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 journalArticlepeer-review

28 Citations (Scopus)
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Abstract

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.
Original languageEnglish
Article number305
JournalBMC Genomics
Volume13
DOIs
Publication statusPublished - 9 Jul 2012

Keywords

  • Animals
  • Ecosystem
  • Female
  • Genome
  • Genomics
  • Male
  • Models, Biological
  • Oligonucleotide Array Sequence Analysis
  • Polymorphism, Single Nucleotide
  • RNA
  • Sequence Analysis, RNA
  • Songbirds
  • Transcriptome

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