De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis)

genomic tools for an ecological model system

Mark P. Peterson, Danielle J. Whittaker, Shruthi Ambreth, Suhas Sureshchandra, Aaron Buechlein, Ram Podicheti, Jeong-Hyeon Choi, Zhao Lai, Keithanne Mockatis, John Colbourne, Haixu Tang, Ellen D. Ketterson

Research output: Contribution to journalArticle

28 Citations (Scopus)

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 (90 %) 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 - extending the historic work on natural history and hormone-mediated phenotypes in this system.

Original languageEnglish (US)
Article number305
JournalBMC Genomics
Volume13
Issue number1
DOIs
StatePublished - Jul 9 2012

Fingerprint

Songbirds
Transcriptome
Ecosystem
Natural History
Genes
Genomics
Nucleotides
Hormones
RNA
Sparrows
Gene Ontology
Gene Regulatory Networks
Microarray Analysis
Titanium
Single Nucleotide Polymorphism
Phenotype
Gene Expression

Keywords

  • 454 titanium cDNA sequencing
  • Aves
  • Junco
  • Microarray
  • Pyrosequencing
  • Single nucleotide polymorphism
  • Transcriptome

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Peterson, M. P., Whittaker, D. J., Ambreth, S., Sureshchandra, S., Buechlein, A., Podicheti, R., ... Ketterson, E. D. (2012). De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system. BMC Genomics, 13(1), [305]. https://doi.org/10.1186/1471-2164-13-305

De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis) : genomic tools for an ecological model system. / Peterson, Mark P.; Whittaker, Danielle J.; Ambreth, Shruthi; Sureshchandra, Suhas; Buechlein, Aaron; Podicheti, Ram; Choi, Jeong-Hyeon; Lai, Zhao; Mockatis, Keithanne; Colbourne, John; Tang, Haixu; Ketterson, Ellen D.

In: BMC Genomics, Vol. 13, No. 1, 305, 09.07.2012.

Research output: Contribution to journalArticle

Peterson, MP, Whittaker, DJ, Ambreth, S, Sureshchandra, S, Buechlein, A, Podicheti, R, Choi, J-H, Lai, Z, Mockatis, K, Colbourne, J, Tang, H & Ketterson, ED 2012, 'De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system', BMC Genomics, vol. 13, no. 1, 305. https://doi.org/10.1186/1471-2164-13-305
Peterson, Mark P. ; Whittaker, Danielle J. ; Ambreth, Shruthi ; Sureshchandra, Suhas ; Buechlein, Aaron ; Podicheti, Ram ; Choi, Jeong-Hyeon ; Lai, Zhao ; Mockatis, Keithanne ; Colbourne, John ; Tang, Haixu ; Ketterson, Ellen D. / De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis) : genomic tools for an ecological model system. In: BMC Genomics. 2012 ; Vol. 13, No. 1.
@article{862622f16edf469f941ae2fcef754c25,
title = "De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system",
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 (90 {\%}) 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 - extending the historic work on natural history and hormone-mediated phenotypes in this system.",
keywords = "454 titanium cDNA sequencing, Aves, Junco, Microarray, Pyrosequencing, Single nucleotide polymorphism, Transcriptome",
author = "Peterson, {Mark P.} and Whittaker, {Danielle J.} and Shruthi Ambreth and Suhas Sureshchandra and Aaron Buechlein and Ram Podicheti and Jeong-Hyeon Choi and Zhao Lai and Keithanne Mockatis and John Colbourne and Haixu Tang and Ketterson, {Ellen D.}",
year = "2012",
month = "7",
day = "9",
doi = "10.1186/1471-2164-13-305",
language = "English (US)",
volume = "13",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "BioMed Central",
number = "1",

}

TY - JOUR

T1 - De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis)

T2 - genomic tools for an ecological model system

AU - Peterson, Mark P.

AU - Whittaker, Danielle J.

AU - Ambreth, Shruthi

AU - Sureshchandra, Suhas

AU - Buechlein, Aaron

AU - Podicheti, Ram

AU - Choi, Jeong-Hyeon

AU - Lai, Zhao

AU - Mockatis, Keithanne

AU - Colbourne, John

AU - Tang, Haixu

AU - Ketterson, Ellen D.

PY - 2012/7/9

Y1 - 2012/7/9

N2 - 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 (90 %) 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 - extending the historic work on natural history and hormone-mediated phenotypes in this system.

AB - 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 (90 %) 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 - extending the historic work on natural history and hormone-mediated phenotypes in this system.

KW - 454 titanium cDNA sequencing

KW - Aves

KW - Junco

KW - Microarray

KW - Pyrosequencing

KW - Single nucleotide polymorphism

KW - Transcriptome

UR - http://www.scopus.com/inward/record.url?scp=84863510246&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84863510246&partnerID=8YFLogxK

U2 - 10.1186/1471-2164-13-305

DO - 10.1186/1471-2164-13-305

M3 - Article

VL - 13

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

IS - 1

M1 - 305

ER -