Genomics Resource for Wheat
We are sequencing a couple of transcriptomes from the dark and light treated seedlings of two diploid wheat (Triticum monococcum) genotypes. The data is available from the following weblink. If you are using this data we request you to cite our publication, Fox et al. (2014) [view]
About Triticum monococcum
"Einkorn wheat Triticum monococcum (2n=2x=14, AmAm) is one of the earliest domesticated crops. However, it was abandoned for cultivation before the Bronze Age and has infrequently been used in wheat breeding. Little is known about the genetic variation in adaptively important biological traits in T. monococcum" (Source:Jing et al 2007). The wild and cultivated germplasms are classified as separate species.
Following plant materials were used for generating the transcriptome sequences of T. monococcum.
Species: Triticum monococcum (Einkorn wheat) NCBI Tax ID = 4568
- DV92 accesion: Subspecies T. monococcum ssp. monococcum. It is a cultivated variety with spring wheat growth habit.
- G3116 accession: Subspecies T. monococcum ssp. Aegilopoides. It is a wild variety with winter wheat growth habit.
Germplasm/Genotypes/Populations: Seed materials are maintained by Dr. Jeff Leonard from the Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon USA..
Source plant material: 8-10-day old seedling shoot
Growth condition: All plants were grown in a growth chamber at Oregon State University campus under continuous dark for 8 days from sowing followed by 2 days (48hrs) of continuous light at 25°C.
- Treatment/Plant Environment Ontology: growth chamber study (EO:0007269); light regimen (EO:0007196) | 8 days dark (no light) followed by 2 days (48hrs) continuous visible spectrum light exposure.
- Plant Sample Collection: (Sample-1) Dark treated samples harvested at 8 days after sowing. (Sample-2) 48 hr continuous light treated samples were harvested on day 10.
From Jaiswal lab
- Transcriptome Sequences (Illumina_reads): DV92 (NCBI:SRX283514, SRR924098) and G3116 (NCBI:SRX257915, SRR922411)- [get data]
- Transcriptome Sequences (cDNA contigs and peptides): fasta format files - [get data]
- Genome alignments to barley and Triticum uratu genomes using BLAT - [get data]
- Genome alignments to barley and Triticum uratu genomes using Exonerate - [get data]
- Annotations (Gene Ontology and InterPro annotations) - [get data]
- Gene expression - [get data]
- SNP markers (VCF and BED file formats) with reference to barley genome - [get data]
- SSR markers - [get data]
Browse other wheat data from external sources
- McCombie lab at CSHL
- GIGAdb: Triticum uratu genome
- GIGAdb: Aegilops tauschii genome
- Ensembl Plants: coming soon
- MIPS wheat database: Visit the page
Fox SE, Geniza M, Hanumappa M, Naithani S, Sullivan C, et al. (2014) De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum. PLoS ONE 9(5): e96855. doi:10.1371/journal.pone.0096855 [view]
- Pubmed - [browse]
- Jing et al 2007; Identification of variation in adaptively important traits and genome-wide analysis of trait–marker associations in Triticum monococcum J. Exp. Bot. (2007) 58 (13): 3749-3764. doi: 10.1093/jxb/erm225
- Ling et al 2013, Draft genome of the wheat A-genome progenitor Triticum urartu Nature, 496, 87–90; doi:10.1038/nature11997
- Jia et al 2013. Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation Nature, 496, 91–95; doi:10.1038/nature12028
- Luo et al. 2013;A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. PNAS, 2013 May 7;110(19):7940-5. doi: 10.1073/pnas.1219082110.
Google Scholar - [browse]
Note: T. monococcum spike image source (WikiMedia Commons)