De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system

Hdl Handle:
http://hdl.handle.net/10675.2/835
Title:
De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system
Authors:
Peterson, Mark P; Whittaker, Danielle J; Ambreth, Shruthi; Sureshchandra, Suhas; Buechlein, Aaron; Podicheti, Ram; Choi, Jeong-Hyeon; Lai, Zhao; Mockatis, Keithanne; Colbourne, John K. ( 0000-0002-6966-2972 ) ; Tang, Haixu; Ketterson, Ellen D
Abstract:
Background: Though genomic-level data are becoming widely available, many of the metazoan species sequenced are laboratory systems whose natural history is not well documented. In contrast, the wide array of species with very well-characterized natural history have, until recently, lacked genomics tools. It is now possible to address significant evolutionary genomics questions by applying high-throughput sequencing to discover the majority of genes for ecologically tractable species, and by subsequently developing microarray platforms from which to investigate gene regulatory networks that function in natural systems. We used GS-FLX Titanium Sequencing (Roche/454-Sequencing) of two normalized libraries of pooled RNA samples to characterize a transcriptome of the dark-eyed junco (Junco hyemalis), a North American sparrow that is a classically studied species in the fields of photoperiodism, speciation, and hormone-mediated behavior.; Results: From a broad pool of RNA sampled from tissues throughout the body of a male and a female junco, we sequenced a total of 434 million nucleotides from 1.17 million reads that were assembled de novo into 31,379 putative transcripts representing 22,765 gene sets covering 35.8 million nucleotides with 12-fold average depth of coverage. Annotation of roughly half of the putative genes was accomplished using sequence similarity, and expression was confirmed for the majority with a preliminary microarray analysis. Of 716 core bilaterian genes, 646 (90â %) were recovered within our characterized gene set. Gene Ontology, orthoDB orthology groups, and KEGG Pathway annotation provide further functional information about the sequences, and 25,781 potential SNPs were identified.; Conclusions: The extensive sequence information returned by this effort adds to the growing store of genomic data on diverse species. The extent of coverage and annotation achieved and confirmation of expression, show that transcriptome sequencing provides useful information for ecological model systems that have historically lacked genomic tools. The junco-specific microarray developed here is allowing investigations of gene expression responses to environmental and hormonal manipulations â extending the historic work on natural history and hormone-mediated phenotypes in this system.
Citation:
BMC Genomics. 2012 Jul 9; 13:305
Issue Date:
9-Jul-2012
URI:
http://hdl.handle.net/10675.2/835
DOI:
10.1186/1471-2164-13-305
PubMed ID:
22776250
PubMed Central ID:
PMC3476391
Type:
Article
ISSN:
1471-2164
Appears in Collections:
Georgia Cancer Center: Faculty Research and Presentations

Full metadata record

DC FieldValue Language
dc.contributor.authorPeterson, Mark Pen_US
dc.contributor.authorWhittaker, Danielle Jen_US
dc.contributor.authorAmbreth, Shruthien_US
dc.contributor.authorSureshchandra, Suhasen_US
dc.contributor.authorBuechlein, Aaronen_US
dc.contributor.authorPodicheti, Ramen_US
dc.contributor.authorChoi, Jeong-Hyeonen_US
dc.contributor.authorLai, Zhaoen_US
dc.contributor.authorMockatis, Keithanneen_US
dc.contributor.authorColbourne, John K.en_US
dc.contributor.authorTang, Haixuen_US
dc.contributor.authorKetterson, Ellen Den_US
dc.date.accessioned2012-10-26T20:35:14Z-
dc.date.available2012-10-26T20:35:14Z-
dc.date.issued2012-07-9en_US
dc.identifier.citationBMC Genomics. 2012 Jul 9; 13:305en_US
dc.identifier.issn1471-2164en_US
dc.identifier.pmid22776250en_US
dc.identifier.doi10.1186/1471-2164-13-305en_US
dc.identifier.urihttp://hdl.handle.net/10675.2/835-
dc.description.abstractBackground: Though genomic-level data are becoming widely available, many of the metazoan species sequenced are laboratory systems whose natural history is not well documented. In contrast, the wide array of species with very well-characterized natural history have, until recently, lacked genomics tools. It is now possible to address significant evolutionary genomics questions by applying high-throughput sequencing to discover the majority of genes for ecologically tractable species, and by subsequently developing microarray platforms from which to investigate gene regulatory networks that function in natural systems. We used GS-FLX Titanium Sequencing (Roche/454-Sequencing) of two normalized libraries of pooled RNA samples to characterize a transcriptome of the dark-eyed junco (Junco hyemalis), a North American sparrow that is a classically studied species in the fields of photoperiodism, speciation, and hormone-mediated behavior.en_US
dc.description.abstractResults: From a broad pool of RNA sampled from tissues throughout the body of a male and a female junco, we sequenced a total of 434 million nucleotides from 1.17 million reads that were assembled de novo into 31,379 putative transcripts representing 22,765 gene sets covering 35.8 million nucleotides with 12-fold average depth of coverage. Annotation of roughly half of the putative genes was accomplished using sequence similarity, and expression was confirmed for the majority with a preliminary microarray analysis. Of 716 core bilaterian genes, 646 (90â %) were recovered within our characterized gene set. Gene Ontology, orthoDB orthology groups, and KEGG Pathway annotation provide further functional information about the sequences, and 25,781 potential SNPs were identified.en_US
dc.description.abstractConclusions: The extensive sequence information returned by this effort adds to the growing store of genomic data on diverse species. The extent of coverage and annotation achieved and confirmation of expression, show that transcriptome sequencing provides useful information for ecological model systems that have historically lacked genomic tools. The junco-specific microarray developed here is allowing investigations of gene expression responses to environmental and hormonal manipulations â extending the historic work on natural history and hormone-mediated phenotypes in this system.en_US
dc.rightsCopyright ©2012 Peterson et al.; licensee BioMed Central Ltd.en_US
dc.subjectResearch Articleen_US
dc.titleDe novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model systemen_US
dc.typeArticleen_US
dc.identifier.pmcidPMC3476391en_US
dc.contributor.corporatenameGHSU Cancer Center-

Related articles on PubMed

All Items in Scholarly Commons are protected by copyright, with all rights reserved, unless otherwise indicated.