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A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B
BACKGROUND: 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...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4534020/ https://www.ncbi.nlm.nih.gov/pubmed/26265254 http://dx.doi.org/10.1186/s12864-015-1803-y |
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author | Kobayashi, Fuminori Wu, Jianzhong Kanamori, Hiroyuki Tanaka, Tsuyoshi Katagiri, Satoshi Karasawa, Wataru Kaneko, Satoko Watanabe, Shota Sakaguchi, Toyotaka Hanawa, Yumiko Fujisawa, Hiroko Kurita, Kanako Abe, Chikako Iehisa, Julio C. M. Ohno, Ryoko Šafář, Jan Šimková, Hana Mukai, Yoshiyuki Hamada, Masao Saito, Mika Ishikawa, Goro Katayose, Yuichi Endo, Takashi R. Takumi, Shigeo Nakamura, Toshiki Sato, Kazuhiro Ogihara, Yasunari Hayakawa, Katsuyuki Doležel, Jaroslav Nasuda, Shuhei Matsumoto, Takashi Handa, Hirokazu |
author_facet | Kobayashi, Fuminori Wu, Jianzhong Kanamori, Hiroyuki Tanaka, Tsuyoshi Katagiri, Satoshi Karasawa, Wataru Kaneko, Satoko Watanabe, Shota Sakaguchi, Toyotaka Hanawa, Yumiko Fujisawa, Hiroko Kurita, Kanako Abe, Chikako Iehisa, Julio C. M. Ohno, Ryoko Šafář, Jan Šimková, Hana Mukai, Yoshiyuki Hamada, Masao Saito, Mika Ishikawa, Goro Katayose, Yuichi Endo, Takashi R. Takumi, Shigeo Nakamura, Toshiki Sato, Kazuhiro Ogihara, Yasunari Hayakawa, Katsuyuki Doležel, Jaroslav Nasuda, Shuhei Matsumoto, Takashi Handa, Hirokazu |
author_sort | Kobayashi, Fuminori |
collection | PubMed |
description | BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1803-y) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4534020 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-45340202015-08-13 A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B Kobayashi, Fuminori Wu, Jianzhong Kanamori, Hiroyuki Tanaka, Tsuyoshi Katagiri, Satoshi Karasawa, Wataru Kaneko, Satoko Watanabe, Shota Sakaguchi, Toyotaka Hanawa, Yumiko Fujisawa, Hiroko Kurita, Kanako Abe, Chikako Iehisa, Julio C. M. Ohno, Ryoko Šafář, Jan Šimková, Hana Mukai, Yoshiyuki Hamada, Masao Saito, Mika Ishikawa, Goro Katayose, Yuichi Endo, Takashi R. Takumi, Shigeo Nakamura, Toshiki Sato, Kazuhiro Ogihara, Yasunari Hayakawa, Katsuyuki Doležel, Jaroslav Nasuda, Shuhei Matsumoto, Takashi Handa, Hirokazu BMC Genomics Research Article BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1803-y) contains supplementary material, which is available to authorized users. BioMed Central 2015-08-12 /pmc/articles/PMC4534020/ /pubmed/26265254 http://dx.doi.org/10.1186/s12864-015-1803-y Text en © Kobayashi et al. 2015 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Kobayashi, Fuminori Wu, Jianzhong Kanamori, Hiroyuki Tanaka, Tsuyoshi Katagiri, Satoshi Karasawa, Wataru Kaneko, Satoko Watanabe, Shota Sakaguchi, Toyotaka Hanawa, Yumiko Fujisawa, Hiroko Kurita, Kanako Abe, Chikako Iehisa, Julio C. M. Ohno, Ryoko Šafář, Jan Šimková, Hana Mukai, Yoshiyuki Hamada, Masao Saito, Mika Ishikawa, Goro Katayose, Yuichi Endo, Takashi R. Takumi, Shigeo Nakamura, Toshiki Sato, Kazuhiro Ogihara, Yasunari Hayakawa, Katsuyuki Doležel, Jaroslav Nasuda, Shuhei Matsumoto, Takashi Handa, Hirokazu A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B |
title | A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B |
title_full | A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B |
title_fullStr | A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B |
title_full_unstemmed | A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B |
title_short | A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B |
title_sort | high-resolution physical map integrating an anchored chromosome with the bac physical maps of wheat chromosome 6b |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4534020/ https://www.ncbi.nlm.nih.gov/pubmed/26265254 http://dx.doi.org/10.1186/s12864-015-1803-y |
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