Microarray and EST database estimates of mRNA expression levels differ: The protein length versus expression curve for C. elegans

Muñoz, Enrique; Bogarad, Leonard D.; Deem, Michael W.

doi:10.1186/1471-2164-5-30

Cited by 27 publications

(15 citation statements)

References 32 publications

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“…The tendency for EST libraries to be biased towards longer transcripts has been previously reported [9]. These studies suggest that the direct use of EST data might be problematic and that it should be normalized for length if transcript abundance is to be used as a measure of expression levels.…”

Section: Resultsmentioning

confidence: 88%

EST Analysis of Ostreococcus lucimarinus, the Most Compact Eukaryotic Genome, Shows an Excess of Introns in Highly Expressed Genes

et al. 2008

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BackgroundThe genome of the pico-eukaryotic (bacterial-sized) prasinophyte green alga Ostreococcus lucimarinus has one of the highest gene densities known in eukaryotes, yet it contains many introns. Phylogenetic studies suggest this unusually compact genome (13.2 Mb) is an evolutionarily derived state among prasinophytes. The presence of introns in the highly reduced O. lucimarinus genome appears to be in opposition to simple explanations of genome evolution based on unidirectional tendencies, either neutral or selective. Therefore, patterns of intron retention in this species can potentially provide insights into the forces governing intron evolution.Methodology/Principal FindingsHere we studied intron features and levels of expression in O. lucimarinus using expressed sequence tags (ESTs) to annotate the current genome assembly. ESTs were assembled into unigene clusters that were mapped back to the O. lucimarinus Build 2.0 assembly using BLAST and the level of gene expression was inferred from the number of ESTs in each cluster. We find a positive correlation between expression levels and both intron number (R = +0.0893, p = <0.0005) and intron density (number of introns/kb of CDS; R = +0.0753, p = <0.005).Conclusions/SignificanceIn a species with a genome that has been recently subjected to a great reduction of non-coding DNA, these results imply the existence of selective/functional roles for introns that are principally detectable in highly expressed genes. In these cases, introns are likely maintained by balancing the selective forces favoring their maintenance with other mutational and/or selective forces acting on genome size.

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Section: Resultsmentioning

confidence: 88%

EST Analysis of Ostreococcus lucimarinus, the Most Compact Eukaryotic Genome, Shows an Excess of Introns in Highly Expressed Genes

et al. 2008

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“…22,49,50 ESTs constitute partial transcriptome representation correlated with gene abundance and expression. 51,52 In 14 Citrus species ( C. aurantifolia ; C. aurantium ; C. clementina ; C. jambhiri ; C. limettioides ; C. limonia ; C. medica ; C. reshni ; C. reticulata ; C. reticulata × C. temple ; C. sinensis × P. trifoliata ; C. unshiu ; C. paradisi ; C. paradisi × P. trifoliata ) and P. trifoliata , we extracted the expression of ESTs count using the CAP3 assembly (.ace files) and compared the usage of codons in accordance with earlier reports. 53–55 We also selected the ribosomal protein-encoding genes and quantified the association of the ribosomal encoding genes with axis 1 (COA/RSCU) and axis 2 (COA/RSCU) of correspondence analysis.…”

Section: Resultsmentioning

confidence: 99%

Evaluation of Codon Biology in Citrus and Poncirus trifoliata Based on Genomic Features and Frame Corrected Expressed Sequence Tags

et al. 2013

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Citrus, as one of the globally important fruit trees, has been an object of interest for understanding genetics and evolutionary process in fruit crops. Meta-analyses of 19 Citrus species, including 4 globally and economically important Citrus sinensis, Citrus clementina, Citrus reticulata, and 1 Citrus relative Poncirus trifoliata, were performed. We observed that codons ending with A- or T- at the wobble position were preferred in contrast to C- or G- ending codons, indicating a close association with AT richness of Citrus species and P. trifoliata. The present study postulates a large repertoire of a set of optimal codons for the Citrus genus and P. trifoliata and demonstrates that GCT and GGT are evolutionary conserved optimal codons. Our observation suggested that mutational bias is the dominating force in shaping the codon usage bias (CUB) in Citrus and P. trifoliata. Correspondence analysis (COA) revealed that the principal axis [axis 1; COA/relative synonymous codon usage (RSCU)] contributes only a minor portion (∼10.96%) of the recorded variance. In all analysed species, except P. trifoliata, Gravy and aromaticity played minor roles in resolving CUB. Compositional constraints were found to be strongly associated with the amino acid signatures in Citrus species and P. trifoliata. Our present analysis postulates compositional constraints in Citrus species and P. trifoliata and plausible role of the stress with GC3 and coevolution pattern of amino acid.

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“…Representation in cDNA library generally correlates with abundance in the original biologic sample [59] although artifacts occur [60,61]. To investigate the difference in the codon usage patterns in highly abundant transcripts as compared with less abundantly expressed genes, as determined by ESTs, we selected five species, each of which is a member of a different clade.…”

Section: Resultsmentioning

confidence: 99%

Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species

et al. 2006

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Microarray and EST database estimates of mRNA expression levels differ: The protein length versus expression curve for C. elegans

Cited by 27 publications

References 32 publications

EST Analysis of Ostreococcus lucimarinus, the Most Compact Eukaryotic Genome, Shows an Excess of Introns in Highly Expressed Genes

EST Analysis of Ostreococcus lucimarinus, the Most Compact Eukaryotic Genome, Shows an Excess of Introns in Highly Expressed Genes

Evaluation of Codon Biology in Citrus and Poncirus trifoliata Based on Genomic Features and Frame Corrected Expressed Sequence Tags

Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species

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