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Sequencing flow-sorted short arm of Haynaldia villosa chromosome 4V provides insights into its molecular structure and virtual gene order.
BMC Genomics. 2017 Oct 16; 18(1):791.BG

Abstract

BACKGROUND

Haynaldia 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.

RESULTS

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.

CONCLUSIONS

The 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.

Authors+Show Affiliations

State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China.Institute of Experimental Botany, Centre of the Haná Region for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-783671, Olomouc, Czech Republic.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, Nanjing, 210095, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China.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, Nanjing, 210095, China.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, Nanjing, 210095, China. xiuew@njau.edu.cn.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

29037165

Citation

Xiao, Jin, et al. "Sequencing Flow-sorted Short Arm of Haynaldia Villosa Chromosome 4V Provides Insights Into Its Molecular Structure and Virtual Gene Order." BMC Genomics, vol. 18, no. 1, 2017, p. 791.
Xiao J, Dai K, Fu L, et al. Sequencing flow-sorted short arm of Haynaldia villosa chromosome 4V provides insights into its molecular structure and virtual gene order. BMC Genomics. 2017;18(1):791.
Xiao, J., Dai, K., Fu, L., Vrána, J., Kubaláková, M., Wan, W., Sun, H., Zhao, J., Yu, C., Wu, Y., Abrouk, M., Wang, H., Doležel, J., & Wang, X. (2017). Sequencing flow-sorted short arm of Haynaldia villosa chromosome 4V provides insights into its molecular structure and virtual gene order. BMC Genomics, 18(1), 791. https://doi.org/10.1186/s12864-017-4211-7
Xiao J, et al. Sequencing Flow-sorted Short Arm of Haynaldia Villosa Chromosome 4V Provides Insights Into Its Molecular Structure and Virtual Gene Order. BMC Genomics. 2017 Oct 16;18(1):791. PubMed PMID: 29037165.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Sequencing flow-sorted short arm of Haynaldia villosa chromosome 4V provides insights into its molecular structure and virtual gene order. AU - Xiao,Jin, AU - Dai,Keli, AU - Fu,Lian, AU - Vrána,Jan, AU - Kubaláková,Marie, AU - Wan,Wentao, AU - Sun,Haojie, AU - Zhao,Jing, AU - Yu,Chunyan, AU - Wu,Yufeng, AU - Abrouk,Michael, AU - Wang,Haiyan, AU - Doležel,Jaroslav, AU - Wang,Xiue, Y1 - 2017/10/16/ PY - 2017/01/22/received PY - 2017/10/12/accepted PY - 2017/10/18/entrez PY - 2017/10/19/pubmed PY - 2018/5/19/medline KW - Chromosome arm 4VS KW - Flow sorting KW - Genome zipper KW - Haynaldia villosa KW - Scaffold SP - 791 EP - 791 JF - BMC genomics JO - BMC Genomics VL - 18 IS - 1 N2 - BACKGROUND: Haynaldia 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. RESULTS: 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. CONCLUSIONS: The 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. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/29037165/Sequencing_flow_sorted_short_arm_of_Haynaldia_villosa_chromosome_4V_provides_insights_into_its_molecular_structure_and_virtual_gene_order_ L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4211-7 DB - PRIME DP - Unbound Medicine ER -