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

Edward S. Rice, Satomi Kohno, Son Pham, Jonathan Howard, Liana F. Lareau, Brendan L. O'Connell, Glenn Hickey, Joel Armstrong, Alden Deran, Ian Fiddes, Roy Platt, Cathy Gresham, Fiona McCarthy, Colin Kern, David Haan, Tan Phan, Carl Schmidt, Jeremy R. Sanford, David Ray, Benedict PatenRichard E. Green, John St John, Louis J. Guillette

Research output: Contribution to journalArticle


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 posterature sensitive period gonads.

Original languageEnglish
Pages (from-to)686-696
Number of pages11
JournalGenome Research
Issue number5
StatePublished - May 2017


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