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

BMC Genomics

Research Article

Federica Di Palma¹  Jessica Alföldi¹  Kerstin Lindblad-Toh²  April N Allen³  Matthew J Huentelman³  Jason J Corneveaux³  Elizabeth D Hutchins⁴  Glenn J Markov⁴  Walter L Eckalbar⁴  Kenro Kusumi⁵ 

[1] Broad Institute of MIT and Harvard, 02142, Cambridge, MA, USA;Broad Institute of MIT and Harvard, 02142, Cambridge, MA, USA;Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;Neurogenomics Division, Translational Genomics Research Institute, 445 N. 5th St., 85004, Phoenix, AZ, USA;School of Life Sciences, Arizona State University, PO Box 874501, 85287-4501, Tempe, AZ, USA;School of Life Sciences, Arizona State University, PO Box 874501, 85287-4501, Tempe, AZ, USA;Neurogenomics Division, Translational Genomics Research Institute, 445 N. 5th St., 85004, Phoenix, AZ, USA;

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

DOI  :  10.1186/1471-2164-14-49

 received in 2012-07-15, accepted in 2013-01-18,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsHere 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.ConclusionsIncorporation 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.

【 授权许可】

Unknown   
© Eckalbar et al.; licensee BioMed Central Ltd. 2013. 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.