Gartersnakes
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA453585 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7084000.fastq.gz | Fastqsanger.gz | |||
| SRR7084010.fastq.gz | Fastqsanger.gz | |||
| SRR7084020.fastq.gz | Fastqsanger.gz | |||
| SRR7084030.fastq.gz | Fastqsanger.gz | |||
| SRR7084040.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 439 |
Similar Datasets
Project description:There are very few studies exploring the genetic diversity of tick-borne encephalitis complex viruses. Most of the viruses have been sequenced using capillary electrophoresis, however, very few viruses have been analyzed using deep sequencing to look at the genotypes in each virus population. In this study, different viruses and strains belonging to the tick-borne encephalitis complex were sequenced and genetic diversity was analyzed. Shannon entropy and single nucleotide variants were used to compare the viruses. Then genetic diversity was compared to the phylogenetic relationship of the viruses.
2023-12-04 | E-MTAB-12112 | biostudies-arrayexpress
Project description:Background: WitchesM-bM-^@M-^Y broom disease of Mexican lime (Citrus aurantifolia L.), which is caused by the phytoplasma M-bM-^@M-^\Candidatus Phytoplasma aurantifoliaM-bM-^@M-^], is a devastating disease that results in significant economic losses. Plants adapt to abiotic stresses by regulating gene expression at the transcriptional and post-transcriptional levels. MicroRNAs (miRNAs) are a recently identified family of molecules that regulate plant responses to environmental stresses through post-transcriptional gene silencing. Methods: Using a high-throughput approach to sequence small RNAs, we compared the expression profiles of miRNAs in healthy Mexican lime trees and in plants infected with M-bM-^@M-^\Ca. Phytoplasma aurantifoliaM-bM-^@M-^]. Results: Our results demonstrated the involvement of different miRNAs in the response of Mexican lime trees to infection by M-bM-^@M-^\Ca. Phytoplasma aurantifoliaM-bM-^@M-^]. We identified miRNA families that are expressed differentially upon infection with phytoplasmas. Most of the miRNAs had variants with small sequence variations (isomiRs), which are expressed differentially in response to pathogen infection. Conclusions: It is likely that the miRNAs that are expressed differentially in healthy and phytoplasma-infected Mexican lime trees are involved in coordinating the regulation of hormonal, nutritional, and stress signalling pathways, and the complex interactions between them. Future research to elucidate the roles of these miRNAs should improve our understanding of the level of diversity of specific plant responses to phytoplasmas. Small mRNA profiles of healthy (H) and Phytoplasma-infected Mexican lime trees were generated by deep sequencing, six replicate, using Illumina Hiseq2000
2013-03-09 | E-GEOD-44279 | biostudies-arrayexpress
Project description:Background: Witches’ broom disease of Mexican lime (Citrus aurantifolia L.), which is caused by the phytoplasma “Candidatus Phytoplasma aurantifolia”, is a devastating disease that results in significant economic losses. Plants adapt to abiotic stresses by regulating gene expression at the transcriptional and post-transcriptional levels. MicroRNAs (miRNAs) are a recently identified family of molecules that regulate plant responses to environmental stresses through post-transcriptional gene silencing. Methods: Using a high-throughput approach to sequence small RNAs, we compared the expression profiles of miRNAs in healthy Mexican lime trees and in plants infected with “Ca. Phytoplasma aurantifolia”. Results: Our results demonstrated the involvement of different miRNAs in the response of Mexican lime trees to infection by “Ca. Phytoplasma aurantifolia”. We identified miRNA families that are expressed differentially upon infection with phytoplasmas. Most of the miRNAs had variants with small sequence variations (isomiRs), which are expressed differentially in response to pathogen infection. Conclusions: It is likely that the miRNAs that are expressed differentially in healthy and phytoplasma-infected Mexican lime trees are involved in coordinating the regulation of hormonal, nutritional, and stress signalling pathways, and the complex interactions between them. Future research to elucidate the roles of these miRNAs should improve our understanding of the level of diversity of specific plant responses to phytoplasmas.
2013-03-09 | GSE44279 | GEO
Project description:Phylogenetic relationships of the Mexican tussilaginioids (Asteraceae)
| PRJEB25760 | ENA
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
Project description:Ogataea polymorpha species complex population genomics
| PRJNA706707 | ENA
Project description:Pangenome arrays contain DNA oligomers targeting several sequenced reference genomes from the same species. In microbiology these can be employed to investigate the often high genetic variability within a species by comparative genome hybridization (CGH). The biological interpretation of pangenome CGH data depends on the ability to compare strains at a functional level, particularly by comparing the presence or absence of orthologous genes. Due to the high genetic variability, available genotype-calling algorithms can not be applied to pangenome CGH data. Therefore, we have developed the algorithm PanCGH that incorporates orthology information about genes to predict the presence or absence of orthologous genes in a query organism using CGH arrays that target the genomes of sequenced representatives of a group of microorganisms. PanCGH was tested and applied in the analysis of genetic diversity among 39 Lactococcus lactis strains from three different subspecies (lactis, cremoris, hordniae) and isolated from two different niches (dairy and plant). Clustering of these strains using the presence/absence data of gene orthologs revealed a clear separation between different subspecies and reflected the niche of the strains. Keywords: CGH, CGH analysis, orthology, Lactococcus lactis We analyzed 39 CGH arrays, where on each array different strain of L. lactis was hybridized.
2010-06-24 | E-GEOD-12638 | biostudies-arrayexpress
Project description:RNA from testis from 4 mus musculus species was hybridized on affymetrix gene chip U74Av2. Subspecies-specific differences in expression level were then extracted by conditioning on outcomes to cases where the expression in one subspecies differed significantly from all others but these did not differ significantly among each other. Keywords: other
2006-04-01 | GSE2471 | GEO
Project description:The Pine Wood Nematode (PWN) Bursaphelenchus xylophilus is a severe forest pathogen in countries where it has been introduced and is considered a worldwide quarantine organism. In this study, protein markers for differentiating populations of this nematode were identified by studying differences among four selected Iberian and one American population. These populations were compared by quantitative proteomics (iTRAQ), which considers the level of protein expression. From a total of 2862 proteins identified using the public database from the B. xylophilus genome project, 216 were unambiguous and significantly differentially expressed in the studied populations. Comparisons of their pairwise ratio were statistically treated and supported in order to convert them into discrete character states, suggesting that 141 proteins were not informative as population specific markers. Application of the Character Compatibility methodology on the remaining 75 proteins (belonging to families with different biological functions) excludes 27 which are incompatible among them. Considering only the compatible proteins, the method selects a subset of 34 specific unique protein markers which allowed the compared classification of the Iberian isolates. This approach makes it easier search for diagnostic tools and phylogenetic inference within species and populations of a pathogen exhibiting a high level of genetic diversity.
2018-07-05 | PXD003129 | Pride