Gene Order Data from a Model Amphibian (Ambystoma): New Perspectives on Vertebrate Genome Structure and Evolution

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2006 Aug 31

PMID 16939647

Citations 21

Authors

Jeramiah J Smith

S Randal Voss

Affiliations

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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.

Citing Articles

Why Do Some Vertebrates Have Microchromosomes?.

Srikulnath K, Ahmad S, Singchat W, Panthum T Cells. 2021; 10(9).

PMID: 34571831 PMC: 8466491. DOI: 10.3390/cells10092182.

Gene and transgenics nomenclature for the laboratory axolotl-Ambystoma mexicanum.

Nowoshilow S, Fei J, Voss S, Tanaka E, Murawala P Dev Dyn. 2021; 251(6):913-921.

PMID: 33896069 PMC: 8542645. DOI: 10.1002/dvdy.351.

A chromosome-scale assembly of the axolotl genome.

Smith J, Timoshevskaya N, Timoshevskiy V, Keinath M, Hardy D, Voss S Genome Res. 2019; 29(2):317-324.

PMID: 30679309 PMC: 6360810. DOI: 10.1101/gr.241901.118.

Miniscule differences between sex chromosomes in the giant genome of a salamander.

Keinath M, Timoshevskaya N, Timoshevskiy V, Voss S, Smith J Sci Rep. 2018; 8(1):17882.

PMID: 30552368 PMC: 6294749. DOI: 10.1038/s41598-018-36209-2.

Amphibian and Avian Karyotype Evolution: Insights from Lampbrush Chromosome Studies.

Zlotina A, Dedukh D, Krasikova A Genes (Basel). 2017; 8(11).

PMID: 29117127 PMC: 5704224. DOI: 10.3390/genes8110311.

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