Wheat chromosome 4D survey sequencing: current progress towards the understanding of its structural organization

HELGUERA M; RIVAROLA M; MARTIS M; VANZETTI L; GARBUS I; LEROY P; CLAVIJO B; ROMERO JR; GONZÁLEZ S; TABBITA F; BONAFEDE M; CATIVELLI M; VALARIK M; SIMKOVA H; WRIGHT J; CÁCCAMO M; DOLEZEL J; FEUILLET C; MAYER K; TRANQUILLI G; PANIEGO N; VIVIANA ECHENIQUE

Yokohama

Simposio; The 12Th International Wheat Genetics Symposium; 2013

International Wheat Genetics Symposium

A draft chromosome 4D genome sequence has been obtained by using the 4D flow-sorted chromosome arms (obtained from cv Chinese Sping) strategy, combined with multiple displacement amplification (MDA) to perform shotgun sequencing with a Roche 454 NGS platform. We have produced sequence data (single and pair- end reads), which was assembled by ?Newbler Large? into contigs and scaffolds. Obtained contigs covered 103 and 120 Mb for 4DS and 4DL, and assembled scaffolds represented 38 and 27 Mb, respectively. Comparison of wheat 4D scaffolds against the Aegilops tauschii genome draft and physical map data allowed anchoring 7410 scaffolds to A tauschii chromosome 4, while 1844 scaffolds were anchored to different chromosomes and 5866 scaffolds remained unanchored. Scaffolds larger than 6kb (2611 = 24.8 Mb) were analyzed using the pipeline Triannot allowing the annotation of 822 gene models. Repeat filtered contigs (67377 = 70 MB) were used to build a syntenic map including 1973 orthologous gene loci with support of at least one of the three grass reference genomes (Brachypodium, Oryza and Sorghum). Three handred and eighty one (381) gene models were also integrated in the virtual ordered linear maps via bi-directional blast hits against the 4Dcontigs and the syntenic conserved reference genes.