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

Comparative genomics continues illuminating amniote genome evolution, but for man

y lineages our understanding remains incom-plete. Here, we refine the assembly (CPI 3.0.3 NCBI AHGY00000000.2) and develop a cytogenetic map of the painted turtle (Chrysemyspicta—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 macrochro-mosomes, 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 re

vealed large heterochromatic blocks in the centromeric region

of only few chromosomes. The nucleolar-org

anizing region (NOR) mapped to a single CPI microchromosome, whereas in some turtles

and lizards the NOR maps to nonhomologous sex-chromosomes, t

hus 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 centromere s 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 ch romosomes, and homology was detected between yet other CPI autosomes and the globally nonhomologous sex chromosomes of chicken, other turtles, and squamates, underscoring the inde-pendent evolution of vertebrate sex-determining mechanisms.