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

MARCELO HELGUERA; RIVAROLA MAXIMO; MARTIS MICHAELA; VANZETTI LEONARDO; GARBUS INGRID,; LEROY PHILIP; CLAVIJO BERNARDO; ROMERO JOSE; GONZÁLEZ SERGIO; TABBITA FACUNDO; CATIVELLI MARIANA; VALARIK MIROSLAV; WRIGHT JOHN; CACCAMO MARIO; DOLEZEL J; FEUILLET CATHERINE; MAYER KLAUS; TRANQUILLI GABRIELA; PANIEGO NORMA; ECHENIQUE VIVIANA C

Yokohama

Congreso; International Wheat Genome Sequencing Consortium; 2013

IWGSC

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 4D contigs and the syntenic conserved reference genes. The short arm of chromosome 4DS exhibited conserved synteny to Brachypodium chromosome Bd1 and Bd4, rice chromosomes Os3 and Os11, and sorghum chromosomes Sb1, Sb2 and Sb5. The long chromosome arm of 4D was conserved with regions on the long chromosome arm of Bd1, short arm of rice chromosome Os3, and long chromosome arm of sorghum Sb1.The analysis of thhe repetitive landscape of chromosome 4D reveals that retroelements represent the 74% and 80% for 4DS and 4DL, respectively. The retroelements are followed in importance by the DNA elements, which comprise 15.4% and 11.2% for 4DS and 4DL, respectively. For both chromosomes arms CACTA/En-Spm and Gypsy were the most represented superfamilies of transposons and retrotransposons, respectively. The use of specific software across the 4DS and 4DL scaffolds allowed the identification, characterization and annotation of four novel LTR retrotransposon families belonging to the Copia superfamily and one belonging to the Gypsy superfamily, as well as one novel LARD retrotransposon family.