次世代シーケンス　参考文献

【 GRAS-Di技術によるジェノタイピング解析 x HiSeq2500 】

Repeated translocation of a supergene underlying rapid sex chromosome turnover in Takifugu pufferfish

Kabir A, Ieda R, Hosoya S, Fujikawa D, Atsumi K, Tajima S, Nozawa A, Koyama T, Hirase S, Nakamura O, Kadota M, Nishimura O, Kuraku S, Nakamura Y, Kobayashi H, Toyoda A, Tasumi S, Kikuchi K. (2022)

Proc Natl Acad Sci U S A. 119: e2121469119.

【 GRAS-Di技術によるジェノタイピング解析 x NovaSeq6000/HiSeq2500 】

Genomic prediction of 10 metamorphic traits of captive-bred Japanese eels (Anguilla japonica) using the GRAS-Di genotyping method

Nomura K, Ishikawa T, Sudo R, Fujiwara A. (2022)

Aquaculture. 548: 737671.

【 GRAS-Di技術によるジェノタイピング解析 x HiSeq4000 】

Artificial Control of the Prunus Self-incompatibility System Using Antisense Oligonucleotides against Pollen Genes

Ono K, Masui K, Tao R. (2022)

The Horticulture Journal. Article ID: QH-002

【 GRAS-Di技術によるジェノタイピング解析 x NovaSeq6000 】

A Y-linked anti-Müllerian hormone type-II receptor is the sex-determining gene in ayu, Plecoglossus altivelis

Nakamoto M, Uchino T, Koshimizu E, Kuchiishi Y, Sekiguchi R, Wang L, Sudo R, Endo M, Guiguen Y, Schartl M, Postlethwait JH, Sakamoto T. (2021)

PLoS Genet. 17: e1009705.

【 GRAS-Di技術によるジェノタイピング解析 x HiSeq4000/2500 】

Genomic evidence for speciation with gene flow in broadcast spawning marine invertebrates.

Hirase S, Yamasaki YY, Sekino M, Nishisako M, Ikeda M, Hara M, Merilä J, Kikuchi K. (2021)

Mol Biol Evol. 38: 4683-4699.

【 GRAS-Di技術によるジェノタイピング解析 x HiSeq4000 】

Effect of Three Types of Ion Beam Irradiation on GerbRepeated translocation of a supergene underlying rapid sex chromosome turnover in Takifugu pufferfishera (Gerbera hybrida) In Vitro Shoots with Mutagenesis Efficiency.

Hosoguchi T, Uchiyama Y, Komazawa H, Yahata M, Shimokawa T, Tominaga A. (2021)

Plants. 10:1480.

【 GRAS-Di技術によるジェノタイピング解析 x HiSeq4000 】

Major and Stable Quantitative Trait Locus qSS2 for Seed Size and Shape Traits in a Soybean RIL Population.

Kumawat G, Xu D. A. (2021)

Front Genet. 12:646102.

【 GRAS-Di技術によるジェノタイピング解析 x HiSeq4000 】

QTL analysis of crown gall disease resistance in apple: first plant R gene candidates effective against Rhizobium rhizogenes (Ti).

Moriya, S., Iwanami, H., Haji, T. et al. (2021)

Tree Genetics & Genomes 17:25.

【 GRAS-Di技術によるジェノタイピング解析 x HiSeq2500 】

Genetic Dissection of a Precocious Phenotype in Male Tiger Pufferfish (Takifugu rubripes) using Genotyping by Random Amplicon Sequencing, Direct (GRAS-Di).

Yoshikawa S, Hamasaki M, Kadomura K, Yamada T, Chuda H, Kikuchi K, Hosoya S. (2021)

Mar Biotechnol (NY). doi: 10.1007/s10126-020-10013-4.

【 GRAS-Di技術によるジェノタイピング解析 x HiSeq2500 】

Random PCR-based genotyping by sequencing technology GRAS-Di (genotyping by random amplicon sequencing, direct) reveals genetic structure of mangrove fishes.

Hosoya S, Hirase S, Kikuchi K, Nanjo K, Nakamura Y, Kohno H, Sano M.

Mol Ecol Resour. 2019 Sep; 19:1153-1163. doi: 10.1111/1755-0998.13025.

【 ゲノム解析 by ショットガンライブラリ x HiSeq2500 】

Variations in mating-type-like (MTL) loci direct PCR-based tracking of Zygosaccharomyces strains formed by mating.

Ogata T, Kuroki K, Ito K, Kondo A, Nakamura K.

J Gen Appl Microbiol. 2018 Jul 23;64(3):127-135. doi: 10.2323/jgam.2017.11.001.

【 ゲノム解析 by ショットガンライブラリ x HiSeq2500/2000 】

Genome resequencing analysis of Salmonella typhimurium LT-2 strains TA98 and TA100 for the establishment of a next-generation sequencing-based mutagenicity assay.

Matsumura S, Ito Y, Morita O, Honda H.

J Appl Toxicol. 2017 Apr 11. doi: 10.1002/jat.3463.

【 De novo 植物ゲノムシーケンシング by 40, 20, 8, 3kb LJDライブラリ x HiSeq2000 】 

The power of single molecule real-time sequencing technology in the de novo assembly of a eukaryotic genome.

Sakai H, Naito K, Ogiso-Tanaka E, Takahashi Y, Iseki K, Muto C, Satou K, Teruya K, Shiroma A, Shimoji M, Hirano T, Itoh T, Kaga A, Tomooka N.

Sci Rep. 2015 Nov 30;5:16780. doi: 10.1038/srep16780.

【 De novo 哺乳類ゲノムシーケンシング by 40, 20, 8, 3kb LJD ライブラリ x HiSeq2000 】 

Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis.

Sato K, Kuroki Y, Kumita W, Fujiyama A, Toyoda A, Kawai J, Iriki A, Sasaki E, Okano H, Sakakibara Y.

Sci Rep. 2015 Nov 20;5:16894. doi: 10.1038/srep16894.

【 De novo 細菌ゲノムシーケンシング by 8kb LPE ライブラリ x GS FLX 】

Genome sequence of the deep-sea denitrifier Pseudomonas sp. strain MT-1, isolated from the mariana trench.

Fujinami S, Oikawa Y, Araki T, Shinmura Y, Midorikawa R, Ishizaka H, Kato C, Horikoshi K, Ito M, Tamegai H.

Genome Announc. 2014 Dec 18;2(6). pii: e01313-14. doi: 10.1128/genomeA.01313-14.

【 De novo 細菌ゲノムシーケンシング by 8kb LPEライブラリ x GS FLX 】

Complete genome sequence of N-acylhomoserine lactone-producing Pseudomonas sp. strain StFLB209, isolated from potato phyllosphere.

Morohoshi T, Kato T, Someya N, Ikeda T.

Genome Announc. 2014 Oct 16;2(5). pii: e01037-14. doi: 10.1128/genomeA.01037-14.

【 De novo 細菌ゲノムシーケンシング by 8kb LPEライブラリ x GS FLX 】

Complete genome sequence of Chryseobacterium sp. strain StRB126, an N-acylhomoserine lactone-degrading bacterium Isolated from potato root.

Morohoshi T, Wang WZ, Someya N, Ikeda T.

Genome Announc. 2014 Sep 25;2(5). pii: e00952-14. doi: 10.1128/genomeA.00952-14.

【De novo 細菌ゲノムシーケンシング by 8kb LPE & ショットガンライブラリ x GS FLX 】

Complete genome sequence of the biocontrol strain Pseudomonas protegens Cab57 discovered in Japan reveals strain-specific diversity of this species.

Takeuchi K, Noda N, Someya N.

PLoS One. 2014 Apr 2;9(4):e93683. doi: 10.1371/journal.pone.0093683. eCollection 2014.

【 De novo 細菌ゲノムシーケンシング by 8kb LPEライブラリ x GS FLX　】

Phenazine antibiotic production and antifungal activity are regulated by multiple quorum-sensing systems in Pseudomonas chlororaphis subsp. aurantiaca StFRB508.

Morohoshi T, Wang WZ, Suto T, Saito Y, Ito S, Someya N, Ikeda T.

J Biosci Bioeng. 2013 Nov;116(5):580-4. doi: 10.1016/j.jbiosc.2013.04.022. Epub 2013 May 30.

【 De novo 植物ゲノムシーケンシング by 40, 20, 8kb LJD & ショットガンライブラリ x HiSeq2000 】

De novo assembly of the complete organelle genome sequences of azuki bean (Vigna angularis) using next-generation sequencers.

Naito K, Kaga A, Tomooka N, Kawase M.

Breed Sci. 2013 Jun;63(2):176-82. doi: 10.1270/jsbbs.63.176. Epub 2013 Jun 1.

【 De novo 細菌ゲノムシーケンシング by 8kb LPE ライブラリ x GS FLX】

Complete genome sequence of Helicobacter cinaedi strain PAGU611, isolated in a case of human bacteremia.

Goto T, Ogura Y, Hirakawa H, Tomida J, Morita Y, Akaike T, Hayashi T, Kawamura Y.

J Bacteriol. 2012 Jul;194(14):3744-5. doi: 10.1128/JB.00645-12.

【 De novo 細菌ゲノムシーケンシング by 8kb LPE & ショットガンライブラリ x GS FLX】

Complete genome sequence and characterization of the N-acylhomoserine lactone-degrading gene of the potato leaf-associated Solibacillus silvestris.

Morohoshi T, Tominaga Y, Someya N, Ikeda T.

J Biosci Bioeng. 2012 Jan;113(1):20-5. doi: 10.1016/j.jbiosc.2011.09.006. Epub 2011 Oct 22.

【 De novo 細菌ゲノムシーケンシング by 8kb LPE & ショットガンライブラリ x GS FLX 】

Genome sequence of Microbacterium testaceum StLB037, an N-acylhomoserine lactone-degrading bacterium isolated from potato leaves.

Morohoshi T, Wang WZ, Someya N, Ikeda T.

J Bacteriol. 2011 Apr;193(8):2072-3. doi: 10.1128/JB.00180-11. Epub 2011 Feb 25.

【 遺伝子発現量解析 by mRNA-Seqライブラリ x NovaSeq6000 】

Expression of ASC splice variant found in Japanese patients with palindromic rheumatism is regulated by rs8056505 single nucleotide polymorphism and interleukin-1 beta.

Hattori M, Yabuuchi A, Tanaka H, Kawara T, Wang H, Inoue K, Shiozawa S, Komai K. (2022)

Asian Pac J Allergy Immunol. doi: 10.12932/AP-010322-1339.

【 遺伝子発現量解析 by mRNA-Seqライブラリ x HiSeq2500/2000 】

Exogenous ABA and endogenous ABA affects ‘Kyoho’ grape berry coloration in different pathway.

Plant Gene. 2018 Jun; 14:74-82. doi: 10.1016/j.plgene.2018.05.001.

【 遺伝子発現量解析 by mRNA-Seqライブラリ x HiSeq2500/2000 】

The Sal-like 4 - integrin α6β1 network promotes cell migration for metastasis via activation of focal adhesion dynamics in basal-like breast cancer cells.

Itou J, Tanaka S, Li W, Iida A, Sehara-Fujisawa A, Sato F, Toi M.

Biochim Biophys Acta. 2016 Oct 20;1864:76-88. doi: 10.1016/j.bbamcr.2016.10.012.

【 De novo 哺乳類トランスクリプトーム by 均一化cDNAライブラリ x GS FLX 】
【 遺伝子発現量解析 by 3’-fragment cDNAライブラリ x HiSeq2000 】

Analysis of gene expression for microminipig liver transcriptomes using parallel long-read technology and short-read sequencing.

Sakai C, Iwano S, Shimizu M, Onodera J, Uchida M, Sakurada E, Yamazaki Y, Asaoka Y, Imura N, Uno Y, Murayama M, Hayashi R, Yamazaki H, Miyamoto Y.

Biopharm Drug Dispos. 2016 May;37(4):220-32. doi: 10.1002/bdd.2007.

【 遺伝子発現量解析 by mRNA-Seqライブラリ x HiSeq2500/2000 】

A homeobox protein, NKX6.1, up-regulates interleukin-6 expression for cell growth in basal-like breast cancer cells.

Li W, Itou J, Tanaka S, Nishimura T, Sato F, Toi M.

Exp Cell Res. 2016 Mar 28. pii: S0014-4827(16)30063-5. doi: 10.1016/j.yexcr.2016.03.023.

【 De novo 動物トランスクリプトーム by 均一化cDNAライブラリ x GS FLX 】 

Transcriptomic study of the rat pinworm Syphacia muris.

Okamoto M,Taira K, Ito R, Asai F.

Helminthologia. 2015 52(4)370-4.

【 De novo 植物トランスクリプトーム by 均一化cDNAライブラリ x GS FLX】

Newly developed SNP-based identification method of hop Varieties.

Yamauchi H, Mukouzaka Y, Taniguchi T, Nakashima K, Furukubo S, Harada M

J Am Soc Brew Chem. 2014 72(4):239-245. doi: 10.1094/ASBCJ-2014-1006-01.

【 De novo 哺乳類トランスクリプトーム by 均一化cDNAライブラリ x GS FLX 】
【 遺伝子発現量解析 by 3’-fragment cDNAライブラリ x HiSeq2000 】

Qualitative de novo analysis of full length cDNA and quantitative analysis of gene expression for common marmoset (Callithrix jacchus) transcriptomes using parallel long-read technology and short-read sequencing.

Shimizu M, Iwano S, Uno Y, Uehara S, Inoue T, Murayama N, Onodera J, Sasaki E, Yamazaki H.

PLoS One. 2014 Jun 30;9(6):e100936. doi: 10.1371/journal.pone.0100936. eCollection 2014.

【 De novo 植物トランスクリプトーム by 3’-fragment cDNAライブラリ x GS FLX】

EST sequencing and microarray analysis of the floral transcriptome of Eustoma　grandiflorum.

Kawabata S, Li Y, Miyamoto K.

Scientia Horticulturae. 2012 Sep 6; 144:230-5. doi: 10.1016/j.scienta.2011.12.024.

【 De novo 動物トランスクリプトーム & 遺伝子発現量解析 by 3’-fragment cDNAライブラリ x GS FLX】

Deep sequencing of ESTs from nacreous and prismatic layer producing tissues and a screen for novel shell formation-related genes in the pearl oyster.

Kinoshita S, Wang N, Inoue H, Maeyama K, Okamoto K, Nagai K, Kondo H, Hirono I, Asakawa S, Watabe S.

PLoS One. 2011;6(6):e21238. doi: 10.1371/journal.pone.0021238. Epub 2011 Jun 22.

【 菌叢メタゲノム解析 by アンプリコンライブラリ x GS Junior 】

Changes in the bacterial community of soybean rhizospheres during growth in the field.

Sugiyama A, Ueda Y, Zushi T, Takase H, Yazaki K.

PLoS One. 2014 Jun 23;9(6):e100709. doi: 10.1371/journal.pone.0100709. eCollection 2014.