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

I. Braasch; A.R. Gehrke; J.J. Smith; K. Kawasaki; T. Manousaki; J. Pasquier; A. Amores; T. Desvignes; P. Batzel; J. Catchen; A.M. Berlin; M.S. Campbell; D. Barrell; K.J. Martin; J.F. Mulley; V. Ravi; A.P. Lee; T. Nakamura; D. Chalopin; S. Fan; D. Wcisel; C. Cañestro; J. Sydes; F.E. Beaudry; Y. Sun; J. Hertel; M.J. Beam; M. Fasold; M. Ishiyama; J. Johnson; S. Kehr; M. Lara; J.H. Letaw; G.W. Litman; R.T. Litman; M. Mikami; T. Ota; N.R. Saha; L. Williams; P.F. Stadler; H. Wang; J.S. Taylor; Q. Fontenot; A. Ferrara; S.M. Searle; B. Aken; M. Yandell; I. Schneider; J.A. Yoder; J. Volff; A. Meyer; C.T. Amemiya; B. Venkatesh; P.W. Holland; Y. Guiguen; J. Bobe; N.H. Shubin; F. Di Palma; J. Alföldi; K. Lindblad-Toh; J.H. Postlethwait

doi:10.1038/ng.3526

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

I. Braasch, A.R. Gehrke, J.J. Smith, K. Kawasaki, T. Manousaki, J. Pasquier, A. Amores, T. Desvignes, P. Batzel, J. Catchen, A.M. Berlin, M.S. Campbell, D. Barrell, K.J. Martin, J.F. Mulley, V. Ravi, A.P. Lee, T. Nakamura, D. Chalopin, S. FanD. Wcisel, C. Cañestro, J. Sydes, F.E. Beaudry, Y. Sun, J. Hertel, M.J. Beam, M. Fasold, M. Ishiyama, J. Johnson, S. Kehr, M. Lara, J.H. Letaw, G.W. Litman, R.T. Litman, M. Mikami, T. Ota, N.R. Saha, L. Williams, P.F. Stadler, H. Wang, J.S. Taylor, Q. Fontenot, A. Ferrara, S.M. Searle, B. Aken, M. Yandell, I. Schneider, J.A. Yoder, J. Volff, A. Meyer, C.T. Amemiya, B. Venkatesh, P.W. Holland, Y. Guiguen, J. Bobe, N.H. Shubin, F. Di Palma, J. Alföldi, K. Lindblad-Toh, J.H. Postlethwait

School of Environmental & Natural Sciences

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Abstract

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.

Original language	English
Journal	Nature Genetics
DOIs	https://doi.org/10.1038/ng.3526
Publication status	Published - 7 Mar 2016

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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

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title = "The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons",

abstract = "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.",

author = "I. Braasch and A.R. Gehrke and J.J. Smith and K. Kawasaki and T. Manousaki and J. Pasquier and A. Amores and T. Desvignes and P. Batzel and J. Catchen and A.M. Berlin and M.S. Campbell and D. Barrell and K.J. Martin and J.F. Mulley and V. Ravi and A.P. Lee and T. Nakamura and D. Chalopin and S. Fan and D. Wcisel and C. Ca{\~n}estro and J. Sydes and F.E. Beaudry and Y. Sun and J. Hertel and M.J. Beam and M. Fasold and M. Ishiyama and J. Johnson and S. Kehr and M. Lara and J.H. Letaw and G.W. Litman and R.T. Litman and M. Mikami and T. Ota and N.R. Saha and L. Williams and P.F. Stadler and H. Wang and J.S. Taylor and Q. Fontenot and A. Ferrara and S.M. Searle and B. Aken and M. Yandell and I. Schneider and J.A. Yoder and J. Volff and A. Meyer and C.T. Amemiya and B. Venkatesh and P.W. Holland and Y. Guiguen and J. Bobe and N.H. Shubin and \{Di Palma\}, F. and J. Alf{\"o}ldi and K. Lindblad-Toh and J.H. Postlethwait",

year = "2016",

month = mar,

day = "7",

doi = "10.1038/ng.3526",

language = "English",

journal = "Nature Genetics",

issn = "1061-4036",

publisher = "Nature Research",

}

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

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

SN - 1061-4036

JO - Nature Genetics

JF - Nature Genetics

ER -

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

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