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Xiphophorus Research Group

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Each of the Xiphophorus genomes have been greatly enhanced by PacBio sequencing and Bionano mapping. To take advantage of the improved genomes, the XGSC configured a platyfish genome hub that is hosted on the UCSC genome browser for genetic data visualization and data mining. See link for details.

The XGSC also configured a gene expression browser link to facilitate data visualization and tracking of genes of interest to determine gene basal expression level through light and dark phases over a 24-hr period.


WELCOME TO THE XIPHOPHORUS RESEARCH GROUP  


Publications for Recent Areas of Research

Warren, W., García-Pérez, R., Xu, S., Lampert, K., Chalopin, D., Stöck, M., Loewe, L., Lu, Y., Kuderna, L., Minx, P., Montague, M., Tomlinson, C., Hillier, L., Murphy, D., Wang, J., Wang, Z., Garcia, C.M., Thomas, G., Volff, J-N., Farias, F., Aken, B., Walter, R.B., Pruitt, K., Marques-Bonet, T., Hahn, M., Kneitz, S., Lynch, M., Schartl. M. (2018). Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly, Nature - Evolution and Ecology, 2:669–679. https://doi/10.1038/s41559-018-0473-y

Shen, Y., Chalopin, D., Garcia, T., Boswell, M., Boswell, W., Shiryayev, S., Agarwala. R., Volff, J-N, Postlethwait, J.H., Schartl, M., Minx, P., Warren, W.C., Walter, R.B. (2016). X. couchianus and X. hellerii genome models provide genomic variation insight among Xiphophorus species, BMC Genomics, 17:37-50.

Amores, A., Catchen, C., Nanda, I., Warren, W., Walter, R.B., and M. Schartl and J.H. Postlethwait (2014).  A Rad-tag genetic map for the playtfish (Xiphophorus maculatus) reveals mechanisms of karyotype evolution among teleost fish. Genetics, 197(2):625-641.

Schartl, M., Walter, R. B., Shen. Y., Garcia, T., Catchen, J., Amores. A., Braasch. I., Chapolin D., Volff, J-N., Lesch, K-P., Bisazza, A., Minx P., Wilson. R.K., Fuerstenberg, S., Boore, J., Postlethwait, J. H. and W.C. Warren (2013). The genome of the platyfish, Xiphophorus maculatus, Nature Genetics, 45(5):567-572.

Walter, R.B., Rains, J.D., Russell, J.E., Guerra, T.M., Daniels, C., Johnston, D.A., Kumar, J., Wheeler, A., Kelnar, K., Khanolkar, V.A., Williams, E.L., Hornecker, J.L., Hollek, L., Mamerow, M., Pedroza, A., and S. Kazianis (2004).  "A Microsatellite Genetic Linkage Map for Xiphophorus."  Genetics, 168:363-372.

 

Lu, Y., Boswell, M., Boswell, W., Kneitz, S., Hausmann, M., Klotz, B., Regneri, J., Savage, M., Amores, A., Postlethwait, J., Warren, W., Schartl, M., Walter, R.B. (2018). Comparison of Xiphophorus and Human Melanoma Transcriptomes Reveals Conserved Pathway Interactions, Pigment Cell Melanoma Res., 2018:1-13, https://doi.org/10.1111/pcmr.12686

Regneri, J., Klotz, B., Wilde, B., Kottler, V., Hausmann, M., Kneitz, S., Regensburger, M., Maurus, K., Götz, R., Lu, Y., Walter, R.B., Herpin, A., Schartl, M. (2018). Analysis of the putative tumor suppressor gene cdkn2ab in pigment cells and melanoma of Xiphophorus and medaka, Pigment Cell Melanoma Res. 2018;00:1–11, https://doi.org/10.1111/pcmr.12729

Lu, Y., Boswell, M., Boswell, W., Kneitz, S., Hausmann, M., Klotz, B., Regneri, J., Savage, M., Amores, A., Postlethwait, J., Warren, W., Schartl, M., Walter, R.B. (2017). Molecular genetic analysis of the melanoma regulatory locus in Xiphophorus Interspecies hybrids, Molecular Carcinogenesis, 56(8):1935-1944.

Kneitz, S., Mishra, R., Chalopin, D., Postlethwait, J.H., Warren, W., Walter, R.B., Schartl, M. (2016). Germ cell and tumor associated piRNAs in the medaka and Xiphophorus melanoma models, BMC Genomics, 17:357, https://doi.org/10.1186/s12864-016-2697-z

Laisney, J., Braasch, I., Walter, R.B., Meierjohann, S. and M. Schartl (2010) Lineage-specific Co-evolution of the EGFR/EGFR Ligand Signalling System. BMC Evolutionary Biology, 10:27-34.

Wood, S.R., Berwick, M., Ley, R.D., Walter, R.B., and G.S. Timmins (2006)  "UV Causation of melanoma in Xiphophorus Is Dominated by Melanin Photosensitized Oxidant Production."  Proc. of the National Academy of Sciences (USA), 103 (11):4111-4115.

 

Boswell, M., W. Boswell, Y. Lu, M. Savage, R. Walter (2020). Deconvoluting Wavelengths Leading to Fluorescent Light Induced Inflammation and Cellular Stress in Zebrafish (Danio rerio), SREP, "In Press".

Lu, Y., Boswell, W., Boswell, M., Klotz, B, Kneitz, S., Regneri, J., Savage, M., Mendoza. C., Postlethwait. J., Warren, W.C., Schartl, M., Walter, R.B. (2018). Application of the Transcriptional Disease Signatures (TDSs) to Screen Melanoma-Effective Compounds in a Small Fish Model, Scientific Reports, 9:530-543. https://doi.org/10.1038/s44158-018-36656-x

Warren, W.C., Kuderna, L., Alexander, A., Catchen, J., Pérez-Silva, J.G., López-Otín, Víctor Quesada, C., Minx, P., Tomlinson, C., Montague, M., Farias, F.H.G., Walter, R.B., Marques-Bonet, T., Glenn, T., Kieran, T.J., Wise, S.S., Wise Jr., J.P., Waterhouse, R.M., and J.P. Wise, Sr. (2018). The novel evolution of the sperm whale genome, Genome Biol. Evolution, 9(12):3260-3264. https://doi.org/10.1093/gbe/evx187

Warren, W., García-Pérez, R., Xu, S., Lampert, K., Chalopin, D., Stöck, M., Loewe, L., Lu, Y., Kuderna, L., Minx, P., Montague, M., Tomlinson, C., Hillier, L., Murphy, D., Wang, J., Wang, Z., Garcia, C.M., Thomas, G., Volff, J-N., Farias, F., Aken, B., Walter, R.B., Pruitt, K., Marques-Bonet, T., Hahn, M., Kneitz, S., Lynch, M., Schartl, M. (2018). Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly, Nature - Evolution & Ecology, 2:669–679, https://doi.org/10.1038/s41559-018-0473-y

Schartl, M., Shen, Y., Maurus, K., Walter, R.B., Wilson, R.K., Postlethwait, J.H., Warren, W.C. (2015). Whole body melanoma Ttranscriptome response in medaka, PLoS-ONE, 10:2 (Dec. 2015), https://doi.org/10.1371/journal.pone.0143057

Garcia T.I., Matos I., Shen, Y., Pabuwal V., Coelho, M.M., Wakamatsu, Y., Schartl, M., and R.B. Walter (2014). Novel Method for Analysis of Allele Specific Expression in Triploid Oryzias latipes Reveals Consistent Pattern of Allele Exclusion. PLOS ONE 9(6): e100250.

Garcia, T.I., Shen, Y., Whitehead, A., Oleksiak, M., Crawford, D.C., and R.B. Walter (2012). RNA-Seq reveals complex genetic response to Deepwater Horizon oil release in Fundulus grandis. BMC Genomics, 13:474-483. 13:474-483.

Whitehead, A., Dubansky, B., Bodiner, C., Garcia, T., Miles, S., Pilley, C., Raghunathan, V., Roach, J., Walker, N., Walter, R.B., Rice, C.D., and F. Glavez  (2012). Genomic and Physiological Footprint of the Deepwater Horizon Oil Spill on Resident Marsh Fishes. Proc. of the National Academy of Sciences (USA), 109(50): 20298-20302.

 

Boswell, M., Lu, Y., Boswell, W., Savage, M., Hildreth, K., Salinas, R., Walter. C.A, Walter, R.B. (2019). Fluorescent light incites a highly conserved immune and inflammatory genetic response within internal and external organs of vertebrates (Danio rerio, Oryzias latipes and Mus musculus), Genes, 10.271.,  https://www.mdpi.com/2073-4425/10/4/271

Walter, R.B., Boswell, M, Chang, J., Boswell, W.T., Lu, Y., Navarro, K, Walter, S.M., Walter, D.J., Salinas, R. and M. Savage (2018). Waveband specific transcriptional control of select genetic pathways in vertebrate Skin, BMC Genomics, 19:355-373.  https://doi.org/10.1186/s12864-018-4735-5

Gonzalez, T. J., Lu, Y., Boswell, M., Boswell, W., Medrano, G., Walter, S., Ellis, S., Savage, M., Varga, Z.M., Lawrence, C., Walter, R.B. (2018). Fluorescent light exposure incites acute and prolonged Immune responses in zebrafish (Danio rerio) skin, Comp. Biochem. & Physiology, Part C, 208:87-95.  https://doi.org/10.1016/j.cbpc.2017.09.009

Boswell, M., Boswell, W., Lu, Y., Savage, M., Mazurek, Z., Chang, J., Muster, J., Walter, R.B. (2018). The Transcriptional response of skin to fluorescent light exposure in viviparous (Xiphophorus) and oviparous (Danio, Oryzias) fishes, Comp. Biochem. & Physiology, Part C, 208:77-86. https://doi.org/10.1016/j.cbpc.2017.10.003