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Open Access Highly Accessed Research article

Genome reannotation of the lizard Anolis carolinensis based on 14 adult and embryonic deep transcriptomes

Walter L Eckalbar1, Elizabeth D Hutchins1, Glenn J Markov1, April N Allen2, Jason J Corneveaux2, Kerstin Lindblad-Toh34, Federica Di Palma3, Jessica Alföldi3, Matthew J Huentelman2 and Kenro Kusumi12*

Author affiliations

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

2 Neurogenomics Division, Translational Genomics Research Institute, 445 N. 5th St., Phoenix, AZ, 85004, USA

3 Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA

4 Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden

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Citation and License

BMC Genomics 2013, 14:49  doi:10.1186/1471-2164-14-49

Published: 23 January 2013

Abstract

Background

The green anole lizard, Anolis carolinensis, is a key species for both laboratory and field-based studies of evolutionary genetics, development, neurobiology, physiology, behavior, and ecology. As the first non-avian reptilian genome sequenced, A. carolinesis is also a prime reptilian model for comparison with other vertebrate genomes. The public databases of Ensembl and NCBI have provided a first generation gene annotation of the anole genome that relies primarily on sequence conservation with related species. A second generation annotation based on tissue-specific transcriptomes would provide a valuable resource for molecular studies.

Results

Here we provide an annotation of the A. carolinensis genome based on de novo assembly of deep transcriptomes of 14 adult and embryonic tissues. This revised annotation describes 59,373 transcripts, compared to 16,533 and 18,939 currently for Ensembl and NCBI, and 22,962 predicted protein-coding genes. A key improvement in this revised annotation is coverage of untranslated region (UTR) sequences, with 79% and 59% of transcripts containing 5’ and 3’ UTRs, respectively. Gaps in genome sequence from the current A. carolinensis build (Anocar2.0) are highlighted by our identification of 16,542 unmapped transcripts, representing 6,695 orthologues, with less than 70% genomic coverage.

Conclusions

Incorporation of tissue-specific transcriptome sequence into the A. carolinensis genome annotation has markedly improved its utility for comparative and functional studies. Increased UTR coverage allows for more accurate predicted protein sequence and regulatory analysis. This revised annotation also provides an atlas of gene expression specific to adult and embryonic tissues.

Keywords:
Annotation; Lizard; Anolis carolinensis; Transcriptome; Genome; RNA-Seq; Gene; Vertebrate; Embryo; Tissue-specific