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

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

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

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.

Original languageEnglish
Article number595
JournalBMC Genomics
Volume16
Issue number1
DOIs
Publication statusPublished - Aug 12 2015

Fingerprint

Bacterial Artificial Chromosomes
Triticum
Chromosomes
Radiation Hybrid Mapping
Genome
Nucleolus Organizer Region
Gene Order
Centromere
Clone Cells

Keywords

  • BAC physical map
  • Centromere
  • Chromosomal rearrangement
  • Chromosome 6B
  • DNA marker
  • Gene order
  • Nucleolus organizer region
  • RH map
  • Synteny
  • Wheat

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Kobayashi, F., Wu, J., Kanamori, H., Tanaka, T., Katagiri, S., Karasawa, W., ... Handa, H. (2015). A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B. BMC Genomics, 16(1), [595]. https://doi.org/10.1186/s12864-015-1803-y

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.

In: BMC Genomics, Vol. 16, No. 1, 595, 12.08.2015.

Research output: Contribution to journalArticle

Kobayashi, F, Wu, J, Kanamori, H, Tanaka, T, Katagiri, S, Karasawa, W, Kaneko, S, Watanabe, S, Sakaguchi, T, Hanawa, Y, Fujisawa, H, Kurita, K, Abe, C, Iehisa, JCM, Ohno, R, Šafář, J, Šimková, H, Mukai, Y, Hamada, M, Saito, M, Ishikawa, G, Katayose, Y, Endo, TR, Takumi, S, Nakamura, T, Sato, K, Ogihara, Y, Hayakawa, K, Doležel, J, Nasuda, S, Matsumoto, T & Handa, H 2015, 'A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B', BMC Genomics, vol. 16, no. 1, 595. https://doi.org/10.1186/s12864-015-1803-y
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. In: BMC Genomics. 2015 ; Vol. 16, No. 1.
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AU - Kobayashi, Fuminori

AU - Wu, Jianzhong

AU - Kanamori, Hiroyuki

AU - Tanaka, Tsuyoshi

AU - Katagiri, Satoshi

AU - Karasawa, Wataru

AU - Kaneko, Satoko

AU - Watanabe, Shota

AU - Sakaguchi, Toyotaka

AU - Hanawa, Yumiko

AU - Fujisawa, Hiroko

AU - Kurita, Kanako

AU - Abe, Chikako

AU - Iehisa, Julio C M

AU - Ohno, Ryoko

AU - Šafář, Jan

AU - Šimková, Hana

AU - Mukai, Yoshiyuki

AU - Hamada, Masao

AU - Saito, Mika

AU - Ishikawa, Goro

AU - Katayose, Yuichi

AU - Endo, Takashi R.

AU - Takumi, Shigeo

AU - Nakamura, Toshiki

AU - Sato, Kazuhiro

AU - Ogihara, Yasunari

AU - Hayakawa, Katsuyuki

AU - Doležel, Jaroslav

AU - Nasuda, Shuhei

AU - Matsumoto, Takashi

AU - Handa, Hirokazu

PY - 2015/8/12

Y1 - 2015/8/12

N2 - 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.

AB - 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.

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KW - Chromosomal rearrangement

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KW - DNA marker

KW - Gene order

KW - Nucleolus organizer region

KW - RH map

KW - Synteny

KW - Wheat

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