IcColElon
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB74680 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR12875211.fastq.gz | Fastqsanger.gz | |||
| ERR12875212.fastq.gz | Fastqsanger.gz | |||
| ERR12893017_1.fastq.gz | Fastqsanger.gz | |||
| ERR12893017_2.fastq.gz | Fastqsanger.gz |
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Project description:Centromeres typically contain repeat sequences, but centromere function does not necessarily depend on these sequences. In aneuploid wheat (Triticum aestivum) and wheat distant hybridization offspring, we found functional centromeres with dramatic changes to centromeric retrotransposon of wheat (CRW) sequences. CRW sequences were greatly reduced in the ditelosomic lines 1BS, 5DS, 5DL, and a wheat-Thinopyrum elongatum addition line. CRWs were completely lost in the ditelosomic line 4DS, but a 994 kb ectopic genomic DNA sequence was involved in de novo centromere formation on the 4DS chromosome. In addition, two ectopic sequences were incorporated in a de novo centromere in a wheat-Th. intermedium addition line. Centromeric sequences were also expanded to the chromosome arm in wide hybridizations. Stable alien chromosomes with two and three regions containing centromeric sequences were found in wheat-Th. elongatum hybrid derivatives, but only one is functional. In wheat-rye (Secale cereale) hybrids, rye centromere specific sequences spread to the chromosome arm and may cause centromere expansion. Thus, distant wheat hybridizations cause frequent and significant changes to the centromere via centromere misdivision, which may affect retention or loss of alien chromosomes in hybrids. ChIP-seq was carried out with anti-CENH3 antibody using material 4DS and control (Chinese Spring, CS as short).
2016-04-02 | E-GEOD-63752 | biostudies-arrayexpress
Project description:Centromeres typically contain repeat sequences, but centromere function does not necessarily depend on these sequences. In aneuploid wheat (Triticum aestivum) and wheat distant hybridization offspring, we found functional centromeres with dramatic changes to centromeric retrotransposon of wheat (CRW) sequences. CRW sequences were greatly reduced in the ditelosomic lines 1BS, 5DS, 5DL, and a wheat-Thinopyrum elongatum addition line. CRWs were completely lost in the ditelosomic line 4DS, but a 994 kb ectopic genomic DNA sequence was involved in de novo centromere formation on the 4DS chromosome. In addition, two ectopic sequences were incorporated in a de novo centromere in a wheat-Th. intermedium addition line. Centromeric sequences were also expanded to the chromosome arm in wide hybridizations. Stable alien chromosomes with two and three regions containing centromeric sequences were found in wheat-Th. elongatum hybrid derivatives, but only one is functional. In wheat-rye (Secale cereale) hybrids, rye centromere specific sequences spread to the chromosome arm and may cause centromere expansion. Thus, distant wheat hybridizations cause frequent and significant changes to the centromere via centromere misdivision, which may affect retention or loss of alien chromosomes in hybrids.
2016-04-02 | GSE63752 | GEO
Project description:The ditelocentric addition line CS-7EL of the spring wheat (Triticum aestivum) cultivar Chinese Spring (CS) contains the long arm of the chromosome 7E from Thinopyrum elongatum (CS-7EL), which confers high resistance to fusarium head blight. It is of great interest to breeders to integrate the resistance locus (loci) from Th. elongatum into commercial wheat varieties. The objectives of this study were to identify candidate genes expressed from the 7EL chromosome of CS-7EL, to develop 7EL-specific molecular markers, and to validate their usefulness to characterize recombination between one of the group 7 chromosomes of wheat and Th. elongatum. High-throughput sequencing of Fusarium graminearum-infected and control CS and CS-7EL cDNA libraries was performed using RNA-Seq. A stepwise bioinformatics strategy was applied to assemble the sequences obtained from RNA-Seq and to create a conservative list of candidate genes expressed from the foreign chromosome 7EL. PCR primer pairs were designed and tested for 135 candidate genes. A total of 48 expressed molecular markers specific for the chromosome 7EL were successfully developed. Screening of progenies from two BC1F2 families from the cross CS-7E(7D)×2*CSph1b showed that these markers are useful to characterize recombination events between the chromosomes 7D from wheat and 7E from Th. elongatum.
2015-09-14 | GSE70797 | GEO
Project description:Analyses of new genomic, transcriptomic or proteomic data commonly result in trashing many unidentified data escaping the ‘canonical’ DNA-RNA-protein scheme. Testing systematic exchanges of nucleotides over long stretches produces inversed RNA pieces (here named “swinger” RNA) differing from their template DNA. These may explain some trashed data. Here analyses of genomic, transcriptomic and proteomic data of the pathogenic Tropheryma whipplei according to canonical genomic, transcriptomic and translational 'rules' resulted in trashing 58.9% of DNA, 37.7% RNA and about 85% of mass spectra (corresponding to peptides). In the trash, we found numerous DNA/RNA fragments compatible with “swinger” polymerization. Genomic sequences covered by «swinger» DNA and RNA are 3X more frequent than expected by chance and explained 12.4 and 20.8% of the rejected DNA and RNA sequences, respectively. As for peptides, several match with “swinger” RNAs, including some chimera, translated from both regular, and «swinger» transcripts, notably for ribosomal RNAs. Congruence of DNA, RNA and peptides resulting from the same swinging process suggest that systematic nucleotide exchanges increase coding potential, and may add to evolutionary diversification of bacterial populations.
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Project description:Gordius_albopunctatus, genomic and transcriptomic data
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Project description:The ditelocentric addition line CS-7EL of the spring wheat (Triticum aestivum) cultivar Chinese Spring (CS) contains the long arm of the chromosome 7E from Thinopyrum elongatum (CS-7EL), which confers high resistance to fusarium head blight. It is of great interest to breeders to integrate the resistance locus (loci) from Th. elongatum into commercial wheat varieties. The objectives of this study were to identify candidate genes expressed from the 7EL chromosome of CS-7EL, to develop 7EL-specific molecular markers, and to validate their usefulness to characterize recombination between one of the group 7 chromosomes of wheat and Th. elongatum. High-throughput sequencing of Fusarium graminearum-infected and control CS and CS-7EL cDNA libraries was performed using RNA-Seq. A stepwise bioinformatics strategy was applied to assemble the sequences obtained from RNA-Seq and to create a conservative list of candidate genes expressed from the foreign chromosome 7EL. PCR primer pairs were designed and tested for 135 candidate genes. A total of 48 expressed molecular markers specific for the chromosome 7EL were successfully developed. Screening of progenies from two BC1F2 families from the cross CS-7E(7D)×2*CSph1b showed that these markers are useful to characterize recombination events between the chromosomes 7D from wheat and 7E from Th. elongatum. Expression profiling of inoculated rachis from CS and CS-7EL heads sampled at 4 days after inoculation. Inoculation of all developed spikelets on each head at mid-anthesis was done with either water or F. graminearum strain DAOM 180378. Three biological replicates were done for each treatment, and 10 to 12 heads were inoculated per biological replicate.
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