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Open Access Highly Accessed Correspondence

Developing a community-based genetic nomenclature for anole lizards

Kenro Kusumi1*, Rob J Kulathinal2*, Arhat Abzhanov3, Stephane Boissinot4, Nicholas G Crawford5, Brant C Faircloth6, Travis C Glenn7, Daniel E Janes3, Jonathan B Losos38, Douglas B Menke9, Steven Poe10, Thomas J Sanger38, Christopher J Schneider5, Jessica Stapley11, Juli Wade12 and Jeanne Wilson-Rawls1

Author affiliations

1 School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ 85287-4501, USA

2 Department of Biology, Temple University, 1900 N. 12th Street, Philadelphia, PA 19122, USA

3 Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA 02138, USA

4 Department of Biology, Queens College, The City University of New York, 65-30 Kissena Boulevard, Flushing, NY 11367-1597; USA

5 Department of Biology, Boston University, 5 Cummington Street, Boston, MA 02215, USA

6 Department of Ecology and Evolutionary Biology, University of California, 621 Charles E. Young Drive South, Los Angeles, CA 90095, USA

7 Department of Environmental Health Science, University of Georgia, 150 East Green Street, Athens, GA 30602, USA

8 Museum of Comparative Zoology, Harvard University, 26 Oxford St., Cambridge, MA 02138, USA

9 Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA 30602-7223, USA

10 Department of Biology, University of New Mexico, 167 Castetter Hall, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131-0001, USA

11 Smithsonian Tropical Research Institute, Unit 9100 BOX 0948, DPO AA 34002-9998, USA

12 Departments of Psychology and Zoology, Michigan State University, 212 Giltner Hall, East Lansing, MI 48824-1101, USA

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Citation and License

BMC Genomics 2011, 12:554  doi:10.1186/1471-2164-12-554

Published: 11 November 2011

Abstract

Background

Comparative studies of amniotes have been hindered by a dearth of reptilian molecular sequences. With the genomic assembly of the green anole, Anolis carolinensis available, non-avian reptilian genes can now be compared to mammalian, avian, and amphibian homologs. Furthermore, with more than 350 extant species in the genus Anolis, anoles are an unparalleled example of tetrapod genetic diversity and divergence. As an important ecological, genetic and now genomic reference, it is imperative to develop a standardized Anolis gene nomenclature alongside associated vocabularies and other useful metrics.

Results

Here we report the formation of the Anolis Gene Nomenclature Committee (AGNC) and propose a standardized evolutionary characterization code that will help researchers to define gene orthology and paralogy with tetrapod homologs, provide a system for naming novel genes in Anolis and other reptiles, furnish abbreviations to facilitate comparative studies among the Anolis species and related iguanid squamates, and classify the geographical origins of Anolis subpopulations.

Conclusions

This report has been generated in close consultation with members of the Anolis and genomic research communities, and using public database resources including NCBI and Ensembl. Updates will continue to be regularly posted to new research community websites such as lizardbase. We anticipate that this standardized gene nomenclature will facilitate the accessibility of reptilian sequences for comparative studies among tetrapods and will further serve as a template for other communities in their sequencing and annotation initiatives.