Metopolophium dirhodum
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA751719 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15711100_1.fastq.gz | Fastqsanger.gz | |||
| SRR15711100_2.fastq.gz | Fastqsanger.gz | |||
| SRR15711101_1.fastq.gz | Fastqsanger.gz | |||
| SRR15711101_2.fastq.gz | Fastqsanger.gz | |||
| SRR15711102_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 36 |
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Project description:Metopolophium dirhodum isolate:CAU Genome sequencing and assembly
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Project description:Saliva was collected from c.40,000 diet reared aphids, pooled and concentrated. Samples were coming from 2 aphid species: Metopolophium dirhodum and Sitobion avenae. Proteins were fractionated using SDS PAGE and visible bands were subjected to in gel digestion. Tryptic peptides were analysised on a Thermo LTQ-FT. Protein identification from the MS/MS data was performed using the TurboSEQUEST algorithm in BioWorks v. 3.2 (Thermo Fisher Scientific) to correlate the data against ACYPIproteins v2.1, the official protein set of the pea aphid genome assembly (33291 predicted protein models; accessed November 2011) available at http://www.aphidbase.com/aphidbase/downloads. The following search parameters were used: precursor-ion mass tolerance of 1.5 Da, fragment ion tolerance of 1.0 Da with methionine oxidation and cysteine carboxyamidomethylation specified as differential modifications and a maximum of two missed cleavage sites allowed. Two filters were applied: XCorr vs. charge state (1, 2, 3 and 4 = 1.50, 2.00, 2.50 and 3.00 respectively) and peptide probability (p<0.001). Matches with multiple unique peptides and a cumulative XCorr >20 are reported. PLoS One accepted: Proteomic profiling of cereal aphid saliva reveals ubiquitous and adaptative secreted proteins. Rao S.A.K., Carolan, J.C. and Wilkinson, T.L.W.
2013-04-09 | PXD000113 | Pride
Project description:RNA-Seq Analyses of Metopolophium dirhodum Reveal the Underlying Resistance to Insecticides
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Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
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Project description:In the field, plants usually have to face combined effects of abiotic and biotic stresses. In our study, two spring wheat cultivars Septima and Quintus were subjected to three water regimes (70, 50, 40 % soil water capacity SWC), aphid (Metopolophium dirhodum) infestation or the combination of both stresses, i.e., drought (50, 40% SWC) and aphids. The study has a 2x3x2 factorial design with three biological replicates. Our previous study (Saska et al. 2022) investigated plant morphophysiological characteristics and aphid life table. In the present study, the results of proteomic analysis using 2D-DIGE followed by MALDI-TOF/TOF protein identification are presented. Drought, but also aphid infestation led to alterations in 113 protein spots including proteins assigned to a variety of biological processes ranging from signalling via energy metabolism, redox regulation, stress and defense responses to secondary metabolism indicating a long-term adaptation to adverse conditions. The absence of specific proteins involved in plant response to herbivorous insects indicates a loss of resistance to aphids in modern wheat cultivars during the breeding process. Septima revealed enhanced tolerance with respect to Quintus as indicated by higher values of morphophysiological characteristics (above-ground biomass, leaf length, osmotic potential per full water saturation) and rel. abundance of proteins involved in mitochondrial respiration and ATP biosynthesis.
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Project description:The naked mole-rat (NMR; Heterocephalus glaber) has recently gained considerable attention in the scientific community for its unique potential to unveil novel insights in the fields of medicine, biochemistry, and evolution. NMRs exhibit unique adaptations that include protracted fertility, cancer resistance, eusociality, and anoxia. This suite of adaptations is not found in other rodent species, suggesting that interrogating conserved and accelerated regions in the NMR genome will find regions of the NMR genome fundamental to their unique adaptations. However, the current NMR genome assembly has limits that make studying structural variations, heterozygosity, and non-coding adaptations challenging. We present a complete diploid naked-mole rat genome assembly by integrating long-read and 10X-linked read genome sequencing of a male NMR and its parents, and Hi-C sequencing in the NMR hypothalamus (N=2). Reads were identified as maternal, paternal or ambiguous (TrioCanu). We then polished genomes with Flye, Racon and Medaka. Assemblies were then scaffolded using the following tools in order: Scaff10X, Salsa2, 3d-DNA, Minimap2-alignment between assemblies, and the Juicebox Assembly Tools. We then subjected the assemblies to another round of polishing, including short-read polishing with Freebayes. We assembled the NMR mitochondrial genome with mitoVGP. Y chromosome contigs were identified by aligning male and female 10X linked reads to the paternal genome and finding male-biased contigs not present in the maternal genome. Contigs were assembled with publicly available male NMR Fibroblast Hi-C-seq data (SRR820318). Both assemblies have their sex chromosome haplotypes merged so that both assemblies have a high-quality X and Y chromosome. Finally, assemblies were evaluated with Quast, BUSCO, and Merqury, which all reported the base-pair quality and contiguity of both assemblies as high-quality. The assembly will next be annotated by Ensembl using public RNA-seq data from multiple tissues (SRP061363). Together, this assembly will provide a high-quality resource to the NMR and comparative genomics communities.
2022-06-27 | E-MTAB-11830 | biostudies-arrayexpress
Project description:The naked mole-rat (NMR; Heterocephalus glaber) has recently gained considerable attention in the scientific community for its unique potential to unveil novel insights in the fields of medicine, biochemistry, and evolution. NMRs exhibit unique adaptations that include protracted fertility, cancer resistance, eusociality, and anoxia. This suite of adaptations is not found in other rodent species, suggesting that interrogating conserved and accelerated regions in the NMR genome will find regions of the NMR genome fundamental to their unique adaptations. However, the current NMR genome assembly has limits that make studying structural variations, heterozygosity, and non-coding adaptations challenging. We present a complete diploid naked-mole rat genome assembly by integrating long-read and 10X-linked read genome sequencing of a male NMR and its parents, and Hi-C sequencing in the NMR hypothalamus (N=2). Reads were identified as maternal, paternal or ambiguous (TrioCanu). We then polished genomes with Flye, Racon and Medaka. Assemblies were then scaffolded using the following tools in order: Scaff10X, Salsa2, 3d-DNA, Minimap2-alignment between assemblies, and the Juicebox Assembly Tools. We then subjected the assemblies to another round of polishing, including short-read polishing with Freebayes. We assembled the NMR mitochondrial genome with mitoVGP. Y chromosome contigs were identified by aligning male and female 10X linked reads to the paternal genome and finding male-biased contigs not present in the maternal genome. Contigs were assembled with publicly available male NMR Fibroblast Hi-C-seq data (SRR820318). Both assemblies have their sex chromosome haplotypes merged so that both assemblies have a high-quality X and Y chromosome. Finally, assemblies were evaluated with Quast, BUSCO, and Merqury, which all reported the base-pair quality and contiguity of both assemblies as high-quality. The assembly will next be annotated by Ensembl using public RNA-seq data from multiple tissues (SRP061363). Together, this assembly will provide a high-quality resource to the NMR and comparative genomics communities.
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Project description:Porcine 60K BeadChip genotyping arrays (Illumina) are increasingly being applied in pig genomics to validate SNPs identified by re-sequencing or assembly-versus-assembly method. Here we report that more than 98% SNPs identified from the porcine 60K BeadChip genotyping array (Illumina) were consistent with the SNPs identified from the assembly-based method. This result demonstrates that whole-genome de novo assembly is a reliable approach to deriving accurate maps of SNPs.
2016-07-05 | GSE83910 | GEO