Vertebrate genomes are comprised of isochores that are relatively long (>100 kb) 
regions with a relatively homogenous (either GC-rich or AT-rich) base 
composition and with rather sharp boundaries with neighboring isochores. Mammals 
and living archosaurs (birds and crocodilians) have heterogeneous genomes that 
include very GC-rich isochores. In sharp contrast, the genomes of amphibians and 
fishes are more homogeneous and they have a lower overall GC content. Because 
DNA with higher GC content is more thermostable, the elevated GC content of 
mammalian and archosaurian DNA has been hypothesized to be an adaptation to 
higher body temperatures. This hypothesis can be tested by examining structure 
of isochores across the reptilian clade, which includes the archosaurs, 
testudines (turtles), and lepidosaurs (lizards and snakes), because reptiles 
exhibit diverse body sizes, metabolic rates, and patterns of thermoregulation. 
This study focuses on a comparative analysis of a new set of expressed genes of 
the red-eared slider turtle and orthologs of the turtle genes in mammalian 
(human, mouse, dog, and opossum), archosaurian (chicken and alligator), and 
amphibian (western clawed frog) genomes. EST (expressed sequence tag) data from 
a turtle cDNA library enriched for genes that have specialized functions 
(developmental genes) revealed using the GC content of the third-codon-position 
to examine isochore structure requires careful consideration of the types of 
genes examined. The more highly expressed genes (e.g., housekeeping genes) are 
more likely to be GC-rich than are genes with specialized functions. However, 
the set of highly expressed turtle genes demonstrated that the turtle genome has 
a GC content that is intermediate between the GC-poor amphibians and the GC-rich 
mammals and archosaurs. There was a strong correlation between the GC content of 
all turtle genes and the GC content of other vertebrate genes, with the slope of 
the line describing this relationship also indicating that the isochore 
structure of turtles is intermediate between that of amphibians and other 
amniotes. These data are consistent with some thermal hypotheses of isochore 
evolution, but we believe that the credible set of models for isochore evolution 
still includes a variety of models. These data expand the amount of genomic data 
available from reptiles upon which future studies of reptilian genomics can 
build.