ArticleBMC genomics2009
Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33 citing papers in PubMed, 96 citations in OpenAlex.
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- The transcriptome of metamorphosing flatfish.BMC genomics · 2016Article
- A gene to organism approach--assessing the impact of environmental pollution in eelpout (Zoarces viviparus) females and larvae.Environmental toxicology and chemistry · 2015Article
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- Model of gene expression in extreme cold - reference transcriptome for the high-Antarctic cryopelagic notothenioid fish Pagothenia borchgrevinki.BMC genomics · 2013Article
- Characterization of the pearl oyster (Pinctada martensii) mantle transcriptome unravels biomineralization genes.Marine biotechnology (New York, N.Y.) · 2013Article
- De novo sequencing and analysis of the Ulva linza transcriptome to discover putative mechanisms associated with its successful colonization of coastal ecosystems.BMC genomics · 2012Article
- Evolutionary force in confamiliar marine vertebrates of different temperature realms: adaptive trends in zoarcid fish transcriptomes.BMC genomics · 2012Article
- Transcriptomic characterization of the larval stage in gilthead seabream (Sparus aurata) by 454 pyrosequencing.Marine biotechnology (New York, N.Y.) · 2012Article
- De novo assembly and characterization of the root transcriptome of Aegilops variabilis during an interaction with the cereal cyst nematode.BMC genomics · 2012Article
- Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development.Open biology · 2012Article
- Genomic toolboxes for conservation biologists.Evolutionary applications · 2012Article
- Transcriptomic analysis of the housefly (Musca domestica) larva using massively parallel pyrosequencing.Molecular biology reports · 2012Article
- Applications for next-generation sequencing in fish ecotoxicogenomics.Frontiers in genetics · 2012Article
- Comparison between Normalised and Unnormalised 454-Sequencing Libraries for Small-Scale RNA-Seq Studies.Comparative and functional genomics · 2012Article
- Gene discovery and tissue-specific transcriptome analysis in chickpea with massively parallel pyrosequencing and web resource development.Plant physiology · 2011Article
- Applications of next generation sequencing in molecular ecology of non-model organisms.Heredity · 2011Review
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe teleost Zoarces viviparus (eelpout) lives along the coasts of Northern Europe and has long been an established model organism for marine ecology and environmental monitoring. The scarce information about this species genome has however restrained the use of efficient molecular-level assays, such as gene expression microarrays.
resultsIn the present study we present the first comprehensive characterization of the Zoarces viviparus liver transcriptome. From 400,000 reads generated by massively parallel pyrosequencing, more than 50,000 pieces of putative transcripts were assembled, annotated and functionally classified. The data was estimated to cover roughly 40% of the total transcriptome and homologues for about half of the genes of Gasterosteus aculeatus (stickleback) were identified. The sequence data was consequently used to design an oligonucleotide microarray for large-scale gene expression analysis.
conclusionOur results show that one run using a Genome Sequencer FLX from 454 Life Science/Roche generates enough genomic information for adequate de novo assembly of a large number of genes in a higher vertebrate. The generated sequence data, including the validated microarray probes, are publicly available to promote genome-wide research in Zoarces viviparus.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.