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4D 454 Survey Sequencing

Targeted chromosomes

4D
4D
Click on a chromosome to access associated data (when available) at URGI Sequences Repository.

Project team

First nameLast nameEmailInstitutionCountry
Viviana Echenique echeniqSPAMFILTER@criba.edu.ar CONICET Argentina
Gabriela Tranquilli gtranquilliSPAMFILTER@cnia.inta.gov.ar INTA Argentina
Norma Paniego npaniegoSPAMFILTER@cnia.inta.gov.ar INTA-CONICET Argentina
Ingrid Garbus igarbusSPAMFILTER@criba.edu.ar CONICET Argentina
Pablo Roncallo roncalloSPAMFILTER@criba.edu.ar CONICET Argentina
Leonardo Vanzetti lvanzettiSPAMFILTER@mjuarez.inta.gov.ar INTA Argentina
Lucio Lombardo llombardoSPAMFILTER@mjuarez.inta.gov.ar INTA-CONICET Argentina
José Romero jromeroSPAMFILTER@criba.edu.ar ANPCyT Argentina
Silvina Lewis slewisSPAMFILTER@cnia.inta.gov.ar INTA Argentina
Mariana Cativelli mcativelliSPAMFILTER@cnia.inta.gov.ar INTA Argentina
Facundo Tabbita ftabbitaSPAMFILTER@cnia.inta.gov.ar ANPCyT Argentina
Máximo Rivarola rivabros2SPAMFILTER@gmail.com CONICET Argentina
Paula Fernandez pfernandezSPAMFILTER@cnia.inta.gov.ar INTA-CONICET Argentina
Darío Principi principidarioSPAMFILTER@yahoo.com.ar INTA Argentina
Bernardo Clavijo bclavijoSPAMFILTER@gmail.com INTA Argentina
Sergio Gonzáles sergioalbgonzSPAMFILTER@gmail.com INTA Argentina

Project collaborators

First nameLast nameEmailInstitutionCountry
Catherine Feuillet catherine.feuilletSPAMFILTER@clermont.inra.fr INRA-Clermont-Ferrand France
Jaroslav Dolezel dolezelSPAMFILTER@ueb.cas.cz IEB Czech Republic
Miroslav Valárik valarikSPAMFILTER@ueb.cas.cz IEB Czech Republic
Kellye Eversole eversoleSPAMFILTER@eversoleassociates.com IWGSC USA

Project funding

The 4D Chromosome Survey project was born as a project from a twinning activity between the PAE3718 Project in Argentina and the EU Triticeae Genome Project at the end of September 2010. The project has been funded by two Argentinean Government Institutions, INTA (Instituto Nacional de Tecnología Agropecuaria) and CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas).

Abstract

The 4D Chromosome Survey Sequencing Project is funded by INTA and CONICET. The aim of the project is to get low coverage coverage sequence of 4DS and 4DL arms. 4DS and 4DL lyophilized DNA was provided by J. Dolozel’s group, IEB-Czech Republic and used to generate approximately 7.2x Roche-454 sequence read coverage of 4DS and approximately 4.1x coverage of 4DL. Single end and long mate pair reads were assembled into contigs (223 Mb) and scaffolds (65 Mb) and aligned to the Aegilops tauschii draft genome to anchor 34Mb to chromosome 4. A virtual gene map containing 5700 genes was constructed and compared, with the chromosome survey sequence generated by the IWGSC.

Publications

Helguera, M., Rivarola, M., Clavijo, B., Martis, M.H., Vanzetti, L., González, S., Garbus, I., Leroy, P., Šimkova, H., Valárik, M., Caccamo, M., Doležel, J., Mayer, K.F.X., Feuillet, C., Tranquilli, G., Paniego, N., Echenique, V. New insights into the wheat chromosome 4D structure and virual gene order, revealed by survey pyrosequencing. Plant Science 233 (2015) 200-212. http://dx.doi.org/10.1016/j.plantsci.2014.12.004

Data accession

The 4D assembly has been deposited at the EBI under accession: GCA_000818885.1 is at EBI