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Developing a community-based genetic nomenclature for anole lizards

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Title: Developing a community-based genetic nomenclature for anole lizards
Author(s): Kusumi, K
Kulathinal, RJ
Abzhanov, A
Boissinot, S
Crawford, NG
Faircloth, BC
Glenn, TC
Janes, DE
Losos, JB
Menke, DB
Poe, S
Sanger, TJ
Schneider, CJ
Stapley, J
Wade, J
Wilson-Rawls, J
Item Type: Journal Article
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.
Publication Date: 11-Nov-2011
Date of Acceptance: 11-Nov-2011
URI: http://hdl.handle.net/10044/1/40770
DOI: http://dx.doi.org/10.1186/1471-2164-12-554
ISSN: 1471-2164
Publisher: BioMed Central
Journal / Book Title: BMC Genomics
Volume: 12
Copyright Statement: This article is published under license to 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.
Keywords: Animals
Conserved Sequence
DNA Transposable Elements
Evolution, Molecular
Genetic Markers
Genomics
Lizards
Microsatellite Repeats
Repetitive Sequences, Nucleic Acid
Terminology as Topic
Animals
Lizards
DNA Transposable Elements
Genetic Markers
Genomics
Evolution, Molecular
Repetitive Sequences, Nucleic Acid
Microsatellite Repeats
Conserved Sequence
Terminology as Topic
Bioinformatics
06 Biological Sciences
11 Medical And Health Sciences
08 Information And Computing Sciences
Publication Status: Published
Article Number: 554
Appears in Collections:Faculty of Natural Sciences



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