Ensembl 2013

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Nucleic Acids Research (Impact Factor: 9.11). 11/2012; 41(Database issue). DOI: 10.1093/nar/gks1236
Source: PubMed


The Ensembl project (http://www.ensembl.org) provides genome information for sequenced chordate genomes with a particular focus on human, mouse, zebrafish and rat. Our
resources include evidenced-based gene sets for all supported species; large-scale whole genome multiple species alignments
across vertebrates and clade-specific alignments for eutherian mammals, primates, birds and fish; variation data resources
for 17 species and regulation annotations based on ENCODE and other data sets. Ensembl data are accessible through the genome
browser at http://www.ensembl.org and through other tools and programmatic interfaces.

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    • "For the assembly, we pooled the filtered reads of all samples and implemented three different trials using SOAP-DENOVO [53] (kmer = 35, min length 200 nucleotides), Velvet/Oases [54, 55]) (kmer = 35, min length 200 nucleotides) and Trinity [56] (trinityrnaseq_r2013-02-25; default kmer 25, min length 200 nucleotides). The three candidate assemblies were evaluated by BLASTn [57] against Oreochromis niloticus, Oryzias latipes and Gasterosteus aculeatus cDNA dataset downloaded from Ensembl database [58] with an e-value threshold of 10-9. The assembly produced by Trinity had the highest number of significant similarity with unique genes from all three teleost species and was selected. "
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    ABSTRACT: Background Teleosts are characterized by a remarkable breadth of sexual mechanisms including various forms of hermaphroditism. Sparidae is a fish family exhibiting gonochorism or hermaphroditism even in closely related species. The sparid Diplodus puntazzo (sharpsnout seabream), exhibits rudimentary hermaphroditism characterized by intersexual immature gonads but single-sex mature ones. Apart from the intriguing reproductive biology, it is economically important with a continuously growing aquaculture in the Mediterranean Sea, but limited available genetic resources. Our aim was to characterize the expressed transcriptome of gonads and brains through RNA-Sequencing and explore the properties of genes that exhibit sex-biased expression profiles. Results Through RNA-Sequencing we obtained an assembled transcriptome of 82,331 loci. The expression analysis uncovered remarkable differences between male and female gonads, while male and female brains were almost identical. Focused search for known targets of sex determination and differentiation in vertebrates built the sex-specific expression profile of sharpsnout seabream. Finally, a thorough genetic marker discovery pipeline led to the retrieval of 85,189 SNPs and 29,076 microsatellites enriching the available genetic markers for this species. Conclusions We obtained a nearly complete source of transcriptomic sequence as well as marker information for sharpsnout seabream, laying the ground for understanding the complex process of sex differentiation of this economically valuable species. The genes involved include known candidates from other vertebrate species, suggesting a conservation of the toolkit between gonochorists and hermaphrodites. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-655) contains supplementary material, which is available to authorized users.
    BMC Genomics 08/2014; 15(1):655. DOI:10.1186/1471-2164-15-655 · 3.99 Impact Factor
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    • "In our initial analysis, we generated a list of the human orthologues of the worm modifier genes using EnsemblCompara [17], and found that 61 out of the 78 worm genes had human counterparts. This ratio is significantly higher than one would expect by chance if one considers that there are only 7,970 worm genes that have human orthologues out of a genome of approximately 20,000 genes [18]. "
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    ABSTRACT: The human Aβ peptide causes progressive paralysis when expressed in the muscles of the nematode worm, C. elegans. We have exploited this model of Aβ toxicity by carrying out an RNAi screen to identify genes whose reduced expression modifies the severity of this locomotor phenotype. Our initial finding was that none of the human orthologues of these worm genes is identical with the genome-wide significant GWAS genes reported to date (the "white zone"); moreover there was no identity between worm screen hits and the longer list of GWAS genes which included those with borderline levels of significance (the "grey zone"). This indicates that Aβ toxicity should not be considered as equivalent to sporadic AD. To increase the sensitivity of our analysis, we then considered the physical interactors (+1 interactome) of the products of the genes in both the worm and the white+grey zone lists. When we consider these worm and GWAS gene lists we find that 4 of the 60 worm genes have a +1 interactome overlap that is larger than expected by chance. Two of these genes form a chaperonin complex, the third is closely associated with this complex and the fourth gene codes for actin, the major substrate of the same chaperonin.
    PLoS ONE 07/2014; 9(7):e102985. DOI:10.1371/journal.pone.0102985 · 3.23 Impact Factor
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    • "According to the UMD 3.1 assembly, chromosome X is the second largest chromosome in the bovine genome [1]. A total of 1128 annotated genes have been reported on the X chromosome in the ENSEMBL version 72 [2]. However, markers on the X chromosome are not used for genomic prediction in some countries and populations. "
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    ABSTRACT: Background Although the X chromosome is the second largest bovine chromosome, markers on the X chromosome are not used for genomic prediction in some countries and populations. In this study, we presented a method for computing genomic relationships using X chromosome markers, investigated the accuracy of imputation from a low density (7K) to the 54K SNP (single nucleotide polymorphism) panel, and compared the accuracy of genomic prediction with and without using X chromosome markers. Methods The impact of considering X chromosome markers on prediction accuracy was assessed using data from Nordic Holstein bulls and different sets of SNPs: (a) the 54K SNPs for reference and test animals, (b) SNPs imputed from the 7K to the 54K SNP panel for test animals, (c) SNPs imputed from the 7K to the 54K panel for half of the reference animals, and (d) the 7K SNP panel for all animals. Beagle and Findhap were used for imputation. GBLUP (genomic best linear unbiased prediction) models with or without X chromosome markers and with or without a residual polygenic effect were used to predict genomic breeding values for 15 traits. Results Averaged over the two imputation datasets, correlation coefficients between imputed and true genotypes for autosomal markers, pseudo-autosomal markers, and X-specific markers were 0.971, 0.831 and 0.935 when using Findhap, and 0.983, 0.856 and 0.937 when using Beagle. Estimated reliabilities of genomic predictions based on the imputed datasets using Findhap or Beagle were very close to those using the real 54K data. Genomic prediction using all markers gave slightly higher reliabilities than predictions without X chromosome markers. Based on our data which included only bulls, using a G matrix that accounted for sex-linked relationships did not improve prediction, compared with a G matrix that did not account for sex-linked relationships. A model that included a polygenic effect did not recover the loss of prediction accuracy from exclusion of X chromosome markers. Conclusions The results from this study suggest that markers on the X chromosome contribute to accuracy of genomic predictions and should be used for routine genomic evaluation.
    Genetics Selection Evolution 07/2014; 46(1):47. DOI:10.1186/1297-9686-46-47 · 3.82 Impact Factor
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