Abstract
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.
CONCLUSION: 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.
Document Type
Article
Publication Date
8-29-2006
Digital Object Identifier (DOI)
http://dx.doi.org/10.1186/1471-2164-7-219
Repository Citation
Smith, Jeramiah J. and Voss, S. Randal, "Gene Order Data from a Model Amphibian (Ambystoma): New Perspectives on Vertebrate Genome Structure and Evolution" (2006). Biology Faculty Publications. 19.
https://uknowledge.uky.edu/biology_facpub/19
Additional file 1
1471-2164-7-219-s2.doc (29 kB)
Additional file 2
1471-2164-7-219-s3.tiff (646 kB)
Additional file 3
1471-2164-7-219-s4.tiff (654 kB)
Additional file 4
1471-2164-7-219-s5.tiff (621 kB)
Additional file 5
1471-2164-7-219-s6.xls (127 kB)
Additional file 6
1471-2164-7-219-s7.txt (538 kB)
Additional file 7
Notes/Citation Information
Published in BMC Genomics, v. 7, 219.
© 2006 Smith and Voss; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Additional files are listed at the end of this page.
Additional file 1:
Summary statistics for Ambystoma-vertebrate genome alignments. This table provides alignment start and end positions and bitscore values for alignments between mapped Ambystoma sequences and genome assemblies for human, mouse, rat, dog, chicken, zebrafish, and T. nigroviridis.
Additional file 2:
Values of the λ association index for comparisons among all eight representative vertebrate species. This table provides values of the λ association index and 95% confidence intervals for all pairwise comparisons among Ambystoma, human, mouse, rat, dog, chicken, zebrafish, and T. nigroviridis.
Additional file 3:
Oxford plot of the positions of presumptive orthologies between Ambystoma linkage groups and rat chromosomes. This plot shows the relative position of orthologies in the Ambystoma (X-axis) and rat (Y-axis) genomes. See Figure 5 for further details.
Additional file 4:
Oxford plot of the positions of presumptive orthologies between Ambystoma linkage groups and dog chromosomes. This plot shows the relative position of orthologies in the Ambystoma (X-axis) and dog (Y-axis) genomes. See Figure 5 for further details.
Additional file 5:
Oxford plot of the positions of presumptive orthologies between Ambystoma linkage groups and zebrafish chromosomes. This plot shows the relative position of orthologies in the Ambystoma (X-axis) and zebrafish (Y-axis) genomes. See Figure 5 for further details.
Additional file 6:
FASTA identifiers, species, and GenBank GIs that are associated with Ambystoma markers. This table provides GenBank and species identifiers for all of the Ambystoma markers that were used in this study.
Additional file 7:
A FASTA file of Ambystoma sequence that were used in this study. This FASTA formatted file provides all of the Ambystoma sequences that were used to generate alignments in this study.