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

F. Kobayashi, J. Wu, H. Kanamori, T. Tanaka, S. Katagiri, W. Karasawa, S. Kaneko, S. Watanabe, T. Sakaguchi, Y. Hanawa, H. Fujisawa, K. Kurita, C. Abe, JC. Iehisa, R. Ohno, J. Šafář, H. Šimková, Y. Mukai, M. Hamada, M. Saito, G. Ishikawa, Y....

. 2015 ; 16 (-) : 595. [pub] 20150812

Jazyk angličtina Země Anglie, Velká Británie

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/bmc16020403

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.

Citace poskytuje Crossref.org

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$a Kobayashi, Fuminori $u Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. kobafumi@affrc.go.jp.
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$a A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B / $c F. Kobayashi, J. Wu, H. Kanamori, T. Tanaka, S. Katagiri, W. Karasawa, S. Kaneko, S. Watanabe, T. Sakaguchi, Y. Hanawa, H. Fujisawa, K. Kurita, C. Abe, JC. Iehisa, R. Ohno, J. Šafář, H. Šimková, Y. Mukai, M. Hamada, M. Saito, G. Ishikawa, Y. Katayose, TR. Endo, S. Takumi, T. Nakamura, K. Sato, Y. Ogihara, K. Hayakawa, J. Doležel, S. Nasuda, T. Matsumoto, H. Handa,
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$a 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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$a Wu, Jianzhong $u Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. jzwu@nias.affrc.go.jp. Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. jzwu@nias.affrc.go.jp.
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$a Kanamori, Hiroyuki $u Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. kanamo@affrc.go.jp.
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$a Tanaka, Tsuyoshi $u Bioinformatics Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. tstanaka@affrc.go.jp.
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$a Karasawa, Wataru $u Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. wkarasawa@affrc.go.jp.
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$a Kaneko, Satoko $u Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan. kaneko_satoko@soken.ac.jp.
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$a Watanabe, Shota $u Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan. watahoshida@gmail.com.
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$a Sakaguchi, Toyotaka $u Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan. ts610821@hotmail.co.jp.
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$a Fujisawa, Hiroko $u Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. fujisawah@affrc.go.jp.
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$a Iehisa, Julio C M $u Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan. masaru_ie@hotmail.com.
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$a Ohno, Ryoko $u Core Research Division, Organization of Advanced Science and Technology, Kobe University, Kobe, 657-8501, Japan. ryohno@people.kobe-u.ac.jp.
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$a Šafář, Jan $u Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ-78371, Olomouc, Czech Republic. safar@ueb.cas.cz.
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$a Saito, Mika $u Wheat Breeding Group, NARO Tohoku Agricultural Research Center, Morioka, 020-0198, Japan. saitom@affrc.go.jp.
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$a Ishikawa, Goro $u Wheat Breeding Group, NARO Tohoku Agricultural Research Center, Morioka, 020-0198, Japan. goro@affrc.go.jp.
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$a Katayose, Yuichi $u Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. katayose@affrc.go.jp.
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$a Endo, Takashi R $u Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan. endo.takashi.2e@gmail.com.
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$a Doležel, Jaroslav $u Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ-78371, Olomouc, Czech Republic. dolezel@ueb.cas.cz.
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