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.
Ordered pseudomolecules from the IWGSC Chromosome Survey Sequence (CSS) 1.0 
The bread wheat genome assembly presented here was produced by the International Wheat Genome Sequencing Consortium (IWGSC) , ordered into chromosomal pseudomolecules using population sequencing (POPSEQ) data generated by the IPK-Gatersleben.
The IWGSC Chromosome survey 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.
With the exception of chromosome 3B, 1,290,751 scaffolds from the CSS were anchored into chromosomal pseudomolecules, for a total length of 4,237,502,413 bp. In addition, Ensembl Plants also incorporates a set of unanchored scaffolds included if they contain a gene model, a sequence variant, or alignment. Additionally, any scaffold longer than 3kb was included, making it a total of 261,251 unanchored scaffolds, with cumulative length of 1,307,508,887 bp.
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.
Chromosome 3B 
The reference sequence of the 1-gigabase chromosome 3B of hexaploid bread wheat was produced by sequencing 8452 bacterial artificial chromosomes in pools, and assembled the reads into a sequence of 774 megabases.
In addition to the reference sequence of 3B chromosome, 1450 unanchored scaffolds are present. Read more.
This reference sequence from the IWGSC replaces the CSS-derived assembly of 3B.
Chloroplast and mitochondrial genome components
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.
For chromosome 3B, the GDEC gene set (See details below) replaces the MIPS gene set for comparative genomics studies purposes. The MIPS genes were nevertherless projected to the new chromosome 3B assembly and are still available in a separate track on the bread wheat genome browser.
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).
Chromosome 3B gene set from GDEC INRA group 
A total 5326 protein-coding genes, 1938 pseudogenes, and 85% of transposable elements were generated on 3B chromosome by the GDEC group at INRA. An additional 251 gene models and 188 pseudogenes were annotated in unanchored scaffolds.
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:
- Illumina RNA-seq data were aligned using STAR, for the following ENA study:
- 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 SNP markers 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, marker sequences mapping to more than 3 loci were discarded, making a total of ~600,000 SNP markers 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 SNP markers of which ~547,000 have been mapped.
- The iSelect 80K Array 
The iSelect Array contains ~81,000 SNP markers of which ~43,500 have been mapped.
- The KASP probeset 
The KASP set contains ~9000 markers of which ~3,284 have been mapped.
Note that a SNP marker can be part of more than one platform.
Triticum aestivum inter-homoeologous variants
Whenever there is a 1-to-1 homoeology relationship for genes between bread wheat component genomes, we report discrepancies between these genes as a distinct variation dataset. These variant entities are called inter-homoeologous variants, and were computed based on the whole genome alignments between bread wheat component genomes.
A total of 10,314,922 inter-homoeologous variants can be visualized or retrieved through Ensembl Plants. Click here for example.
SIFT predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations.
SIFT scores and predictions (whether it is 'tolerated' or 'deleterious') have been calculated for all missense variants across all bread wheat variation datasets. See SIFT predictions for missense variants present in psbO gene, as an example.
We used all protein sequences available from UniRef90 (release 2014_07) as the protein database.
Wheat sequence search v2.0 online
Full sequence-based searching of the wheat genome is now available within the standard Ensembl Genomes sequence search facilities (ENA search and BLAST). The previous custom wheat-only search has now been discontinued.
- International Wheat Genome Sequencing Consortium (IWGSC)
- URGI Wheat Portal
- GDEC 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
- ENA study ERP004505: Analysis of the bread wheat grain transcriptome reveals complex genome interplay in a hexaploid cereal
- Triticum aestivum ESTs at ENA
- Triticum aestivum Unigene cluster sequences at NCBI
- CerealsDB from the Functional Genomics Group at the University of Bristol
- A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome.
2014. Science. 345:1251788.
- Structural and functional partitioning of bread wheat chromosome 3B.
Choulet F, Alberti A, Theil S, Glover N, Barbe V, Daron J, Pingault L, Sourdille P, Couloux A, Paux E et al. 2014. Science. 345:1249721.
- 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.
- Genome interplay in the grain transcriptome of hexaploid bread wheat.
Pfeifer M, Kugler KG, Sandve SR, Zhan B, Rudi H, Hvidsten TR, , Mayer KF, Olsen OA. 2014. Science. 345:1250091.
- 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.
General information about this species can be found in Wikipedia.
|Assembly:||IWGSC2, Nov 2014|
|Golden Path Length:||4,294,967,295|
|Genebuild method:||Imported from IWGSC|
Genes and/or transcript that contains an open reading frame (ORF).:
|Small non coding genes:||10,128|
|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.:||111,488|
|T. aestivum RNA-seq alignments:||39,237|
|T. turgidum RNA-seq alignments:||83,160|