UZH-Logo

Maintenance Infos

The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution


Raats, Dina; Frenkel, Zeev; Krugman, Tamar; Dodek, Itay; Sela, Hanan; Šimková, Hana; Magni, Federica; Cattonaro, Federica; Vautrin, Sonia; Bergès, Hélène; Wicker, Thomas; Keller, Beat; Leroy, Philippe; Philippe, Romain; Paux, Etienne; Doležel, Jaroslav; Feuillet, Catherine; Korol, Abraham; Fahima, Tzion (2013). The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution. Genome Biology, 14(12):R138.

Abstract

BACKGROUND: The wheat genome sequence is an essential tool for advanced genomic research and improvements. The generation of a high-quality wheat genome sequence is challenging due to its complex 17 Gb polyploid genome. To overcome these difficulties, sequencing through the construction of BAC-based physical maps of individual chromosomes is employed by the wheat genomics community. Here, we present the construction of the first comprehensive physical map of chromosome 1BS, and illustrate its unique gene space organization and evolution. RESULTS: Fingerprinted BAC clones were assembled into 57 long scaffolds, anchored and ordered with 2,438 markers covering 83% of chromosome 1BS. The BAC-based chromosome 1BS physical map and gene order of the orthologous regions of model grass species were consistent, providing strong support for the reliability of the chromosome 1BS assembly. Chromosome 1BS gene space spans the entire length of the chromosome arm, with 76% of the genes organized in small gene-islands, accompanied by a two fold increase in gene density from the centromere to the telomere. CONCLUSIONS: This study provides new evidence on common and chromosome-specific features in the organization and evolution of the wheat genome, including a non-uniform distribution of gene density along the centromere-telomere axis, abundance of non-syntenic genes, the degree of colinearity with other grass genomes, and a non-uniform size expansion along the centromere-telomere axis, compared with other model cereal genomes. The high quality physical map constructed in this study provides a solid basis for the assembly of a reference sequence of chromosome 1BS and for breeding applications.

BACKGROUND: The wheat genome sequence is an essential tool for advanced genomic research and improvements. The generation of a high-quality wheat genome sequence is challenging due to its complex 17 Gb polyploid genome. To overcome these difficulties, sequencing through the construction of BAC-based physical maps of individual chromosomes is employed by the wheat genomics community. Here, we present the construction of the first comprehensive physical map of chromosome 1BS, and illustrate its unique gene space organization and evolution. RESULTS: Fingerprinted BAC clones were assembled into 57 long scaffolds, anchored and ordered with 2,438 markers covering 83% of chromosome 1BS. The BAC-based chromosome 1BS physical map and gene order of the orthologous regions of model grass species were consistent, providing strong support for the reliability of the chromosome 1BS assembly. Chromosome 1BS gene space spans the entire length of the chromosome arm, with 76% of the genes organized in small gene-islands, accompanied by a two fold increase in gene density from the centromere to the telomere. CONCLUSIONS: This study provides new evidence on common and chromosome-specific features in the organization and evolution of the wheat genome, including a non-uniform distribution of gene density along the centromere-telomere axis, abundance of non-syntenic genes, the degree of colinearity with other grass genomes, and a non-uniform size expansion along the centromere-telomere axis, compared with other model cereal genomes. The high quality physical map constructed in this study provides a solid basis for the assembly of a reference sequence of chromosome 1BS and for breeding applications.

Citations

16 citations in Web of Science®
18 citations in Scopus®
Google Scholar™

Altmetrics

Downloads

148 downloads since deposited on 09 Jan 2014
57 downloads since 12 months
Detailed statistics

Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Department of Plant and Microbial Biology
Dewey Decimal Classification:580 Plants (Botany)
Language:English
Date:2013
Deposited On:09 Jan 2014 09:59
Last Modified:14 Nov 2016 11:46
Publisher:BioMed Central
ISSN:1465-6906
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1186/gb-2013-14-12-r138
PubMed ID:24359668
Permanent URL: https://doi.org/10.5167/uzh-88009

Download

[img]
Preview
Content: Accepted Version
Filetype: PDF
Size: 717kB
View at publisher
[img]
Preview
Content: Published Version
Filetype: PDF
Size: 1MB
Licence: Creative Commons: Attribution 2.0 Generic (CC BY 2.0)

TrendTerms

TrendTerms displays relevant terms of the abstract of this publication and related documents on a map. The terms and their relations were extracted from ZORA using word statistics. Their timelines are taken from ZORA as well. The bubble size of a term is proportional to the number of documents where the term occurs. Red, orange, yellow and green colors are used for terms that occur in the current document; red indicates high interlinkedness of a term with other terms, orange, yellow and green decreasing interlinkedness. Blue is used for terms that have a relation with the terms in this document, but occur in other documents.
You can navigate and zoom the map. Mouse-hovering a term displays its timeline, clicking it yields the associated documents.

Author Collaborations