Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Shotgun metagenomics of honey DNA: evaluation of a methodological approach to describe a multi-kingdom honey bee derived environmental DNA signature

ABSTRACT: Shotgun metagenomics of honey DNA: evaluation of a methodological approach to describe a multi-kingdom honey bee derived environmental DNA signature

PROVIDER: PRJEB26884 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR2592240.fastq.gz	Fastqsanger.gz
	ERR2592241.fastq.gz	Fastqsanger.gz

Items per page:

1 - 2 of 2

Similar Datasets

Shotgun metagenomics of honey DNA: Evaluation of a methodological approach to describe a multi-kingdom honey bee derived environmental DNA signature.

Project description:Honey bees are considered large-scale monitoring tools due to their environmental exploration and foraging activities. Traces of these activities can be recovered in the honey that also may reflect the hive ecological micro-conditions in which it has been produced. This study applied a next generation sequencing platform (Ion Torrent) for shotgun metagenomic analysis of honey environmental DNA (eDNA). The study tested a methodological framework to interpret DNA sequence information useful to describe the complex ecosystems of the honey bee colony superorganism, its pathosphere and the heterogeneity of the agroecological environments and environmental sources that left DNA marks in the honey. Analysis of two honeys reported sequence reads from five main organism groups (kingdoms or phyla): arthropods (that mainly included reads from Apis mellifera, several other members of the Hymenotpera, in addition to members of the Diptera, Coleoptera and Lepidoptera, as well as aphids and mites), plants (that clearly confirmed the botanical origin of the two honeys, i.e. orange tree blossom and eucalyptus tree blossom honeys), fungi and bacteria (including common hive and honey bee gut microorganisms, honey bee pathogens and plant pathogens), and viruses (which accounted for the largest number of reads in both honeys, mainly assigned to Apis mellifera filamentous virus). The shotgun metagenomic approach that was used in this study can be applied in large scale experiments that might have multiple objectives according to the multi-kingdom derived eDNA that is contained in the honey.

| S-EPMC6209200 | biostudies-literature

Hologenomic signatures from honey

Project description:Shotgun metagenomic analysis of honey DNA at high sequencing depth can describe a multi-kingdom and multi-level honey bee derived environmental DNA signature and the honey bee hologenome complexity

| PRJEB36075 | ENA

Shotgun sequencing of honey DNA can describe honey bee derived environmental signatures and the honey bee hologenome complexity.

Project description:Honey bees are large-scale monitoring tools due to their extensive environmental exploration. In their activities and from the hive ecosystem complex, they get in close contact with many organisms whose traces can be transferred into the honey, which can represent an interesting reservoir of environmental DNA (eDNA) signatures and information useful to analyse the honey bee hologenome complexity. In this study, we tested a deep shotgun sequencing approach of honey DNA coupled with a specifically adapted bioinformatic pipeline. This methodology was applied to a few honey samples pointing out DNA sequences from 191 organisms spanning different kingdoms or phyla (viruses, bacteria, plants, fungi, protozoans, arthropods, mammals). Bacteria included the largest number of species. These multi-kingdom signatures listed common hive and honey bee gut microorganisms, honey bee pathogens, parasites and pests, which resembled a complex interplay that might provide a general picture of the honey bee pathosphere. Based on the Apis mellifera filamentous virus genome diversity (the most abundant detected DNA source) we obtained information that could define the origin of the honey at the apiary level. Mining Apis mellifera sequences made it possible to identify the honey bee subspecies both at the mitochondrial and nuclear genome levels.

| S-EPMC7283317 | biostudies-literature

Intronic Non-CG DNA Hydroxymethylation and Alternative mRNA Splicing in Honey Bees

Project description:Honey bee non-CG DNA hydroxymethylation is enriched in the introns, which supplements previous findings that honey bee CG DNA methylation is enriched in exons.

2013-09-19 | GSE50990 | GEO

Identification of Mblk-1-binding DNA regions in honey bee brains by ChIP-seq.

Project description:Examination of Mblk-1-binding DNA regions in honey bee adult mushroom bodies(MBs) and pupal whole brains

2022-12-14 | GSE173409 | GEO

Intronic Non-CG DNA Hydroxymethylation and Alternative mRNA Splicing in Honey Bees

Project description:Honey bee non-CG DNA hydroxymethylation is enriched in the introns, which supplements previous findings that honey bee CG DNA methylation is enriched in exons. Bisulfite sequencing combined with Pvu-Seq to distinguish 5-methylcytosine from 5-hydroxymethylcytosine and RNA-Seq

2013-09-19 | E-GEOD-50990 | biostudies-arrayexpress

Apis mellifera population genomics using honey DNA.

Project description:Apis mellifera population genomics using honey DNA.

| PRJEB55169 | ENA

Honey

Project description:Honey Metagenome

| PRJNA1364200 | ENA

CRISPR-induced deletion of honey bee orco gene [DNA]

Project description:Honey bee embryos were injected either with a CRISPR contruct targeting the orco gene or an injection buffer control. RNA-Sequencing was performed on the antennal mRNA from adult bees within 24 hours of eclosion.

2020-10-09 | GSE147713 | GEO

Honey

Project description:Microbial diversity in honey

| PRJNA943093 | ENA