Ontology highlight
ABSTRACT:
PROVIDER: PRJNA743326 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR15083976_1.fastq.gz | Fastqsanger.gz | |||
| SRR15083977_1.fastq.gz | Fastqsanger.gz | |||
| SRR15083978_1.fastq.gz | Fastqsanger.gz | |||
| SRR15083979_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 13 |
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Project description:A comparative genomic approach was used to identify large sequence polymorphisms among Mycobacterium avium isolates obtained from a variety of host species. DNA microarrays were used as a platform for comparing mycobacteria field isolates with the sequenced bovine isolate Mycobacterium avium subsp. paratuberculosis (Map) K10. ORFs were classified as present or divergent based on the relative fluorescent intensities of the experimental samples compared to Map K10 DNA. Map isolates cultured from cattle, bison, sheep, goat, avian, and human sources were hybridized to the Map microarray. Three large deletions were observed in the genomes of four Map isolates obtained from sheep and four clusters of ORFs homologous to sequences in the Mycobacterium avium subsp. avium (Maa) 104 genome were identified as being present in these isolates. One of these clusters encodes glycopeptidolipid biosynthesis enzymes. One of the Map sheep isolates had a genome profile similar to a group of Mycobacterium avium subsp. silvaticum (Mas) isolates which included four independent laboratory stocks of the organism traditionally identified as Maa strain 18. Genome diversity in Map appears to be mostly restricted to large sequence polymorphisms that are often associated with mobile genetic elements. Keywords: Comparative genomic hybridization
2007-04-27 | GSE7622 | GEO
Project description:Potato yellow vein virus (PYVV) was detected by RT-PCR in potatoes grown in the Central Colombian highlands, north of Bogotá (~3000 mt height). At this altitude viral whitefly vectors are largely absent, but infection persists because of the use of uncertified tubers. Plants with typical PYVV-induced yellowing symptoms, as well as with atypical yellowing or non-symptomatic were sampled at three separate geographical locations. And five of them were subjected to Next Generation Sequencing (NGS) of their small RNA (sRNA) populations. Contigs to any virus were assembled, and complete or almost complete sequences of four PYVV isolates were thus re-constructed, all from symptomatic plants. Three viral isolates infected plants singly, while the fourth one co-infected the plant together with a potyvirus (potato virus Y, PVY). Relative proportions of sRNAs to each of the three viral genomic RNAs were assessed and found to remain comparable between the four infections. Genomic regions were identified as hotspots to sRNA formation, or as regions that induced poorly sRNAs. Furthermore, PYVV titers in the mixed vs. the single infections were found to be remained comparable, indicating absence of synergistic/antagonistic effect of the potyvirus on the accumulation of PYVV.
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Project description:With the aid of a biochip, carrying representative sequences from approximately 2200 sequences from the genome of isolate 9a5c from X. fastidiosa (Xf), microarray-based comparisons have been performed with 6 different Xf isolates obtained from citrus plants (Table 1). Four of these isolates (56a, 9.12c, 187b, and 36f) were obtained from CVC-affected trees and are representatives of the most prevalent Xf haplotypes found in sweet orange orchards across the state of São Paulo, while isolate CV21 was obtained from a non-symptomatic tree from the same region. Isolate Fb7, on the other hand, was obtained from a sweet orange tree that displayed symptoms of “Pecosita”, a disease similar to CVC that occurs in some citrus-growing regions of Argentina. Keywords: Comparative Genomic Hybridization
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Project description:A comparative genomic approach was used to identify large sequence polymorphisms among Mycobacterium avium isolates obtained from a variety of host species. DNA microarrays were used as a platform for comparing mycobacteria field isolates with the sequenced bovine isolate Mycobacterium avium subsp. paratuberculosis (Map) K10. ORFs were classified as present or divergent based on the relative fluorescent intensities of the experimental samples compared to Map K10 DNA. Map isolates cultured from cattle, bison, sheep, goat, avian, and human sources were hybridized to the Map microarray. Three large deletions were observed in the genomes of four Map isolates obtained from sheep and four clusters of ORFs homologous to sequences in the Mycobacterium avium subsp. avium (Maa) 104 genome were identified as being present in these isolates. One of these clusters encodes glycopeptidolipid biosynthesis enzymes. One of the Map sheep isolates had a genome profile similar to a group of Mycobacterium avium subsp. silvaticum (Mas) isolates which included four independent laboratory stocks of the organism traditionally identified as Maa strain 18. Genome diversity in Map appears to be mostly restricted to large sequence polymorphisms that are often associated with mobile genetic elements. Keywords: Comparative genomic hybridization Each isolate was competitively hybridized against Map K10 with a minimum of 2 dye flip hybridizations per isolate.
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