Triticum aestivum Assembly and Gene Annotation
About Triticum aestivum
Triticum aestivum (bread wheat) is a major global cereal grain essential to human nutrition. Wheat was one of the first cereals to be domesticated, originating in the fertile crescent around 7000 years ago. Bread wheat is hexaploid, with a genome size estimated at ~17 Gbp, composed of three closely-related and independently maintained genomes that are the result of a series of naturally occuring hybridization events. The ancestral progenitor genomes are considered to be Triticum urartu (the A-genome donor) and an unknown grass thought to be related to Aegilops speltoides (the B-genome donor). This first hybridization event produced tetraploid emmer wheat (AABB, T. dicoccoides) which hybridized again with Aegilops tauschii (the D-genome donor) to produce modern bread wheat.
IWGSC Chromosome survey sequence 
The bread wheat genome in Ensembl Plants is version 1.0 of the chromosome survey sequence for Triticum aestivum cv. Chinese Spring generated by the International Wheat Genome Sequencing Consortium. The gene models are provided by MIPS (version 2.2).
The sequence has been generated using the Illumina platform from flow-sorted chromosome arms. The resulting assemblies are fragmented and resolution of repetitive regions is still limited. Nonetheless, assembly of gene-containing regions is reasonably good (N50 of 2.5kb) and the predicted gene models are close in terms of length and exon count to those previously predicted for other closely related species.
Due to the large number of scaffolds in the assembly, only a subset is visible in the browser, comprising all scaffolds equal or greater than 3kb and all scaffolds to which a gene was predicted, or a wheat cDNA alignment has been made, or a SNP is present (~740,000 scaffolds). This set has been included in the Ensembl Plants BLAST and ENA search services.
The complete set of survey sequences may be downloaded from The Genome Analysis Centre, and may be searched using the TGAC blast server. The data are also available in the archives of the International Nucleotide Sequence Database Consortium, under the PRJEB3955 project.
In addition to sequence assemblies and gene models, a number of additional data sets have been aligned to the survey sequence, including the complete genomes of Brachypodium distachyon, rice (Oryza sativa), and barely (Hordeum vulgare), as well as wheat UniGene clusters from NCBI, and wheat RNA-seq data deposited in the INSDC archives.
Protein-coding gene set from MIPS
The structure of the gene models were computed by spliced-alignments (GenomeThreader) of publically available wheat fl-cDNAs and protein sequences of related grass species barley, Brachypodium, rice and Sorghum, respectively. Thereby, redundant transcript structures (sharing intron boundaries) from different references were merged. Additionally, a comprehensive RNA-seq dataset including five different tissues (root, leaf, spike, stem, grain) and different developmental stages was also used to identify wheat specific genes and additional splicing variants. Wheat RNA-seq short-reads were aligned stringently against the sequence survey assembly (using Bowtie and TopHat) and the transcript structure assembled using Cufflinks.
A total of 99,386 protein-coding genes and transcripts were predicted. For every gene loci, 193,667 additional splice variants were predicted. To simplify the display, these alternative splice variants were loaded separately and can be visualized in a different track on the contig view. Click here for example. This track is not set by default, to turn it on, Use "Configure This page" menu.
Non coding RNA genes have been annotated using tRNAScan-SE (Lowe, T.M. and Eddy, S.R. 1997), RFAM (Griffiths-Jones et al 2005), and RNAmmer (Lagesen K.,et al 2007).
Triticeae-CAP predicted transcripts set - Krasileva et al. 
Predicted transcripts annotations have also been inferred from Exonerate alignments of wheat coding sequences (CDS) from two sets of transcripts: Triticum turgidum assembled RNAseq data (Krasileva et al., Genome Biology 2013, 14:R66, Supplemental dataset 7) and a collection of publicly available wheat transcripts filtered to exclude pseudogenes, sequences shorter than 90 bp, and ORFs similar to those present in the T. turgidum set. Click here for example. The program findorf was used to predict the CDS within these transcripts as described in Krasileva et al. . See Triticeae-CAP project page for more information.
Additional standard annotations are described here.
Wheat RNA-Seq, ESTs, and UniGene datasets have been aligned to the Triticum aestivum genome:
- 454 RNA-seq data were aligned using STAR, for the following ENA studies:
- Wheat UniGene cluster sequence data were aligned using Exonerate, following the standard Ensembl pipeline. Click here for example.
- All publicly available wheat EST data were aligned using STAR. Click here for example.
- TriFLDB  sequences were aligned using STAR. Click here for example.
Analysis of the bread wheat genome using comparative whole genome shotgun sequencing - Brenchley et al. 
The wheat genome assemblies previously generated by Brenchley et al. (PMID:23192148) have also been aligned to the survey sequence, Brachypodium, barley and the wild wheat progenitors (Triticum urartu and Aegilops tauschii). Homoeologous variants inferred between the three wheat genomes (A, B, and D) are displayed in the context of the gene models of these five genomes.
Sequences of diploid progenitor and ancestral species permitted homoeologous variants to be classified into two groups, 1) SNPs that differ between the A and D genomes (where the B genome is unknown) and, 2) SNPs that are the same between the A and D genomes, but differ in B.
The wheat gene alignments and the projected wheat SNPs are available on the Location view of the Triticum aestivum, Brachypodium distachyon and Hordeum vulgare genomes, as additional tracks under the "Wheat SNPs and alignments" section of the "Configure This page" menu. Click here for a bread wheat example. Click here for a Brachypodium example. Click here for a barley example.
Transcriptome assembly in diploid einkorn wheat Triticum monococcum - Fox et al. 
Genome-wide transcriptomes of two Triticum monococcum subspecies were constructed, the wild winter wheat T. monococcum ssp. aegilopoides (accession G3116) and the domesticated spring wheat T. monococcum ssp. monococcum (accession DV92) by generating de novo assemblies of RNA-Seq data derived from both etiolated and green seedlings. Assembled data is available from the Jaiswal lab and raw reads are available from INSDC projects PRJNA203221 and PRJNA195398.
The de novo transcriptome assemblies of DV92 and G3116 represent 120,911 and 117,969 transcripts, respectively. They were mapped to the bread wheat, barley and Triticum urartu genomes using STAR. Click here for a bread wheat example.
Triticum aestivum variation data from CerealsDB
~900,000 SNPs provided by CerealsDB, from the University of Bristol, were mapped to the IWGSC Chromosome survey sequence using Exonerate, running on ungapped model, with the following filtering criteria, 100% coverage, and 100% identity match. Also, SNPs mapping to more than 3 loci were discarded, making a total of ~745,000 SNPs successfully mapped to the survey sequence, for a total of ~725,000 non-redundant SNP loci.
These SNPs can be part of the following platforms:
- The Axiom 820K SNP Array
The Axiom Array contains 820,000 SNPs of which ~684,000 have been mapped.
- The iSelect 80K Array 
The iSelect Array contains over 80,000 SNP loci of which ~58,000 have been mapped.
- The KASP probeset 
The KASP set contains ~3,900 SNP loci of which ~3,100 have been loaded in Ensembl Plants.
Note that a SNP marker can be part of more than one platform.
Wheat sequence search
In addition to the normal sequence search facilities, provided against any reference genome, a dedicated wheat sequence search service allows you to find alignments between your favourite genes and all the publicly available bread wheat genome sequences. The matched wheat sequences can be visualized in the context of reference models from the Hordeum vulgare and Brachypodium distachyon genomes.
Search is performed via the ENA search service, and currently includes:
- The 5x 454 whole genome assembly,
- ~1.3 million wheat EST sequences, and
- ~57,000 wheat Unigene cluster sequences.
This sequence search service, specific to bread wheat, will be disabled in the next release of Ensembl Plants (Fall 2014).
- International Wheat Genome Sequencing Consortium (IWGSC)
- URGI Wheat Portal
- MIPS International Wheat Survey Genome Database
- MIPS 5x 454 Survey Wheat Genome Database
- Triticeae Genomics For Sustainable Agriculture resource page
- Triticeae-CAP in UC Davis University
- Triticum monococcum resources from Jaiswal Lab in Oregon State University
- TREP, the Triticeae Repeat Sequence Database
- TriFLDB, the triticeae full-length CDS database
- ENA study ERP000319: 454 pyrosequencing of the Triticum aestivum (bread wheat) genome to 5X coverage
- ENA study ERP001415: 454 sequencing of Triticum aestivum (bread wheat) cv. Chinese spring cDNA samples from a pool of tissues, from plants under drought stress and from circadian-sampled leaves
- Triticum aestivum ESTs at ENA
- Triticum aestivum Unigene cluster sequences at NCBI
- A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome.
2014. Science. 345:1251788.
- Analysis of the bread wheat genome using whole-genome shotgun sequencing.
Brenchley R, Spannagl M, Pfeifer M, Barker GL, D'Amore R, Allen AM, McKenzie N, Kramer M, Kerhornou A, Bolser D et al. 2012. Nature. 491:705-710.
- Homoeolog-specific transcriptional bias in allopolyploid wheat.
Akhunova AR, Matniyazov RT, Liang H, Akhunov ED. 2010. BMC Genomics. 11:505.
- Separating homeologs by phasing in the tetraploid wheat transcriptome.
Krasileva KV, Buffalo V, Bailey P, Pearce S, Ayling S, Tabbita F, Soria M, Wang S, Consortium I, Akhunov E et al. 2013. Genome Biol.. 14:R66.
- TriFLDB: a database of clustered full-length coding sequences from Triticeae with applications to comparative grass genomics.
Mochida K, Yoshida T, Sakurai T, Ogihara Y, Shinozaki K. 2009. Plant Physiol.. 150:1135-1146.
- De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum.
Fox SE, Geniza M, Hanumappa M, Naithani S, Sullivan C, Preece J, Tiwari VK, Elser J, Leonard JM, Sage A et al. 2014. PLoS ONE. 9:e96855.
- Characterization of polyploid wheat genomic diversity using a high-density 90000 single nucleotide polymorphism array.
Wang S, Wong D, Forrest K, Allen A, Chao S, Huang BE, Maccaferri M, Salvi S, Milner SG, Cattivelli L et al. 2014. Plant Biotechnol. J..
- Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.).
Allen AM, Barker GL, Berry ST, Coghill JA, Gwilliam R, Kirby S, Robinson P, Brenchley RC, D'Amore R, McKenzie N et al. 2011. Plant Biotechnol. J.. 9:1086-1099.
- CerealsDB 2.0: an integrated resource for plant breeders and scientists.
Wilkinson PA, Winfield MO, Barker GL, Allen AM, Burridge A, Coghill JA, Edwards KJ. 2012. BMC Bioinformatics. 13:219.
General information about this species can be found in Wikipedia.
|Assembly:||IWGSP1, Jul 2013|
|Golden Path Length:||4,294,967,295|
|Genebuild method:||Imported from MIPS|
Genes and/or transcript that contains an open reading frame (ORF).:
|Short non coding genes
Short non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as short non coding genes: miRNA, miscRNA, rRNA, tRNA, ncRNA, scRNA, snlRNA, snoRNA, snRNA, tRNA, and also the pseudogenic form of these biotypes. The majority of the short non coding genes in Ensembl are annotated automatically by our ncRNA pipeline.:
|Long non coding genes
Long non coding genes are usually greater than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as long non coding genes: 3prime_overlapping_ncrna, ambiguous_orf, antisense, antisense_RNA, lincRNA, ncrna_host, non_coding, non_stop_decay, processed_transcript, retained_intron, sense_intronic, sense_overlapping. The majority of the long non coding genes in Ensembl are annotated manually by HAVANA.:
A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.:
|Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.:||109,331|
|T. aestivum RNA-seq alignments:||41,648|
|T. turgidum RNA-seq alignments:||89,353|