and Biological Sciences

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Sharma, P. K., Ahmed, H. I., Heuberger, M., Koo, D. H., Quiroz-Chavez, J., Adhikari, L., Raupp, J., Cauet, S., Rodde, N., Cravero, C., Callot, C., Yadav, I. S., Kathiresan, N., Athiyannan, N., Ramirez-Gonzalez, R. H., Uauy, C., Wicker, T., Abrouk, M., Gu, Y. Q., ... Tiwari, V. K. (2023). An online database for einkorn wheat to aid in gene discovery and functional genomics studies. Database, 2023, Article baad079. https://doi.org/10.1093/database/baad079

@article{30b47f6a613e4785b05c330667e4d91b,

title = "An online database for einkorn wheat to aid in gene discovery and functional genomics studies",

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 and domesticated). This work reports an einkorn genome database that provides an interface to the cereals research community to perform comparative genomics, applied genetics and breeding 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 wheat research and breeding.",

author = "Sharma, {Parva Kumar} and Ahmed, {Hanin Ibrahim} and Matthias Heuberger and Koo, {Dal Hoe} and Jesus Quiroz-Chavez and Laxman Adhikari and John Raupp and St{\'e}phane Cauet and Nathalie Rodde and Charlotte Cravero and Caroline Callot and Yadav, {Inderjit Singh} and Nagarajan Kathiresan and Naveenkumar Athiyannan and Ramirez-Gonzalez, {Ricardo H.} and Cristobal Uauy and Thomas Wicker and Michael Abrouk and Gu, {Yong Q.} and Jesse Poland and Krattinger, {Simon G.} and Lazo, {Gerard R.} and Tiwari, {Vijay K.}",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2023.",

year = "2023",

doi = "10.1093/database/baad079",

language = "English (US)",

volume = "2023",

journal = "Database",

issn = "1758-0463",

publisher = "Oxford University Press",

}

Sharma, PK, Ahmed, HI, Heuberger, M, Koo, DH, Quiroz-Chavez, J, Adhikari, L, Raupp, J, Cauet, S, Rodde, N, Cravero, C, Callot, C, Yadav, IS, Kathiresan, N, Athiyannan, N, Ramirez-Gonzalez, RH, Uauy, C, Wicker, T, Abrouk, M, Gu, YQ, Poland, J , Krattinger, SG, Lazo, GR & Tiwari, VK 2023, 'An online database for einkorn wheat to aid in gene discovery and functional genomics studies', Database, vol. 2023, baad079. https://doi.org/10.1093/database/baad079

TY - JOUR

T1 - An online database for einkorn wheat to aid in gene discovery and functional genomics studies

AU - Sharma, Parva Kumar

AU - Ahmed, Hanin Ibrahim

AU - Heuberger, Matthias

AU - Koo, Dal Hoe

AU - Quiroz-Chavez, Jesus

AU - Adhikari, Laxman

AU - Raupp, John

AU - Cauet, Stéphane

AU - Rodde, Nathalie

AU - Cravero, Charlotte

AU - Callot, Caroline

AU - Yadav, Inderjit Singh

AU - Kathiresan, Nagarajan

AU - Athiyannan, Naveenkumar

AU - Ramirez-Gonzalez, Ricardo H.

AU - Uauy, Cristobal

AU - Wicker, Thomas

AU - Abrouk, Michael

AU - Gu, Yong Q.

AU - Poland, Jesse

AU - Krattinger, Simon G.

AU - Lazo, Gerard R.

AU - Tiwari, Vijay K.

PY - 2023

Y1 - 2023

N2 - 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 and domesticated). This work reports an einkorn genome database that provides an interface to the cereals research community to perform comparative genomics, applied genetics and breeding 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 wheat research and breeding.

AB - 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 and domesticated). This work reports an einkorn genome database that provides an interface to the cereals research community to perform comparative genomics, applied genetics and breeding 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 wheat research and breeding.

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DO - 10.1093/database/baad079

M3 - Article

C2 - 37971714

AN - SCOPUS:85177479774

SN - 1758-0463

VL - 2023

JO - Database

JF - Database

M1 - baad079

ER -

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

Abstract

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