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 2 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 with 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 organizing, analyzing and visualizing genome-scale information for important crop and model plants. Available data include 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 of the gene family, are made available for visualization and analysis. Driven by the 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.
Highlights
The first cereal genome sequenced was rice in 2002 (Goff et al, 2002; Yu et al, 2002)
Triticeae resources are a prioritised within the resource, and we aim to include new data sets rapidly after publication and data release
Terms are calculated using a standard pipeline based on domain annotation (Jones et al, 2014) and are projected between orthologues defined by gene tree analyis. http://ensemblgenomes.org/info/data/cross_references
Summary
The first cereal genome sequenced was rice in 2002 (Goff et al, 2002; Yu et al, 2002). Progress has accelerated with the publication of the genome sequence of maize in 2009 (Schnable et al, 2009), barley in 2012 (IBSC, 2012), progenitors of the bread wheat A and D genomes in 2013 (Jia et al, 2013; Ling et al, 2013), and the draft bread wheat genome itself in 2014 (IWGSC, 2014; Brenchley et al, 2012) These four cereals, barley, maize, rice and wheat, together account for 30% of global food production or 2.4 out of 3.8 billion tonnes annually. The improvement of sequencing technologies, those capable of capturing long-range information, will be necessary to achieve this goal Even in their existing condition, these resources are already sufficiently complete to be usefully represented through data analysis and visualisation platforms designed for genomes with finished assemblies, such as Ensembl Plants
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