TriticeaeExpDB

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Tissue and Stage

Project ID	Title	Related Publication	Sequencing Type	Description	Notes
PRJNA945064	Transcriptome data of triticeae species	Mating systems and recombination landscape strongly shape genetic diversity and selection in wheat relatives	Illumina HiSeq 3000	This study investigate the effects of mating system and linked selection on genetic diversity and the efficacy of selection in a group of grass species	Mix of flower and leaf
PRJDB2406	RNASeq from leaves of Triticum boeoticum and T. monococcum	-	454 GS FLX Titanium	Large-scale de novo analysis of RNA-seq from from leaves of T. boeoticum (KT1-1) and T. monococcum (KT3-5) and development of high-confidence SNPs between them.	Leaf
PRJNA470527	Comparative transcriptome profile during grain filling of cultivated wheat genotypes and their progenitors	Transcriptome Analysis Reveals Important Candidate Genes Related to Nutrient Reservoir, Carbohydrate Metabolism, and Defence Proteins during Grain Development of Hexaploid Bread Wheat and Its Diploid Progenitors	Illumina HiSeq 4000	Gene expression of Hexaploid (AABBDD), tetraploid (AABB) and their diploid progenitors ( AA, BB and DD) during grain development (transcriptome profile of individual genotypes and studies on differentially expressed genes)	Developing grain
PRJNA910827	RNA-seq of Triticeae pollen and stigma samples	The triticale mature pollen and stigma proteomes – assembling the proteins for a productive encounter	NextSeq 500	The pollen and stigma transcriptomes of different Triticeae species were sequenced.	Pollen and stigma
PRJDB7642	Genome-wide polymorphisms from RNA sequencing assembly of leaf transcripts facilitate phylogenetic analysis and molecular marker development in wild einkorn wheat	Genome-wide polymorphisms from RNA sequencing assembly of leaf transcripts facilitate phylogenetic analysis and molecular marker development in wild einkorn wheat.	Illumina MiSeq	Two wild diploid wheat species, Triticum monococcum ssp. aegilopoides and T. urartu, are closely related, and respectively harbour the Am and A genomes. The A-genome donor of tetraploid and common wheat is T. urartu, and T. monococcum ssp. monococcum is the cultivated form derived from the wild einkorn wheat T. monococcum ssp. aegilopoides. Although T. monococcum ssp. aegilopoides has been a useful genetic resource for wheat breeding, genome-wide molecular markers have not been sufficiently developed in the subspecies aegilopoides. Here, we obtained the genome-wide polymorphisms such as single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) from the RNA sequencing (RNA-seq) data of leaf transcripts in 15 accessions of the two diploid wheat species. The detected SNPs and indels covered the entire chromosomes, discriminating between between T. monococcum ssp. aegilopoides and ssp. monococcum that had recently diverged. The polymorphism information contributed to compare the genetic diversity of einkorn wheat with those of two related diploid Aegilops species, Ae. tauschii and Ae. umbellulata. Cleaved amplified polymorphic sequence (CAPS) markers converted from the SNP data were efficiently developed to confirm the chromosome addition of the subspecies aegilopoides chromosomes to tetraploid wheat in nascent allohexaploid lines with AABBAmAm genome. In addition, the CAPS markers were available for linkage map construction in mapping population of the subspecies aegilopoides accessions. The SNP and indel data are applicable to further genetic studies in einkorn wheat.	Leaf
PRJNA553311	Transcriptome Sequencing of Different Ploidy Wheat	Changes in Alternative Splicing in Response to Domestication and Polyploidization in Wheat	Illumina HiSeq X Ten	Alternative splicing changes during domestication and polyploidization were revealed by transcriptome sequencing of wheat materials with different ploidy.	Leaf and root
PRJNA515803	Triticum monococcum Raw sequence reads	-	HiSeq X Ten	Transcriptome Analysis Identifies the Key Genes Responsible for the white Coleoptile Trait in Triticum monococcum	Coleoptile
PRJEB61155	Gemomic resources of einkorn wheat (Triticum monococcum) – wild and domesticated einkorn	Einkorn genomics sheds light on history of the oldest domesticated wheat	Illumina NovaSeq 6000	Einkorn (Triticum monococcum) is the first domesticated wheat species, being central to the birth of agriculture and the Neolithic Revolution in the Fertile Crescent ~10,000 years ago. Here, we generate and analyze 5.2-gigabase genome assemblies for wild and domesticated einkorn, which represent the most contiguous Triticeae assemblies to date, including completely assembled centromeres. Einkorn centromeres are highly dynamic, showing evidence of ancient and recent centromere shifts caused by structural rearrangements. Whole-genome sequencing of a diversity panel uncovered the population structure and evolutionary history of einkorn, revealing complex patterns of hybridizations and introgressions following the dispersal of domesticated einkorn from the Fertile Crescent. We also discovered that around 1% of the modern bread wheat (Triticum aestivum) A subgenome originates from einkorn. These resources and findings highlight the history of einkorn evolution and provide a basis to accelerate the genomics-assisted improvement of einkorn and bread wheat.	Roots, whole aerial parts at the seedling stage, flag leaves, fully emerged spikes, glumes and grains
PRJNA993781	Triticum monococcum subsp. monococcum Raw sequence reads	A near-complete genome sequence of einkorn wheat provides insight into the evolution of wheat A subgenomes.	Illumina NovaSeq 6000	Triticum monococcum subsp. monococcum played a significant role in the development of agriculture and was widely cultivated for centuries in the Middle East, Europe, Central Asia, and Africa before being replaced by free-threshing polyploid wheats. We report de novo assembly and annotation of T. monococcum genome by sequencing a cultivated accession PI 306540 collected in Romania.	Stem, leaf, root, grain, spike
PRJNA532455	The Evolution of Gene Expression in Polyploid Wheats and Their Diploid Ancestors during Embryogenesis	Alternative splicing dynamics and evolutionary divergence during embryogenesis in wheat species.	Illumina HiSeq 2500	we present an atlas of global gene expression as well as the evolutionary divergence covering embryo, endosperm and seed coat development in wheats and their diploid ancestors, providing insights into the evolution of gene expression in embryogenesis and grain development of wheat species. Overall design: We investigate the dynamics and evolution of gene expression throughout seven stages of embryo development (including the two cell, pre-embryo, transition, leaf early, leaf middle, leaf late and mature embryo), two stages of endosperm (transition stage endosperm and leaf late stage endosperm), and one pericarp stage (leaf early stage pericarp) across five wheat and ancestral grass species (AC -hexaploid, SF-tetraploid, DV-A genome diploid, SP-B genome diploid and TA-D genome diploid), two replicates for each stage.	Two cell, pre-embryo, transition, leaf early, leaf middle, leaf late and mature embryo

Stress and Treatment

Project ID	Title	Related Publication	Sequencing Type	Description	Notes
PRJNA932462	RNA-seq raw reads of Triticum monococcum genotypes	High-resolution mapping of SrTm4, a recessive resistance gene to wheat stem rust	Illumina NovaSeq 6000	This study used RNA-seq data to annalyze the Differentially expressed genes (DEGs) between the homozygous susceptible T. monococcum lines (G3116, S-A13 and S-E14) and the homozygous resistant lines (PI 306540, R-F14 and R-K18). The result helps to identify candidate genes within the physical maps of the SrTm4 region.	Puccinia graminis f. sp. tritici
PRJEB21284	Transcriptome analysis of Triticum monococcum in response to cold stress (4 degrees C for 24 hours)	-	Illumina HiSeq 2500	24-hour cold shock treatment applied to winter wheat T. monococcum ssp. aegilopoides (accession G3116) and the domesticated spring wheat T. monococcum ssp. monococcum (accession DV92). Tissues were harvested and homogenized using liquid nitrogen. RNA extraction was conducted using a modified chloroform extraction protocol (Plant Purification Reagent) followed by RNeasy Plant Mini Kit (50) for purification. Samples included: three G3116 control, three G3116 cold shock, three DV92 control, and three DV92 cold shock. Illumina samples were prepped using TruSeq RNA prep kit v.2 and sequenced on the Illumina Hiseq 2500 sequencing platform.	Cold
PRJNA421442	Integrative analysis of the einkorn (Triticum monococum) grain reveals new mechanisms of response to sulfur deficiency	Omics Data Reveal Putative Regulators of Einkorn Grain Protein Composition under Sulfur Deficiency.	Illumina HiSeq 2500	In wheat, the main staple crop in many regions of the word, one major challenge is to improve the yield potential while maintaining the grain quality, which is mainly defined by its protein concentration and composition. To achieve this goal, it is essential to considerate the nitrogen (N) and sulfur (S) nutrition, which strongly influences the grain storage protein (GSP) composition. Nowadays, the limitation of nitrogen inputs and the sulfur deficiency recently observed in soils represent major difficulties to control the grain quality. Thus, identification of the molecular mechanisms that control the accumulation of GSP in response to N and S supply is necessary. In this study, we applied four post-anthesis N and S treatments to an einkorn (Triticum monococcum) culture. Effects of the treatments on the grain transcriptome and metabolome were evaluated at different times during grain development. From the 386 differentially expressed genes and the 21 metabolites differentially accumulated, our results have revealed a strong impact of a high-N supply without any added S. A large majority of genes were transiently influenced by the treatments while others showed strong modifications of their kinetics of expression during grain filling. We hypothesized the role of several genes (e.ge.g. sulfate transporters, transcriptional regulators) in the adjustment of the N-to-S ratio in response to a S deficiency. These genes could coordinate the amino acid pool necessary for GSP synthesis. These new results contribute in facing the challenge of maintaining wheat grain quality for the development of more sustainable agriculture. Overall design: Transcriptome comparisons between four N and S treatments and between six grain develomental stages in three replicates	Nitrogen (N) and sulfur (S)