4D 454 Survey Sequencing
Targeted chromosomes
|
Project team
| First name | Last name | Institution | Country | |
|---|---|---|---|---|
| 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 name | Last name | Institution | Country | |
|---|---|---|---|---|
| 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