ZFIN ID: ZDB-LAB-170706-1
Braasch Lab
PI/Director: Braasch, Ingo
Contact Person: Braasch, Ingo
Email: braasch@msu.edu
URL: https://www.researchgate.net/profile/Ingo_Braasch
Address: Michigan State University Department of Integrative Biology (IBIO) College of Natural Science 288 Farm Lane, Nat Sci 203 East Lansing, MI 48824 USA
Country: United States
Phone: +1 517 432 3484 (office) 3485 (lab)
Line Designation: msu


Research in the Braasch FishEvoDevoGeno Lab addresses fundamental questions about the genomic and developmental basis of major transitions during the course of vertebrate evolution. We study genomic and morphological novelties in vertebrates at the levels of genome structure, gene family dynamics, and gene regulation and combine comparative genomics with analyses of molecular evolution and developmental genetic approaches using teleost fishes such as zebrafish and medaka and ‘ancient’ fishes such as spotted gar (Lepisosteus oculatus) as model systems. Through comparative genomic approaches, we also aim to improve connectivity of human to zebrafish and medaka as biomedical models.

Thompson, Andrew W. Post-Doc Kozel, Carrie Fish Facility Staff

Vigouroux, R.J., Duroure, K., Vougny, J., Albadri, S., Kozulin, P., Herrera, E., Nguyen-Ba-Charvet, K., Braasch, I., Suárez, R., Del Bene, F., Chédotal, A. (2021) Bilateral visual projections exist in non-teleost bony fish and predate the emergence of tetrapods. Science (New York, N.Y.). 372:150-156
Thompson, W.A., Vijayan, M.M. (2020) Zygotic Venlafaxine Exposure Impacts Behavioral Programming by Disrupting Brain Serotonin in Zebrafish. Environmental science & technology. 54:14578-14588
Ganz, J., Melancon, E., Wilson, C., Amores, A., Batzel, P., Strader, M., Braasch, I., Diba, P., Kuhlman, J.A., Postlethwait, J.H., Eisen, J.S. (2019) Epigenetic factors Dnmt1 and Uhrf1 coordinate intestinal development. Developmental Biology. 455:473-484
Cal, L., Suarez-Bregua, P., Braasch, I., Irion, U., Kelsh, R., Cerdá-Reverter, J.M., Rotllant, J. (2019) Loss-of-function mutations in the melanocortin-1-receptor (Mc1r) cause disruption of dorso-ventral countershading in teleost fish. Pigment cell & melanoma research. 32(6):817-828
Cal, L., Suarez-Bregua, P., Comesaña, P., Owen, J., Braasch, I., Kelsh, R., Cerdá-Reverter, J.M., Rotllant, J. (2019) Countershading in zebrafish results from an Asip1 controlled dorsoventral gradient of pigment cell differentiation. Scientific Reports. 9:3449
Spiewak, J.E., Bain, E.J., Liu, J., Kou, K., Sturiale, S.L., Patterson, L.B., Diba, P., Eisen, J.S., Braasch, I., Ganz, J., Parichy, D.M. (2018) Evolution of Endothelin signaling and diversification of adult pigment pattern in Danio fishes. PLoS Genetics. 14:e1007538
Heap, L.A.L., Vanwalleghem, G., Thompson, A.W., Favre-Bulle, I.A., Scott, E.K. (2018) Luminance Changes Drive Directional Startle through a Thalamic Pathway. Neuron. 99(2):293-301.e4
Cal, L., MegÍas, M., Cerdá-Reverter, J.M., Postlethwait, J.H., Braasch, I., Rotllant, J. (2017) BAC Recombineering of the Agouti Loci from Spotted Gar and Zebrafish Reveals the Evolutionary Ancestry of Dorsal-Ventral Pigment Asymmetry in Fish. Journal of experimental zoology. Part B, Molecular and developmental evolution. 328(7):697-708
Pasquier, J., Braasch, I., Batzel, P., Cabau, C., Montfort, J., Nguyen, T., Jouanno, E., Berthelot, C., Klopp, C., Journot, L., Postlethwait, J.H., Guiguen, Y., Bobe, J. (2017) Evolution of gene expression after whole-genome duplication: New insights from the spotted gar genome. Journal of experimental zoology. Part B, Molecular and developmental evolution. 328(7):709-721
Suarez-Bregua, P., Torres-Nuñez, E., Saxena, A., Guerreiro, P., Braasch, I., Prober, D.A., Moran, P., Cerda-Reverter, J.M., Du, S.J., Adrio, F., Power, D.M., Canario, A.V., Postlethwait, J.H., Bronner, M.E., Cañestro, C., Rotllant, J. (2017) Pth4, an ancient parathyroid hormone lost in eutherian mammals, reveals a new brain-to-bone signaling pathway. FASEB journal : official publication of the Federation of American Societies for Experimental Biology. 31:569-583
Sukeena, J.M., Galicia, C.A., Wilson, J.D., McGinn, T., Boughman, J.W., Robison, B.D., Postlethwait, J.H., Braasch, I., Stenkamp, D.L., Fuerst, P.G. (2016) Characterization and Evolution of the Spotted Gar Retina. Journal of experimental zoology. Part B, Molecular and developmental evolution. 326(7):403-421
Askary, A., Smeeton, J., Paul, S., Schindler, S., Braasch, I., Ellis, N.A., Postlethwait, J., Miller, C.T., Crump, J.G. (2016) Ancient origin of lubricated joints in bony vertebrates. eLIFE. 5
Pasquier, J., Cabau, C., Nguyen, T., Jouanno, E., Severac, D., Braasch, I., Journot, L., Pontarotti, P., Klopp, C., Postlethwait, J.H., Guiguen, Y., Bobe, J. (2016) Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database. BMC Genomics. 17:368
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., Fan, S., Wcisel, D., Cañestro, C., Sydes, J., Beaudry, F.E., Sun, Y., Hertel, J., Beam, M.J., Fasold, M., Ishiyama, M., Johnson, J., Kehr, S., Lara, M., Letaw, J.H., Litman, G.W., Litman, R.T., Mikami, M., Ota, T., Saha, N.R., Williams, L., Stadler, P.F., Wang, H., Taylor, J.S., Fontenot, Q., Ferrara, A., Searle, S.M., Aken, B., Yandell, M., Schneider, I., Yoder, J.A., Volff, J.N., Meyer, A., Amemiya, C.T., Venkatesh, B., Holland, P.W., Guiguen, Y., Bobe, J., Shubin, N.H., Di Palma, F., Alföldi, J., Lindblad-Toh, K., Postlethwait, J.H. (2016) The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature Genetics. 48(4):427-37
Braasch, I., Peterson, S.M., Desvignes, T., McCluskey, B.M., Batzel, P., Postlethwait, J.H. (2015) A new model army: Emerging fish models to study the genomics of vertebrate Evo-Devo. Journal of experimental zoology. Part B, Molecular and developmental evolution. 324(4):316-41
Gehrke, A.R., Schneider, I., de la Calle-Mustienes, E., Tena, J.J., Gomez-Marin, C., Chandran, M., Nakamura, T., Braasch, I., Postlethwait, J.H., Gómez-Skarmeta, J.L., Shubin, N.H. (2015) Deep conservation of wrist and digit enhancers in fish. Proceedings of the National Academy of Sciences of the United States of America. 112(3):803-8
Ganz, J., Kroehne, V., Freudenreich, D., Machate, A., Geffarth, M., Braasch, I., Kaslin, J., Brand, M. (2014) Subdivisions of the adult zebrafish pallium based on molecular marker analysis. F1000Research. 3:308
Santos, M.E., Braasch, I., Boileau, N., Meyer, B.S., Sauteur, L., Böhne, A., Belting, H.G., Affolter, M., Salzburger, W. (2014) The evolution of cichlid fish egg-spots is linked with a cis-regulatory change. Nature communications. 5:5149
Braasch, I., Guiguen, Y., Loker, R., Letaw, J.H., Ferrara, A., Bobe, J., and Postlethwait, J.H. (2014) Connectivity of vertebrate genomes: Paired-related homeobox (Prrx) genes in spotted gar, basal teleosts, and tetrapods. Comparative biochemistry and physiology. Toxicology & pharmacology : CBP. 163:24-36
Meng, F., Braasch, I., Phillips, J.B., Lin, X., Titus, T., Zhang, C., and Postlethwait, J.H. (2013) Evolution of the eye transcriptome under constant darkness in Sinocyclocheilus cavefish. Mol. Biol. Evol.. 30(7):1527-1543
Schartl, M., Walter, R.B., Shen, Y., Garcia, T., Catchen, J., Amores, A., Braasch, I., Chalopin, D., Volff, J.N., Lesch, K.P., Bisazza, A., Minx, P., Hillier, L., Wilson, R.K., Fuerstenberg, S., Boore, J., Searle, S., Postlethwait, J.H., and Warren, W.C. (2013) The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits. Nature Genetics. 45(5):567-572
Amemiya, C.T., Alfoldi, J., Lee, A.P., Fan, S., Philippe, H., MacCallum, I., Braasch, I., Manousaki, T., Schneider, I., Rohner, N., Organ, C., Chalopin, D., Smith, J.J., Robinson, M., Dorrington, R.A., Gerdol, M., Aken, B., Biscotti, M.A., Barucca, M., Baurain, D., Berlin, A.M., Blatch, G.L., Buonocore, F., Burmester, T., Campbell, M.S., Canapa, A., Cannon, J.P., Christoffels, A., de Moro, G., Edkins, A.L., Fan, L., Fausto, A.M., Feiner, N., Forconi, M., Gamieldien, J., Gnerre, S., Gnirke, A., Goldstone, J.V., Haerty, W., Hahn, M.E., Hesse, U., Hoffmann, S., Johnson, J., Karchner, S.I., Karaku, S., Lara, M., Levin, J.Z., Litman, G.W., Mauceli, E., Miyake, T., Mueller, M.G., Nelson, D.R., Nitsche, A., Olmo, E., Ota, T., Pallavicini, A., Panji, S., Picone, B., Ponting, C.P., Prohaska, S.J., Przybylski, D., Saha, N.R., Ravi, V., Ribeiro, F.J., Sauka-Spengler, T., Scapigliati, G., Searle, S.M.J., Sharpe, T., Simakov, O., Stadler, P.F., Stegeman, J.J., Sumiyama, K., Tabbaa, D., Tafer, H., Turner-Maier, J., van Heusden, P., White, S., Williams, L., Yandell, M., Brinkmann, H., Volff, J.N., Tabin, C.J., Shubin, N., Schartl, M., Jaffe, D.B., Postlethwait, J.H., Venkatesh, B., Palma, F.D., Lander, E.S., Meyer, A., and Lindblad-Toh, K. (2013) The African coelacanth genome provides insights into tetrapod evolution. Nature. 496:311-316
Delaurier, A., Nakamura, Y., Braasch, I., Khanna, V., Kato, H., Wakitani, S., Postlethwait, J.H., and Kimmel, C.B. (2012) Histone deacetylase-4 is required during early cranial neural crest development for generation of the zebrafish palatal skeleton. BMC Developmental Biology. 12(1):16
Anderson, J.L., Rodriguez-Mari, A., Braasch, I., Amores, A., Hohenlohe, P., Batzel, P., and Postlethwait, J.H. (2012) Multiple Sex-Associated Regions and a Putative Sex Chromosome in Zebrafish Revealed by RAD Mapping and Population Genomics. PLoS One. 7(7):e40701
McFarlane, L., Svingen, T., Braasch, I., Koopman, P., Schartl, M., and Wilhelm, D. (2011) Expansion of the Ago gene family in the teleost clade. Development genes and evolution. 221(2):95-204
Braasch, I., and Postlethwait, J.H. (2011) The teleost agouti-related protein 2 gene is an ohnolog gone missing from the tetrapod genome. Proceedings of the National Academy of Sciences of the United States of America. 108(13):E47-E48
Catchen, J.M., Braasch, I., and Postlethwait, J.H. (2011) Conserved synteny and the zebrafish genome. Methods in cell biology. 104:259-285
Herpin, A., Braasch, I., Kraeussling, M., Schmidt, C., Thoma, E.C., Nakamura, S., Tanaka, M., and Schartl, M. (2010) Transcriptional rewiring of the sex determining dmrt1 gene duplicate by transposable elements. PLoS Genetics. 6(2):e1000844
Laisney, J.A., Braasch, I., Walter, R.B., Meierjohann, S., and Schartl, M. (2010) Lineage-specific co-evolution of the Egf receptor/ligand signaling system. BMC Evolutionary Biology. 10:27
Braasch, I., Liedtke, D., Volff, J.N., and Schartl, M. (2009) Pigmentary function and evolution of tyrp1 gene duplicates in fish. Pigment cell & melanoma research. 22(6):839-850
Braasch, I., Brunet, F., Volff, J.N., and Schartl, M. (2009) Pigmentation pathway evolution after whole-genome duplication in fish. Genome biology and evolution. 1:479-493
Braasch, I., Volff, J.N., and Schartl, M. (2009) The endothelin system: evolution of vertebrate-specific ligand-receptor interactions by three rounds of genome duplication. Mol. Biol. Evol.. 26(4):783-799
Klüver, N., Herpin, A., Braasch, I., Driessle, J., and Schartl, M. (2009) Regulatory back-up circuit of medaka Wt1 co-orthologs ensures PGC maintenance. Developmental Biology. 325(1):179-188
Braasch, I., Volff, J.N., and Schartl, M. (2008) The evolution of teleost pigmentation and the fish-specific genome duplication. Journal of Fish Biology. 73(8):1891-1918
Salzburger, W., Renn, S.C., Steinke, D., Braasch, I., Hofmann, H.A., and Meyer, A. (2008) Annotation of expressed sequence tags for the East African cichlid fish Astatotilapia burtoni and evolutionary analyses of cichlid ORFs. BMC Genomics. 9:96
Selz, Y., Braasch, I., Hoffmann, C., Schmidt, C., Schultheis, C., Schartl, M., and Volff, J.N. (2007) Evolution of melanocortin receptors in teleost fish: The melanocortin type 1 receptor. Gene. 401(1-2):114-122
Siegel, N., Hoegg, S., Salzburger, W., Braasch, I., and Meyer, A. (2007) Comparative genomics of ParaHox clusters of teleost fishes: gene cluster breakup and the retention of gene sets following whole genome duplications. BMC Genomics. 8:312
Braasch, I., Schartl, M., and Volff, J.N. (2007) Evolution of pigment synthesis pathways by gene and genome duplication in fish. BMC Evolutionary Biology. 7(1):74
Braasch, I., Salzburger, W., and Meyer, A. (2006) Asymmetric evolution in two fish-specifically duplicated receptor tyrosine kinase paralogons involved in teleost coloration. Mol. Biol. Evol.. 23(6):1192-1202
Steinke, D., Salzburger, W., Braasch, I., and Meyer, A. (2006) Many genes in fish have species-specific asymmetric rates of molecular evolution. BMC Genomics. 7(1):20
Taylor, J.S., Braasch, I., Frickey, T., Meyer, A., and van de Peer, Yves (2003) Genome duplication, a trait shared by 22,000 species of ray-finned fish. Genome research. 13(3):382-390
Taylor, J.S., van de Peer, Y., Braasch, I., and Meyer, A. (2001) Comparative genomics provides evidence for an ancient genome duplication event in fish. Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 356(1414):1661-1679
van de Peer, Y., Taylor, J.S., Braasch, I., and Meyer, A. (2001) The ghost of selection past: rates of evolution and functional divergence of anciently duplicated genes. Journal of molecular evolution. 53(4-5):436-446