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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...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
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.
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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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