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A high-resolution mRNA expression time course of embryonic development in zebrafish
[article]
2017
bioRxiv
pre-print
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We have produced an mRNA expression time course of zebrafish development across 18 time points from 1-cell to 5 days post-fertilisation sampling individual and pools of embryos. Using poly(A) pulldown stranded RNA-seq and a 3′ end transcript counting method we characterise the temporal expression profiles of 23,642 genes. We identify temporal and functional transcript co-variance that associates 5,024 unnamed genes with distinct developmental time points. Specifically, a class of over 100
doi:10.1101/107631
fatcat:crrp2axbqrcrvhjrh5qfssvn5e
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... usly uncharacterised zinc finger domain containing genes, located on the long arm of chromosome 4, is expressed in a sharp peak during zygotic genome activation. The data reveal complex and widespread differential use of exons and previously unidentified 3′ ends across development, new primary microRNA transcripts and temporal divergence of gene paralogues generated in the teleost genome duplication. To make this dataset a useful baseline reference, the data are accessible to browse and download at Expression Atlas and Ensembl.
A high-resolution mRNA expression time course of embryonic development in zebrafish
2017
eLife
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Author ORCIDs Richard J White, http://orcid.org/0000-0003-1842-412X Konstantinos Billis, http://orcid.org/0000-0001-8568-4306 Thibaut Hourlier, http://orcid.org/0000-0003-4894-7773 Anja Fü llgrabe, http ...
doi:10.7554/elife.30860
pmid:29144233
pmcid:PMC5690287
fatcat:kfjyomsqkvdvzntjeuxyjvye2e
Transcriptomic analysis of the interaction between Helianthus annuus and its obligate parasite Plasmopara halstedii shows single nucleotide polymorphisms in CRN sequences
2011
BMC Genomics
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scriptomic analysis of the interaction between Helianthus annuus and its obligate parasite Plasmopara halstedii shows single nucleotide polymorphisms in CRN sequences. Abstract Background: Downy mildew in sunflowers (Helianthus annuus L.) is caused by the oomycete Plasmopara halstedii (Farl.) Berlese et de Toni. Despite efforts by the international community to breed mildew-resistant varieties, downy mildew remains a major threat to the sunflower crop. Very few genomic, genetic and molecular
doi:10.1186/1471-2164-12-498
pmid:21988821
pmcid:PMC3204308
fatcat:hhhyf5owjre5rgxwg5ejgrxivu
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... ources are currently available to study this pathogen. Using a 454 sequencing method, expressed sequence tags (EST) during the interaction between H. annuus and P. halstedii have been generated and a search was performed for sites in putative effectors to show polymorphisms between the different races of P. halstedii. Results: A 454 pyrosequencing run of two infected sunflower samples (inbred lines XRQ and PSC8 infected with race 710 of P. halstedii, which exhibit incompatible and compatible interactions, respectively) generated 113,720 and 172,107 useable reads. From these reads, 44,948 contigs and singletons have been produced. A bioinformatic portal, HP, was specifically created for in-depth analysis of these clusters. Using in silico filtering, 405 clusters were defined as being specific to oomycetes, and 172 were defined as non-specific oomycete clusters. A subset of these two categories was checked using PCR amplification, and 86% of the tested clusters were validated. Twenty putative RXLR and CRN effectors were detected using PSI-BLAST. Using corresponding sequences from four races (100, 304, 703 and 710), 22 SNPs were detected, providing new information on pathogen polymorphisms. Conclusions: This study identified a large number of genes that are expressed during H. annuus/P. halstedii compatible or incompatible interactions. It also reveals, for the first time, that an infection mechanism exists in P. halstedii similar to that in other oomycetes associated with the presence of putative RXLR and CRN effectors. SNPs discovered in CRN effector sequences were used to determine the genetic distances between the four races of P. halstedii. This work therefore provides valuable tools for further discoveries regarding the H. annuus/P. halstedii pathosystem.
A Gene-Phenotype Network Based on Genetic Variability for Drought Responses Reveals Key Physiological Processes in Controlled and Natural Environments
2012
PLoS ONE
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Identifying the connections between molecular and physiological processes underlying the diversity of drought stress responses in plants is key for basic and applied science. Drought stress response involves a large number of molecular pathways and subsequent physiological processes. Therefore, it constitutes an archetypical systems biology model. We first inferred a gene-phenotype network exploiting differences in drought responses of eight sunflower (Helianthus annuus) genotypes to two
doi:10.1371/journal.pone.0045249
pmid:23056196
pmcid:PMC3466295
fatcat:vz2n57xqanhnpaqomdncqpx2pa
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... stress scenarios. Large transcriptomic data were obtained with the sunflower Affymetrix microarray, comprising 32423 probesets, and were associated to nine morpho-physiological traits (integrated transpired water, leaf transpiration rate, osmotic potential, relative water content, leaf mass per area, carbon isotope discrimination, plant height, number of leaves and collar diameter) using sPLS regression. Overall, we could associate the expression patterns of 1263 probesets to six phenotypic traits and identify if correlations were due to treatment, genotype and/or their interaction. We also identified genes whose expression is affected at moderate and/or intense drought stress together with genes whose expression variation could explain phenotypic and drought tolerance variability among our genetic material. We then used the network model to study phenotypic changes in less tractable agronomical conditions, i.e. sunflower hybrids subjected to different watering regimes in field trials. Mapping this new dataset in the gene-phenotype network allowed us to identify genes whose expression was robustly affected by water deprivation in both controlled and field conditions. The enrichment in genes correlated to relative water content and osmotic potential provides evidence of the importance of these traits in agronomical conditions.
The Ensembl gene annotation system
2016
Database: The Journal of Biological Databases and Curation
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The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts
doi:10.1093/database/baw093
pmid:27337980
pmcid:PMC4919035
fatcat:jsnympsq4rczzhh5nupzv5b4ha
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... y leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail. Database URL: http://www.ensembl.org/index.html Species are listed along with assembly names, assembly accessions, the Ensembl release numbers where the annotations were first made available, the dates of these Ensembl releases, and the references for each of the respective published genome projects. The rhesus macaque assembly (MMUL 1.0) was published before the Browser Genome Release Agreement came into effect and therefore was not assigned an assembly accession.
Ensembl 2016
2015
Nucleic Acids Research
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The Ensembl project (http://www.ensembl.org) is a system for genome annotation, analysis, storage and dissemination designed to facilitate the access of genomic annotation from chordates and key model organisms. It provides access to data from 87 species across our main and early access Pre! websites. This year we introduced three newly annotated species and released numerous updates across our supported species with a concentration on data for the latest genome assemblies of human, mouse,
doi:10.1093/nar/gkv1157
pmid:26687719
pmcid:PMC4702834
fatcat:ucvvl4dvujeu3ieixlk7vpzjie
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... fish and rat. We also provided two data updates for the previous human assembly, GRCh37, through a dedicated website (http://grch37.ensembl.org). Our tools, in particular the VEP, have been improved significantly through integration of additional third party data. REST is now capable of larger-scale analysis and our regulatory data BioMart can deliver faster results. The website is now capable of displaying long-range interactions such as those found in cis-regulated datasets. Finally we have launched a website optimized for mobile devices providing views of genes, variants and phenotypes. Our data is made available without restriction and all code is available from our GitHub organization site (http: //github.com/Ensembl) under an Apache 2.0 license.
An improved pig reference genome sequence to enable pig genetics and genomics research
[article]
2019
biorxiv/medrxiv
pre-print
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AbstractThe domestic pig (Sus scrofa) is important both as a food source and as a biomedical model with high anatomical and immunological similarity to humans. The draft reference genome (Sscrofa10.2) represents a purebred female pig from a commercial pork production breed (Duroc), and was established using older clone-based sequencing methods. The Sscrofa10.2 assembly was incomplete and unresolved redundancies, short range order and orientation errors and associated misassembled genes limited
doi:10.1101/668921
fatcat:k4bclu6iovdodndojtnhdgqnhu
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... ts utility. We present two genome assemblies created with more recent long read technologies and a whole genome shotgun strategy, one for the same Duroc female (Sscrofa11.1) and one for an outbred, composite breed male animal commonly used for commercial pork production (USMARCv1.0). Both assemblies are of substantially higher (>90-fold) continuity and accuracy compared to the earlier reference, and the availability of two independent assemblies provided an opportunity to identify large-scale variants and to error-check the accuracy of representation of the genome. We propose that the improved Duroc breed assembly (Sscrofa11.1) become the reference genome for genomic research in pigs.
Ensembl 2017
2016
Nucleic Acids Research
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Ensembl (www.ensembl.org) is a database and genome browser for enabling research on vertebrate genomes. We import, analyse, curate and integrate a diverse collection of large-scale reference data to create a more comprehensive view of genome biology than would be possible from any individual dataset. Our extensive data resources include evidence-based gene and regulatory region annotation, genome variation and gene trees. An accompanying suite of tools, infrastructure and programmatic access
doi:10.1093/nar/gkw1104
pmid:27899575
pmcid:PMC5210575
fatcat:hzc4nlutrnfo5obbhqtlljr724
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... hods ensure uniform data analysis and distribution for all supported species. Together, these provide a comprehensive solution for large-scale and targeted genomics applications alike. Among many other developments over the past year, we have improved our resources for gene regulation and comparative genomics, and added CRISPR/Cas9 target sites. We released new browser functionality and tools, including improved filtering and prioritization of genome variation, Manhattan plot visualization for linkage disequilibrium and eQTL data, and an ontology search for phenotypes, traits and disease. We have also enhanced data discovery and access with a track hub registry and a se-lection of new REST end points. All Ensembl data are freely released to the scientific community and our source code is available via the open source Apache 2.0 license.
Ensembl 2015
2014
Nucleic Acids Research
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Ensembl (http://www.ensembl.org) is a genomic interpretation system providing the most up-to-date annotations, querying tools and access methods for chordates and key model organisms. This year we released updated annotation (gene models, comparative genomics, regulatory regions and variation) on the new human assembly, GRCh38, although we continue to support researchers using the GRCh37.p13 assembly through a dedicated site (http://grch37. ensembl.org). Our Regulatory Build has been revamped
doi:10.1093/nar/gku1010
pmid:25352552
pmcid:PMC4383879
fatcat:cqhfyssywrcm5iuxojhi33h3he
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... identify regulatory regions of interest and to efficiently highlight their activity across disparate epigenetic data sets. A number of new interfaces allow users to perform large-scale comparisons of their data against our annotations. The REST server (http://rest.ensembl.org), which allows programs written in any language to query our databases, has moved to a full service alongside our upgraded website tools. Our online Variant Effect Predictor tool has been updated to process more variants and calculate summary statistics. Lastly, the WiggleTools package enables users to summarize large collections of data sets and view them as single tracks in Ensembl. The Ensembl code base itself is more accessible: it is now hosted on our GitHub organization page (https://github.com/Ensembl) under an Apache 2.0 open source license.
The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease
2014
Nature Biotechnology
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An improved pig reference genome sequence to enable pig genetics and genomics research
2020
GigaScience
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Background The domestic pig (Sus scrofa) is important both as a food source and as a biomedical model given its similarity in size, anatomy, physiology, metabolism, pathology, and pharmacology to humans. The draft reference genome (Sscrofa10.2) of a purebred Duroc female pig established using older clone-based sequencing methods was incomplete, and unresolved redundancies, short-range order and orientation errors, and associated misassembled genes limited its utility. Results We present 2
doi:10.1093/gigascience/giaa051
pmid:32543654
pmcid:PMC7448572
fatcat:75gn5f2hfzeqnclwumqnonttsm
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... ted highly contiguous chromosome-level genome assemblies created with more recent long-read technologies and a whole-genome shotgun strategy, 1 for the same Duroc female (Sscrofa11.1) and 1 for an outbred, composite-breed male (USMARCv1.0). Both assemblies are of substantially higher (>90-fold) continuity and accuracy than Sscrofa10.2. Conclusions These highly contiguous assemblies plus annotation of a further 11 short-read assemblies provide an unprecedented view of the genetic make-up of this important agricultural and biomedical model species. We propose that the improved Duroc assembly (Sscrofa11.1) become the reference genome for genomic research in pigs.
Ensembl 2014
2013
Nucleic Acids Research
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Ensembl (http://www.ensembl.org) creates tools and data resources to facilitate genomic analysis in chordate species with an emphasis on human, major vertebrate model organisms and farm animals. Over the past year we have increased the number of species that we support to 77 and expanded our genome browser with a new scrollable overview and improved variation and phenotype views. We also report updates to our core datasets and improvements to our gene homology relationships from the addition of
doi:10.1093/nar/gkt1196
pmid:24316576
pmcid:PMC3964975
fatcat:knxp7akjtnbvnm7hlxajhvnzra
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... new species. Our REST service has been extended with additional support for comparative genomics and ontology information. Finally, we provide updated information about our methods for data access and resources for user training.
Ensembl 2018
2017
Nucleic Acids Research
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The Ensembl project has been aggregating, processing, integrating and redistributing genomic datasets since the initial releases of the draft human genome, with the aim of accelerating genomics research through rapid open distribution of public data. Large amounts of raw data are thus transformed into knowledge, which is made available via a multitude of channels, in particular our browser (http://www.ensembl. org). Over time, we have expanded in multiple directions. First, our resources
doi:10.1093/nar/gkx1098
pmid:29155950
pmcid:PMC5753206
fatcat:g7pg5j5vpfgilgtr2bflfiqyei
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... e multiple fields of genomics, in particular gene annotation, comparative genomics, genetics and epigenomics. Second, we cover a growing number of genome assemblies; Ensembl Release 90 contains exactly 100. Third, our databases feed simultaneously into an array of services designed around different use cases, ranging from quick browsing to genome-wide bioinformatic analysis. We present here the latest developments of the Ensembl project, with a focus on managing an increasing number of assemblies, supporting efforts in genome interpretation and improving our browser.
Ensembl 2013
2012
Nucleic Acids Research
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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.
doi:10.1093/nar/gks1236
pmid:23203987
pmcid:PMC3531136
fatcat:5hwmkwmozbcpbk3bzrzuhwdqhe
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... l data are accessible through the genome browser at http://www.ensembl.org and through other tools and programmatic interfaces.
GENCODE reference annotation for the human and mouse genomes
2018
Nucleic Acids Research
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The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics. Over the last 15 years, the GENCODE consortium has been producing reference quality gene annotations to provide this foundational resource. The GENCODE consortium includes both experimental and computational biology groups who work together to improve and extend the GENCODE gene annotation.
doi:10.1093/nar/gky955
pmid:30357393
pmcid:PMC6323946
fatcat:vg5kuecy5rc7xewce5u3xczdba
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... ifically, we generate primary data, create bioinformatics tools and provide analysis to support the work of expert manual gene annotators and automated gene annotation pipelines. In addition, manual and computational annotation workflows use any and all publicly available data and analysis, along with the research literature to identify and characterise gene loci to the highest standard. GENCODE gene annotations are accessible via the Ensembl and UCSC Genome Browsers, the Ensembl FTP site, Ensembl Biomart, Ensembl Perl and REST APIs as well as https://www.gencodegenes.org.
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