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

Jin Xiao,Xiue Wang,Lian Fu,Chunyan Yu,Haiyan Wang,Jan Vrána,Yufeng Wu,Michael Abrouk,Jaroslav Doležel,Haojie Sun,Wentao Wan,Jing Zhao,Keli Dai,Marie Kubaláková

doi:10.1186/s12864-017-4211-7

Abstract

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.

Highlights

Haynaldia villosa (H. villosa) has been recognized as a species potentially useful for wheat improvement
Purity in the sorted fractions was determined after fluorescence in situ hybridization (FISH) with two probes on sorted chromosomes spread on the microscope slides
Identification of syntenic regions in Brachypodium, rice and sorghum To identify syntenic regions in the three model genomes, all the 1977 gene sequences predicted from H. villosa chromosome 4VS scaffolds were compared by blastn search against the coding sequence (CDS) database of Brachypodium, rice and sorghum

Summary

Results

Shotgun sequencing and assembling of H. villosa chromosome 4VS The DAPI-based flow karyotypes of wheat-H. villosa ditelosomic addition line Dt4VS showed 5 peaks (Fig. 1). Non-protein coding DNA sequences A total of 386 different putative miRNAs and 121 tRNA genes were identified in the 4VS scaffolds (Table 2). The detailed criterions were described in the Material and Methods Using both Ab initio and evidence-based gene predictions, we identified a total of 1977 high-confidence protein-coding loci on 1069 scaffolds of chromosome 4VS (Table 2; Additional file 2: Table S2). After filtering (Materials and Methods), a total of 942 out of these 1977 (47.6%) 4VS evidenced genes had blastn hits to the genes in at least one of three species Brachypodium, rice and sorghum, with gene number of 922, 878 and 890, respectively (Additional file 3: Figure S3A). By taking the advantage of the release of Ae. tauschii genetic map, we generated a “genome zipper” containing 1137 4VS genes by referring to 4D scaffolds which was anchored to chromosome 4D of Ae. tauschii (Additional file 2: Table S4). Our work provides an example for genome sequencing of the remained H. villosa chromosomes

Conclusions

Background

Methods

Conclusion