次世代シーケンサーデータの解析手法 第 9 回 ゲノムアノテーションとその可視化、DDBJ への登録
論文発表は研究の一部である。そして多くの学術雑誌は、論文発表される塩基配列を国際塩基配列データベース（International Nucleotide Sequence Database Collaboration; INSDC）に登録することを義務付けている。この意味において、これまで本連載で述べてきた解析手法に関する事柄とは若干スタンスが異なるが、ゲノム配列の登録作業もまた研究の一環といえる。第 9 回は、前回までに構築したゲノム配列 Lactobacillus hokkaidonensis LOOC260T の総仕上げとして、染色体複製開始点の同定と回転、ゲノムアノテーション、INSDC...
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| Published in | 日本乳酸菌学会誌 Vol. 28; no. 1; pp. 3 - 11 |
|---|---|
| Main Authors | , , , , , , |
| Format | Journal Article |
| Language | Japanese |
| Published |
日本乳酸菌学会
10.03.2017
|
| Subjects | |
| Online Access | Get full text |
| ISSN | 1343-327X 2186-5833 |
| DOI | 10.4109/jslab.28.3 |
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| Abstract | 論文発表は研究の一部である。そして多くの学術雑誌は、論文発表される塩基配列を国際塩基配列データベース（International Nucleotide Sequence Database Collaboration; INSDC）に登録することを義務付けている。この意味において、これまで本連載で述べてきた解析手法に関する事柄とは若干スタンスが異なるが、ゲノム配列の登録作業もまた研究の一環といえる。第 9 回は、前回までに構築したゲノム配列 Lactobacillus hokkaidonensis LOOC260T の総仕上げとして、染色体複製開始点の同定と回転、ゲノムアノテーション、INSDC を構成する日米欧三極の一つであるDNA Data Bank of Japan（DDBJ）への登録、そしてDNAPlotter を用いたアノテーション結果の描画について解説する。ウェブサイト（Rで）塩基配列解析（URL: http:// www.iu.a.u-tokyo.ac.jp/~kadota/r_seq.html）中に本連載をまとめた項目（URL: http://www.iu.a.u-tokyo.ac.jp/~kadota/r_seq.html#about_book_ JSLAB）が存在する。ウェブ資料（以下、W）や関連ウェブサイトなどを効率的に活用してほしい。 |
|---|---|
| AbstractList | 論文発表は研究の一部である。そして多くの学術雑誌は、論文発表される塩基配列を国際塩基配列データベース（International Nucleotide Sequence Database Collaboration; INSDC）に登録することを義務付けている。この意味において、これまで本連載で述べてきた解析手法に関する事柄とは若干スタンスが異なるが、ゲノム配列の登録作業もまた研究の一環といえる。第 9 回は、前回までに構築したゲノム配列 Lactobacillus hokkaidonensis LOOC260T の総仕上げとして、染色体複製開始点の同定と回転、ゲノムアノテーション、INSDC を構成する日米欧三極の一つであるDNA Data Bank of Japan（DDBJ）への登録、そしてDNAPlotter を用いたアノテーション結果の描画について解説する。ウェブサイト（Rで）塩基配列解析（URL: http:// www.iu.a.u-tokyo.ac.jp/~kadota/r_seq.html）中に本連載をまとめた項目（URL: http://www.iu.a.u-tokyo.ac.jp/~kadota/r_seq.html#about_book_ JSLAB）が存在する。ウェブ資料（以下、W）や関連ウェブサイトなどを効率的に活用してほしい。 |
| Author | 李, 慶範 藤澤, 貴智 谷澤, 靖洋 中村, 保一 門田, 幸二 真島, 淳 清水, 謙多郎 |
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| Copyright | 2017 日本乳酸菌学会 |
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| References | 32) Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A. (1987) Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J Bacteriol 169: 5429-5433. 3) Field D, Tiwari B, Booth T, Houten S, Swan D, et al. (2006) Open software for biologists: from famine to feast. Nat Biotechnol 24: 801-803. 22) Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ. (2017) GenBank. Nucleic Acids Res 45: D37-D42. 27) Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, et al. (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res 12: 1611- 1618. 1) Tanizawa Y, Tohno M, Kaminuma E, Nakamura Y, Arita M. (2015) Complete genome sequence and analysis of Lactobacillus hokkaidonensis LOOC260T, a psychrotrophic lactic acid bacterium isolated from silage. BMC Genomics 16: 240. 14) Ogasawara N, Moriya S, von Meyenburg K, Hansen FG, Yoshikawa H. (1985) Conservation of genes and their organization in the chromosomal replication origin region of Bacillus subtilis and Escherichia coli. EMBO J 4: 3345-3350. 29) Goto N, Prins P, Nakao M, Bonnal R, Aerts J, et al. (2010) BioRuby: bioinformatics software for the Ruby programming language. Bioinformatics 26: 2617-2619. 5) Rudner R, Karkas JD, Chargaff E. (1968) Separation of B. subtilis DNA into complementary strands. 3. Direct analysis. Proc Natl Acad Sci U S A 60: 921-922. 36) Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25: 1043-1055. 28) Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, et al. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25: 1422-1423. 16) Gao F, Zhang CT. (2008) Ori-Finder: a web-based system for finding oriCs in unannotated bacterial genomes. BMC Bioinformatics 9: 79. 30) Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277: 1453-1462. 19) De Bodt S1, Raes J, Florquin K, Rombauts S, Rouzé P, et al. (2003) Genomewide structural annotation and evolutionary analysis of the type I MADS-box genes in plants. J Mol Evol 56: 573-586. 31) Seemann T. (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30: 2068-2069. 24) 孫建強，三浦文，清水謙多郎，門田幸二（2015）次世代シーケンサーデータの解析手法：第 3 回 Linux 環境構築から NGS データ取得まで．日本乳酸菌学会誌 26: 32-41 17) Zhang R, Zhang CT. (1994) Z curves, an intutive tool for visualizing and analyzing the DNA sequences. J Biomol Struct Dyn 11: 767-782. 15) Tanizawa Y, Fujisawa T, Kaminuma E, Nakamura Y., Arita M. (2016) DFAST and DAGA: Web-based integrated genome annotation tools and resources. Biosci Microbiota Food Health 35: 173-184. 13) Kimura M, Miki T, Hiraga S, Nagata T, Yura T. (1979) Conditionally lethal amber mutations in the dnaA region of the Escherichia coli chromosome that affect chromosome replication. J Bacteriol 140: 825- 834. 33) Eddy SR. (2011) Accelerated Profile HMM Searches. PLoS Comput Biol 7: e1002195. 34) Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, et al. (2016) The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res 44: D279-285. 35) Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK, et al. (2013) TIGRFAMs and Genome Properties in 2013. Nucleic Acids Res 41: D387- 395. 21) Mashima J, Kodama Y, Fujisawa T, Katayama T, Okuda Y, et al. (2017) DNA Data Bank of Japan. Nucleic Acids Res 45: D25-D31. 40) Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J. (2009) DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 25: 119-120. 11) Arakawa K, Tomita M. (2012) Measures of compositional strand bias related to replication machinery and its applications. Curr Genomics 13: 4-15. 37) Endo A, Tanizawa Y, Tanaka N, Maeno S, Kumar H, et al. (2015) Comparative genomics of Fructobacillus spp. and Leuconostoc spp. reveals niche-specific evolution of Fructobacillus spp. BMC Genomics 16: 1117. 9) Prescott DM, Kuempel PL. (1972) Bidirectional replication of the chromosome in Escherichia coli. Proc Natl Acad Sci U S A 69: 2842- 2845. 4) Chargaff E. (1951) Structure and function of nucleic acids as cell constituents. Fed Proc 10: 654-659. 8) Bird RE, Louarn J, Martuscelli J, Caro L. (1972) Origin and sequence of chromosome replication in Escherichia coli. J Mol Biol 70: 549-566. 25) Kodama Y, Shumway M, Leinonen R; International Nucleotide Sequence Database Collaboration. (2012) The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Res 40: D54-56. 6) Lobry JR. (1996) Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol 13: 660-665. 7) Rocha E. (2002) Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes? Trends Microbiol 10: 393- 395. 20) Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, et al. (2001) Functional annotation of a full-length mouse cDNA collection. Nature 409: 685-690. 39) Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, et al. (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57: 81-91. 10) Hiasa H, Marians KJ. (1994) Primase couples leading- and lagging-strand DNA synthesis from oriC. J Biol Chem 269: 6058-6063. 2) 谷澤靖洋，神沼英里，中村保一，遠野雅徳、寺田朋子、清水謙多郎，門田幸二（2016）次世代シーケンサーデータの解析手法：第 8 回ア センブリ後の解析．日本乳酸菌学会誌 27: 187-195 23) Toribio AL, Alako B, Amid C, Cerdeño-Tarrága A, Clarke L. (2017) European Nucleotide Archive in 2016. Nucleic Acids Res 45: D32-D36. 26) 門田幸二，孫建強，湯敏，西岡輔，清水謙多郎（2014）次世代シーケンサーデータの解析手法：第 1 回イントロダクション．日本乳酸菌 学会誌 25: 87-94 38) Maeno S, Tanizawa Y, Kanesaki Y, Kubota E, Kumar H, et al. (2016) Genomic characterization of a fructophilic bee symbiont Lactobacillus kunkeei reveals its niche-specific adaptation. Syst Appl Microbiol 39: 516-526. 12) Meijer M, Beck E, Hansen FG, Bergmans HE, Messer W, et al. (1979) Nucleotide sequence of the origin of replication of the Escherichia coli K-12 chromosome. Proc Natl Acad Sci U S A 76: 580-584. 18) Rice P, Longden I, Bleasby A. (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16: 276-277. |
| References_xml | – reference: 19) De Bodt S1, Raes J, Florquin K, Rombauts S, Rouzé P, et al. (2003) Genomewide structural annotation and evolutionary analysis of the type I MADS-box genes in plants. J Mol Evol 56: 573-586. – reference: 34) Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, et al. (2016) The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res 44: D279-285. – reference: 14) Ogasawara N, Moriya S, von Meyenburg K, Hansen FG, Yoshikawa H. (1985) Conservation of genes and their organization in the chromosomal replication origin region of Bacillus subtilis and Escherichia coli. EMBO J 4: 3345-3350. – reference: 11) Arakawa K, Tomita M. (2012) Measures of compositional strand bias related to replication machinery and its applications. Curr Genomics 13: 4-15. – reference: 31) Seemann T. (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30: 2068-2069. – reference: 13) Kimura M, Miki T, Hiraga S, Nagata T, Yura T. (1979) Conditionally lethal amber mutations in the dnaA region of the Escherichia coli chromosome that affect chromosome replication. J Bacteriol 140: 825- 834. – reference: 28) Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, et al. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25: 1422-1423. – reference: 18) Rice P, Longden I, Bleasby A. (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16: 276-277. – reference: 40) Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J. (2009) DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 25: 119-120. – reference: 36) Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25: 1043-1055. – reference: 3) Field D, Tiwari B, Booth T, Houten S, Swan D, et al. (2006) Open software for biologists: from famine to feast. Nat Biotechnol 24: 801-803. – reference: 5) Rudner R, Karkas JD, Chargaff E. (1968) Separation of B. subtilis DNA into complementary strands. 3. Direct analysis. Proc Natl Acad Sci U S A 60: 921-922. – reference: 20) Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, et al. (2001) Functional annotation of a full-length mouse cDNA collection. Nature 409: 685-690. – reference: 1) Tanizawa Y, Tohno M, Kaminuma E, Nakamura Y, Arita M. (2015) Complete genome sequence and analysis of Lactobacillus hokkaidonensis LOOC260T, a psychrotrophic lactic acid bacterium isolated from silage. BMC Genomics 16: 240. – reference: 23) Toribio AL, Alako B, Amid C, Cerdeño-Tarrága A, Clarke L. (2017) European Nucleotide Archive in 2016. Nucleic Acids Res 45: D32-D36. – reference: 26) 門田幸二，孫建強，湯敏，西岡輔，清水謙多郎（2014）次世代シーケンサーデータの解析手法：第 1 回イントロダクション．日本乳酸菌 学会誌 25: 87-94． – reference: 2) 谷澤靖洋，神沼英里，中村保一，遠野雅徳、寺田朋子、清水謙多郎，門田幸二（2016）次世代シーケンサーデータの解析手法：第 8 回ア センブリ後の解析．日本乳酸菌学会誌 27: 187-195． – reference: 24) 孫建強，三浦文，清水謙多郎，門田幸二（2015）次世代シーケンサーデータの解析手法：第 3 回 Linux 環境構築から NGS データ取得まで．日本乳酸菌学会誌 26: 32-41． – reference: 32) Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A. (1987) Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J Bacteriol 169: 5429-5433. – reference: 9) Prescott DM, Kuempel PL. (1972) Bidirectional replication of the chromosome in Escherichia coli. Proc Natl Acad Sci U S A 69: 2842- 2845. – reference: 25) Kodama Y, Shumway M, Leinonen R; International Nucleotide Sequence Database Collaboration. (2012) The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Res 40: D54-56. – reference: 30) Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277: 1453-1462. – reference: 15) Tanizawa Y, Fujisawa T, Kaminuma E, Nakamura Y., Arita M. (2016) DFAST and DAGA: Web-based integrated genome annotation tools and resources. Biosci Microbiota Food Health 35: 173-184. – reference: 37) Endo A, Tanizawa Y, Tanaka N, Maeno S, Kumar H, et al. (2015) Comparative genomics of Fructobacillus spp. and Leuconostoc spp. reveals niche-specific evolution of Fructobacillus spp. BMC Genomics 16: 1117. – reference: 29) Goto N, Prins P, Nakao M, Bonnal R, Aerts J, et al. (2010) BioRuby: bioinformatics software for the Ruby programming language. Bioinformatics 26: 2617-2619. – reference: 7) Rocha E. (2002) Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes? Trends Microbiol 10: 393- 395. – reference: 22) Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ. (2017) GenBank. Nucleic Acids Res 45: D37-D42. – reference: 33) Eddy SR. (2011) Accelerated Profile HMM Searches. PLoS Comput Biol 7: e1002195. – reference: 16) Gao F, Zhang CT. (2008) Ori-Finder: a web-based system for finding oriCs in unannotated bacterial genomes. BMC Bioinformatics 9: 79. – reference: 27) Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, et al. (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res 12: 1611- 1618. – reference: 39) Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, et al. (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57: 81-91. – reference: 35) Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK, et al. (2013) TIGRFAMs and Genome Properties in 2013. Nucleic Acids Res 41: D387- 395. – reference: 21) Mashima J, Kodama Y, Fujisawa T, Katayama T, Okuda Y, et al. (2017) DNA Data Bank of Japan. Nucleic Acids Res 45: D25-D31. – reference: 8) Bird RE, Louarn J, Martuscelli J, Caro L. (1972) Origin and sequence of chromosome replication in Escherichia coli. J Mol Biol 70: 549-566. – reference: 10) Hiasa H, Marians KJ. (1994) Primase couples leading- and lagging-strand DNA synthesis from oriC. J Biol Chem 269: 6058-6063. – reference: 12) Meijer M, Beck E, Hansen FG, Bergmans HE, Messer W, et al. (1979) Nucleotide sequence of the origin of replication of the Escherichia coli K-12 chromosome. Proc Natl Acad Sci U S A 76: 580-584. – reference: 4) Chargaff E. (1951) Structure and function of nucleic acids as cell constituents. Fed Proc 10: 654-659. – reference: 6) Lobry JR. (1996) Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol 13: 660-665. – reference: 17) Zhang R, Zhang CT. (1994) Z curves, an intutive tool for visualizing and analyzing the DNA sequences. J Biomol Struct Dyn 11: 767-782. – reference: 38) Maeno S, Tanizawa Y, Kanesaki Y, Kubota E, Kumar H, et al. (2016) Genomic characterization of a fructophilic bee symbiont Lactobacillus kunkeei reveals its niche-specific adaptation. Syst Appl Microbiol 39: 516-526. |
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| Title | 次世代シーケンサーデータの解析手法 第 9 回 ゲノムアノテーションとその可視化、DDBJ への登録 |
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| ispartofPNX | 日本乳酸菌学会誌, 2017/03/10, Vol.28(1), pp.3-11 |
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