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

BMC Genomics

Research Article

Jan Vrána¹  Marie Kubaláková¹  Jaroslav Doležel¹  Michael Abrouk¹  Jing Zhao²  Yufeng Wu²  Haojie Sun²  Jin Xiao²  Keli Dai²  Lian Fu²  Haiyan Wang²  Wentao Wan²  Chunyan Yu²  Xiue Wang² 

[1] Institute of Experimental Botany, Centre of the Haná Region for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-783671, Olomouc, Czech Republic;State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, 210095, Nanjing, China;

关键词: Haynaldia villosa;    Flow sorting;    Chromosome arm 4VS;    Scaffold;    Genome zipper;   

DOI  :  10.1186/s12864-017-4211-7

 received in 2017-01-22, accepted in 2017-10-12,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundHaynaldia villosa (H. villosa) has been recognized as a species potentially useful for wheat improvement. The availability of its genomic sequences will boost its research and application.ResultsIn 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.ConclusionsThe sequences provided valuable information for mapping and positional-cloning genes located on 4VS, such as the wheat yellow mosaic virus resistance gene Wss1. The work on 4VS provided detailed insights into the genome of H. villosa, and may also serve as a model for sequencing the remaining parts of H. villosa genome.

【 授权许可】

CC BY   
© The Author(s). 2017