A BAC-based integrated linkage map of the silkworm Bombyx mori

Kimiko Yamamoto, Junko Nohata, Keiko Kadono-Okuda, Junko Narukawa, Motoe Sasanuma, Shun Ichi Sasanuma, Hiroshi Minami, Michihiko Shimomura, Yoshitaka Suetsugu, Yutaka Banno, Kazutoyo Osoegawa, Pieter J. de Jong, Marian R. Goldsmith, Kazuei Mita

研究成果: ジャーナルへの寄稿記事

77 引用 (Scopus)

抄録

Background: In 2004, draft sequences of the model lepidopteran Bombyx mori were reported using whole-genome shotgun sequencing. Because of relatively shallow genome coverage, the silkworm genome remains fragmented, hampering annotation and comparative genome studies. For a more complete genome analysis, we developed extended scaffolds combining physical maps with improved genetic maps. Results: We mapped 1,755 single nucleotide polymorphism (SNP) markers from bacterial artificial chromosome (BAC) end sequences onto 28 linkage groups using a recombining male backcross population, yielding an average inter-SNP distance of 0.81 cM (about 270 kilobases). We constructed 6,221 contigs by fingerprinting clones from three BAC libraries digested with different restriction enzymes, and assigned a total of 724 single copy genes to them by BLAST (basic local alignment search tool) search of the BAC end sequences and high-density BAC filter hybridization using expressed sequence tags as probes. We assigned 964 additional expressed sequence tags to linkage groups by restriction fragment length polymorphism analysis of a nonrecombining female backcross population. Altogether, 361.1 megabases of BAC contigs and singletons were integrated with a map containing 1,688 independent genes. A test of synteny using Oxford grid analysis with more than 500 silkworm genes revealed six versus 20 silkworm linkage groups containing eight or more orthologs of Apis versus Tribolium, respectively. Conclusion: The integrated map contains approximately 10% of predicted silkworm genes and has an estimated 76% genome coverage by BACs. This provides a new resource for improved assembly of whole-genome shotgun data, gene annotation and positional cloning, and will serve as a platform for comparative genomics and gene discovery in Lepidoptera and other insects.

元の言語英語
記事番号R21
ジャーナルGenome biology
9
発行部数1
DOI
出版物ステータス出版済み - 1 28 2008

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Bacterial Artificial Chromosomes
bacterial artificial chromosomes
Bombyx
Bombyx mori
silkworms
chromosome mapping
chromosome
genome
Genome
gene
linkage groups
polymorphism
Expressed Sequence Tags
Firearms
expressed sequence tags
genes
single nucleotide polymorphism
Genes
Single Nucleotide Polymorphism
molecular cloning

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

これを引用

Yamamoto, K., Nohata, J., Kadono-Okuda, K., Narukawa, J., Sasanuma, M., Sasanuma, S. I., ... Mita, K. (2008). A BAC-based integrated linkage map of the silkworm Bombyx mori. Genome biology, 9(1), [R21]. https://doi.org/10.1186/gb-2008-9-1-r21

A BAC-based integrated linkage map of the silkworm Bombyx mori. / Yamamoto, Kimiko; Nohata, Junko; Kadono-Okuda, Keiko; Narukawa, Junko; Sasanuma, Motoe; Sasanuma, Shun Ichi; Minami, Hiroshi; Shimomura, Michihiko; Suetsugu, Yoshitaka; Banno, Yutaka; Osoegawa, Kazutoyo; de Jong, Pieter J.; Goldsmith, Marian R.; Mita, Kazuei.

:: Genome biology, 巻 9, 番号 1, R21, 28.01.2008.

研究成果: ジャーナルへの寄稿記事

Yamamoto, K, Nohata, J, Kadono-Okuda, K, Narukawa, J, Sasanuma, M, Sasanuma, SI, Minami, H, Shimomura, M, Suetsugu, Y, Banno, Y, Osoegawa, K, de Jong, PJ, Goldsmith, MR & Mita, K 2008, 'A BAC-based integrated linkage map of the silkworm Bombyx mori', Genome biology, 巻. 9, 番号 1, R21. https://doi.org/10.1186/gb-2008-9-1-r21
Yamamoto K, Nohata J, Kadono-Okuda K, Narukawa J, Sasanuma M, Sasanuma SI その他. A BAC-based integrated linkage map of the silkworm Bombyx mori. Genome biology. 2008 1 28;9(1). R21. https://doi.org/10.1186/gb-2008-9-1-r21
Yamamoto, Kimiko ; Nohata, Junko ; Kadono-Okuda, Keiko ; Narukawa, Junko ; Sasanuma, Motoe ; Sasanuma, Shun Ichi ; Minami, Hiroshi ; Shimomura, Michihiko ; Suetsugu, Yoshitaka ; Banno, Yutaka ; Osoegawa, Kazutoyo ; de Jong, Pieter J. ; Goldsmith, Marian R. ; Mita, Kazuei. / A BAC-based integrated linkage map of the silkworm Bombyx mori. :: Genome biology. 2008 ; 巻 9, 番号 1.
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abstract = "Background: In 2004, draft sequences of the model lepidopteran Bombyx mori were reported using whole-genome shotgun sequencing. Because of relatively shallow genome coverage, the silkworm genome remains fragmented, hampering annotation and comparative genome studies. For a more complete genome analysis, we developed extended scaffolds combining physical maps with improved genetic maps. Results: We mapped 1,755 single nucleotide polymorphism (SNP) markers from bacterial artificial chromosome (BAC) end sequences onto 28 linkage groups using a recombining male backcross population, yielding an average inter-SNP distance of 0.81 cM (about 270 kilobases). We constructed 6,221 contigs by fingerprinting clones from three BAC libraries digested with different restriction enzymes, and assigned a total of 724 single copy genes to them by BLAST (basic local alignment search tool) search of the BAC end sequences and high-density BAC filter hybridization using expressed sequence tags as probes. We assigned 964 additional expressed sequence tags to linkage groups by restriction fragment length polymorphism analysis of a nonrecombining female backcross population. Altogether, 361.1 megabases of BAC contigs and singletons were integrated with a map containing 1,688 independent genes. A test of synteny using Oxford grid analysis with more than 500 silkworm genes revealed six versus 20 silkworm linkage groups containing eight or more orthologs of Apis versus Tribolium, respectively. Conclusion: The integrated map contains approximately 10{\%} of predicted silkworm genes and has an estimated 76{\%} genome coverage by BACs. This provides a new resource for improved assembly of whole-genome shotgun data, gene annotation and positional cloning, and will serve as a platform for comparative genomics and gene discovery in Lepidoptera and other insects.",
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AU - Yamamoto, Kimiko

AU - Nohata, Junko

AU - Kadono-Okuda, Keiko

AU - Narukawa, Junko

AU - Sasanuma, Motoe

AU - Sasanuma, Shun Ichi

AU - Minami, Hiroshi

AU - Shimomura, Michihiko

AU - Suetsugu, Yoshitaka

AU - Banno, Yutaka

AU - Osoegawa, Kazutoyo

AU - de Jong, Pieter J.

AU - Goldsmith, Marian R.

AU - Mita, Kazuei

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Y1 - 2008/1/28

N2 - Background: In 2004, draft sequences of the model lepidopteran Bombyx mori were reported using whole-genome shotgun sequencing. Because of relatively shallow genome coverage, the silkworm genome remains fragmented, hampering annotation and comparative genome studies. For a more complete genome analysis, we developed extended scaffolds combining physical maps with improved genetic maps. Results: We mapped 1,755 single nucleotide polymorphism (SNP) markers from bacterial artificial chromosome (BAC) end sequences onto 28 linkage groups using a recombining male backcross population, yielding an average inter-SNP distance of 0.81 cM (about 270 kilobases). We constructed 6,221 contigs by fingerprinting clones from three BAC libraries digested with different restriction enzymes, and assigned a total of 724 single copy genes to them by BLAST (basic local alignment search tool) search of the BAC end sequences and high-density BAC filter hybridization using expressed sequence tags as probes. We assigned 964 additional expressed sequence tags to linkage groups by restriction fragment length polymorphism analysis of a nonrecombining female backcross population. Altogether, 361.1 megabases of BAC contigs and singletons were integrated with a map containing 1,688 independent genes. A test of synteny using Oxford grid analysis with more than 500 silkworm genes revealed six versus 20 silkworm linkage groups containing eight or more orthologs of Apis versus Tribolium, respectively. Conclusion: The integrated map contains approximately 10% of predicted silkworm genes and has an estimated 76% genome coverage by BACs. This provides a new resource for improved assembly of whole-genome shotgun data, gene annotation and positional cloning, and will serve as a platform for comparative genomics and gene discovery in Lepidoptera and other insects.

AB - Background: In 2004, draft sequences of the model lepidopteran Bombyx mori were reported using whole-genome shotgun sequencing. Because of relatively shallow genome coverage, the silkworm genome remains fragmented, hampering annotation and comparative genome studies. For a more complete genome analysis, we developed extended scaffolds combining physical maps with improved genetic maps. Results: We mapped 1,755 single nucleotide polymorphism (SNP) markers from bacterial artificial chromosome (BAC) end sequences onto 28 linkage groups using a recombining male backcross population, yielding an average inter-SNP distance of 0.81 cM (about 270 kilobases). We constructed 6,221 contigs by fingerprinting clones from three BAC libraries digested with different restriction enzymes, and assigned a total of 724 single copy genes to them by BLAST (basic local alignment search tool) search of the BAC end sequences and high-density BAC filter hybridization using expressed sequence tags as probes. We assigned 964 additional expressed sequence tags to linkage groups by restriction fragment length polymorphism analysis of a nonrecombining female backcross population. Altogether, 361.1 megabases of BAC contigs and singletons were integrated with a map containing 1,688 independent genes. A test of synteny using Oxford grid analysis with more than 500 silkworm genes revealed six versus 20 silkworm linkage groups containing eight or more orthologs of Apis versus Tribolium, respectively. Conclusion: The integrated map contains approximately 10% of predicted silkworm genes and has an estimated 76% genome coverage by BACs. This provides a new resource for improved assembly of whole-genome shotgun data, gene annotation and positional cloning, and will serve as a platform for comparative genomics and gene discovery in Lepidoptera and other insects.

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