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Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling

    • 1Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA;
    • 2Department of Biology, St. Cloud State University, St. Cloud, Minnesota 56301, USA;
    • 3Driver Group, LLC, San Francisco, California 94158, USA;
    • 4BioTuring, Incorporated, San Diego, California 92121, USA;
    • 5Department of Biochemistry, Stanford University, Stanford, California 94305, USA;
    • 6California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA;
    • 7Dovetail Genomics, LLC, Santa Cruz, California 95060, USA;
    • 8Department of Biological Sciences, Texas Tech University, Lubbock, Texas 79409, USA;
    • 9Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, Mississippi 39762, USA;
    • 10School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona 85721, USA;
    • 11Department of Animal Science, University of California, Davis, California 95616, USA;
    • 12HCM University of Science, Ho Chí Minh, Vietnam 748500;
    • 13Department of Animal and Food Sciences, University of Delaware, Newark, Delaware 19717, USA;
    • 14Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, California 95064, USA;
    • 15Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA;
    • 16Department of Obstetrics and Gynecology, Marine Biomedicine and Environmental Science Center, Hollings Marine Laboratory, Medical University of South Carolina, Charleston, South Carolina 29412, USA
    • † Deceased August 6, 2015.
Published January 30, 2017. Vol 27 Issue 5, pp. 686-696. https://doi.org/10.1101/gr.213595.116
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cover of Genome Research Vol 36 Issue 4
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Abstract

The American alligator, Alligator mississippiensis, like all crocodilians, has temperature-dependent sex determination, in which the sex of an embryo is determined by the incubation temperature of the egg during a critical period of development. The lack of genetic differences between male and female alligators leaves open the question of how the genes responsible for sex determination and differentiation are regulated. Insight into this question comes from the fact that exposing an embryo incubated at male-producing temperature to estrogen causes it to develop ovaries. Because estrogen response elements are known to regulate genes over long distances, a contiguous genome assembly is crucial for predicting and understanding their impact. We present an improved assembly of the American alligator genome, scaffolded with in vitro proximity ligation (Chicago) data. We use this assembly to scaffold two other crocodilian genomes based on synteny. We perform RNA sequencing of tissues from American alligator embryos to find genes that are differentially expressed between embryos incubated at male- versus female-producing temperature. Finally, we use the improved contiguity of our assembly along with the current model of CTCF-mediated chromatin looping to predict regions of the genome likely to contain estrogen-responsive genes. We find that these regions are significantly enriched for genes with female-biased expression in developing gonads after the critical period during which sex is determined by incubation temperature. We thus conclude that estrogen signaling is a major driver of female-biased gene expression in the post-temperature sensitive period gonads.

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