Dataset Information

A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B.

ABSTRACT: A complete genome sequence is an essential tool for the genetic improvement of wheat. Because the wheat genome is large, highly repetitive and complex due to its allohexaploid nature, the International Wheat Genome Sequencing Consortium (IWGSC) chose a strategy that involves constructing bacterial artificial chromosome (BAC)-based physical maps of individual chromosomes and performing BAC-by-BAC sequencing. Here, we report the construction of a physical map of chromosome 6B with the goal of revealing the structural features of the third largest chromosome in wheat.We assembled 689 informative BAC contigs (hereafter reffered to as contigs) representing 91% of the entire physical length of wheat chromosome 6B. The contigs were integrated into a radiation hybrid (RH) map of chromosome 6B, with one linkage group consisting of 448 loci with 653 markers. The order and direction of 480 contigs, corresponding to 87% of the total length of 6B, were determined. We also characterized the contigs that contained a part of the nucleolus organizer region or centromere based on their positions on the RH map and the assembled BAC clone sequences. Analysis of the virtual gene order along 6B using the information collected for the integrated map revealed the presence of several chromosomal rearrangements, indicating evolutionary events that occurred on chromosome 6B.We constructed a reliable physical map of chromosome 6B, enabling us to analyze its genomic structure and evolutionary progression. More importantly, the physical map should provide a high-quality and map-based reference sequence that will serve as a resource for wheat chromosome 6B.

SUBMITTER: Kobayashi F

PROVIDER: S-EPMC4534020 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B.

Kobayashi Fuminori F Wu Jianzhong J Kanamori Hiroyuki H Tanaka Tsuyoshi T Katagiri Satoshi S Karasawa Wataru W Kaneko Satoko S Watanabe Shota S Sakaguchi Toyotaka T Hanawa Yumiko Y Fujisawa Hiroko H Kurita Kanako K Abe Chikako C Iehisa Julio C M JC Ohno Ryoko R Šafář Jan J Šimková Hana H Mukai Yoshiyuki Y Hamada Masao M Saito Mika M Ishikawa Goro G Katayose Yuichi Y Endo Takashi R TR Takumi Shigeo S Nakamura Toshiki T Sato Kazuhiro K Ogihara Yasunari Y Hayakawa Katsuyuki K Doležel Jaroslav J Nasuda Shuhei S Matsumoto Takashi T Handa Hirokazu H

BMC genomics 20150812

<h4>Background</h4>A complete genome sequence is an essential tool for the genetic improvement of wheat. Because the wheat genome is large, highly repetitive and complex due to its allohexaploid nature, the International Wheat Genome Sequencing Consortium (IWGSC) chose a strategy that involves constructing bacterial artificial chromosome (BAC)-based physical maps of individual chromosomes and performing BAC-by-BAC sequencing. Here, we report the construction of a physical map of chromosome 6B wi ...[more]

PMID: 26265254

Similar Datasets

Project description:BackgroundThe Hessian fly (Mayetiola destructor) is an important insect pest of wheat. It has tractable genetics, polytene chromosomes, and a small genome (158 Mb). Investigation of the Hessian fly presents excellent opportunities to study plant-insect interactions and the molecular mechanisms underlying genome imprinting and chromosome elimination. A physical map is needed to improve the ability to perform both positional cloning and comparative genomic analyses with the fully sequenced genomes of other dipteran species.ResultsAn FPC-based genome wide physical map of the Hessian fly was constructed and anchored to the insect's polytene chromosomes. Bacterial artificial chromosome (BAC) clones corresponding to 12-fold coverage of the Hessian fly genome were fingerprinted, using high information content fingerprinting (HIFC) methodology, and end-sequenced. Fluorescence in situ hybridization (FISH) co-localized two BAC clones from each of the 196 longest contigs on the polytene chromosomes. An additional 70 contigs were positioned using a single FISH probe. The 266 FISH mapped contigs were evenly distributed and covered 60% of the genome (95,668 kb). The ends of the fingerprinted BACs were then sequenced to develop the capacity to create sequenced tagged site (STS) markers on the BACs in the map. Only 3.64% of the BAC-end sequence was composed of transposable elements, helicases, ribosomal repeats, simple sequence repeats, and sequences of low complexity. A relatively large fraction (14.27%) of the BES was comprised of multi-copy gene sequences. Nearly 1% of the end sequence was composed of simple sequence repeats (SSRs).ConclusionThis physical map provides the foundation for high-resolution genetic mapping, map-based cloning, and assembly of complete genome sequencing data. The results indicate that restriction fragment length heterogeneity in BAC libraries used to construct physical maps lower the length and the depth of the contigs, but is not an absolute barrier to the successful application of the technology. This map will serve as a genomic resource for accelerating gene discovery, genome sequencing, and the assembly of BAC sequences. The Hessian fly BAC-clone assembly, and the names and positions of the BAC clones used in the FISH experiments are publically available at (http://genome.purdue.edu/WebAGCoL/Hfly/WebFPC/).

Dataset Information

A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B.

Publications

A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets