Hexaploid wheat mitochondrion sequencing
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB50328 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR8091036_1.fastq.gz | Fastqsanger.gz | |||
| ERR8091036_2.fastq.gz | Fastqsanger.gz | |||
| ERR8091037_1.fastq.gz | Fastqsanger.gz | |||
| ERR8091037_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 7 |
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Project description:Tetraploid wheat mitochondrion sequencing
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Project description:affy_hexaploid_wheat - hexa - Changes upon polyploidization in hexaploid wheat - transcriptomic changes in synthetic hexaploid derived from a cross between tetraploid and natural diploid. Study aims to understand regulation of gene expression in synthetic and natural wheat allohexaploids (Triticum aestivum), that combines the AB genome of T. turgidum and the D genome of Aegilops tauschii; and which we have recently characterized as genetically stable. We conducted a comprehensive genome-wide analysis of gene expression that allowed us to compare the effect of variability of the D genome progenitor, the trans-generation stability as well as comparison to natural wheat allohexaploid. We used the Affymetrix GeneChip® Wheat Genome Array, on which 55,049 transcripts are represented. Additive expression was shown to represent majority of expression regulation in the synthetic allohexaploids, where expression for more than 93% of transcripts was equal to the one evaluated from equal mixture of parental RNA. This leaves ~2000 (~7%) transcripts, which expression was non-additive. No global gene expression bias or dominance towards any of the progenitor genomes was observed whereas high trans-generational stability and low effect of the D genome progenitor variability were revealed. Our study suggests that gene expression regulation in wheat allohexaploids is early established upon allohexaploidization and highly conserved over generations, as demonstrated by the high similarity of expression with natural wheat allohexaploids. Keywords: genotype and ecotype comparison
2010-02-18 | GSE20169 | GEO
Project description:Many crop species have complex genomes, making the conventional pathway to associating molecular markers with trait variation, which includes genome sequencing, both expensive and time-consuming. We used a streamlined approach to rapidly develop a genomics platform for hexaploid wheat based on the inferred order of expressed sequences. This involved assembly of the transcriptomes for the progenitor genomes of bread wheat, the development of a genetic linkage map comprising 9495 mapped transcriptome-based SNP markers, use of this map to rearrange the genome sequence of Brachypodium distachyon into pseudomolecules representative of the genome organization of wheat and sequence similarity-based mapping onto this resource of the transcriptome assemblies. To demonstrate that this approximation of gene order in wheat is appropriate to underpin association genetics analysis, we undertook Associative Transcriptomics for straw biomass traits, identifying associations and even candidate genes for height, weight and width.
2014-01-31 | E-MTAB-4414 | biostudies-arrayexpress
Project description:affy_hexaploid_wheat - hexa - Changes upon polyploidization in hexaploid wheat - transcriptomic changes in synthetic hexaploid derived from a cross between tetraploid and natural diploid. Study aims to understand regulation of gene expression in synthetic and natural wheat allohexaploids (Triticum aestivum), that combines the AB genome of T. turgidum and the D genome of Aegilops tauschii; and which we have recently characterized as genetically stable. We conducted a comprehensive genome-wide analysis of gene expression that allowed us to compare the effect of variability of the D genome progenitor, the trans-generation stability as well as comparison to natural wheat allohexaploid. We used the Affymetrix GeneChip® Wheat Genome Array, on which 55,049 transcripts are represented. Additive expression was shown to represent majority of expression regulation in the synthetic allohexaploids, where expression for more than 93% of transcripts was equal to the one evaluated from equal mixture of parental RNA. This leaves ~2000 (~7%) transcripts, which expression was non-additive. No global gene expression bias or dominance towards any of the progenitor genomes was observed whereas high trans-generational stability and low effect of the D genome progenitor variability were revealed. Our study suggests that gene expression regulation in wheat allohexaploids is early established upon allohexaploidization and highly conserved over generations, as demonstrated by the high similarity of expression with natural wheat allohexaploids. Keywords: genotype and ecotype comparison 18 arrays - wheat
2010-02-21 | E-GEOD-20169 | biostudies-arrayexpress
Project description:Plants of two non-restorer varieties of hexaploid winter wheat (Astoria, Grana) and two restorers ones (Patres and Primépi) were used to identify effective Rf (fertility restorer) genes by next generation sequencing on whole transcriptomes (RNA-seq).
2021-06-30 | E-MTAB-10131 | biostudies-arrayexpress
Project description: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 ânullisomic-tetrasomicâ 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 obtained mRNA-Seq datasets from non-normalized cDNA libraries created from shoot and root tissues of the euploid bread wheat cultivar Chinese Spring, from which the nullitetra lines are derived, from complete sets of chromosome 1 and 5 nullitetras, and from extant relatives of the diploid A (Triticum urartu) and D (Aegilops tauschii) genome donors, herein referred to as A and D genome diploids
2014-04-22 | E-MTAB-4223 | biostudies-arrayexpress
Project description:To study the expression profiles of hexaploid wheat chromosome 3B genes during the life cycle of a wheat plant and establish a transcriptome atlas for this chromosome, deep transcriptome sequencing was conducted in duplicates in 15 wheat samples corresponding to five different organs (leaf, shoot, root, spike, and grain) at three developmental stages each. Strand-non-specific and strand-specific libraries were used to produce 2.52 billion paired-end reads (232 Gb) and 615.3 single-end reads (62 Gb), respectively.
2014-09-08 | E-MTAB-4484 | biostudies-arrayexpress
Project description:Wheat is a cereal grain and one of the world’s major food crops. Recent advances in wheat genome sequencing are by now facilitating genomic and proteomic analyses of this crop. However, little is known about the protein levels of hexaploid versus tetraploid wheat cultivars, and knowledge on phosphorylated proteins still limited. Using our recently established (phospho)proteomic workflow, we performed a parallel analysis of the proteome and phosphoproteome on seedling leaves from two hexaploid wheat cultivars (Pavon 76 and USU-Apogee) and a tetraploid wheat (Senatore Cappelli). This revealed that a large portion of proteins and phosphosites can be quantified in all cultivars. Our shotgun proteomics data revealed a high similarity between hexaploid and tetraploid varieties with respect to protein abundance. However, we could identify a set of proteins that were differentially abundant between hexaploid and tetraploid cultivars. In addition, already at seedling stage, a small set of proteins were differential between the small (USU-Apogee) and larger hexaploid wheat cultivar (Pavon 76), which could potentially act as growth predictors. Finally, the phosphosites identified in this study can be retrieved from the in-house developed plant PTM-Viewer (bioinformatics.psb.ugent.be/webtools/ptm_viewer/), making this the first repository for phosphorylated wheat proteins. This paves the way for further in depth, quantitative (phospho)proteome-wide differential analyses upon a specific trigger or environmental change.
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Project description:[hexa-] Transcriptomic changes in synthetic hexaploid wheat
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Project description:Transcriptome-based association genetics in hexaploid wheat
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