PuSH - Publikationsserver des Helmholtz Zentrums München

Helguera, E.* ; Rivarola, M.* ; Clavijo, B.J.* ; Martis, M.M. ; Vanzetti, L.S.* ; González, S.* ; Garbus, I.* ; Leroy, P.* ; Šimková, H.* ; Valárik, M.* ; Caccamo, M.* ; Dolezel, J.* ; Mayer, K.F.X. ; Feuillet, C.* ; Tranquilli, G.E.* ; Paniego, N.B.* ; Echenique, V.C.*

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

Plant Sci. 233, 200-212 (2015)
Verlagsversion DOI PMC
Open Access Gold (Paid Option)
Creative Commons Lizenzvertrag
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.
Altmetric
Weitere Metriken?
[➜Einloggen]
Zusatzinfos bearbeiten [➜Einloggen]
Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Korrespondenzautor
Schlagwörter Chromosome 4d Survey Sequence ; Gene Annotation ; Gene Content ; Synteny ; Triticum Aestivum ; Virtual Gene Order; Streak Mosaic-virus; Nuclear-dna Amounts; Polyploid Wheat; Physical Map; Comparative Genomics; Aegilops-tauschii; Open Software; Draft Genome; Common Wheat; Stripe Rust
ISSN (print) / ISBN 0168-9452
e-ISSN 0168-9452
Zeitschrift Plant Science
Quellenangaben Band: 233, Heft: , Seiten: 200-212 Artikelnummer: , Supplement: ,
Verlag Elsevier
Verlagsort Clare
Nichtpatentliteratur Publikationen
Begutachtungsstatus Peer reviewed
Institut(e) Research Unit Plant Genome and Systems Biology (PGSB)