Tools:

• Wheat expression browser (JIC)

A total of 850 RNA-Seq samples derived from 32 tissues at different growth stages and/or challenged by different stress treatments were mapped to the IWGSC RefSeq Annotations v1.0 and v1.1.

The visualisation interface allows users to group, filter, sort and download the data according to the categories specified above. This design provides control over precise categories to be used in the database and the visualisation interface will adjust accordingly. The interface allow users to query one gene, compare two genes or visualise up to 50 genes in a heatmap interface. A detailed tutorial can be found in this link (https://github.com/homonecloco/expvip-web/wiki/Tutorial-expVIP-Graphical-Interface-(Wheat-Expression-Browser-example) and all the analysed data and source code is also available (https://github.com/homonecloco/expvip-web/wiki ).

• WheatExp (UCDavis)

Quality and adapter-trimmed RNA-seq reads were mapped to the full cDNA set of wheat transcripts from the International Wheat Genome Sequencing Consortium which are hosted by the Ensembl database . Diploid datasets were mapped to A-genome (32,091 cDNAs), tetraploid datasets were mapped to the A- and B-genomes (68,166 cDNAs) and hexaploid datasets were mapped to the A-, B- and D- genomes (101,245 cDNAs). Current expression data is generated from Ensembl release 26. Reference FASTA and GTF files, as well as all expression data in tabular format, are available for download from the following FTP site.

Triticum aestivum RNA-Seq download

RNA-Seq expression data from JIC (C. Uauy) are publicly available to download as reads counts and transcripts per kilobase million (TPM) for the IWGSC RefSeq v1.1 annotation.

It is a transcriptome atlas developed from 850 RNA-Seq datasets representing a diverse range of tissues, development stages and environmental condition

RNA-Seq data from INRA GDEC (L. Pingault, E. Paux) are publicly  available to download .

• Deep transcriptome sequencing was conducted on two RNA-Seq library types:

(i) non-oriented library (TruSeq, Illumina) sequenced on Illumina HiSeq2000 2x100bp (PE) for 15 different conditions corresponding to five wheat organs (root, leaf, stem, spike, grain) at three developmental stages each in duplicates

(ii) oriented library (ScriptSeq, Epicentre) sequenced on Illumina HiSeq2000 1x100bp (SE) for five conditions corresponding to five wheat organs (root, leaf, stem, spike, grain) without duplicates.

Mapping RNA-Seq reads to the chromosome 3B reference sequence allowed to validate gene prediction, as well as to identify a significant number of novel transcribed regions in which no gene structure was predicted and that might correspond to long non-coding RNAs. Transcription profiles, alternative splicing and expression breadth were also studied, providing new insights into the structural and functional compartmentalization of the wheat chromosome 3B. In combination with the IWGSC survey sequences, these data also proved to be extremely useful to decipher the specific evolutionary history of wheat chromosomes as well as to study the relative expression of homoeologous and paralogous copies of wheat genes.

• RNA-Seq meiosis data (4 conditions in duplicate) are publicly  available to download .

non-oriented library (TruSeq, Illumina, fragmentation time: 12min), sequenced on HiSeq2000 2x100bp paired-end.

Thanks to P. Sourdille and P. Leroy for data submission.

Diploid and tetraploid transcriptome

GrainGenes has implemented a new BLAST site to search transcriptome data from diploid (T.urartu) and tetraploid wheat (T. turgidum ssp. durum cultivar Kronos) at http://wheat.pw.usda.gov/GG2/WheatTranscriptome/

Data has been deposited in GenBank (T. urartu; GAKL00000000; PID PRJNA191053 and T. turgidum; GAKM00000000; PID PRJNA191054). Separate datasets (with explanations) are available for download without any restrictions on use at our project website: http://maswheat.ucdavis.edu/Transcriptome/index.htm

All datasets in one file are available to download on the Sequence Repository here

Open access paper: http://genomebiology.com/content/pdf/gb-2013-14-6-r66.pdf .

Authors: K.V. Krasileva, V. Buffalo, P. Bailey, S. Pearce, S. Ayling, F. Tabbita, M. Soria, S. Wang, IWGS Consortium, E. Akhunov, C. Uauy and J.Dubcovsky