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Triticeae resources in Ensembl Plants

View ORCID ProfileDan M. Bolser, View ORCID ProfileArnaud Kerhornou, View ORCID ProfileBrandon Walts, View ORCID ProfilePaul Kersey
doi: https://doi.org/10.1101/011585
Dan M. Bolser
1Ensembl Genomes, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
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Arnaud Kerhornou
1Ensembl Genomes, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
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Brandon Walts
1Ensembl Genomes, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
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Paul Kersey
1Ensembl Genomes, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
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Abstract

Recent developments in DNA sequencing have enabled the large and complex genomes of many crop species to be determined for the first time, even those previously intractable due to their polyploid nature. Indeed, over the course of the last two years, the genome sequences of several commercially important cereals, notably barley and bread wheat, have become available, as well as those of related wild species. While still incomplete, comparison to other, more completely assembled species suggests that coverage of genic regions is likely to be high.

Ensembl Plants (http://plants.ensembl.org) is an integrative resource organising, analysing and visualising genome-scale information for important crop and model plants. Available data includes reference genome sequence, variant loci, gene models and functional annotation. For variant loci, individual and population genotypes, linkage information and, where available, phenotypic information, are shown. Comparative analyses are performed on DNA and protein sequence alignments. The resulting genome alignments and gene trees, representing the implied evolutionary history the gene family, are made available for visualisation and analysis. Driven by the use case of bread wheat, specific extensions to the analysis pipelines and web interface have recently been developed to support polyploid genomes.

Data in Ensembl Plants is accessible through a genome browser incorporating various specialist interfaces for different data types, and through a variety of additional methods for programmatic access and data mining. These interfaces are consistent with those offered through the Ensembl interface for the genomes of non-plant species, including those of plant pathogens, pests and pollinators, facilitating the study of the plant in its environment.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted November 18, 2014.
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Triticeae resources in Ensembl Plants
Dan M. Bolser, Arnaud Kerhornou, Brandon Walts, Paul Kersey
bioRxiv 011585; doi: https://doi.org/10.1101/011585
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Triticeae resources in Ensembl Plants
Dan M. Bolser, Arnaud Kerhornou, Brandon Walts, Paul Kersey
bioRxiv 011585; doi: https://doi.org/10.1101/011585

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