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. 2015 Jun 24;7(7):2038-50.
doi: 10.1093/gbe/evv119.

Physical Mapping and Refinement of the Painted Turtle Genome (Chrysemys Picta) Inform Amniote Genome Evolution and Challenge Turtle-Bird Chromosomal Conservation

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Free PMC article

Physical Mapping and Refinement of the Painted Turtle Genome (Chrysemys Picta) Inform Amniote Genome Evolution and Challenge Turtle-Bird Chromosomal Conservation

Daleen Badenhorst et al. Genome Biol Evol. .
Free PMC article

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.

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.

Figures

F<sc>ig</sc>. 1.
Fig. 1.
— G-banded (a), C-banded (b), and Ag-NOR stained (c) metaphase chromosomes of CPI, and the distribution of telomeric DNA (d) and 18S rDNA repeats (e) on CPI metaphase spreads. Arrows indicate C-positive interstitial bands (b) and NOR localization (c).
F<sc>ig</sc>. 2.
Fig. 2.
— CPI GTG-banded karyotype and ideogram showing the physical location of FISH-anchored BAC clones, with sex-linked BACs in red, along with the homology of gene blocks to chicken (GGA) and human (HSA) chromosomes, depicted as colored blocks, and with the NOR location on CPI 14. “UL” indicates uncharacterized loci, that is, CPI BACs that did not map to annotated scaffolds and thus homology to GGA and HSA was precluded. Note that BACs 45D19, 35H18, 39D13 colocate with 39B2 in CPI-5, and BAC 6L20 shows some hybridization to this region as well, likely due to the presence of shared repeat sequences (see supplementary table S2, Supplementary Material online).
F<sc>ig</sc>. 3.
Fig. 3.
— Examples of BAC FISH mapping showing the hybridization pattern of BACs containing genes related to sexual development (a, b), CR1 and Gypsy-enriched BACs (c), and simpler repeat-enriched BACs (d).
F<sc>ig</sc>. 4.
Fig. 4.
— Chromosomal homology, synteny, and rearrangements identified between CPI turtles and the chicken and human genomes. Multiple gene blocks may be encompassed by the start and stop positions listed within each chromosome and are detailed in the supplementary table S1, Supplementary Material online, along with their gene content.
F<sc>ig</sc>. 4.
Fig. 4.
— Chromosomal homology, synteny, and rearrangements identified between CPI turtles and the chicken and human genomes. Multiple gene blocks may be encompassed by the start and stop positions listed within each chromosome and are detailed in the supplementary table S1, Supplementary Material online, along with their gene content.
F<sc>ig</sc>. 4.
Fig. 4.
— Chromosomal homology, synteny, and rearrangements identified between CPI turtles and the chicken and human genomes. Multiple gene blocks may be encompassed by the start and stop positions listed within each chromosome and are detailed in the supplementary table S1, Supplementary Material online, along with their gene content.

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