Triticeae resources in Ensembl Plants

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.

Keywords: Comparative genomics; Functional genomics; Genetic variation; Genome browser; Transcriptomics; Triticeae.

Fig. 1

Visualizing the bread wheat genome through the Ensembl Genomes browser interface. The user can view many layers of genome annotation in a highly customizable way. Tracks shown include (A) gene models, (B) assemblies and interhomoeologous variations from Brenchley et al. (2012), (C) RNA-Seq data, (D) variations from the AXIOM array and (E) transcript assemblies from T. turgidum. Additional tracks are shown for T. aestivum ESTs and UniGenes (purple and green), alignment blocks to O. sativa and B. distachyon (pink), repeats (grey) and GC content.

Fig. 2

Detailed view of a gene tree in Ensembl Plants. The tree shows the inferred evolutionary history of the sucrose-6F-phosphate phosphohydrolase family protein in H. vulgare. The gene tree (left) shows the expected phylogenetic relationship for the gene between the species shown. Note that the sequence identifier of the wheat genes includes the name of the chromosome arm to which it belongs, i.e. 5DS for the short arm of chromosome 5 in the D-genome. Red squares indicate inferred duplication events in the history of the gene, and shaded gray triangles indicate collapsed branches. A pictographic representation of the underlying multiple sequence alignment is included on the gene tree pages (right).

Fig. 3

The transcript variation image for the H. vulgare MLOC_42.1 protein-coding transcript in Ensembl Plants. The image gives an overview of all the variants within the transcript in the context of the functional domains assigned to the protein. Upper boxes highlight the amino acid change, where applicable, and lower boxes give the alleles. Variants are color coded according to their consequence type, missense, synonymous and positional. A full list of consequence types is given here: http://www.ensembl.org/info/genome/variation/predicted_data.html. The transcripts, features and variations can be clicked to explore more information about each object.

Fig. 4

The matrix of whole-genome alignments between pairs of monocot genomes in Ensembl Plants. Cyan indicates that an alignment exists for the pair. Only one representative rice is shown, O. sativa, although each of the 10 rice genomes was aligned against each other (not shown).

Fig. 5

View of the whole-genome alignment between wheat, rice and Brachypodium in Ensembl Plants. Pink bars and green blocks indicate aligned blocks between the rice and wheat (upper) and wheat and Brachypodium (lower) pairs of genomes. Transcripts are shown in red but the genomic features shown on each track are configurable.

Fig. 6

Polyploid view of the whole-genome alignment within the bread wheat A, B and D component genomes. The image is defined as in Fig. 5. An additional feature track shows repeats annotated in all three genomes.