ArticleBMC genomics2010
Digital gene expression analysis of the zebra finch genome.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
30 citing papers in PubMed, 45 citations in OpenAlex.
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- De novo assembly of the dual transcriptomes of a polymorphic raptor species and its malarial parasite.BMC genomics · 2015Article
- Using genomics to characterize evolutionary potential for conservation of wild populations.Evolutionary applications · 2014Article
- Highly variable recombinational landscape modulates efficacy of natural selection in birds.Genome biology and evolution · 2014Article
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- Overview of the functional virulent genome of the coffee leaf rust pathogen Hemileia vastatrix with an emphasis on early stages of infection.Frontiers in plant science · 2014Article
- Identification of differentially expressed genes in breast muscle and skin fat of postnatal Pekin duck.PloS one · 2014Article
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- Brain transcriptome of the violet-eared waxbill Uraeginthus granatina and recent evolution in the songbird genome.Open biology · 2013Article
- Characterisation of a transcriptome to find sequence differences between two differentially migrating subspecies of the willow warbler Phylloscopus trochilus.BMC genomics · 2013Article
- Transcriptome of the dead: characterisation of immune genes and marker development from necropsy samples in a free-ranging marine mammal.BMC genomics · 2013Article
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- Sequencing of the core MHC region of black grouse (Tetrao tetrix) and comparative genomics of the galliform MHC.BMC genomics · 2012Article
- Gene expression divergence and nucleotide differentiation between males of different color morphs and mating strategies in the ruff.Ecology and evolution · 2012Article
- Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development.Open biology · 2012Article
- Application of high-resolution, massively parallel pyrosequencing for estimation of haplotypes and gene expression levels of swine leukocyte antigen (SLA) class I genes.Immunogenetics · 2012Article
- Survey of the Applications of NGS to Whole-Genome Sequencing and Expression Profiling.Genomics & informatics · 2012Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundIn order to understand patterns of adaptation and molecular evolution it is important to quantify both variation in gene expression and nucleotide sequence divergence. Gene expression profiling in non-model organisms has recently been facilitated by the advent of massively parallel sequencing technology. Here we investigate tissue specific gene expression patterns in the zebra finch (Taeniopygia guttata) with special emphasis on the genes of the major histocompatibility complex (MHC).
resultsAlmost 2 million 454-sequencing reads from cDNA of six different tissues were assembled and analysed. A total of 11,793 zebra finch transcripts were represented in this EST data, indicating a transcriptome coverage of about 65%. There was a positive correlation between the tissue specificity of gene expression and non-synonymous to synonymous nucleotide substitution ratio of genes, suggesting that genes with a specialised function are evolving at a higher rate (or with less constraint) than genes with a more general function. In line with this, there was also a negative correlation between overall expression levels and expression specificity of contigs. We found evidence for expression of 10 different genes related to the MHC. MHC genes showed relatively tissue specific expression levels and were in general primarily expressed in spleen. Several MHC genes, including MHC class I also showed expression in brain. Furthermore, for all genes with highest levels of expression in spleen there was an overrepresentation of several gene ontology terms related to immune function.
conclusionsOur study highlights the usefulness of next-generation sequence data for quantifying gene expression in the genome as a whole as well as in specific candidate genes. Overall, the data show predicted patterns of gene expression profiles and molecular evolution in the zebra finch genome. Expression of MHC genes in particular, corresponds well with expression patterns in other vertebrates.
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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.