Sequencing flow-sorted short arm of Haynaldia villosa chromosome 4V provides insights into its molecular structure and virtual gene order

0481223 - ÚEB 2018 RIV GB eng J - Journal Article
Xiao, J. - Dai, K. - Fu, S. - Vrána, Jan - Kubaláková, Marie - Wan, W. - Sun, H. - Zhao, J. - Yu, C. - Wu, Y. - Abrouk, Michael - Wang, H. - Doležel, Jaroslav - Wang, X.
Sequencing flow-sorted short arm of Haynaldia villosa chromosome 4V provides insights into its molecular structure and virtual gene order.
BMC Genomics. Roč. 18, č. 1 (2017), č. článku 791. ISSN 1471-2164. E-ISSN 1471-2164
R&D Projects: GA MŠMT(CZ) LO1204; GA ČR GBP501/12/G090
Institutional support: RVO:61389030
Keywords : Chromosome arm 4VS * Flow sorting * Genome zipper * Haynaldia villosa * Scaffold
OECD category: Plant sciences, botany
Impact factor: 3.730, year: 2017

In this work, the short arm of H. villosa chromosome 4V (4VS) was sorted by flow cytometry and sequenced using Illumina platform. About 170.6 Mb assembled sequences were obtained. Further analysis showed that repetitive elements accounted for about 64.6% of 4VS, while the coding fraction, which is corresponding to 1977 annotated genes, represented 1.5% of the arm. The syntenic regions of the 4VS were searched and identified on wheat group 4 chromosomes 4AL, 4BS, 4DS, Brachypodium chromosomes 1 and 4, rice chromosomes 3 and 11, and sorghum chromosomes 1, 5 and 8. Based on genome-zipper analysis, a virtual gene order comprising 735 gene loci on 4VS genome was built by referring to the Brachypodium genome, which was relatively consistent with the scaffold order determined for Ae. tauschii chromosome 4D. The homologous alleles of several cloned genes on wheat group 4 chromosomes including Rht-1 gene were identified.
Permanent Link: http://hdl.handle.net/11104/0276821