Number of the records: 1
New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing
- 1.
SYSNO ASEP 0446524 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing Author(s) Helguera, M. (AR)
Rivarola, M. (AR)
Clavijo, B. (GB)
Martis, M.M. (DE)
Vanzetti, L.S. (AR)
Gonzalez, S. (AR)
Garbus, I. (AR)
LeRoy, P. (FR)
Šimková, Hana (UEB-Q) RID, ORCID
Valárik, Miroslav (UEB-Q) RID, ORCID
Caccamo, M. (GB)
Doležel, Jaroslav (UEB-Q) RID, ORCID
Mayer, K. F. X. (DE)
Feuillet, C. (US)
Tranquilli, G. (AR)
Paniego, N. (AR)
Echenique, V. (AR)Source Title Plant Science. - : Elsevier - ISSN 0168-9452
Roč. 233, APR 2015 (2015), s. 200-212Number of pages 13 s. Language eng - English Country IE - Ireland Keywords Chromosome 4D survey sequence ; Gene annotation ; Gene content Subject RIV EB - Genetics ; Molecular Biology R&D Projects GBP501/12/G090 GA ČR - Czech Science Foundation (CSF) LO1204 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) Institutional support UEB-Q - RVO:61389030 UT WOS 000351247300020 DOI 10.1016/j.plantsci.2014.12.004 Annotation 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 (7.2x) and 4DL (4.1x) 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 similar to 5700 genes (similar to 2200 on 4DS and similar to 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. Workplace Institute of Experimental Botany Contact David Klier, knihovna@ueb.cas.cz, Tel.: 220 390 469 Year of Publishing 2016
Number of the records: 1