Publications by SQC users

SQC Publication Archives
(last update 2020.10)

SQC members in Author

Chuya Shinzato, Konstantin Khalturin, Jun Inoue, Yuna Zayasu, Miyuki Kanda, Mayumi Kawamitsu, Yuki Yoshioka, Hiroshi Yamashita, Go Suzuki, Noriyuki Satoh 
Eighteen coral genomes reveal the evolutionary origin of Acropora strategies to accommodate environmental changes 
Molecular Biology and Evolution 
Published: 02 September 2020 
https://doi.org/10.1093/molbev/msaa216  

 
Koki Nishitsuji; Asuka Arimoto; Yoshitaka Yonashiro; Kanako Hisata; Manabu Fujie; Mayumi Kawamitsu; Eiichi Shoguchi; Noriyuki Satoh 
Comparative genomics of four strains of the edible brown alga, Cladosiphon okamuranus 
BMC Genomics 
Published: 26 June 2020 
https://doi.org/10.1186/s12864-020-06792-8 

 
Akito Ishikawa, Keisuke Shimizu, Yukinobu Isowa, Takeshi Takeuchi, Ran Zhao, Keiji Kito, Manabu Fujie, Noriyuki Satoh, and Kazuyoshi Endo 
Functional shell matrix proteins tentatively identified by asymmetric snail shell morphology 
Scientific Reports 
Published: 17 June 2020 
https://doi.org/10.1038/s41598-020-66021-w 
 

Fabienne Ziadi-Künzli, Taha Soliman, Hideyuki Imai, Momoko Sakurai, Ken Maeda, Katsunori Tachihara   
Re-evaluation of deep-sea dogfishes (genus Squalus) in Japan using phylogenetic inference
Deep-Sea Research Part I: Oceanographic Research Papers.
Published: June 2020 
https://doi.org/10.1016/j.dsr.2020.103261 

 
Kazuo Shin-ya, Takuya Hashimoto, Ikuko Kozone, Junko Hashimoto, Hikaru Suenaga, Manabu Fujie, Noriyuki Sato, and Haruo Ikeda 
Identification, cloning and heterologous expression of biosynthetic gene cluster for desertomycin 
The Journal of Antibiotics 
Published: 26 May 2020 
https://doi.org/10.1038/s41429-020-0319-0 

 
Takashi Miyake, Natsuki Aihara, Ken Maeda, Chuya Shinzato, Ryo Koyanagi, Hirozumi Kobayashi, Kazunori Yamahira
Bloodmeal host identification with inferences to feeding habits of a fish-fed mosquito, Aedes baisasi
Scientific Reports 9: 4002 (2019)
Published: 8 March 2019
https://doi.org/10.1038/s41598-019-40509-6 

Kazuo Shin-ya, Takuya Hashitomo, Ikuko Kozone, Junko Hashimoto, Reiko Ueoka, Noritaka Kagaya, Manabu Fujie, Noriyuki Sato, Haruo Ikeda
Novel macrolactam compound produced by heterologous expression of a large cryptic biosynthetic gene cluster of Streptomyces rochei IFO12908
Journal of Antibiotics
Published: 18 Dec 2019
https://doi.org/10.1038/s41429-019-0265-x


Takeshi Takeuchi, Tetsuji Masaoka, Hideo Aoki, Ryo Koyanagi, Manabu Fujie, Noriyuki Satoh
Divergent northern and southern populations and demographic history of the pearl oyster in the western Pacific revealed with genomic SNPs
Evolutionary Applications
Published: 13 December 2019
https://doi.org/10.1111/eva.12905 


Nozomi Hanahara, Takuo Higashiji, Chuya Shinzato, Ryo Koyanagi, Ken Maeda
First record of Larsonella pumilus (Teleostei: Gobiidae) from Japan, with phylogenetic placement of the genus Larsonella
Zootaxa
Published: 11 Nov 2019
https://doi.org/10.11646/zootaxa.4695.4.4 


Yutaka Satou, Ryohei Nakmura, Yu Deli,  Reiko Yoshida, Mayuko Hamada, Manabu Fujie, Kanako Hisata, Hiroyuki Takeda, and Noriyuki Satoh
A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona
Genome Biol. Evol. In Press. 
Published: 22 October 2019
https://doi.org/10.1093/gbe/evz228


Ogawa T, Oda-Ueda N, Hisata K, Nakamura H, Chijiwa T, Hattori S, Isomoto A, Yugeta H, Yamasaki S, Fukumaki Y, Ohno M, Satoh N, Shibata H
Alternative mRNA Splicing in Three Venom Families Underlying a Possible Production of Divergent Venom Proteins of the Habu Snake, Protobothrops flavoviridis.
Toxins (Basel). 2019 Oct 9;11(10). pii: E581
Published online: 9 Oct 2019
https://doi.org/10.3390/toxins11100581


Lu TM, Kanda M, Furuya H, Satoh N.
Dicyemid Mesozoans: a unique parasitic lifestyle and a reduced genome.
Genome biology and evolution. 2019 Aug;11(8):2232-43. 
Published: 26 July 2019
https://doi.org/10.1093/gbe/evz157


Hosam E.Elsaieda, Taha Soliman, Hany T .Abu-Taleb, Hiroki Goto, and Holger Jenke-Kodam.
Phylogenetic characterization of eukaryotic and prokaryotic gut flora of Nile tilapia, Oreochromis niloticus, along niches of Lake Nasser, Egypt, based on rRNA gene high-throughput sequences
Ecological Genetics and Genomics. Volume 11
Published: May 2019
https://doi.org/10.1016/j.egg.2019.100037


Konstantin Khalturin, Chuya Shinzato, Maria Khalturina, Mayuko Hamada, Manabu Fujie, Ryo Koyanagi, Miyuki Kanda, Hiroki Goto, Friederike Anton-Erxleben, Masaya Toyokawa, Sho Toshino, and Noriyuki Satoh
Medusozoan genomes inform the evolution of the jellyfish body plan
Nature Ecology & Evolution volume 3, pages 811–822 (2019)  
Published: 15 April 2019
https://doi.org/10.1038/s41559-019-0853-y


Arimoto A, Nishitsuji K, Higa Y, Arakaki N, Hisata K, Shinzato C, Satoh N, Shoguchi E. 
A siphonous macroalgal genome suggests convergent functions of homeobox genes in algae and land plants
DNA Research. 2019 Apr 1;26(2):183-92
Published: 28 March 2019
https://doi.org/10.1093/dnares/dsz002


Nishitsuji, K., Arimoto, A., Higa, Y., Mekaru, M., Kawamitsu, M., Satoh, N., and Shoguchi, E.
Draft genome of the brown alga, Nemacystus decipiens, Onna-1 strain: Fusion of genes involved in the sulfated fucan biosynthesis pathway
Scientific Reports, 9: 4607, 2019
Published: 14 March 2019
https://doi.org/10.1038/s41598-019-40955-2

 

Iwasaka H, Koyanagi R, Satoh R, Nagano A, Watanabe K, Hisata K, Satoh N, Aki T.
A Possible Trifunctional β-Carotene Synthase Gene Identified in the Draft Genome of Aurantiochytrium sp. Strain KH105.
Genes 2018, 9(4), 200
Published: 9 April 2018
https://doi.org/10.3390/genes9040200


Shinzato C, Zayasu Y,  Kanda M, Kawamitsu M, Satoh N, Yamashita H and Suzuki G
Using seawater to document coral-zoothanthella diversity: A new approach to coral reef monitoring using environmental DNA.
Front. Mar. Sci. 
Published: 20 February 2018
https://doi.org/10.3389/fmars.2018.00028


Nakano H, Miyazawa H, Maeno A, Shiroishi T, Kakui K, Koyanagi R, Kanda M, Satoh N, Omori A, Kohtsuka H.
A new species of Xenoturbella from the western Pacific Ocean and the evolution of Xenoturbella.
BMC Evol Biol. 2017 Dec 18;17(1):245. 
Published: 18 December 2017
https://doi.org/10.1186/s12862-017-1080-2


Luo YJ, Kanda M, Koyanagi R, Hisata K, Akiyama T, Sakamoto H, Sakamoto T, Satoh N.
Nemertean and phoronid genomes reveal lophotrochozoan evolution and the origin of bilaterian heads.
Nat Ecol Evol. 2017
Published: 04 December 2017
https://doi.org/10.1038/s41559-017-0389-y


Maeda K, Saeki T, Shinzato C, Koyanagi R, and Satoh N.
Review of Schismatogobius (Gobiidae) from Japan, with the description of a new species.
Ichtyol. Res. (2017)
Published: 25 July 2017
https://doi.org/10.1007/s10228-017-0593-4


Hasan Z, Koizumi S, Sasaki D, Yamada H, Arakaki N, Fujihara Y, Okitsu S, Shirahata H, and Ishikawa H.
JunB is essential for IL-23-dependent pathogenicity of Th17 cells.
Nature Communications, 8: 15628 (2017)
Published: 30 May 2017
https://doi.org/10.1038/ncomms15628


Lu TM, Kanda M, Satoh N, and Furuya H.
The phylogenetic position of dicyemid mesozoans offers insights into spiralian evolution.
Zoological Letters 3: 6 (2017)
Published: 29 May 2017
https://doi.org/10.1186/s40851-017-0068-5


Hall MR, Kocot KM, Baughman KW, Fernandez-Valverde SL, Gauthier MEA, Hatleberg WL, Krishnan A, McDougall C, Motti CA, Shoguchi E, Wang T, Xiang X, Zhao M, Bose U, Shinzato C, Hisata K, Fujie M, Kanda M, Cummins SF, Satoh N, Degnan SM, and Degnan BM.
The crown-of-thorns starfish genome as a guide for biocontrol of this coral reef pest.
Nature (2017)
Published: 13 April 2017
https://doi.org/10.1038/nature22033


Campbell MA, Nielsen JG, Sado T, Shinzato C, Kanda M, Satoh TP, and Miya M.
Evolutionary affinities of the unfathomable Parabrotulidae: Molecular data indicate placement of Parabrotula within the family Bythitidae, Ophidiiformes.
Molecular Phylogenetics and Evolution, 109, 337-342 (2017)
Published online: 6 February 2017
https://doi.org/10.1016/j.ympev.2017.02.004 

 

SQC in Acknowledgement

Jun Inoue,Kanako Hisata,Nina Yasuda,Noriyuki Satoh 
An Investigation into the Genetic History of Japanese Populations of Three Starfish,Acanthaster planci,Linckia laevigata,and Asterias amurensis,Based on Complete Mitochondrial DNA Sequences 
G3 Genes|Genomes|Genetics 
Published: July 1, 2020 
https://doi.org/10.1534/g3.120.401155 


Takahashi A, Suzuki T, Soeda S, Takaoka S, Kobori S, Yamaguchi T, Mohamed HM, Yanagiya A, Abe T, Shigeta M, Furuta Y. 
The CCR4–NOT complex maintains liver homeostasis through mRNA deadenylation
Life science alliance;3(5)
Published: 1 April 2020
https://doi.org/10.26508/lsa.201900494


Ilsley GR, Suyama R, Noda T, Satoh N, Luscombe NM. 
Finding cell-specific expression patterns in the early Ciona embryo with single-cell RNA-seq
Scientific reports;10(1):1-0
Published: 18 Mar 2020
https://doi.org/10.1038/s41598-020-61591-1


Espinas NA, Furci L, Shimajiri Y, Harukawa Y, Miura S, Takuno S, Saze H. 
Transcriptional regulation of genes bearing intronic heterochromatin in the rice genome
PLoS genetics;16(3):e1008637.
Published: 18 March 2020
https://doi.org/10.1371/journal.pgen.1008637


Shoguchi E, Yoshioka Y, Shinzato C, Arimoto A, Bhattacharya D, Satoh N.
Correlation between organelle genetic variation and RNA editing in dinoflagellates associated with the coral Acropora digitifera. 
Genome biology and evolution;12(3):203-9.
Published: 27 February 2020
https://doi.org/10.1093/gbe/evaa042


Mostafa D, Takahashi A, Yanagiya A, Yamaguchi T, Abe T, Kureha T, Kuba K, Kanegae Y, Furuta Y, Yamamoto T, Suzuki T. 
Essential functions of the CNOT7/8 catalytic subunits of the CCR4-NOT complex in mRNA regulation and cell viability. 
RNA biology. 
Published: 10 Jan 2020
https://doi.org/10.1080/15476286.2019.1709747


Sanchez G, Jolly J, Reid A, Sugimoto C, Azama C, Marlétaz F, Simakov O, Rokhsar DS. 
New bobtail squid (Sepiolidae: Sepiolinae) from the Ryukyu islands revealed by molecular and morphological analysis
Communications biology; 2(1):1-5
Published: 11 December 2019
https://doi.org/10.1038/s42003-019-0661-6


Darwell CT, Fischer G, Sarnat EM, Friedman NR, Liu C, Baiao G, Mikheyev AS, Economo EP.
Genomic and phenomic analysis of island ant community assembly
Molecular Ecology. 
Published: 10 Dec 2019
https://doi.org/10.1111/mec.15326


Lu TM, Furuya H, Satoh N. 
Gene expression profiles of dicyemid life-cycle stages may explain how dispersing larvae locate new hosts. 
Zoological Letters; 1;5(1):32
Published: Dec 2019
https://doi.org/10.1186/s40851-019-0146-y


Arimoto A, Nishitsuji K, Narisoko H, Shoguchi E, Satoh N. 
Differential gene expression in fronds and stolons of the siphonous macroalga, Caulerpa lentillifera
Development, growth & differentiation
Published: 11 November 2019
https://doi.org/10.1111/dgd.12634


Takahashi A, Takaoka S, Kobori S, Yamaguchi T, Ferwati S, Kuba K, Yamamoto T, Suzuki T. 
The CCR4–NOT deadenylase complex maintains adipocyte identity
International journal of molecular sciences. 20(21):5274
Published: 24 Oct 2019
https://doi.org/10.3390/ijms20215274


Techer MA, Rane RV, Grau ML, Roberts JM, Sullivan ST, Liachko I, Childers AK, Evans JD, Mikheyev AS. 
Divergent selection following speciation in two ectoparasitic honey bee mites.
bioRxiv
Published: 1 Oct 2019
https://doi.org/10.1038/s42003-019-0606-0


Techer MA, Rane RV, Grau ML, Roberts JMK, Sullivan ST, Liachko I, Childers AK, Evans JD, Mikheyev AS
Divergent evolutionary trajectories following speciation in two ectoparasitic honey bee mites.
Communications Biology; 2:357
Published: 1 Oct 2019
https://doi.org/10.1038/s42003-019-0606-0


Nomura Y, Yokobayashi Y. 
Systematic minimization of RNA ligase ribozyme through large-scale design-synthesis-sequence cycles.
Nucleic acids research; 47(17):8950-60
Published: 26 Sep 2019
https://doi.org/10.1093/nar/gkz729


Kawamura K, Maruyama IN. 
Forward genetic screen for Caenorhabditis elegans mutants with a shortened locomotor healthspan
G3: Genes, Genomes, Genetics;9(8):2415-23
Published: 8 Aug 2019
https://doi.org/10.1534/g3.119.400241


Techer MA, Rane RV, Grau ML, Roberts JM, Sullivan ST, Liachko I, Childers AK, Evans JD, Mikheyev AS. 
Genomic analyses of sibling honey bee ectoparasitic mite species show divergent strategies of adaptation.
bioRxiv
Published: 2 July 2019
https://doi.org/10.1101/512988


Marion Mennesson, Ken Maeda, Philippe Keith
Evolutionary aspects of cephalic sensory papillae of the Indo-Pacific species of Eleotris (Teleostei: Eleotridae).
Zoologica Scripta 48: 627–639 (2019)
Published: 2 July 2019
https://doi.org/10.1111/zsc.12366


Dehm D, Krumbholz J, Baunach M, Wiebach V, Hinrichs K, Guljamow A, Tabuchi T, Jenke-Kodama H, Sussmuth RD, Dittmann E. 
Unlocking the spatial control of secondary metabolism uncovers hidden natural product diversity in Nostoc punctiforme.
ACS chemical biology ;14(6):1271-9
Published: 24 May 2019
https://doi.org/10.1021/acschembio.9b00240


Beedessee G. 
Genomic insights on secondary metabolism in symbiotic dinoflagellates
Thesis or Dissertation
Published: 2019 Apr
https://doi.org/10.15102/1394.00000779


Brisbin MM, Conover AE, Mitarai S. 
Hydrothermal activity and water mass composition shape microbial eukaryote diversity and biogeography in the Okinawa Trough
bioRxiv
Published: 1 Jan 2019
https://doi.org/10.1101/714816


Kawamura, Kazuto. 
Forward genetic screen for Caenorhabditis elegans mutants with a progressive decline in adult locomotor function
Thesis or Dissertation
Published: Jan 2019
https://doi.org/10.15102/1394.00000766

 

Poetsch AR, Boulton SJ, Luscombe NM
Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis.
BioRxiv
Published: 07 December 2018
https://doi.org/10.1101/168153


Brisbin MM, Mesrop LY, Grossmann MM, Mitarai S.
Intra-host symbiont diversity and extended symbiont maintenance in photosymbiotic Acantharea (clade F).
bioRxiv
Published: 27 August 2018
https://doi.org/10.1101/299495


Inoue T, Barker CS, Matsunami H, Aizawa SI, Samatey FA.
The FlaG regulator is involved in length control of the polar flagella of Campylobacter jejuni.
Microbiology
Published: 01 May 2018
https://doi.org/10.1099/mic.0.000648


Sajiki K, Tahara Y, Villar-Briones A, Pluskal T, Teruya T, Mori A, Hatanaka M, Ebe M, Nakamura T, Aoki K, Nakaseko Y, Yanagida M.
Genetic defects in SAPK signalling, chromatin regulation, vesicle transport and CoA-related lipid metabolism are rescued by rapamycin in fission yeast.
Open Biol. 2018 Mar;8(3). pii: 170261. 
Published:28 March 2018
https://doi.org/10.1098/rsob.170261


Kobori S, Yokobayashi Y.
Analyzing and Tuning Ribozyme Activity by Deep Sequencing to Modulate Gene Expression Level in Mammalian Cells.
ACS Synthetic Biolology.
Published: 17 Jan 2018
https://doi.org/10.1021/acssynbio.7b00367


Soliman T, Yang SY, Yamazaki T, Jenke-Kodama H.
Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise.
PeerJ. 2017 Dec 19;5:e4178.
Published: 19 Dec 2017
https://doi.org/10.7717/peerj.4178


Soliman T, Reimer JD, Yang SY, Villar-Briones A, Roy MC, Jenke-Kodama H.
Diversity of Microbial Communities and Quantitative Chemodiversity in Layers of Marine Sediment Cores from a Causeway (Kaichu-Doro) in Okinawa Island, Japan.
Front Microbiol.
Published: 11 Dec 2017
https://doi.org/10.3389/fmicb.2017.02451


Nomura Y, Chien HC, Yokobayashi Y.
Direct screening for ribozyme activity in mammalian cells.
Chem Commun (Camb).
Published: 7 Nov 2017
https://doi.org/10.1039/c7cc07815c


Dhamodharan V, Kobori S, Yokobayashi Y.
Large Scale Mutational and Kinetic Analysis of a Self-Hydrolyzing Deoxyribozyme.
ACS Chem Biol. 
Published: 23 Oct 2017
https://doi.org/10.1021/acschembio.7b00621


Mikheyev AS, Zwick A, Magrath MJL, Grau ML, Qiu L, Su YN, Yeates D.
Museum Genomics Confirms that the Lord Howe Island Stick Insect Survived Extinction.
Curr Biol. 2017 Oct 4. pii: S0960-9822(17)31098-9.
Published: 23 October 2017
https://doi.org/10.1016/j.cub.2017.08.058


Khilyas IV, Sorokin AA, Kiseleva L, Simpson DJW, Fedorovich V, Sharipova MR, Kainuma M, Cohen MF, Goryanin I.
Comparative Metagenomic Analysis of Electrogenic Microbial Communities in Differentially Inoculated Swine Wastewater-Fed Microbial Fuel Cells.
Scientifica (Cairo). 
Published: 12 Oct 2017
https://doi.org/10.1155/2017/7616359


Aird SD, Arora J, Barua A, Qiu L, Terada K, Mikheyev AS.
Population Genomic Analysis of a Pitviper Reveals Microevolutionary Forces Underlying Venom Chemistry.
Genome Biol Evol. 2017 Oct 1;9(10):2640-2649. 
Published: 27 September 2017
https://doi.org/10.1093/gbe/evx199


Kobori S, Takahashi K, and Yokobayashi Y.
Deep Sequencing Analysis of Aptazyme Variants Based on a Pistol Ribozyme.
ACS Synthetic Biology (2017)
Published: 11 April 2017
https://doi.org/10.1021/acssynbio.7b00057

 

SQC in Materials and Methods

Mars Brisbin M, Mitarai S.
Differential Gene Expression Supports a Resource‐Intensive, Defensive Role for Colony Production in the Bloom‐Forming Haptophyte, Phaeocystis globosa
Journal of Eukaryotic Microbiology;66(5):788-801.
Published: 12 March 2019
https://doi.org/10.1111/jeu.12727


Marlétaz F, Peijnenburg KT, Goto T, Satoh N, Rokhsar DS.
A new spiralian phylogeny places the enigmatic arrow worms among gnathiferans
Current Biology ;29(2):312-8.
Published: 21 Jan 2019 
https://doi.org/10.1016/j.cub.2018.11.042

 

Past Publications by SQC users

Please click the link below to see the past publications by SQC users by year.