title: Physical Mapping and Refinement of the Painted Turtle Genome (Chrysemys picta) Inform Amniote Genome Evolution and Challenge Turtle-Bird Chromosomal Conservation.
abstract: Comparative genomics continues illuminating amniote genome evolution, but for many lineages our understanding remains incomplete. Here, we refine the assembly (CPI 3.0.3 NCBI AHGY00000000.2) and develop a cytogenetic map of the painted turtle (Chrysemys picta-CPI) genome, the first in turtles and in vertebrates with temperature-dependent sex determination. A comparison of turtle genomes with those of chicken, selected nonavian reptiles, and human revealed shared and novel genomic features, such as numerous chromosomal rearrangements. The largest conserved syntenic blocks between birds and turtles exist in four macrochromosomes, whereas rearrangements were evident in these and other chromosomes, disproving that turtles and birds retain fully conserved macrochromosomes for greater than 300 Myr. C-banding revealed large heterochromatic blocks in the centromeric region of only few chromosomes. The nucleolar-organizing region (NOR) mapped to a single CPI microchromosome, whereas in some turtles and lizards the NOR maps to nonhomologous sex-chromosomes, thus revealing independent translocations of the NOR in various reptilian lineages. There was no evidence for recent chromosomal fusions as interstitial telomeric-DNA was absent. Some repeat elements (CR1-like, Gypsy) were enriched in the centromeres of five chromosomes, whereas others were widespread in the CPI genome. Bacterial artificial chromosome (BAC) clones were hybridized to 18 of the 25 CPI chromosomes and anchored to a G-banded ideogram. Several CPI sex-determining genes mapped to five chromosomes, and homology was detected between yet other CPI autosomes and the globally nonhomologous sex chromosomes of chicken, other turtles, and squamates, underscoring the independent evolution of vertebrate sex-determining mechanisms.
authors.affiliation: Department of Ecology, Evolution, and Organismal Biology, Iowa State University.
authors.forename: Daleen
authors.initials: D
authors.lastname: Badenhorst
authors.affiliation: The Genome Institute at Washington University, St Louis.
authors.forename: LaDeana W
authors.initials: LW
authors.lastname: Hillier
authors.affiliation: Department of Ecology, Evolution, and Organismal Biology, Iowa State University.
authors.forename: Robert
authors.initials: R
authors.lastname: Literman
authors.affiliation: Department of Ecology, Evolution, and Organismal Biology, Iowa State University.
authors.forename: Eugenia Elisabet
authors.initials: EE
authors.lastname: Montiel
authors.affiliation: Department of Ecology, Evolution, and Organismal Biology, Iowa State University.
authors.forename: Srihari
authors.initials: S
authors.lastname: Radhakrishnan
authors.affiliation: The Genome Institute at Washington University, St Louis.
authors.forename: Yingjia
authors.initials: Y
authors.lastname: Shen
authors.affiliation: The Genome Institute at Washington University, St Louis.
authors.forename: Patrick
authors.initials: P
authors.lastname: Minx
authors.affiliation: Department of Ecology, Evolution, and Organismal Biology, Iowa State University Department of Organismic and Evolutionary Biology, Harvard University.
authors.forename: Daniel E
authors.initials: DE
authors.lastname: Janes
authors.affiliation: The Genome Institute at Washington University, St Louis.
authors.forename: Wesley C
authors.initials: WC
authors.lastname: Warren
authors.affiliation: Department of Organismic and Evolutionary Biology, Harvard University.
authors.forename: Scott V
authors.initials: SV
authors.lastname: Edwards
authors.affiliation: Department of Ecology, Evolution, and Organismal Biology, Iowa State University nvalenzu@iastate.edu.
authors.forename: Nicole
authors.initials: N
authors.lastname: Valenzuela
mesh_terms: D000818:Animals; D001717:Birds / Q000235:genetics; D002478:Cells, Cultured; D002871:Chromosome Banding; D022202:Chromosomes, Artificial, Bacterial; D019143:Evolution, Molecular; D016678:Genome; D006801:Humans; D007621:Karyotyping; D008969:Molecular Sequence Data; D020161:Physical Chromosome Mapping; D026801:Synteny; D014426:Turtles / Q000235:genetics*
keywords: chicken; chromosomal rearrangements; genome and chromosome evolution; human; nonmodel vertebrates; physical molecular cytogenetic BAC clone mapping; temperature-dependent and genotypic sex determination; translocations and inversions; turtles