title: The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage.
abstract: BACKGROUND
  We describe the genome of the western painted turtle, Chrysemys picta bellii, one of the most widespread, abundant, and well-studied turtles. We place the genome into a comparative evolutionary context, and focus on genomic features associated with tooth loss, immune function, longevity, sex differentiation and determination, and the species' physiological capacities to withstand extreme anoxia and tissue freezing.
  
  
  RESULTS
  Our phylogenetic analyses confirm that turtles are the sister group to living archosaurs, and demonstrate an extraordinarily slow rate of sequence evolution in the painted turtle. The ability of the painted turtle to withstand complete anoxia and partial freezing appears to be associated with common vertebrate gene networks, and we identify candidate genes for future functional analyses. Tooth loss shares a common pattern of pseudogenization and degradation of tooth-specific genes with birds, although the rate of accumulation of mutations is much slower in the painted turtle. Genes associated with sex differentiation generally reflect phylogeny rather than convergence in sex determination functionality. Among gene families that demonstrate exceptional expansions or show signatures of strong natural selection, immune function and musculoskeletal patterning genes are consistently over-represented.
  
  
  CONCLUSIONS
  Our comparative genomic analyses indicate that common vertebrate regulatory networks, some of which have analogs in human diseases, are often involved in the western painted turtle's extraordinary physiological capacities. As these regulatory pathways are analyzed at the functional level, the painted turtle may offer important insights into the management of a number of human health disorders.
authors.forename: H Bradley
authors.initials: HB
authors.lastname: Shaffer
authors.forename: Patrick
authors.initials: P
authors.lastname: Minx
authors.forename: Daniel E
authors.initials: DE
authors.lastname: Warren
authors.forename: Andrew M
authors.initials: AM
authors.lastname: Shedlock
authors.forename: Robert C
authors.initials: RC
authors.lastname: Thomson
authors.forename: Nicole
authors.initials: N
authors.lastname: Valenzuela
authors.forename: John
authors.initials: J
authors.lastname: Abramyan
authors.forename: Chris T
authors.initials: CT
authors.lastname: Amemiya
authors.forename: Daleen
authors.initials: D
authors.lastname: Badenhorst
authors.forename: Kyle K
authors.initials: KK
authors.lastname: Biggar
authors.forename: Glen M
authors.initials: GM
authors.lastname: Borchert
authors.forename: Christopher W
authors.initials: CW
authors.lastname: Botka
authors.forename: Rachel M
authors.initials: RM
authors.lastname: Bowden
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authors.initials: EL
authors.lastname: Braun
authors.forename: Anne M
authors.initials: AM
authors.lastname: Bronikowski
authors.forename: Benoit G
authors.initials: BG
authors.lastname: Bruneau
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authors.initials: LT
authors.lastname: Buck
authors.forename: Blanche
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authors.lastname: Castoe
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authors.lastname: Czerwinski
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authors.initials: KD
authors.lastname: Delehaunty
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authors.initials: SV
authors.lastname: Edwards
authors.forename: Catrina C
authors.initials: CC
authors.lastname: Fronick
authors.forename: Matthew K
authors.initials: MK
authors.lastname: Fujita
authors.forename: Lucinda
authors.initials: L
authors.lastname: Fulton
authors.forename: Tina A
authors.initials: TA
authors.lastname: Graves
authors.forename: Richard E
authors.initials: RE
authors.lastname: Green
authors.forename: Wilfried
authors.initials: W
authors.lastname: Haerty
authors.forename: Ramkumar
authors.initials: R
authors.lastname: Hariharan
authors.forename: Omar
authors.initials: O
authors.lastname: Hernandez
authors.forename: LaDeana W
authors.initials: LW
authors.lastname: Hillier
authors.forename: Alisha K
authors.initials: AK
authors.lastname: Holloway
authors.forename: Daniel
authors.initials: D
authors.lastname: Janes
authors.forename: Fredric J
authors.initials: FJ
authors.lastname: Janzen
authors.forename: Cyriac
authors.initials: C
authors.lastname: Kandoth
authors.forename: Lesheng
authors.initials: L
authors.lastname: Kong
authors.forename: A P Jason
authors.initials: AP
authors.lastname: de Koning
authors.forename: Yang
authors.initials: Y
authors.lastname: Li
authors.forename: Robert
authors.initials: R
authors.lastname: Literman
authors.forename: Suzanne E
authors.initials: SE
authors.lastname: McGaugh
authors.forename: Lindsey
authors.initials: L
authors.lastname: Mork
authors.forename: Michelle
authors.initials: M
authors.lastname: O'Laughlin
authors.forename: Ryan T
authors.initials: RT
authors.lastname: Paitz
authors.forename: David D
authors.initials: DD
authors.lastname: Pollock
authors.forename: Chris P
authors.initials: CP
authors.lastname: Ponting
authors.forename: Srihari
authors.initials: S
authors.lastname: Radhakrishnan
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Raney
authors.forename: Joy M
authors.initials: JM
authors.lastname: Richman
authors.forename: John
authors.initials: J
authors.lastname: St John
authors.forename: Tonia
authors.initials: T
authors.lastname: Schwartz
authors.forename: Arun
authors.initials: A
authors.lastname: Sethuraman
authors.forename: Phillip Q
authors.initials: PQ
authors.lastname: Spinks
authors.forename: Kenneth B
authors.initials: KB
authors.lastname: Storey
authors.forename: Nay
authors.initials: N
authors.lastname: Thane
authors.forename: Tomas
authors.initials: T
authors.lastname: Vinar
authors.forename: Laura M
authors.initials: LM
authors.lastname: Zimmerman
authors.forename: Wesley C
authors.initials: WC
authors.lastname: Warren
authors.forename: Elaine R
authors.initials: ER
authors.lastname: Mardis
authors.forename: Richard K
authors.initials: RK
authors.lastname: Wilson
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000818:Animals; D001482:Base Composition / Q000235:genetics; D019143:Evolution, Molecular; D005260:Female; D005615:Freezing; D016678:Genome / Q000235:genetics*; D006801:Humans; D000860:Hypoxia / Q000235:genetics / Q000503:physiopathology; D007107:Immune System / Q000378:metabolism; D032085:Isochores / Q000235:genetics; D016013:Likelihood Functions; D008136:Longevity / Q000235:genetics; D008297:Male; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D008957:Models, Genetic; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D010802:Phylogeny; D011544:Pseudogenes / Q000235:genetics; D012015:Reference Standards; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D012641:Selection, Genetic; D019849:Sex Determination Processes; D013696:Temperature; D014426:Turtles / Q000235:genetics*
chemical_list: D032085:Isochores; D035683:MicroRNAs
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