Triticum aestivum Assembly and Gene Annotation

IWGSCThe bread wheat genome in Ensembl Plants is the Chromosome Survey Sequence (CSS) for Triticum aestivum cv. Chinese Spring, combined with the reference sequence of chromosome 3B, both generated by the International Wheat Genome Sequencing Consortium. The CSS assemblies have been further refined into chromosomal pseudomolecules using POPSEQ data generated by Chapman et al. The gene models for 3B were annotated by the GDEC group at INRA. For all other chromosomes, gene models were generated by PGSB (version 2.2). The data presented here has been prepared as part of the Triticeae Genomics for Sustainable Agriculture project, funded by the U.K. Biotechnology and Biological Sciences Reseach Council.

See also the wheat homepage at URGI logo

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 occurring 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.

Assembly

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) [1], ordered into chromosomal pseudomolecules using population sequencing (POPSEQ) data generated by Chapman et al. [2].

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 [3]

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

The chloroplast and mitochondrial genome components and their gene annotation are also present. They were imported respectively from the following ENA entries, KC912694 and AP008982.

Annotation

Protein-coding gene set from PGSB [1]

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 PGSB gene set for comparative genomics studies purposes. The PGSB genes have been 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 [3]

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. [4]

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. [4]. See Triticeae-CAP project page for more information.

Repeat Annotation

Repbase repeats as well as Triticeae repeats from TREP were aligned to the T. aestivum genome using RepeatMasker. Read more about our repeat feature annotations.

Sequence alignments

Transcriptome mappings

Wheat RNA-Seq, ESTs, and UniGene datasets have been aligned to the Triticum aestivum genome:

Analysis of the bread wheat genome using comparative whole genome shotgun sequencing - Brenchley et al. [6]

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. [9]

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.

Variation

Data from CerealsDB [10]

~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 [11]
    The iSelect Array contains ~81,000 SNP markers of which ~43,500 have been mapped.
  • The KASP probeset [12]
    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.

Data from the Wheat Hapmap project [13]

The data were generated by re-sequencing 62 diverse wheat lines using whole exome capture (WEC) and genotyping-by-sequencing (GBS) approaches. 1.57 million SNPs and 161,719 small indels, distributed across all 21 chromosomes, were identified.

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 scores

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 2015_04) 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.

Links

References

  1. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome.
    2014. Science. 345:1251788.
  2. A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome.
    Chapman JA, Mascher M, Bulu A, Barry K, Georganas E, Session A, Strnadova V, Jenkins J, Sehgal S, Oliker L et al. 2015. Genome Biol.. 16:26.
  3. 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.
  4. 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.
  5. Homoeolog-specific transcriptional bias in allopolyploid wheat.
    Akhunova AR, Matniyazov RT, Liang H, Akhunov ED. 2010. BMC Genomics. 11:505.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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..
  12. 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.
  13. A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes.
    Jordan KW, Wang S, Lun Y, Gardiner LJ, MacLachlan R, Hucl P, Wiebe K, Wong D, Forrest KL, et al. 2015. Genome Biol.. 16:48.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

Assembly: IWGSC1.0+popseq, Nov 2014
Database version: 80.2
Base Pairs: 6,591,259,146
Golden Path Length: 6,483,288,884
Data source: IWGSC
Genebuild version: 2.2
Genebuild method: Imported from IWGSC

Gene counts

Coding genes: 100,934
Non coding genes: 9,993
    Small non coding genes: 9,971
    Long non coding genes: 14
    Misc non coding genes: 8
Pseudogenes: 1,569
Gene transcripts: 112,496

Feature counts

T. Aestivum Rna-Seq Alignments: 39,237
T. Turgidum Rna-Seq Alignments: 83,160
Short Variants: 9,433,868

Coordinate Systems

chromosome
23 sequences
SequenceLength (bp)
1A248437066
1B295113561
1D135633378
2A254944609
2B345274828
2D150381694
3A185052605
3B774434471
3D124322642
4A215863839
4B317344599
4D121193423
5A148252673
5B273623383
5D161539237
6A207910053
6B204046169
6D177000238
7A182007620
7B251517909
7D238042887
Mt452528
Pt114984
scaffold 1610065 sequences