ZFIN ID: ZDB-PERS-000504-1
Taylor, John
Email: taylorjs@uvic.ca
Address: Department of Biology University of Victoria P.O. Box 3020 Station CSC Victoria, British Columbia, V8W 2N5 Canada
Phone: Office: (250) 472-5206; Lab: (250) 472-5213
Fax: (250) 721-7120

The discovery of extra Hox gene clusters in zebrafish (Danio rerio), medaka (Oryzias latipes) and pufferfish (Fugu rubripes) has led to the hypothesis that a genome duplication event occurred after the divergence of ray-finned and lobe-finned fishes. Teleostei is the most diverse of all vertebrate groups with approximately 25,000 species and genome duplication may have facilitated this radiation.

The fish-specific genome duplication hypothesis makes clear predictions about the number of genes in fish compared to tetrapods and about the topology of gene trees. Fish should have twice the number of genes found in tetrapods, a gene tree should match the expected organismal tree but each tetrapod gene should have two orthologs in fish. Furthermore, the fish orthologs should be sister sequences in a phylogenetic analysis and different gene trees should all indicate that duplicated genes in fish were formed at the same time.

I have been collecting human and zebrafish protein sequences from the protein database at NCBI to determine whether gene numbers and gene phylogenies support the fish-specific duplication hypothesis. I have also collected sequences from Mus musculus, Gallus gallus,and Xenopus laevisin order to reconstruct phylogenies necessary to identify orthologous genes among the many sequences retrieved in NCBI BLAST searches. Phylogenies of 25 genes fit the predictions of the fish-specific genome duplication hypothesis. These genes that appear to have been produced during the same duplication event are distributed throughout the zebrafish genome.

I am currently reviewing the gene expression literature in order to study variation in expression patterns among genes produced during the fish-specific genome duplication event. I am also reconstructing phylogenies of zebrafish genes listed in a recent mapping study (Woods et al., 2000, Genome Res. 10:1903-1914) that are thought to have been produced during the fish-specific genome duplication event. This study has recently expanded to include all protein sequences available from Actinopterygii and nucleotide sequence data from Tetradon. Furthermore, all available human CDS sequences have been used as BLAST query sequences.

Choi, J., Zhang, T., Vu, A., Ablain, J., Makowski, M.M., Colli, L.M., Xu, M., Hennessey, R.C., Yin, J., Rothschild, H., Gräwe, C., Kovacs, M.A., Funderburk, K.M., Brossard, M., Taylor, J., Pasaniuc, B., Chari, R., Chanock, S.J., Hoggart, C.J., Demenais, F., Barrett, J.H., Law, M.H., Iles, M.M., Yu, K., Vermeulen, M., Zon, L.I., Brown, K.M. (2020) Massively parallel reporter assays of melanoma risk variants identify MX2 as a gene promoting melanoma. Nature communications. 11:2718
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
Bourgenot, C., Saunter, C.D., Taylor, J.M., Girkin, J.M., and Love, G.D. (2012) 3D adaptive optics in a light sheet microscope. Optics express. 20(12):13252-13261
Rennison, D.J., Owens, G.L., and Taylor, J.S. (2012) Opsin gene duplication and divergence in ray-finned fish. Molecular phylogenetics and evolution. 62(3):986-1008
Hoegg, S., Brinkmann, H., Taylor, J.S., and Meyer, A. (2004) Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish. Journal of molecular evolution. 59(2):190-203
Klinger, M., Taylor, J.S., Oertle, T., Schwab, M.E., Stürmer, C.A., and Diekmann, H. (2004) Identification of Nogo-66 receptor (NgR) and homologous genes in fish. Mol. Biol. Evol.. 21(1):76-85
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
van de Peer, Y., Taylor, J.S., and Meyer, A. (2003) Are all fishes ancient polyploids?. Journal of structural and functional genomics. 3(1-4):65-73
van de Peer, Y., Frickey, T., Taylor, J., and Meyer, A. (2002) Dealing with saturation at the amino acid level: a case study based on anciently duplicated zebrafish genes. Gene. 295(2):205-211
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
Taylor, J.S., van de Peer, Y., and Meyer, A. (2001) Genome duplication, divergent resolution and speciation. Trends in genetics : TIG. 17:299-301

Taylor, J.S. and Brinkmann, H. (2001) 2R or not 2R? Meeting Report: Gene and Genome Duplications and the Evolution of Novel Gene Functions (Jacques Monod conference, Aussois, France, April 2001). Trends in Genetics 17:488-489.

Taylor, J.S. and Breden, F. (2000) Slipped-strand mispairing at noncontiguous repeats in Poecilia reticulata: a model for minisatellite birth. Genetics 155:1313-1320.

Taylor, J.S., Durkin, J.M.H., and Breden, F. (1999) The death of a microsatellite: a phylogenetic perspective on microsatellite interruptions. Mol. Biol. Evol. 16:567-572.

Taylor, J.S., Sanny, S.P., and Breden, F. (1999) Microsatellite homoplasy in the guppy (Poecilia reticulata). J. Mol. Evol. 48:245-247.

Packer, L., Taylor, J.S., Savignano, D.A., Bleser, C.A., Lane, C.P., and Sommer, L.A. (1998) Taxonomic status, genetic variation and gene flow in an endangered butterfly, Lycaeides melissa samuelis (Lepidoptera; Lycaenidae). Can. J. Zool. 76:320-329.

Packer, L. and Taylor, J.S. (1997) How many hidden species are there? An application of the phylogenetic species concept to genetic data for some comparatively well known bee 'species'. Can. Ent. 129:587-594.

Fenton, M.B., Rautenbach, I.L., Chipese, D., Cumming, M.B., Musgrave, M.K., Taylor, J.S., and Volpers, T. (1993) Variation in foraging behaviour, habitat use, and diet of large slit-faced bats (Nycteris grandis). Zeitschrift für Säugetierkunde 58:65-74.