New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing

Helguera, M., Rivarola, M., Clavijo, B., Martis, M.M., Vanzetti, L.S., González, S., Garbus, I., Leroy, P., Šimková, H., Valárik, M., Caccamo, M., Doležel, J., Mayer, K.F.X., Feuillet, C., Tranquilli, G., Paniego, N., Echenique, V.
PLANT SCIENCE 233: 200-212, 2015

Keywords: Chromosome 4D survey sequence, Gene annotation, Gene content, Synteny, Virtual gene order, Triticum aestivum
Abstract: tSurvey sequencing of the bread wheat (Triticum aestivum L.) genome (AABBDD) has been approachedthrough different strategies delivering important information. However, the current wheat sequenceknowledge is not complete. The aim of our study is to provide different and complementary set of datafor chromosome 4D. A survey sequence was obtained by pyrosequencing of flow-sorted 4DS (7.2×) and4DL (4.1×) arms. Single ends (SE) and long mate pairs (LMP) reads were assembled into contigs (223 Mb)and scaffolds (65 Mb) that were aligned to Aegilops tauschii draft genome (DD), anchoring 34 Mb to chro-mosome 4. Scaffolds annotation rendered 822 gene models. A virtual gene order comprising 1973 wheatorthologous gene loci and 381 wheat gene models was built. This order was largely consistent with thescaffold order determined based on a published high density map from the Ae. tauschii chromosome 4,using bin-mapped 4D ESTs as a common reference. The virtual order showed a higher collinearity withhomeologous 4B compared to 4A. Additionally, a virtual map was constructed and ∼5700 genes (∼2200on 4DS and ∼3500 on 4DL) predicted. The sequence and virtual order obtained here using the 454 platformwere compared with the Illumina one used by the IWGSC, giving complementary information.
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IEB authors: Jaroslav Doležel, Hana Šimková, Miroslav Valárik