Mapping Reference
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.
Ensembl Release 26 mapping
rates
|
Dataset |
Wheat
species |
Tissues |
Developmental
stage/treatment |
RNA-seq
reads |
%
uniquely mapped reads |
Data
source |
Reference |
|
Wheat development
timecourse |
T.
aestivum cv.
Chinese Spring |
Shoot, root, grain, spike
and stem. |
Three stages for each
tissue |
101bp Paired End (PE) |
61.7% |
ENA: ERP004714 |
|
|
Photomorphogenesis |
T.
monococcum ssp. monococcum Acc. DV92 |
Whole seedlings |
Etiolated and
light-exposed seedlings. |
50bp
Single end (SE) |
53.4% |
SRA:
SRX283514 |
|
|
T.
monococcum
ssp. aegilopoides Acc. G3116 |
Whole seedlings |
Etiolated and
light-exposed seedlings. |
101bp
PE |
68.0% |
SRA:
SRX257915 |
||
|
Drought and heat stress |
T.
aestivum cv.
TAM 107 |
Whole seedlings |
Drought, heat and
combined stress. |
101bp PE |
45.9% |
SRA: SRP045409 |
|
|
Grain layers |
T.
aestivum cv.
Holdfast |
Endosperm, inner
pericarp, outer pericarp. |
12 days after anthesis |
50bp SE |
31.4% |
ENA: ERP008767 |
|
|
Senescing leaf timecourse |
T.
turgidum ssp. durum L. cv. Kronos |
Flag leaves |
Heading date, 12 and 22
days after anthesis |
50bp SE |
33.9% |
GEO: GSE60635 |
|
|
Grain development
timecourse |
T. aestivum
cv.
Chinese Spring |
Grain layers |
10, 20 and 30 days after
anthesis |
101bp PE |
56.1% |
ENA: ERP004505 |
Limitations
The main application of WheatExp is to compare the relative expression levels of the different homoeologues of a single gene across different tissues, developmental stages, environmental conditions and genetic backgrounds. Comparisons among genes are valid only when the genes being compared have the same number of homoeologues in the reference genome. In a simulated RNA-seq experiment using a set of confirmed homoeologous triplets, 98.4% of reads map uniquely to their transcript of origin when their homoeologous genes are absent from the reference. When mapping to the full reference, unique mapping rates fall to 82.2% due to the loss of reads which map equally well to different homoeologues. Consequently, genes where one homoeologue is absent from the reference will exhibit a higher proportion of uniquely-mapped reads and the expression levels of the two remaining homoeologues may also be inflated by the incorrect mapping of reads from the absent homoeologue. Additionally, no expression data will be reported for any genes which lack annotation within the current IWGSC release and any contig assemblies which are duplicated in the reference assembly will exhibit a reduced number of uniquely mapped reads. Therefore, caution is advised when comparing the expression levels of different genes.
Citation
Pearce S, Vazquez-Gross H, Herin SY, Hane D, Wang Y, Gu YQ, Dubcovsky J. WheatExp: an RNA-seq expression database for polyploid wheat. BMC Plant Biol. 2015;15:299. PDF available here WheatExp: an RNA-seq expression database for polyploid wheat
Database Implementation and System Architecture
WheatExp database implementation uses a flexible storage schema to house the data. The storage table has the following MySQL (https://www.mysql.com/) storage datatypes: study_id (varchar), seq_id (varchar), tissue (varchar), mean (float), se (float), se_low (float) and se_high (float). Binary search tree indices (BTREE) were implemented to increase the speed of queries using the study_id and seq_id columns. The web and database is running on a ThinkMate ThinkTank IQ4 system with four Intel Xeon E7-4820 at 2.00 GHz with 52 GB of RAM. It is currently running Linux Kernel 3.13 distribution Ubuntu 14.04 long term support with PHP version 5.5.9 and MySQL version 5.5.43.