title: Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling.
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.
authors.affiliation: Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA.
authors.forename: Edward S
authors.initials: ES
authors.lastname: Rice
authors.affiliation: Department of Biology, St. Cloud State University, St. Cloud, Minnesota 56301, USA.
authors.forename: Satomi
authors.initials: S
authors.lastname: Kohno
authors.affiliation: Driver Group, LLC, San Francisco, California 94158, USA.
authors.forename: John St
authors.initials: JS
authors.lastname: John
authors.affiliation: BioTuring, Incorporated, San Diego, California 92121, USA.
authors.forename: Son
authors.initials: S
authors.lastname: Pham
authors.affiliation: Department of Biochemistry, Stanford University, Stanford, California 94305, USA.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Howard
authors.affiliation: California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA.
authors.forename: Liana F
authors.initials: LF
authors.lastname: Lareau
authors.affiliation: Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA.|Dovetail Genomics, LLC, Santa Cruz, California 95060, USA.
authors.forename: Brendan L
authors.initials: BL
authors.lastname: O'Connell
authors.affiliation: Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA.
authors.forename: Glenn
authors.initials: G
authors.lastname: Hickey
authors.affiliation: Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA.
authors.forename: Joel
authors.initials: J
authors.lastname: Armstrong
authors.affiliation: Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA.
authors.forename: Alden
authors.initials: A
authors.lastname: Deran
authors.affiliation: Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA.
authors.forename: Ian
authors.initials: I
authors.lastname: Fiddes
authors.affiliation: Department of Biological Sciences, Texas Tech University, Lubbock, Texas 79409, USA.
authors.forename: Roy N
authors.initials: RN
authors.lastname: Platt
authors.affiliation: Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, Mississippi 39762, USA.
authors.forename: Cathy
authors.initials: C
authors.lastname: Gresham
authors.affiliation: School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona 85721, USA.
authors.forename: Fiona
authors.initials: F
authors.lastname: McCarthy
authors.affiliation: Department of Animal Science, University of California, Davis, California 95616, USA.
authors.forename: Colin
authors.initials: C
authors.lastname: Kern
authors.affiliation: Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA.
authors.forename: David
authors.initials: D
authors.lastname: Haan
authors.affiliation: HCM University of Science, Ho Chí Minh, Vietnam 748500.
authors.forename: Tan
authors.initials: T
authors.lastname: Phan
authors.affiliation: Department of Animal and Food Sciences, University of Delaware, Newark, Delaware 19717, USA.
authors.forename: Carl
authors.initials: C
authors.lastname: Schmidt
authors.affiliation: Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, California 95064, USA.
authors.forename: Jeremy R
authors.initials: JR
authors.lastname: Sanford
authors.affiliation: Department of Biological Sciences, Texas Tech University, Lubbock, Texas 79409, USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Ray
authors.affiliation: Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA.
authors.forename: Benedict
authors.initials: B
authors.lastname: Paten
authors.affiliation: Department of Obstetrics and Gynecology, Marine Biomedicine and Environmental Science Center, Hollings Marine Laboratory, Medical University of South Carolina, Charleston, South Carolina 29412, USA.
authors.forename: Louis J
authors.initials: LJ
authors.lastname: Guillette
authors.affiliation: Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA.|California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA.|Dovetail Genomics, LLC, Santa Cruz, California 95060, USA.
authors.forename: Richard E
authors.initials: RE
authors.lastname: Green
mesh_terms: D000489:Alligators and Crocodiles / Q000196:embryology / Q000235:genetics*; D000818:Animals; D000076246:CCCTC-Binding Factor / Q000378:metabolism; D002843:Chromatin / Q000378:metabolism; D017124:Conserved Sequence; D020451:Contig Mapping; D004967:Estrogens / Q000235:genetics* / Q000378:metabolism; D005260:Female; D016678:Genome; D008297:Male; D017422:Sequence Analysis, DNA; D019849:Sex Determination Processes / Q000235:genetics; D015398:Signal Transduction; D026801:Synteny
chemical_list: D000076246:CCCTC-Binding Factor; D002843:Chromatin; D004967:Estrogens