Ontology highlight
ABSTRACT:
PROVIDER: PRJNA523452 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8599510.fastq.gz | Fastqsanger.gz | |||
| SRR8599510_1.fastq.gz | Fastqsanger.gz | |||
| SRR8599510_2.fastq.gz | Fastqsanger.gz | |||
| SRR8599520.fastq.gz | Fastqsanger.gz | |||
| SRR8599520_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 72 |
Similar Datasets
Project description:Experiment evaluating aplicability of PlasTi-microarray for cross-species hybridization studies. PlasTi-microarray is a tiling oligonucleotide microarray originally designed for cucumber plastome analysis.Chloroplast RNA from Arabidopsis, tomato and spinach leaves was extracted, labelled and hybridized to PlasTi-microarray with the cucumber samples labelled with the second dye as a control. For each species, one biological sample and one technical replicate (labelled in a dye-swap orientation) were analyzed, resulting in two microarray hybridizations per species and six microarrays (a-f) in total.
2011-05-27 | E-MEXP-3220 | biostudies-arrayexpress
Project description:Groupers (Epinephelidae) are ecologically, commercially, and culturally important predatory fishes throughout their global distribution range in tropical, subtropical and occasionally temperate regions. They are key species for modern and ancient fisheries in the Mediterranean which have been heavily overfished in the past century leading to smaller catch sizes, lower CPUE, and decreased biomass. There are four species of grouper native to the Mediterranean within the Epinephelus genus.The abundance and distribution of grouper species prior to the 20th century in the Mediterranean remains poorly known. Using peptide mass fingerprinting, also known as Zooarchaeology by Mass Spectrometry (ZooMS), we investigated if ZooMS is a viable method for identifying intra-genus grouper bones to species level. Due to the lack of publicly available genomic sequences and for validation of ZooMS markers, we reconstructed collagen type I amino acid sequences using LC-MS/MS for four Epinephelus spp. Adequate variation between collagen sequences enabled the production of the best supported phylogenetic tree for Mediterranean Epinephelus spp. to date. We identified 23 previously undescribed ZooMS biomarkers capable of distinguishing groupers to the species level. Our novel biomarkers were applied to a case study of 23 grouper/comber fish bones from the Middle to Late Holocene archaeological site of Kinet Höyük, located along the coast of Iskenderun Bay, Turkey. ZooMS markers enabled species level identification of 19 bones with 18 identified as Epinephelus aeneus and 1 identified as Epinephelus marginatus. Combining ZooMS identifications with catch size reconstructions has revealed that E. aeneus is capable of growing ca. 30 cm larger than previously reported. This abundance and dominance of E. aeneus locally at Kinet Höyük is consistent with E. aeneus being the most prevalent grouper species in Iskenderun Bay today, testifying to several millennia of this species local population persistence despite fishing pressure, habitat degradation, and climatic changes.
2023-10-23 | PXD042430 | Pride
Project description:<p>Plant monocultures growing for extended periods face severe losses of productivity. This phenomenon, known as 'yield decline', is often caused by the accumulation of above- and below-ground plant antagonists. The effectiveness of plant defences against antagonists might help explain differences in yield decline among species. Using a trait-based approach, we studied the role of 20 physical and chemical defence traits of leaves and fine roots on yield decline of 4- and 18-year-old monocultures of 27 grassland species. We hypothesized that yield decline is lower for species with high defences, that root defences are better predictors of yield decline than leaf defences, and that in roots, physical defences better predict yield decline than chemical defences, while the reverse is true for leaves. We additionally hypothesized that the relationship between defences and yield decline increase with time and that species increasing the expression of defence traits after long-term monoculture growth would suffer less yield decline. We summarized leaf and fine root defence traits using principal component analysis and analysed the relationship between the most informative components as well as their temporal changes and monoculture yield decline. The significant predictors of yield decline were traits related to the so-called collaboration gradient of the root economics space (specific root length and root diameter) as well as their temporal changes and traits related to the leaf physical vs chemical defence trade-off (leaf dry matter, silicon and cellulose content, toughness and phytochemical diversity). We were unable to unequivocally identify the mechanisms relating the effect of those traits to yield decline as they could mediate plant responses to several stressor such as antagonist nutrient depletion and drought. Further studies are needed to differentiate between these alternative mechanisms and gain a comprehensive understanding of the drivers behind the impact of root and leaf defence traits on yield decline.</p>
2023-11-03 | MTBLS4286 | MetaboLights