9 research outputs found

    GENCODE: reference annotation for the human and mouse genomes in 2023.

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    GENCODE produces high quality gene and transcript annotation for the human and mouse genomes. All GENCODE annotation is supported by experimental data and serves as a reference for genome biology and clinical genomics. The GENCODE consortium generates targeted experimental data, develops bioinformatic tools and carries out analyses that, along with externally produced data and methods, support the identification and annotation of transcript structures and the determination of their function. Here, we present an update on the annotation of human and mouse genes, including developments in the tools, data, analyses and major collaborations which underpin this progress. For example, we report the creation of a set of non-canonical ORFs identified in GENCODE transcripts, the LRGASP collaboration to assess the use of long transcriptomic data to build transcript models, the progress in collaborations with RefSeq and UniProt to increase convergence in the annotation of human and mouse protein-coding genes, the propagation of GENCODE across the human pan-genome and the development of new tools to support annotation of regulatory features by GENCODE. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org

    Del genoma als gens

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    In the 20th century, scientists established the molecular nature of genes – the basic units of biological inheritance – and of the processes involved in the flow of information from genes to proteins. The generalization of sequencing techniques facilitated the determination of the sequence of genomes, but their usability was limited without a map of all the genes involved. In order to build it, a combination of experimental and computational methods are used. The new sequencing technologies that allow the determination of the complete sequence of messenger RNAs are preferred, but they cannot always be used and this is why computational methods are essential. These methods include the identification of regions in the genome with sequence composition biases similar to those in the regions known to code for proteins. The ongoing projects that will sequence the genome of all the eukaryote species will make it necessary to develop more accurate and efficient computational methods.Durant el segle xx es va establir la naturalesa molecular dels gens — les unitats bàsiques de l’herència biològica— i dels processos involucrats en el flux d’informació dels gens a les proteïnes. La generalització de les tècniques de seqüenciació va facilitar l’obtenció de la seqüència dels genomes, però la seva utilitat és limitada sense un mapa dels gens. Per tal de construir-lo, hom utilitza una combinació de mètodes experimentals i computacionals. Les noves tecnologies que permeten l’obtenció de la seqüència completa dels RNA missatgers són les preferides, però no sempre es poden utilitzar. Per aquest motiu, els mètodes computacionals són essencials. Aquests mètodes inclouen la localització de regions en el genoma amb uns biaixos en la composició de la seqüència característics de les regions codificants de proteïnes. Els projectes en marxa que seqüenciaran el genoma de totes les espècies eucariotes faran necessari el desenvolupament de mètodes computacionals cada cop més acurats i eficients

    GENCODE: reference annotation for the human and mouse genomes in 2023

    No full text
    GENCODE produces high quality gene and transcript annotation for the human and mouse genomes. All GENCODE annotation is supported by experimental data and serves as a reference for genome biology and clinical genomics. The GENCODE consortium generates targeted experimental data, develops bioinformatic tools and carries out analyses that, along with externally produced data and methods, support the identification and annotation of transcript structures and the determination of their function. Here, we present an update on the annotation of human and mouse genes, including developments in the tools, data, analyses and major collaborations which underpin this progress. For example, we report the creation of a set of non-canonical ORFs identified in GENCODE transcripts, the LRGASP collaboration to assess the use of long transcriptomic data to build transcript models, the progress in collaborations with RefSeq and UniProt to increase convergence in the annotation of human and mouse protein-coding genes, the propagation of GENCODE across the human pan-genome and the development of new tools to support annotation of regulatory features by GENCODE. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org

    The hologenome of <i>Daphnia magna</i> reveals possible DNA methylation and microbiome-mediated evolution of the host genome

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    Properties that make organisms ideal laboratory models in developmental and medical research are often the ones that also make them less representative of wild relatives. The waterflea Daphnia magna is an exception, by both sharing many properties with established laboratory models and being a keystone species, a sentinel species for assessing water quality, an indicator of environmental change and an established ecotoxicology model. Yet, Daphnia's full potential has not been fully exploited because of the challenges associated with assembling and annotating its gene-rich genome. Here, we present the first hologenome of Daphnia magna, consisting of a chromosomal-level assembly of the D. magna genome and the draft assembly of its metagenome. By sequencing and mapping transcriptomes from exposures to environmental conditions and from developmental morphological landmarks, we expand the previously annotates gene set for this species. We also provide evidence for the potential role of gene-body DNA-methylation as a mutagen mediating genome evolution. For the first time, our study shows that the gut microbes provide resistance to commonly used antibiotics and virulence factors, potentially mediating Daphnia's environmental-driven rapid evolution. Key findings in this study improve our understanding of the contribution of DNA methylation and gut microbiota to genome evolution in response to rapidly changing environments.NERC highlights grant [NE/N016777/1]; European Union's Horizon 2020 research and innovation programme [965406]; the work presented in this publication was performed as part of ASPIS; the results and conclusions reflect only the author's view and that the European Commission cannot be held responsible for any use that may be made of the information contained therein; This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie SkƂodowska-Curie grant agreement No 101028700; China−UK Research of Safeguarding Natural Water project, funded by the Royal Society International Collaboration Award [IC160121]. Funding for open access charge: Natural Environment Research Council

    The hologenome of <i>Daphnia magna</i> reveals possible DNA methylation and microbiome-mediated evolution of the host genome

    No full text
    Properties that make organisms ideal laboratory models in developmental and medical research are often the ones that also make them less representative of wild relatives. The waterflea Daphnia magna is an exception, by both sharing many properties with established laboratory models and being a keystone species, a sentinel species for assessing water quality, an indicator of environmental change and an established ecotoxicology model. Yet, Daphnia’s full potential has not been fully exploited because of the challenges associated with assembling and annotating its gene-rich genome. Here, we present the first hologenome of Daphnia magna, consisting of a chromosomal-level assembly of the D. magna genome and the draft assembly of its metagenome. By sequencing and mapping transcriptomes from exposures to environmental conditions and from developmental morphological landmarks, we expand the previously annotates gene set for this species. We also provide evidence for the potential role of gene-body DNA-methylation as a mutagen mediating genome evolution. For the first time, our study shows that the gut microbes provide resistance to commonly used antibiotics and virulence factors, potentially mediating Daphnia's environmental-driven rapid evolution. Key findings in this study improve our understanding of the contribution of DNA methylation and gut microbiota to genome evolution in response to rapidly changing environments.</p

    Thermal Analysis

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