Chromosome 4D survey sequencing analysis: present status and perspectives

CLAVIJO B; WRIGHT J; MARTIS M; CÁCCAMO M; VALARIK M; TABBITA F; JOSÉ ROMERO; VANZETTI L; BONAFEDE M; INGRID GARBUS; CATIVELLI M; PABLO RONCALLO; SIMKOVA H; MAYER K; DOLEZEL J; TRANQUILLI G; PANIEGO N; VIVIANA ECHENIQUE; HELGUERA M

México DF

Workshop; ITMI Workshop and Pre-Conference IWSC, CIMMYT; 2011

CIMMYT

Sequencing wheat genome has always been viewed as a complex task because of its large size, a high repetitive DNA content and polyploidy. Several of previously mentioned constrains (large size, polyploidy) can be overcome by flow sorting of individual chromosomes followed by shotgun sequencing using next generation sequencing (NGS) technologies. In this study we used 4D flow-sorted chromosome arms (obtained from cv Chinese Sping) to perform shotgun sequencing with a Roche 454 NGS platform producing sequence data equivalent to a 3.6x chromosome coverage. In order to reach a reliable and preliminary de novo assembly, short reads are being analyzed using different algorithms, strategies and parameters. Assembly performance is being evaluated by output comparison using rapid alignment tools to generate a correspondence relation between contigs on the assemblies. The identification of common (ie. emerging on various assemblies) and trustable (arguably emerging as better or more trustworthy variants when comparing different assemblies) contigs will allow downstream processes like molecular marker discovery and gene content evaluation using Genome Zipper. In the near future, additional multiplatform reads including pair end (considering Roche and Illumina technologies), will also be generated and evaluated to corroborate and enrich previous data.