Project description:In daily practice biomolecules are usually extracted with their own specific protocols for downstream omics analysis. However, when sample material is limited, an all-in-one strategy is preferable. DNA, RNA and proteins can be isolated with phenol guanidine thiocyanate based extraction, yet lysis with Urea is the accepted standard for phosphoproteomic applications. Here we compared Urea with RNA-Bee mediated protein extraction for use in mass spectrometry (MS) based phosphoproteomics analysis of cells and tissues. We profile the DNA damage response after ionizing irradiation of U2OS cells as proof of principle for cultured human cells as well as mouse liver and three different human tissues. We show high overlap and similarity of phosphosite data and kinase activity for RNA-bee extraction when compared to standard Urea approach. Phenol guanidine thiocyanate lysis might thus be an appropriate way for multi-omics or MS profiling workflows in order to obtain several data types from a single sample.

2021-04-22 | PXD023665 | Pride

Colletes gigas

Project description:Colletes gigas Genome sequencing

| PRJNA768143 | ENA

Abundant small RNAs in the reproductive tissues of the honey bee, Apis mellifera, are a plausible mechanism for epigenetic inheritance and parental manipulation of gene expression

Project description:Here we present the first characterisation of small RNAs in honey bee reproductive tissues. We conclude that small RNAs are likely to play an integral role in honey bee gametogenesis and reproduction and provide a plausible mechanism for parent-of origin-effects on gene expression and reproductive physiology. present in honey bee reproductive tissues: ovaries, spermatheca, semen, fertilised and unfertilised eggs, and testes.

2022-04-13 | GSE182720 | GEO

The First Draft Genome of the Plasterer Bee Colletes gigas (Hymenoptera: Colletidae: Colletes).

Project description:Despite intense interest in bees, no genomes are available for the bee family Colletidae. Colletes gigas, one of the largest species of the genus Colletes in the world, is an ideal candidate to fill this gap. Endemic to China, C. gigas has been the focus of studies on its nesting biology and pollination of the economically important oil tree Camellia oleifera, which is chemically defended. To enable deeper study of its biology, we sequenced the whole genome of C. gigas using single-molecule real-time sequencing on the Pacific Bioscience Sequel platform. In total, 40.58 G (150×) of long reads were generated and the final assembly of 326 scaffolds was 273.06 Mb with a N50 length of 8.11 Mb, which captured 94.4% complete Benchmarking Universal Single-Copy Orthologs. We predicted 11,016 protein-coding genes, of which 98.50% and 84.75% were supported by protein- and transcriptome-based evidence, respectively. In addition, we identified 26.27% of repeats and 870 noncoding RNAs. The bee phylogeny with this newly sequenced colletid genome is consistent with available results, supporting Colletidae as sister to Halictidae when Stenotritidae is not included. Gene family evolution analyses identified 9,069 gene families, of which 70 experienced significant expansions (33 families) or contractions (37 families), and it appears that olfactory receptors and carboxylesterase may be involved in specializing on and detoxifying Ca. oleifera pollen. Our high-quality draft genome for C. gigas lays the foundation for insights on the biology and behavior of this species, including its evolutionary history, nesting biology, and interactions with the plant Ca. oleifera.

| S-EPMC7313665 | biostudies-literature

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