Gene order data from a model amphibian (Ambystoma): new perspectives on vertebrate genome structure and evolution.
BACKGROUND
Because amphibians arise from a branch of the vertebrate evolutionary tree that is juxtaposed between fishes and amniotes, they provide important comparative perspective for reconstructing character changes that have occurred during vertebrate evolution. Here, we report the first comparative study of vertebrate genome structure that includes a representative amphibian. We used 491 transcribed sequences from a salamander (Ambystoma) genetic map and whole genome assemblies for human, mouse, rat, dog, chicken, zebrafish, and the freshwater pufferfish Tetraodon nigroviridis to compare gene orders and rearrangement rates.


RESULTS
Ambystoma has experienced a rate of genome rearrangement that is substantially lower than mammalian species but similar to that of chicken and fish. Overall, we found greater conservation of genome structure between Ambystoma and tetrapod vertebrates, nevertheless, 57% of Ambystoma-fish orthologs are found in conserved syntenies of four or more genes. Comparisons between Ambystoma and amniotes reveal extensive conservation of segmental homology for 57% of the presumptive Ambystoma-amniote orthologs.


CONCLUSIONS
Our analyses suggest relatively constant interchromosomal rearrangement rates from the euteleost ancestor to the origin of mammals and illustrate the utility of amphibian mapping data in establishing ancestral amniote and tetrapod gene orders. Comparisons between Ambystoma and amniotes reveal some of the key events that have structured the human genome since diversification of the ancestral amniote lineage.
Smith
Jeramiah J
JJ
Department of Biology and Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY 40506, USA. jjsmit3@uky.edu
Voss
S Randal
SR
D000557:Ambystoma / Q000235:genetics*; D000818:Animals; D002645:Chickens / Q000235:genetics; D002874:Chromosome Mapping; D002875:Chromosomes; D004285:Dogs; D019143:Evolution, Molecular; D005787:Gene Frequency; D023061:Gene Order; D008040:Genetic Linkage; D049810:Genetic Speciation; D006801:Humans; D051379:Mice; D023421:Models, Animal; D010802:Phylogeny; D051381:Rats; D012689:Sequence Homology, Nucleic Acid; D026801:Synteny; D014714:Vertebrates / Q000235:genetics*; D015027:Zebrafish / Q000235:genetics