TriticeaeExpDB

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Tissue and Stage

Project ID	Title	Related Publication	Sequencing Type	Description	Notes
PRJNA914861	RNA-seq of Triticum urartu, Aegilops tauschii, their reciprocal F1 hybrids and allotetraploids	Genome shock in a synthetic allotetraploid wheat invokes subgenome-partitioned gene regulation, meiotic instability, and karyotype variation	Illumina NovaSeq 6000	Transcriptome sequencing and analysis of Triticum urartu, Aegilops tauschii, their reciprocal F1 hybrids and allotetraploids.	Inflorescence,leaf
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
PRJNA905376	RNA-seq data for synthetic hexaploid wheat lines and their corresponding tetraploid and diploid parents	Global transcriptome analysis of allopolyploidization reveals large-scale repression of the D-subgenome in synthetic hexaploid wheat	Illumina NovaSeq 6000	We performed transcriptome sequencing of four SHW lines and their corresponding two tetraploid (Triticum turgidum) and diploid (Aegilops tauschii) parents to capture the gene expression dynamics upon allopolyploidization	Glume, root, pistil when anthers are mature, head at boot, pistil one day after anthesis, shoot, mature anther, palea+lemma, hypocotyl, pistil when anthers are immature
PRJNA579337	RNA-seq of hybrid hexaploid wheat from progenitor species Triticum turgidum (durum wheat, AABB) variety HOH501 and two Aegilops tauschii lines (Clae23 and ENT336, DD) Transcriptome	-	NextSeq 500	Poly-A and smRNA sequencing of hybrid hexaploid wheat	Leaf
PRJDB7401	Triticinae strain:Tetra Chinese Spring and Aegilops tauschii	-	Illumina HiSeq 4000	Triticum aestivum (Bread wheat) has a hexaploid AABBDD genome. The duplicated gene copies, called homeologs, from A, B and D subgenomes may have biased expression levels influencing the phenotype. Though there are different methods for transcripts quantification of homeolog genes, it remains unclear which method performs better given the same RNA-seq data set. To test this, RNA-seq data was collected from two bread wheat-related species, tetra Chinese Spring and Aegilops tauschii, which have tetraploid AABB and diploid DD genomes, respectively.	Leaf
PRJDB1854	RNASeq from seedling leaves of Aegilops tauschii	Discovery of High-Confidence Single Nucleotide Polymorphisms from Large-Scale De Novo Analysis of Leaf Transcripts of Aegilops tauschii, A Wild Wheat Progenitor	454 GS FLX Titanium	Large-scale de novo analysis of RNA-seq from seedling leaves of Aegilops tauschii (diploid wild wheat) and development of high-confidence SNPs between Ae. tauschii of PI476874 and IG47812. Iehisa et al. (2012) DNA Research 19:487-497.	Leaf
PRJNA213168	mRNA-Seq for homoeologous gene expression analysis in hexaploid bread wheat	Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat	Illumina Genome Analyzer II	Bread wheat (Triticum aestivum) has a large, complex and hexaploid genome consisting of A, B and D homoeologous chromosome sets. Therefore each wheat gene potentially exists as a trio of A, B and D homoeoalleles, each of which may contribute differentially to wheat phenotypes. We describe a novel approach combining wheat cytogenetic resources (chromosome substitution ‘nullisomic-tetrasomic’ lines) with next generation deep sequencing of gene transcripts (RNA-seq), to directly and accurately identify homoeologue-specific single nucleotide variants and quantify the relative homoeoallelic contribution to gene expression. We discover, based on a sample comprising ~5-10% of the total wheat gene content, that at least 40% of wheat genes are expressed from all three distinct homoeoalleles. Most of these genes show strikingly biased expression patterns in which expression is dominated by a single homoeoallele. The remaining ~60% of wheat genes are expressed from either one or two homoeoalleles only, through a combination of extensive transcriptional silencing and homoeoallele loss. We conclude that wheat is tending towards functional diploidy, through a variety of mechanisms causing single homoeoalleles to become the predominant source of gene transcripts. This discovery has profound consequences for wheat breeding and our understanding of wheat evolution.	Root and shoot
PRJNA965956	Aegilops tauschii Raw sequence reads	Whole genome doubling-induced the enrichment of H3K27me3 in genes carrying specific TEs in Aegilops tauschii	Illumina NovaSeq 6000	Raw data of RNA-seq and H3K27me3 in roots and leaves of diploid and tetraploid Aegilops tauschii 60 days after seed germination	Root and 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
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
PRJNA790482	RNA sequencing of the whole grains at early development from SHWs and their parents	-	HiSeq X Ten	We sequenced the grains at 0, 2, 4, 6, 8, and 10 days after pollinations for SHWs and their parents	Whole grain
PRJNA418048	Aegilops tauschii Raw sequence reads	AetMYC1, the Candidate Gene Controlling the Red Coleoptile Trait in Aegilops tauschii Coss. Accession As77	Illumina MiSeq	The transcriptome analysis of red coleoptile and white coleoptile of Aegilops tauschii was employed for isolating the candidate genes controlling the white coleoptile trait.	Coleoptile
PRJNA609457	H3K27me2 and H3K27me3 ChIP-seq in wheat evolution	Histone H3K27 dimethylation landscapes contribute to genome stability and genetic recombination during wheat polyploidization	HiSeq X Ten	Bread wheat is a widely cultivated allohexaploid arise via two recent polyploidization events. Growing evidence suggests histone modifications are involved in response to genomic shock and adaption to adverse environments during formation of polyploid plants. However, the roles of histone modifications in wheat evolution remain elusive. We analyzed profiles of H3K27me2 and H3K27me3 during polyploidization and hybridization of wheat using hexaploid bread and its tetraploid and diploid relatives. H3K27me2 levels positively correlated with the ploidy levels and the increased H3K27me2 may contributed to repress massively amplified transposons to maintain genome stability during wheat evolution. H3K27me2 is involved in silencing euchromatic TEs and the distribution of H3K27me2 is mutually exclusive with another repressive mark H3K9me2. Regions of H3K27me2 canyons were highly related with formation of DNA double-strand breaks in genomes of wheat, maize and Arabidopsis, revealing a novel histone modification contributing to recombination regulation. Our results provided comprehensive view of H3K27me2 and H3K27me3 distribution during wheat evolution and proposed potential roles of H3K27me2 on genome stability and genetic recombination, which may contribute to accelerate crop breeding.	Leaf
PRJDB8961	Introgression of chromosomal segments conferring early heading time from wheat diploid progenitor, Aegilops tauschii Coss., into Japanese elite wheat cultivars	Introgression of chromosomal segments conferring early heading date from wheat diploid progenitor, Aegilops tauschii Coss., into Japanese elite wheat cultivars	Illumina MiSeq	We backcrossed two early heading lines of synthetic hexaploid wheat with four Japanese elite cultivars to develop the early heading lines of bread wheat. In total, nine early heading lines, which showed two to eight days earlier heading time than their parental cultivars in the field conditions, were selected and established from the selfed progenies of the two- or three-times backcrossed populations. RNA sequencing-based genotyping was performed to detect single nucleotide polymorphisms between the selected lines and their parental wheat cultivars, which revealed the chromosomal regions transmitted from the parental synthetic wheat to the selected lines.	Leaf
PRJDB7401	transcript quantification of wheat homeologs	-	Illumina HiSeq 4000	Triticum aestivum (Bread wheat) has a hexaploid AABBDD genome. The duplicated gene copies, called homeologs, from A, B and D subgenomes may have biased expression levels influencing the phenotype. Though there are different methods for transcripts quantification of homeolog genes, it remains unclear which method performs better given the same RNA-seq data set. To test this, RNA-seq data was collected from two bread wheat-related species, tetra Chinese Spring and Aegilops tauschii, which have tetraploid AABB and diploid DD genomes, respectively.	Leaf, root
PRJNA553311	Transcriptome Sequencing of Different Ploidy Wheat	Changes in Alternative Splicing in Response to Domestication and Polyploidization in Wheat	Illumina HiSeq 2500	Alternative splicing changes during domestication and polyploidization were revealed by transcriptome sequencing of wheat materials with different ploidy.	Leaf and root
PRJNA532455	The Evolution of Gene Expression in Polyploid Wheats and Their Diploid Ancestors during Embryogenesis	The Transcriptional Landscape of Polyploid Wheats and Their Diploid Ancestors during Embryogenesis and Grain Development	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.	Embryo, endosperm and seed coat
PRJEB29860	RNAseq data for Aegilops tauschii ENT331	Reduced chromatin accessibility underlies gene expression differences in homologous chromosome arms of diploid Aegilops tauschii and hexaploid wheat	Illumina HiSeq 2500	Leaf (14dd) RNAseq data for Aegilops tauschii ENT331.	Leaf
PRJNA322418	Triticum aestivum Transcriptome or Gene expression	Genomic Imprinting Was Evolutionarily Conserved during Wheat Polyploidization	Illumina HiSeq 2500	Transcriptome of hexaploid wheat, tetroploid wheat and Aegilops tauschii endosperm, used for gene imprinting analysis	Endosperm
PRJEB23317	Tracriptome data from 5 tissues in Aegilops tauschii	Genome sequence of the progenitor of the wheat D genome Aegilops tauschii	Illumina HiSeq 2500	These are the trancriptome data of leaf, root, seedling, deleveloping grain 10dd and deleveloping grain 27dd in Aegilops tauschii. All the reads are clean, adaptor-free and high quiality.	Leaf, root, seedling, deleveloping grain 10dd and deleveloping grain 27dd
PRJNA406980	Subgenome Interplay Shapes Genomic Variations and Transcriptomic Changes during Wheat Hexaploidization Events	-	Illumina HiSeq 2500	Genomic variations and transcriptomic changes extensively occur in newly formed polyploids to reconcile immediate challenges caused by divergent subgenomes in one nucleus. To comprehensively investigate sequence elimination and expression alteration in wheat hexaploidization, here we performed whole exome capture experiments coupled with high throughput sequencing analysis by exploiting three sets of newly synthesized wheat species. We observed that the whole wheat chromosomes were subjected to extensive genomic elimination partially regulated by sequence homology in response to hexaploidization. But homeologous subgenomes exhibited distinct features that DNA sequences were preferentially eliminated on DD genome compared with AA and BB genome. In addition, a higher proportion of eliminated sequences occurred in exonic regions than in intergenic regions on DD genome, whereas a significant enrichment was observed in the repeat-rich intergenic regions for AA and BB genome, exhibiting a contrast distribution pattern compared to the gene density. Furthermore, we detected 488 overlapped genes with sequence elimination on DD genome but few on the other two genomes across three nascent hexaploid wheats. Interestingly, GO enrichment analysis showed genes with sequence elimination were enriched in distinct functional pathways between subgenomes. Transcriptome analysis indicates polyploidization enhanced gene expression differentiation between root and leaf and led to rapid and extensive gene expression changes in synthetic hexaploid wheat. AA and BB genome exhibited synergistic expression profiling which was distinct from DD genome, and interestingly, expression bias was observed for a proportion of homeologs in synthetic hexaploid wheat. Strikingly, only 3.3-23.6% genes with sequence elimination exhibited expression changes in synthetic hexaploid wheat compared with their respective progenitors, indicating genomic variation is not the major cause resulting in the transcirptomic changes during wheat polyploidization events, whereas epigenetic modifications might play an important role in regulating expression profiling alterations.	Leaf, root
PRJNA383463	Asymmetrical changes in chromatin and small RNAs contribute to altered gene expression and endosperm development in resynthesized wheat allotetraploids	Asymmetrical changes of gene expression, small RNAs and chromatin in two resynthesized wheat allotetraploids	Illumina HiSeq 2000	We performed genome-wide analyses of mRNA and small RNA transcriptomes in the endosperm of two synthetic wheats SSAA and AADD that differ in seed fertility and size. Transcriptomes between the endosperm and root of AADD were also analyzed to test a developmental role. Immunostaining experiments were performed to analyze the changes of histone H3K9me2 modifications in the chromosomes of two wheat allotetraploids and their progenitors.	Endosperm, seedling root
PRJNA353049	Transcriptome and Epigenome analysis in Polyploidy Wheat and its progenitors	-	Illumina HiSeq 2000	We analyzed sequence features of intergenic spacer (IGS) in the progenitors of common wheat Triticum aestivum (AABBDD), which revealed nucleolar organizing region (NOR) dominance hierarchy (BB > DD > AA). The hierarchy is based on the length, transcript start site, number and sequence variation of Rep1 (promoter-like repeat) unit. Transcriptome and epigenome in the synthetic tetraploid wheat (AADD / DDAA) and their progenitors T. urartu (AA) and Ae. tauschii (DD) were further investigated to explore the mechanism for NOR silencing. We found that long non-coding RNAs and 24-nt small interfering RNAs were highly abundant in the IGS regions of the DD, and scarcity in AA. After polyploidy formation, NORs of AA subgenome were silenced and associated with increased levels of 24-nt siRNAs derived from active NOR of the DD subgenome. These DD-subgenome 24-nt siRNAs may trans-act on AA-genome IGS to induce DNA methylation via RNA directed DNA methylation (RdDM). Furthermore, BS-Seq and MeDIP-Seq assay show siRNA-targeted regions in AA-subgenome IGS were hypermethylated. Additionally, the increased H3K27me3 and decreased H4K12ac were found in AA-subgenome IGS after polyploidization. This similar phenomenon of BB 24-nt siRNAs trans-act on DD was detected in hexaploid wheat.	Leaf
PRJDB4683	RNA sequencing of 10 Aegilops tauschii accessions	Genome-wide identification of novel genetic markers from RNA sequencing assembly of diverse Aegilops tauschii accessions.	Illumina MiSeq	To generate novel genetic markers, we performed RNA sequencing of 10 accessions of Ae. tauschii. Transcripts were deduced from de novo assembly of short reads for each accession.	Leaf
PRJDB2161	RNASeq from spikes of Aegilops tauschii	Genome-wide marker development for the wheat D genome based on single nucleotide polymorphisms identified from transcripts in the wild wheat progenitor Aegilops tauschii.	454 GS FLX Titanium	Genome-wide marker development in the wheat D genome based on transcirpts-derived SNP of wild wheat progenitor Aegilops tauschii. Iehisa JCM, Shimizu A., Sato K., Nishijima R., Sakaguchi K., Matsuda R., Nasuda S, Takumi S.(2014) Theoretical and Applied Genetics 127:261-271.	Spikes
PRJNA244006	mRNA and sRNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation for Allopolyploid Heterosis in Nascent Hexaploid Wheat	mRNA and Small RNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation of Allopolyploid Heterosis in Nascent Hexaploid Wheat.	Illumina HiSeq 2000	Nascent allohexaploid wheat may represent the initial genetic state for the evolution and domestication of common wheat, which arose by combining the AB genomes of tetraploid Triticum turgidum with the D genome from Aegilops tauschii and out-competed its parents in growth vigor and adaptability. To better understand the molecular basis for this success, we performed mRNA and small RNA expression analyses in three tissues of nascent allohexaploid wheat and its following generations, their progenitors, and Chinese Spring, with the assistance of newly released A and D genome sequences. We found that nonadditive expression was rare among protein-coding genes which exhibited profound parental expression level dominance, with genes of total homoeolog expression level in nascent allohexaploid progeny similar to their expression levels in T. turgidum functionally enriched for development and those to Ae. tauschii distinctively for adaptation. In contrast, miRNAs appeared to be sensitive to polyploidization, with nonadditively expressed miRNAs potentially involved in growth vigor and adaptation. Meanwhile, siRNAs may contribute to biased repression of D homoeolog, possibly due to increased siRNA density on transposable element (TE)-associated D homoeologs. Together, our data provide new insights into homoeolog regulatory mechanisms that may be essential to heterosis in nascent hexaploid wheat. Overall design: We performed mRNA and small RNA analyses in three tissues of nascent allohexaploid wheat and its following generations, their progenitors, and Chinese Spring.Among these samples, Samples 1-6 and 26-31, tetraploid progenitors; Samples 7-12 and 32-37, diploid progenitors; Samples 13-22 and 38-47, following generations; Samples 23-25 and 48-50, Chinese Spring.	Seed、 spike、 seeding
PRJNA139957	High through put screen of small RNA in parental, hybrid and allopolyploid wheat	Wheat hybridization and polyploidization results in deregulation of small RNAs.	Illumina Genome Analyzer	Speciation via interspecific or intergeneric hybridization and polyploidization triggers genomic responses Overall design: Examination of small RNA of diploid Parent, Tetraploid parent, F1 hybrid and hexaploid amhiploid. Four pools of plants for each sample	whole plant

Stress and Treatment

Project ID	Title	Related Publication	Sequencing Type	Description	Notes
PRJNA951712	Aegilops tauschii subsp. tauschii Raw sequence reads	Transcriptome analysis in Aegilops tauschii unravels further insights into genetic control of stripe rust resistance	Illumina HiSeq 2500	This project contains four samples (two from susceptible accession, two from resistant accession) of RNA-Seq prepared from leaf tissue at seedling stage	Puccinia striiformis f. sp. tritici
PRJNA882581	Transcriptome analysis under shading stress of Aegilops tauschii	Transcriptomic analysis provides insight into the genetic regulation of shade avoidance in Aegilops tauschii	Illumina HiSeq 2500	To study on the hub gene of Aegilops tauschii under shading stress	Mono-cropping or inter-cropping
PRJNA868361	Transcriptome analysis of Iranian KC-2226 genotype of Aegilops tauschii under drought stress	Identification of drought-tolerant hub genes in Iranian KC-2226 genotype of Aegilops tauschii using transcriptomic analysis	Illumina NovaSeq 6000	Transcriptome analysis of Iranian KC-2226 genotype of Aegilops tauschii under drought stress	Drought
PRJNA815810	AADD RNA-seq Raw Data Raw sequence reads	Homoeologous exchange enables rapid evolution of tolerance to salinity and hyper-osmotic stresses in a synthetic allotetraploid wheat	Illumina HiSeq 2500	-	Salinity and hyper-osmotic
PRJNA748580	RNA sequencing of Aegilops tauschii	Comparative transcriptome analysis of two contrasting resistant and susceptible Aegilops tauschii accessions to wheat leaf rust (Puccinia triticina) using RNA-sequencing	Illumina HiSeq 2500	compatible and incompatible Aegilops accessions were challenged with leaf rust in order to evaluate strengths and weaknesses of Aegilops against the rust	Leaf rust
PRJNA680816	Aegilops tauschii and Triticum aestivum raw sequence reads	Regulation of 2,4-D Isooctyl Ester on Triticum aestivum and Aegilops tauschii Tillering and Endogenous Phytohormonal Responses	Illumina HiSeq 4000	The transcriptomic response of Aegilops tauschii and Triticum aestivum to 2,4-D isooctyl ester spray	2,4-D isooctyl ester spray
PRJNA624969	Aegilops tauschii Coss raw sequence reads	Regulation of Aegilops tauschii Coss Tiller Bud Growth by Plant Density: Transcriptomic, Physiological and Phytohormonal Responses	Illumina HiSeq 4000	indetification some tiller-related genes	Plant density
PRJNA604114	Aegilops tauschii subsp. strangulata Raw sequence reads	Cloning of the broadly effective wheat leaf rust resistance gene Lr42 transferred from Aegilops tauschii	Illumina HiSeq 2000	BSR-Seq of Lr42 using two F2:3 Ae. tauschii populations	Leaf rust race PNMRJ
PRJNA505880	Two selenium-accumulating genotypes of Aegilops tauschii in response to selenium and Description: Aegilops tauschii Transcriptome or Gene expression in Se treatments	Comparative transcriptome analysis of two selenium-accumulating genotypes of Aegilops tauschii Coss. in response to selenium	Illumina HiSeq 2500	-	Selenium
PRJNA342899	Aegilops tauschii Transcriptome or Gene expression	-	Illumina HiSeq 2000	Transcriptomic analysis of Aegilops tauschii during salinity stress	Salt