Jun Inoue

Last updated: Jun 11, 2019 at 09:04

Name	Jun Inoue
E-mail	jun.inouenig.ac.jp
Affiliation	National Institute of Genetics
Research funding number	10596779

Research Interests

Chordata(1) , Actinopterygii(1) , Genome comparison(1) , Molecular Phylogenetics(18)

Research Areas

Genome science / Genome biology /
Biological Science / Molecular biology / Molecular phylogenetics

Awards & Honors

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Aug 2016

Young Scientist Initiative Award, The Society of Evolutionary Studies, Japan

Oct 2014

Open science award, Database Center for Life Science

Jul 2011

The Award for Education and Enlightenment, The Society of Evolutionary Studies, Japan

Oct 2006

Encouraging prize, The Ichthyological Society of Japan

Published Papers

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A key metabolic gene for recurrent freshwater colonization and radiation in fishes

Ishikawa, A, Kabeya, N, Ikeya, K, Kakioka, R, Cech, JN, Osada, N, Leal, MC, Inoue J, Kume, M, Toyoda, A, Tezuka, A, Nagano, AJ, Yamasaki, YY, Suzuki, Y, Kokita, T, Takahashi, H, Lucek, K, Marques, D, Takehana, Y, Naruse, K, Mori, S, Monroig, O, Ladd, N, Schubert, C, Matthews, B, Peichel, CL, Seehausen, O, Yoshizaki, G, Kitano J.

Science 364 886-889 May 2019 [Refereed]

ORTHOSCOPE Analysis Reveals the Presence of the Cellulose Synthase Gene in All Tunicate Genomes but Not in Other Animal Genomes

Inoue J, Nakashima K, Satoh, N.

Genes 10 294 Apr 2019 [Refereed]

Tunicates or urochordates—comprising ascidians, larvaceans, and salps—are the only metazoans that can synthesize cellulose, a biological function usually associated with bacteria and plants but not animals. Tunicate cellulose or tunicine is a majo...

Repertoires of G protein-coupled receptors for Ciona-specific neuropeptides

Shiraishi A, Okuda T, Miyasaka N, Osugi T, Okuno Y, Inoue J, Satake H

Proceedings of the National Academy of Sciences 116(16) 7847 Apr 2019 [Refereed]

Deuterostome genomics: Lineage-specific protein expansions that enabled chordate muscle evolution.

Inoue J, Satoh N.

Molecular Biology and Evolution. 35(4) 914-924 Apr 2018 [Refereed]

ORTHOSCOPE: An Automatic Web Tool for Phylogenetically Inferring Bilaterian Orthogroups with User-Selected Taxa

Inoue J, Satoh N,

Molecular Biology and Evolution Mar 2019 [Refereed]

The chordate ancestor possessed a single copy of the Brachyury gene for notochord acquisition.

Inoue J, Yasuoka Y, Takahashi H, Satoh N.

Zoological Letters. 3 4 Dec 2017 [Refereed]

Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling.

Inoue J, Sato Y, Sinclair R, Tsukamoto K, Nishida M.

Proceedings of the National Academy of Sciences of the United States of America 112(48) 14918-14923 Dec 2015 [Refereed]

A draft genome of the striped catfish, Pangasianodon hypophthalmus, for comparative analysis of genes relevant to development and a resource for aquaculture improvement.

Kim OTP, Nguyen PT, Shoguchi E, Hisata K, Vo TTB, Inoue J, Shinzato C, Le BTN, Nishitsuji K, Kanda M, et al.

BMC Genomics 19 733 2018 [Refereed]

Evolutionary origin of the Scombridae (tunas and mackerels): members of a paleogene adaptive radiation with 14 other pelagic fish families.

Miya M., Friedman M, Satoh TP., Takeshima H., Sado T., Iwasaki W., Yamanoue Y., Nakatani M., Mabuchi K., Inoue JG., Poulsen JY., Fukunaga T., Sato Y., Nishida M.

Plos One 8(9) e73535 2013 [Refereed]

Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny.

dos Reis M, Inoue J, Hasegawa M, Asher RJ, Donoghue PCJ, Yang Z

Proceedings of the Royal Soceity B. 279(1742) 3491-3500 2012 [Refereed]

Best practices for justifying fossil calibrations.

Parham, J.F., Donoghue, P.C.J., Bell, C.J., Calway, T.D., Head, J.J., Holroyd, P.A., Inoue J.G., Irmis, R.B., Joyce, W.G., Ksepka, D.T., Patané, J.S.L., Smith, N.D., Tarver, J.E., van Tuinen, M., Yang, Z., Angielczyk, K.D., Greenwood, J., Hipsley, C.A., Jacobs, L., Makovicky, P.J., Müller, J., Smith, K.T., Theodor, J.M., Warnock, R.C.M., Benton, M.J.

Systematic Biology 61(2) 346-359 2012 [Refereed]

Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time and place of basal divergence of cypriniform fishes (Actinopterygii: Ostariophysi).

Saitoh, K., Sado, T., Doosey, M.H., Bart, Jr., H.L., Inoue J.G., Nishida, M., Mayden, R.L., Miya, M.

Zoological Journal of the Linnean Society, Zoological Journal of the Linnean Society 161(3) 633-662 2011 [Refereed]

Body plan convergence in the evolution of skates and rays (Chondrichthyes: Batoidea)

Aschliman N.C., Nishida M., Miya M., Inoue J.G., Rosana K.M., Naylor G.J.P.

Molecular Phylogenetics and Evolution 63(1) 28-42 2011 [Refereed]

The Impact of the Representation of Fossil Calibrations on Bayesian Estimation of Species Divergence Times

Inoue J.G., Donoghue P.C.J, Yang Z.

Systematic Biology 59(1) 74-89 2010 [Refereed]

Inter- specific and subspecific genetic divergences of freshwater eels, genus Anguilla including a recently described species, A. luzonensis, based on whole mitochondrial genome sequences.

Minegishi, Y., Aoyama, J., Inoue J.G., Azanza, R.V., Tsukamoto, K.

Coastal Marine Science 33 64-77 2010 [Refereed]

Evolutionary origin and phylogeny of the modern holocephalans (Chondrichthyes: Chimaeriformes): a mitogenomic perspective.

Inoue J.G., Miya, M., Lam, K., Tay B.H., Danks, J.A., Bell, J., Walker, T.I., Venkatesh, B.

Molecular Biology and Evolution 27(11) 2576-2586 2010 [Refereed]

The impact of the representation of fossil calibration on Bayesian estimation of species divergence times.

Inoue, J., Donoghue, P.C.J., Yang, Z.

Systematic Biology 59 74-89 2010 [Refereed]

The historical biogeography of the freshwater knifefishes using mitogenomic approaches: A Mesozoic origin of the Asian notopterids (Actinopterygii: Osteoglossomorpha)

Inoue J.G., Kumazawa, Y., Miya, M., Nishida, M.

Molecular Phylogenetics and Evolution 51(3) 486-499 2009 [Refereed]

Deep-ocean origin of the freshwater eels.

Inoue J.G., Miya, M., Miller, M.J., Sado, T., Hanel, R., Hatooka, K., Aoyama, J., Minegishi, M., Nishida, M., Tsukamoto, K.

Biology Letters 6(3) 363-366 2010 [Refereed]

Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates.

Setiamarga, D.H., Miya, M., Inoue J.G., Ishiguro, N.B., Mabuchi, K., Nishida, M.

Biology Letters 23(6) 812-816 2009 [Refereed]

Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): a new perspective based on whole mitogenome sequences from 75 higher teleosts

Kawahara, R., Miya, M. Mabuchi, K., Lavoue, S., Inoue J.G., Satoh, T. P., Kawaguchi, A., Nishida. M.

Molecular Phylogenetics and Evolution 46(1) 224-236 2008 [Refereed]

Interrelationships of Atherinomorpha (medakas, flyingfishes, killifishes, silversides, and their relatives): The first evidence based on whole mitogenome sequences.

Setiamarga, D.H., Miya, M., Yamanoue, Y., Mabuchi, K., Satoh, T.P., Inoue J.G., Nishida, M.

Molecular Phylogenetics and Evolution 49(2) 598-605 2008 [Refereed]

Genetic identification of two types of Ariosoma leptocephali.

Ma, T., Miller, M. J., Aoyama, J., Minagawa, M., Inoue J.G., Watanabe, S., Tsukamoto, K.

Coastal Marine Science 32 48-53 2008 [Refereed]

Genetic differentiation in the genus Uroconger in the Indo-Pacific region.

Ma, T., Aoyama, J., Miller, M.J., Minegishi, Y., Inoue J.G., Tsukamoto, K.

Aquatic Biology 2(1) 29-35 2008 [Refereed]

The mitochondrial genome of spotted green pufferfish Tetraodon nigroviridis (Teleostei: Tetraodontiformes) and divergence time estimation among model organisms in fishes.

Yamanoue, Y., Miya, M., Inoue J.G., Matsuura, K., Nishida, M.

Gene and Genetic Systems 81(1) 29-39 2006 [Refereed]

The mitochondrial genome of Indonesian coelacanth Latimeria menadoensis (Sarcopterygii: Coelacanthiformes) and divergence time estimation between the two coelacanths.

Inoue J.G., Miya, M., Venkatesh, B., Nishida, M.

Gene and Genetic Systems 349 227-235 2005 [Refereed]

Sundasalanx (Sundasalangidae) is a progenetic clupeiform, not a closely-related group of salangids (Osmeriformes): Mitogenomic evidence.

Ishiguro, N. B., Miya, M., Inoue J.G., Nishida, M.

Journal of Fish Biology 67(2) 561-569 2005 [Refereed]

Molecular systematics of the gonorynchiform fishes (Teleostei) based on whole mitogenome sequences: Implications for higher-level relationships within the Otocephala.

Lavoue, S., Miya, M., Inoue J.G., Saitoh, K., Ishiguro, N. B., Nishida, M.

Molecular Phylogenetics and Evolution 37(1) 165-177 2005 [Refereed]

Molecular phylogeny and evolution of the freshwater eels genus Anguilla based on the whole mitochondrial genome sequences

Minegishi, Y., Aoyama, J., Inoue J.G., Miya, M., Nishida, M., Tsukamoto, K.

Molecular Phylogenetics and Evolution 34(1) 134-146 2005 [Refereed]

Mitogenomic evidence for the monophyly of elopomorph fishes (Teleostei) and the evolutionary origin of the leptocephalus larva.

Inoue J.G., Miya, M., Tsukamoto, K., Nishida, M.

Molecular Phylogenetics and Evolution 32(1) 274-286 2004 [Refereed]

Ecological aspects of the downstream migration of introduced European eels in the Uono River, Japan

Miyai, T., Aoyama, J., Sasai, S., Inoue J.G., Miller, M. J., Tsukamoto, K.

Environmental Biology of Fishes 71(1) 105-114 2004 [Refereed]

Mitochondrial genomics of ostariophysan fishes: perspectives on phylogeny and biogeography

Saitoh, K., Miya, M., Inoue J.G., Ishiguro, N. B., Nishida, M.

Journal of Molecular Evolution 56(4) 464-472 2003 [Refereed]

Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences.

Miya, M., Takeshima, H., Endo, H., Ishiguro, N. B., Inoue J.G., Mukai, T., Satoh, T. P., Yamaguchi, M., Kawaguchi, A., Mabuchi, K., Shirai, S. M., Nishida, M.

Molecular Phylogenetics and Evolution 26(1) 121-138 2003 [Refereed]

Evolution of the deep-sea gulper eel mitochondrial genomes: large-scale gene rearrangements originated within the eels

Inoue J.G., Miya, M., Tsukamoto, K., Nishida, M.

Molecular Biology and Evolution 20(11) 1917-1924 2003 [Refereed]

Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the "ancient fish."

Inoue J.G., Miya, M., Tsukamoto, K., Nishida, M.

Molecular Phylogenetics and Evolution 26(1) 110-120 2003 [Refereed]

Phylogeny of the basal teleosts, with special reference to the Elopomorpha.

Inoue J.G., Miya, M.

Japanese Journal of Ichthyology 48 75-91 2001 [Refereed]

Molecular approach to species identification of eggs with respect to determination of the spawning site of the Japanese eel Anguilla japonica.

Aoyama, J., Ishikawa S., Otake, T., Mochioka, N., Suzuki, Y., Watanabe, S., Shinoda, A., Inoue J.G., et al.