Generation, analysis and functional annotation of expressed sequence tags from the sheepshead minnow (Cyprinodon variegatus)

Mehdi Pirooznia, Alexander Pozhitkov, Edward J. Perkins, Youping Deng, Marius Brouwer

Research output: Contribution to journalArticlepeer-review

Abstract

Background: Sheepshead minnow (Cyprinodon variegatus) are small fish capable of withstanding exposure to very low levels of dissolved oxygen, as well as extreme temperatures and salinities. It is an important model in understanding the impacts and biological response to hypoxia and co-occurring compounding stressors such as polycyclic aromatic hydrocarbons, endocrine disrupting chemicals, metals and herbicides. Here, we initiated a project to sequence and analyze over 10,000 ESTs generated from the Sheepshead minnow (Cyprinodon variegatus) as a resource for investigating stressor responses.Results: We sequenced 10,858 EST clones using a normalized cDNA library made from larval, embryonic and adult suppression subtractive hybridization-PCR (SSH) libraries. Post- sequencing processing led to 8,099 high quality sequences. Clustering analysis of these ESTs indentified 4,223 unique sequences containing 1,053 contigs and 3,170 singletons. BLASTX searches produced 1,394 significant (E-value <10-5) hits and further Gene Ontology (GO) analysis annotated 388 of these genes. All the EST sequences were deposited by Expressed Sequence Tags database (dbEST) in GenBank (GenBank: GE329585 to GE337683). Gene discovery and annotations are presented and discussed. This set of ESTs represents a significant proportion of the Sheepshead minnow (Cyprinodon variegatus) transcriptome, and provides a material basis for the development of microarrays useful for further gene expression studies in association with stressors such as hypoxia, cadmium, chromium and pyrene.

Original languageEnglish (US)
Article numberS4
JournalBMC Genomics
Volume11
Issue numberSUPPL. 2
DOIs
StatePublished - Nov 2 2010

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Fingerprint Dive into the research topics of 'Generation, analysis and functional annotation of expressed sequence tags from the sheepshead minnow (Cyprinodon variegatus)'. Together they form a unique fingerprint.

Cite this