W427 Towards A Reference Sequence of the Bread Wheat Chromosome 3B

Date: Saturday, January 14, 2012
Time: 9:00 AM
Room: Town and Country
Frederic Choulet , INRA GDEC, Clermont-Ferrand, France
Etienne Paux , INRA GDEC, Clermont-Ferrand, France
Sébastien Theil , INRA GDEC, Clermont-Ferrand, France
Philippe Leroy , INRA GDEC, Clermont-Ferrand, France
Nicolas Guilhot , INRA GDEC, Clermont-Ferrand, France
Pierre Sourdille , INRA GDEC, Clermont-Ferrand, France
Michael Alaux , INRA - URGI, Research Unit Genomic-Info, Versailles, France
Arnaud Bellec , INRA-CNRGV, Castanet-Tolosan, France
Hana Simkova , Institute of Experimental Botany, Olomouc, Czech Republic
Arnaud Couloux , CEA - Genoscope, Evry Cedex, France
Adriana Alberti , CEA - Genoscope, Evry Cedex, France
Helene Berges , INRA-CNRGV, Castanet Tolosan, France
Jaroslav Dolezel , Institute of Experimental Botany, Olomouc, Czech Republic
Hadi Quesneville , INRA - URGI, Versailles, France
Patrick Wincker , CEA - Genoscope, Evry Cedex, France
Catherine Feuillet , INRA GDEC, Clermont-Ferrand, France
To produce a reference sequence of the 1Gb hexaploid wheat chromosome 3B, a total of 8441 BAC clones representing the minimal tiling path (MTP) of the 3B physical map was sequenced with the Roche-454 Titanium technology on barcoded pools of about 10 BACs each. 8 kb mate-pair libraries were built for each pool to ensure the assembly of large sequence scaffolds. In addition, more than 40’000 BAC-end sequences were produced and a 82X coverage of sorted 3B chromosomes was generated by Illumina sequencing. Assembly of 922 pools generated 1027 Mb of sequence with 16159 scaffolds having a N50 of 277 Kb. For 80% of the BAC pools, less than 5 scaffolds cover 90% of the sequenced region, revealing that the assembled sequence is of high quality. Sequence quality was evaluated by comparing de novo assemblies with 13 reference contig sequences generated previously. This revealed that genes are correctly assembled and fully included into large sequence contigs, suggesting that the whole 3B gene space will be assessed through this approach. Moreover, even though some TE rich regions still contain large gaps because of unresolved read pairs, scaffolds are properly assembled and the size of the gaps is correctly estimated. Finishing is underway using BAC end, whole genome profiling tags and Illumina sequences information. The automated annotation of the 3B sequence is underway using the annotation pipeline TriAnnot. Results about sequencing, assembling and annotation will be discussed. For more details about the 3BSEQ project see: http://urgi.versailles.inra.fr/Projects/3BSeq.