• Login
    View Item 
    •   Home
    • Centers & Institutes
    • Georgia Cancer Center
    • Georgia Cancer Center: Faculty Research and Presentations
    • View Item
    •   Home
    • Centers & Institutes
    • Georgia Cancer Center
    • Georgia Cancer Center: Faculty Research and Presentations
    • View Item
    JavaScript is disabled for your browser. Some features of this site may not work without it.

    Browse

    All of Scholarly CommonsCommunitiesTitleAuthorsIssue DateSubmit DateSubjectsThis CollectionTitleAuthorsIssue DateSubmit DateSubjects

    My Account

    LoginRegister

    About

    AboutCreative CommonsAugusta University LibrariesUSG Copyright Policy

    Statistics

    Display statistics

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

    • CSV
    • RefMan
    • EndNote
    • BibTex
    • RefWorks
    Thumbnail
    Name:
    1471-2164-13-305.pdf
    Size:
    309.3Kb
    Format:
    PDF
    Download
    Thumbnail
    Name:
    1471-2164-13-305-S1.pdf
    Size:
    11.45Kb
    Format:
    PDF
    Download
    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.
    Tang, Haixu
    Ketterson, Ellen D
    Show allShow less
    Issue Date
    2012-07-9
    URI
    http://hdl.handle.net/10675.2/835
    
    Metadata
    Show full item record
    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
    ae974a485f413a2113503eed53cd6c53
    10.1186/1471-2164-13-305
    Scopus Count
    Collections
    Georgia Cancer Center: Faculty Research and Presentations

    entitlement

    Related articles

    • Transcriptome sequencing and microarray design for functional genomics in the extremophile Arabidopsis relative Thellungiella salsuginea (Eutrema salsugineum).
    • Authors: Lee YP, Giorgi FM, Lohse M, Kvederaviciute K, Klages S, Usadel B, Meskiene I, Reinhardt R, Hincha DK
    • Issue date: 2013 Nov 14
    • Characterization of the transcriptome of an ecologically important avian species, the Vinous-throated Parrotbill Paradoxornis webbianus bulomachus (Paradoxornithidae; Aves).
    • Authors: Chu JH, Lin RC, Yeh CF, Hsu YC, Li SH
    • Issue date: 2012 Apr 24
    • Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation database.
    • Authors: Blavet N, Charif D, Oger-Desfeux C, Marais GA, Widmer A
    • Issue date: 2011 Jul 26
    • A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing.
    • Authors: Hoang NV, Furtado A, Mason PJ, Marquardt A, Kasirajan L, Thirugnanasambandam PP, Botha FC, Henry RJ
    • Issue date: 2017 May 22
    • Speciation on oceanic islands: rapid adaptive divergence vs. cryptic speciation in a Guadalupe Island songbird (Aves: Junco).
    • Authors: Aleixandre P, Hernández Montoya J, Milá B
    • Issue date: 2013
    DSpace software (copyright © 2002 - 2021)  DuraSpace
    Quick Guide | Contact Us
    Open Repository is a service operated by 
    Atmire NV
     

    Export search results

    The export option will allow you to export the current search results of the entered query to a file. Different formats are available for download. To export the items, click on the button corresponding with the preferred download format.

    By default, clicking on the export buttons will result in a download of the allowed maximum amount of items.

    To select a subset of the search results, click "Selective Export" button and make a selection of the items you want to export. The amount of items that can be exported at once is similarly restricted as the full export.

    After making a selection, click one of the export format buttons. The amount of items that will be exported is indicated in the bubble next to export format.