Ontology highlight
ABSTRACT:
PROVIDER: PRJNA811959 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18242742.fastq.gz | Fastqsanger.gz | |||
| SRR18242743.fastq.gz | Fastqsanger.gz | |||
| SRR18242744.fastq.gz | Fastqsanger.gz |
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Project description:Genomic safe harbors (GSHs) are utilized as an ideal integration site for generating transgenic organisms and cells. Discovery of GSHs is one of the crucial factors for the advancement of basic and applied biology in the species. Such GSHs were discovered in Pv11 (Polypedilum vanderplanki) cell line, which can survive extreme desiccation. To identify the integration sites, high-molecular-weight genomic DNAs were extracted. The DNA libraries were prepared and sequenced with a Nanopore MinION sequencer. In the way to confirm that GSHs loci are localized in open chromatin regions we prepared ATAC-seq libraries, which were sequenced in Illumina HiSeq2500.
2022-03-01 | GSE190481 | GEO
Project description:Colletotrichum is a large genus of fungal phytopathogens that cause major economic losses on a wide range of crop plants throughout the world. These pathogenes vary widely in their host specificity and may have either broad or narrow host ranges. Here, we report the first complete genome of the alfalfa (Medicago sativa) pathogen, Colletotrichum destructivum, which will facilitate the genomic analysis of host adaptation and comparison with other members of the Destructivum clade. We identified a specific 1.2Mb region within chromosome 1 displaying all the hallmarks of fungal accessory chromosomes, which may have arisen through the integration of a mini-chromosome into a core chromosome and possibly linked with the pathogenicity of this fungus. We show this region is also a focus for chromosomal rearrangements, which may contribute to generating genetic diversity for adaptive evolution. Finally, we report infection by this fungus of the model legume, Medicago truncatula, providing a novel pathosystem for studying fungal-plant interactions.
2023-12-18 | GSE246592 | GEO
Project description:We here describe the first successful construction of a targeted tandem duplication of a large chromosomal segment in Aspergillus oryzae. The targeted tandem chromosomal duplication was achieved by using strains that had 5M-bM-^@M-^YM-NM-^TpyrG upstream of the region targeted for tandem chromosomal duplication and 3M-bM-^@M-^YM-NM-^TpyrG downstream of the target region. Consequently, strains bearing a 210-kb targeted tandem chromosomal duplication near the centromeric region of chromosome 8 and strains bearing a targeted tandem chromosomal duplication of a 700-kb region of chromosome 2 were successfully constructed. The strains bearing the tandem chromosomal duplication were efficiently obtained from the regenerated protoplast of the parental strains. However, the generation of the chromosomal duplication did not depend on the introduction of double-stranded breaks (DSBs) by I-SceI. The chromosomal duplications of these strains were stably maintained after five generations of culture under non-selective conditions. The strains bearing the tandem chromosomal duplication in the 700-kb region of chromosome 2 showed highly increased protease activity in solid-state culture, indicating that the duplication of large chromosomal segments could be a useful new breeding technology and gene analysis method. A. oryzae strain bearing a 210-kb targeted tandem chromosomal duplication, A. oryzae strain bearing a 700-kb targeted tandem chromosomal duplication, and A. oryzae RIB40 (wild type strain), were cultivated in Polypeptone-dextrin medium. After 3 days cultivation, genomic DNAs from the samples were extracted, and array CGH analysis was carried out to confirm the chromosomal duplications in the strains.
2014-06-30 | E-GEOD-57246 | biostudies-arrayexpress
Project description:Purpose. Simian virus 40 (SV40)-immortalized human corneal epithelial (HCE-T) cells have been widely used as an in vitro model of human corneal epithelial cells. To better understand the nature of this cell line, we assessed it for genomic aberrations and cellular heterogeneity. Methods. For the quantitative measurement of genomic aberrations, array based comparative genomic hybridization (CGH) analysis was performed. For identification of cellular heterogeneity, cell morphology, growth kinetics, trans-epithelial electrical resistance and transcriptional efficiency were analyzed. We also carried out real-time PCR and chromosomal fluorescent in situ hybridization (cFISH) against some gained or lost loci in order to assess genomic heterogeneity. To assess differences in the gene expression profiles between HCE-T cells and normal corneal epithelial cells, we collected expressed sequence tags (ESTs) for this cell line. Southern blotting and inverse PCR analyses were used to determine the genomic integration site of the SV40 large T antigen gene (LTAG). Results. Array CGH analysis indicated that the genomic content of HCE-T cells is different from the normal healthy genome. Our results from cellular functional assays, real-time PCR and cFISH strongly showed that HCE-T cells consist of a not insignificant number of heterogeneous cell populations. The genomic integration site of the SV40 large T antigen was at p22.1 of chromosome 9. Conclusions. Our results indicate that HCE-T cells have an altered genomic content and that they are composed of heterogeneous cell populations. This should be considered when conducting experiments or interpreting the results of studies which use this cell line. Keywords: comparative genomic hybridization Genomic DNAs from HCE-T cells, immortalized cell line of human corneal epithelial cells and normal female duploid cells were subjected to array CGH analysis to identify genomic alterations in the HCE-T cells. These DNAs were labeled with Cy5 and Cy3, respectively.
2008-04-15 | E-GEOD-11101 | biostudies-arrayexpress
Project description:Phylogenetic, microbiological and comparative genomic analysis was used to examine the diversity among members of the genus Caldicellulosiruptor with an eye towards the capacity of these extremely thermophilic bacteria for degrading the complex carbohydrate content of plant biomass. Seven species from this genus (C. saccharolyticus, C. bescii (formerly Anaerocellum thermophilum), C. hydrothermalis, C. owensensis, C. kronotskyensis, C. lactoaceticus, and C. kristjanssonii) were compared on the basis of 16S rRNA phylogeny and cross-species DNA-DNA hybridization to a whole genome C. saccharolyticus oligonucleotide microarray. Growth physiology of the seven Caldicellulosiruptor species on a range of carbohydrates showed that, while all could be cultivated on acid pre-treated switchgrass, only C. saccharolyticus, C. besci, C. kronotskyensis, and C. lactoaceticus were capable of hydrolyzing Whatman No. 1 filter paper. Two-dimensional gel electrophoresis of the secretomes from cells grown on microcrystalline cellulose revealed that species capable of crystalline cellulose hydrolysis also had diverse secretome fingerprints. The two-dimensional secretome of C. saccharolyticus revealed a prominent S-layer protein that appears to be also indicative of highly cellulolytic Caldicellulosiruptor species, suggesting a possible role in cell-substrate interaction. These growth physiology results were also linked to glycoside hydrolase and carbohydrate-binding module inventories for the seven bacteria, deduced from draft genome sequence information. These preliminary inventories indicated that the absence of a single glycoside hydrolase family and carbohydrate binding motif family appear to be responsible for some Caldicellulosiruptor species’ diminished cellulolytic capabilities. Overall, the genus Caldicellulosiruptor appears to contain more genomic and physiological diversity than previously reported, and is well suited for biomass deconstruction applications. Six dye-flip experiments were conducted using C. saccharolyticus genomic DNA as the reference in each dye-flip, and one of six different Caldicellulosiruptor spp. as a tester in each dye-flip
2010-11-29 | E-GEOD-23606 | biostudies-arrayexpress