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

Abstract
Survey sequencing of the bread wheat (Triticum aestivum L.) genome (AABBDD) has been approached through different strategies delivering important information. However, the current wheat sequence knowledge is not complete. The aim of our study is to provide different and complementary set of data for chromosome 4D. A survey sequence was obtained by pyrosequencing of flow-sorted 4DS (7.2×) and 4DL (4.1×) arms. Single ends (SE) and long mate pairs (LMP) [ver mas...]
Survey sequencing of the bread wheat (Triticum aestivum L.) genome (AABBDD) has been approached through different strategies delivering important information. However, the current wheat sequence knowledge is not complete. The aim of our study is to provide different and complementary set of data for chromosome 4D. A survey sequence was obtained by pyrosequencing of flow-sorted 4DS (7.2×) and 4DL (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 chromosome 4. Scaffolds annotation rendered 822 gene models. A virtual gene order comprising 1973 wheat orthologous gene loci and 381 wheat gene models was built. This order was largely consistent with the scaffold 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 with homeologous 4B compared to 4A. Additionally, a virtual map was constructed and ∼5700 genes (∼2200 on 4DS and ∼3500 on 4DL) predicted. The sequence and virtual order obtained here using the 454 platform were compared with the Illumina one used by the IWGSC, giving complementary information [Cerrar]
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Author
Helguera, Marcelo;   Rivarola, Maximo Lisandro;   Clavijo, Bernardo;   Martis, Mihaela M.;   Vanzetti, Leonardo Sebastian;   Gonzalez, Sergio Alberto;   Garbus, Ingrid;   Leroy, Phillippe;   Simková, Hana;   Valárik, Miroslav;   Caccamo, Mario;   Dolezel, Jaroslav;   Mayer, Klaus F.X.;   Feuillet, Catherine;   Tranquilli, Gabriela;   Paniego, Norma Beatriz;   Echenique, Carmen Viviana;  
Fuente
Plant science 233 : 200-212. (Apr. 2015)
Date
2015
ISSN
0168-9452
URI
http://hdl.handle.net/20.500.12123/1142
https://www.sciencedirect.com/science/article/pii/S016894521400291X?via%3Dihub
DOI
https://doi.org/10.1016/j.plantsci.2014.12.004
Formato
pdf
Tipo de documento
artículo
Palabras Claves
Trigo; Triticum Aestivum; Genes; Cromosomas; Chromosomes; Cromosoma 4 D;
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Excepto donde se diga explicitamente, este item se publica bajo la siguiente descripción: Creative Commons Attribution-NonCommercial-ShareAlike 2.5 Unported (CC BY-NC-SA 2.5)
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