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The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

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The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. / Braasch, I.; Gehrke, A.R.; Smith, J.J. et al.
In: Nature Genetics, 07.03.2016.

Research output: Contribution to journal › Article › peer-review

HarvardHarvard

Braasch, I, Gehrke, AR, Smith, JJ, Kawasaki, K, Manousaki, T, Pasquier, J, Amores, A, Desvignes, T, Batzel, P, Catchen, J, Berlin, AM, Campbell, MS, Barrell, D, Martin, KJ, Mulley, JF, Ravi, V, Lee, AP, Nakamura, T, Chalopin, D, Fan, S, Wcisel, D, Cañestro, C, Sydes, J, Beaudry, FE, Sun, Y, Hertel, J, Beam, MJ, Fasold, M, Ishiyama, M, Johnson, J, Kehr, S, Lara, M, Letaw, JH, Litman, GW, Litman, RT, Mikami, M, Ota, T, Saha, NR, Williams, L, Stadler, PF, Wang, H, Taylor, JS, Fontenot, Q, Ferrara, A, Searle, SM, Aken, B, Yandell, M, Schneider, I, Yoder, JA, Volff, J, Meyer, A, Amemiya, CT, Venkatesh, B, Holland, PW, Guiguen, Y, Bobe, J, Shubin, NH, Di Palma, F, Alföldi, J, Lindblad-Toh, K & Postlethwait, JH 2016, 'The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons', Nature Genetics. https://doi.org/10.1038/ng.3526

APA

Braasch, I., Gehrke, A. R., Smith, J. J., Kawasaki, K., Manousaki, T., Pasquier, J., Amores, A., Desvignes, T., Batzel, P., Catchen, J., Berlin, A. M., Campbell, M. S., Barrell, D., Martin, K. J., Mulley, J. F., Ravi, V., Lee, A. P., Nakamura, T., Chalopin, D., ... Postlethwait, J. H. (2016). The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature Genetics. https://doi.org/10.1038/ng.3526

CBE

Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, et al. 2016. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature Genetics. https://doi.org/10.1038/ng.3526

MLA

Braasch, I. et al. "The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons". Nature Genetics. 2016. https://doi.org/10.1038/ng.3526

VancouverVancouver

Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J et al. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature Genetics. 2016 Mar 7. doi: 10.1038/ng.3526

Author

Braasch, I. ; Gehrke, A.R. ; Smith, J.J. et al. / The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. In: Nature Genetics. 2016.

RIS

TY - JOUR

T1 - The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

AU - Braasch, I.

AU - Gehrke, A.R.

AU - Smith, J.J.

AU - Kawasaki, K.

AU - Manousaki, T.

AU - Pasquier, J.

AU - Amores, A.

AU - Desvignes, T.

AU - Batzel, P.

AU - Catchen, J.

AU - Berlin, A.M.

AU - Campbell, M.S.

AU - Barrell, D.

AU - Martin, K.J.

AU - Mulley, J.F.

AU - Ravi, V.

AU - Lee, A.P.

AU - Nakamura, T.

AU - Chalopin, D.

AU - Fan, S.

AU - Wcisel, D.

AU - Cañestro, C.

AU - Sydes, J.

AU - Beaudry, F.E.

AU - Sun, Y.

AU - Hertel, J.

AU - Beam, M.J.

AU - Fasold, M.

AU - Ishiyama, M.

AU - Johnson, J.

AU - Kehr, S.

AU - Lara, M.

AU - Letaw, J.H.

AU - Litman, G.W.

AU - Litman, R.T.

AU - Mikami, M.

AU - Ota, T.

AU - Saha, N.R.

AU - Williams, L.

AU - Stadler, P.F.

AU - Wang, H.

AU - Taylor, J.S.

AU - Fontenot, Q.

AU - Ferrara, A.

AU - Searle, S.M.

AU - Aken, B.

AU - Yandell, M.

AU - Schneider, I.

AU - Yoder, J.A.

AU - Volff, J.

AU - Meyer, A.

AU - Amemiya, C.T.

AU - Venkatesh, B.

AU - Holland, P.W.

AU - Guiguen, Y.

AU - Bobe, J.

AU - Shubin, N.H.

AU - Di Palma, F.

AU - Alföldi, J.

AU - Lindblad-Toh, K.

AU - Postlethwait, J.H.

PY - 2016/3/7

Y1 - 2016/3/7

N2 - To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.

AB - To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.

UR - https://static-content.springer.com/esm/art%3A10.1038%2Fng.3526/MediaObjects/41588_2016_BFng3526_MOESM269_ESM.pdf

U2 - 10.1038/ng.3526

DO - 10.1038/ng.3526

M3 - Article

JO - Nature Genetics

JF - Nature Genetics

SN - 1061-4036

ER -