Wheat chromosome 3B resequencing
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB31708 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3236870_1.fastq.gz | Fastqsanger.gz | |||
| ERR3236870_2.fastq.gz | Fastqsanger.gz | |||
| ERR3236880_1.fastq.gz | Fastqsanger.gz | |||
| ERR3236880_2.fastq.gz | Fastqsanger.gz | |||
| ERR3236890_1.fastq.gz | Fastqsanger.gz |
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Project description:To improve our understanding of the organization and regulation of the wheat gene space, we established the first transcription map of a wheat chromosome (3B) by hybridizing the newly developed INRA GDEC Triticum aestivum NimbleGen 12x40k unigenes microarray with BAC pools from a new version of the 3B physical map as well as with cDNA probes from five tissues at three developmental stages each. By hybridizing the BAC pools with the wheat NimbleGen 40K unigenes chip we managed to map almost 3000 unigenes on the wheat chromosome 3B BACs and to study the organization of the wheat gene space along chromosome 3B. The sequences of the unigenes helped to perform functional and evolutionary analyses of these unigenes. By hybridizing the 15 cDNA samples from five organs at three developmental stages each we established the expression profiles of more than 32000 wheat unigenes. Particularly we focused on the expression of the unigenes mapped on wheat chromosome 3B to perform coexpression analyses.
2011-11-03 | E-TABM-1095 | biostudies-arrayexpress
Project description:Wheat chromosome 3B survey sequence
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Project description:Wheat chromosome 3B survey sequence.
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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:Background Because of its size, allohexaploid nature and high repeat content, the wheat genome has always been perceived as too complex for efficient molecular studies. However, we recently constructed the first physical map of a wheat chromosome (3B). But gene mapping is still laborious in wheat because of high redundancy between the three homoeologous genomes. In contrast, in the closely related diploid species, barley, numerous gene-based markers have been developed. This study aims at combining the unique genomic resources developed in wheat and barley to decipher the organisation of gene space on wheat chromosome 3B. Results Three dimensional pools of the minimal tiling path of wheat chromosome 3B physical map were hybridized to a barley Agilent 15K expression microarray. This led to the identification of 738 barley genes with a homolog on wheat chromosome 3B. In addition, comparative analyses revealed that 68% of the genes identified were syntenic between the wheat chromosome 3B and barley chromosome 3H and 59% between wheat chromosome 3B and rice chromosome 1, together with some wheat-specific rearrangements. Finally, it indicated an increasing gradient of gene density from the centromere to the telomeres positively correlated with the number of genes clustered in islands on wheat chromosome 3B. Conclusion Our study shows that novel structural genomics resources now available in wheat and barley can be combined efficiently to overcome specific problems of genetic anchoring of physical contigs in wheat and to perform high-resolution comparative analyses with rice for deciphering the organisation of the wheat gene space.
2010-12-02 | E-TABM-1011 | biostudies-arrayexpress
Project description:Barley contains a much higher content of bioactive substances than wheat. In order to investigate the effect of genome interaction between barley and wheat on phytosterol content, we used a series of barley chromosome addition lines of common wheat. The wheat 38k-microarray was utilized for screening of genes with expression levels specifically increased by an additive effect or synergistic action between wheat and barley chromosomes. We determined the overall expression pattern of genes related to phytosterol biosynthesis in wheat and in each addition line. Together with determining the phytosterol levels of wheat, barley and each addition line, we assess the critical genes in the phytosterol pathway that can be expressed to promote phytosterol levels.
2011-12-08 | GSE28023 | GEO
Project description:Barley contains a much higher content of bioactive substances than wheat. In order to investigate the effect of genome interaction between barley and wheat on phytosterol content, we used a series of barley chromosome addition lines of common wheat. The wheat 38k-microarray was utilized for screening of genes with expression levels specifically increased by an additive effect or synergistic action between wheat and barley chromosomes. We determined the overall expression pattern of genes related to phytosterol biosynthesis in wheat and in each addition line. Together with determining the phytosterol levels of wheat, barley and each addition line, we assess the critical genes in the phytosterol pathway that can be expressed to promote phytosterol levels. Gene expression levels of each barley chromosome addition line of common wheat were compared to that of common wheat. Total RNA samples were isolated from the 2-week-old seedling leaves. The experiments were replicated three times for each addition line using independent samples.
2011-12-08 | E-GEOD-28023 | biostudies-arrayexpress
Project description:Using 270K Nimblegen Comparative Genomic Hybridization (CGH) array on a set of cv. Chinese Spring deletion lines, a total of 3,671 sequence contigs and scaffolds (~7.8% of chromosome 7B physical length) were mapped into nine deletion bins. In our study we have developed 270K CGH Nimblegen array containing wheat 7B chromosome specific probes and genotyped wheat 7B deletion stocks which have terminal deletions in 7B. Our main aim was to identify absent probes (sequences) in deletion lines. Initially, spatial normalization and M-A loess normalization was performed for comparison test/reference and then clustering analysis (Mcust) was carried out. Further analysis was done on scaffolds (i.e. on larger sequences instead of probes; probes are designed from scaffolds)
2014-05-09 | GSE57461 | GEO
Project description:Using 270K Nimblegen Comparative Genomic Hybridization (CGH) array on a set of cv. Chinese Spring deletion lines, a total of 3,671 sequence contigs and scaffolds (~7.8% of chromosome 7B physical length) were mapped into nine deletion bins. In our study we have developed 270K CGH Nimblegen array containing wheat 7B chromosome specific probes and genotyped wheat 7B deletion stocks which have terminal deletions in 7B. Our main aim was to identify absent probes (sequences) in deletion lines. Initially, spatial normalization and M-A loess normalization was performed for comparison test/reference and then clustering analysis (Mcust) was carried out. Further analysis was done on scaffolds (i.e. on larger sequences instead of probes; probes are designed from scaffolds) Hybridization of DNA from 13 wheat lines, including 11 Chinese Spring cytogenetic stocks (Del7BL-9, DT7BL, DT7BS, Del7BL-13, Del7BL-14, Del7BL-5, Del7BL-1, Del7BL-7Del1DS-3, Del7BL-2,Del7BS-2, Del7BL-3) and 2 replicates of Langdon (LDN) tetraploid wheat. A set of 49,500 7B chromosome specific features (ISBP probes and random genomic features) and 18,000 control probes with each probe replicated four times on the 270K chip.
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