Challenges and Resources for the Post-genomic Era of Anole Research

The Anolis carolinensis genome represents the first annotated squamate genome and provides a valuable resource for those interested in anole morphology, development, physiology, systematics, and behavior (yes, even behavior!).  Since the release of the original A. carolinensis draft genome in March 2007, no fewer than 20 papers have mined it for a deeper understanding of the amniote genome and its evolution. Many more labs are currently developing tools and resources for functional genomics and we can expect a number of exciting advancements in coming years. But with increased genomic information comes the need for community-wide organization and discussion about how to handle, store, label, and communicate these data. These well-known hurdles have each been faced in other communities. In addition, the community of Anolis researchers can also expect new challenges due to the number of comparative studies being conducted among populations and species (compared to research being done within relatively homogeneous strains or lines). To handle at least a few of these challenges, the Anolis Gene Nomenclature Committee was formed, comprised of researchers from diverse biological disciplines and representatives from public genomic databases. Culminating nearly two years of discussion, the first publication from this group is now available online (for free!) from BMC Genomics, outlining basic guidelines for the terminology and symbols used in future work on anole genomics. This paper represents an evolving document and is presented here to elicit further discussion.

The major consideration of the AGNC when developing these guidelines for gene nomenclature was flexibility in comparisons among amniote genomes. In their inaugural publication, the AGNC describes a series of guidelines for Anolis gene names and symbols, assigning gene orthology, and tracking orthologous sequences from different Anolis species. Briefly, there was a consensus that gene symbols should be written in lowercase, italicized font (e.g., shh, fgf8, bmp4, etc.) while protein symbols should be all uppercase and without italics (e.g., SHH, FGF8, BMP4, etc.). Guidelines for non-coding elements such as regulatory elements and transposons are not well established and will be discussed in greater detail in the future. To clearly distinguish sequence data collected from different Anolis species the AGNC recommends using a four-letter suffix appended to each gene symbol that is unique to each species (e.g., shh-Asag, fgf8-Acar, bmp4-Acyb, etc., see Table 2 of the paper). Please see the publication for further details of the recommendations.

In closing, I thought that it would be useful to the community to summarize the growing number of genomic resources that are becoming publicly available. If anyone knows of additional resources or would like to provide comments/suggestions to the AGNC, please add your comments below or contact one of its members.

Genomic databases
NCBI Unigene                                Sequence data from 26,575 transcripts
Ensemble                                         1.7Gb of sequence information for ~12,000 annotated loci
UCSC                                                Portal for comparative genomics
lizardbase                                       Anolis genome browser, Gene nomenclature resources
–                                                        (new comparative data coming soon)

Database of expression data
AnolisGenome.org                       Genomic and expression data (relaunch Nov. 28)

Mapping and geographic variation
lizardbase                                      GIS data mapping for genetic, ecological, and
–                                                        morphological data

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2 Responses to Challenges and Resources for the Post-genomic Era of Anole Research

  1. Rich Glor says:

    I’m glad to see the emergence of some of these new databases. I hope that they continue to grow. For the time being, lizardbase is definitely not the place to go for GIS data. The interface looks nice, but there are no underlying data. Try HerpNet or VertNet if you want GIS data.

  2. Pingback: Anoles on Genbank |

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