Journal of Molecular Evolution: Vol. 65 pp. 259-266
Patterns of Vertebrate Isochore Evolution Revealed by Comparison of Expressed Mammalian, Avian, and Crocodilian Genes
Jena L. Chojnowski*, James Franklin, Yoshinao Katsu, Taisen Iguchi, Louis J. Guillette Jr., Rebecca T. Kimball and Edward L. Braun
Department of Zoology, University of Florida, Gainesville, Florida 32611 (J.L.C., J.F., L.J.G., R.T.K., E.L.B.); Division of Molecular Environmental Endocrinology, Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan (Y.K., T.I.); Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan (Y.K., T.I.)
Vertebrate genomes are mosaics of isochores, defined as long (>100 kb) regions with relatively homogeneous within-region base composition. Birds and mammals have more GC-rich isochores than amphibians and fish, and the GC-rich isochores of birds and mammals have been suggested to be an adaptation to homeothermy. If this hypothesis is correct, all poikilothermic (cold-blooded) vertebrates, including the nonavian reptiles, are expected to lack a GC-rich isochore structure. Previous studies using various methods to examine isochore structure in crocodilians, turtles, and squamates have led to different conclusions. We collected more than 6000 expressed sequence tags (ESTs) from the American alligator to overcome sample size limitations suggested to be the fundamental problem in the previous reptilian studies. The alligator ESTs were assembled and aligned with their human, mouse, chicken, and western clawed frog orthologs, resulting in 366 alignments. Analyses of third-codon-position GC content provided conclusive evidence that the poikilothermic alligator has GC-rich isochores, like homeothermic birds and mammals. We placed these results in a theoretical framework able to unify available models of isochore evolution. The data collected for this study allowed us to reject the models that explain the evolution of GC content using changes in body temperature associated with the transition from poikilothermy to homeothermy. Falsification of these models places fundamental constraints upon the plausible pathways for the evolution of isochores.
This work was supported in part by grants to Y.K. and T.I. (Grant-in-Aid for Scientific Research from the Ministry of Education, Science, Sports and Culture of Japan and grants from the Ministry of Environment, Japan) and to E.L.B. and L.J.G. (University of Florida Opportunity Fund).
* Corresponding author