TriticeaeExpDB

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Tissue and Stage

Project ID	Title	Related Publication	Sequencing Type	Description	Notes
PRJEB19929	Wild emmer wheat genome sequencing project	-	Illumina HiSeq 2500	Wheat (Triticum spp.) is one of the founder crops that drove the Neolithic transition from hunter-gatherer to sedentary agrarian societies in the Fertile Crescent over 10,000 years ago. Identifying the suite of genetic modifications underlying wheat's domestication requires knowledge of the genome of its allotetraploid progenitor, wild emmer (T. turgidum ssp. dicoccoides). Here we report a 10.1-gigabase assembly of the 14 chromosomes of wild tetraploid wheat.	Root, lemma, leaf, grain, glume, flower, flag leaf, DS
PRJNA272886	Triticeae Transcriptome or Gene expression	Transcriptome asymmetry in synthetic and natural allotetraploid wheats, revealed by RNA-sequencing	Illumina HiSeq 2000	Genome-wide homeolog gene expression in synthetic and natural allotetraploid wheats, revealed by RNA-seq	Seeding and develop spike
PRJNA288606	Transcriptome profiling of wheat glumes in wild emmer, hulled landraces, and modern cultivars	Transcriptome profiling of wheat glumes in wild emmer, hulled landraces and modern cultivars	Illumina HiSeq 2000	Wheat domestication is considered as one of the most important events in the development of human civilization. Wheat spikelets have undergone significant changes during evolution under domestication, resulting in soft glumes and larger kernels that are released easily upon threshing. Our main goal was to explore changes of transcripome expression in glumes genome expression accompanied with wheat evolution under domestication. For this project, transcriptome profiles of wheat glume in wild emmer, landraces, and modern cultivars were compared using next generation sequencing (RNA-seq).	Glume
PRJNA507457	Triticum dicoccoides Genome Sequencing Using RNA Seq	-	Illumina HiSeq 2500	Ten populations of wild emmer (Triticum dicoccoides) were collected 28 years apart. Single nucleotide polymorphisms (SNPs) were detected using RNA Seq sequences. Focus was placed on those SNPs that were deleterious and associated with the two sample times to examine the change in diversity over time.	4th leaf
PRJNA624178	RNA sequencing of wild and domesticated wheat genotypes	Comparative transcriptomic and metabolic analysis of wild and domesticated wheat genotypes reveals differences in chemical and physical defense responses against aphids.	Illumina HiSeq 4000	Comparative transcriptomic analysis of Triticum turgidum ssp. durum cv. Svevo, Triticum turgidum ssp. dicoccoides (accession Zavitan) and Triticum aestivum cv. Chinese Spring for elucidation of defense mechanisms against aphids.	Leaf
PRJNA894592	Wild emmer wheat hybrids and parental populations	-	Illumina HiSeq 2500	This study compared transcriptome alternation between two wild emmer wheat natural populations and their hybrids	Leaf
PRJNA953608	Hybridization and genome doubling shape codon usage landscapes in the subgenomes of bread wheat	-	Sequel	The success of allopolyploids is partly attributable to their ability to resolve deadly genomic conflicts in early generations. Codon usage patterns are genomic signatures, and codon usage bias is thought to play a key role in shaping patterns of gene expression and cellular function through its effects on diverse processes. To date, little is known about the mechanism by which subgenomic conflicts in codon usage are resolved within allopolyploids. Here, we characterized changes in codon usage from wild progenitors to bread wheat. Our results indicated that evolutionarily divergent genomes in bread wheat have the same codon usage patterns, and the codon usage patterns of bread wheat are distinct from those of its wild progenitors, which tend to have a high GC content in the third codon site (GC3). The direct cause of the above phenomenon might be asymmetries in the increase in subgenome GC3 from wild progenitors to bread wheat. Increases in GC3 might also stem from sharp decreases in the average number of transcripts per GC3-poor genes from wild progenitors to bread wheat. Finally, we found that both hybridization and genome doubling can resolve genomic conflicts in codon usage during bread wheat allopolyploidization. Genome doubling induces increases in GC3, which results in a GC3-rich codon bias in bread wheat. The results of this study provide novel insights into the occurrence and consequences of allopolyploidization-induced genomic changes.	Leaf

Stress and Treatment

Project ID	Title	Related Publication	Sequencing Type	Description	Notes
PRJEB20904	Root precursors of microRNAs in wild emmer and modern wheats show major differences in response to drought stress	Root precursors of microRNAs in wild emmer and modern wheats show major differences in response to drought stress.	Illumina HiSeq 2000	MicroRNAs, small regulatory molecules with significant impacts on the transcriptional network of all living organisms, have been the focus of several studies conducted mostly on modern wheat cultivars. In this study, we investigated miRNA repertoires of modern durum wheat and its wild relatives, with differing degrees of drought tolerance, to identifymiRNA candidates and their targets involved in drought stress response. Root transcriptomes of Triticum turgidum ssp. durum variety Kızıltan and two Triticum turgidum ssp. dicoccoides genotypes TR39477 and TTD-22 under control and drought conditions were assembled from individual RNA-Seq reads and used for in silico identification of miRNAs. A total of 66 miRNAs were identified from all species, across all conditions, of which 46 and 38 of the miRNAs identified from modern durum wheat and wild genotypes, respectively, had not been previously reported. Genotype and/or stress-specific miRNAs provide insights into our understandingof the complex drought response. Particularly, miR1435, miR5024, and miR7714, identified only from drought-stress roots of drought-tolerant genotype TR39477, can be candidates for future studies to explore and exploit the drought response to develop tolerant varieties.	Drought

Mutant and Experimental Genetic Population

Project ID	Title	Related Publication	Sequencing Type	Description	Notes
PRJNA795708	Mutation analysis of Triticum dicoccoides accession carrying Pm gene	"Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69"	Illumina NovaSeq 6000	Mutation analysis of Triticum dicoccoides accession carrying powdery mildew resistance gene in four independent loss of function mutants aiming to clone the gene .	Pm69