Amplicon sequencing of pollen foraged by Bombus affinis for compositional analysis
Dates
Publication Date
2024-01-26
Start Date
2020-07-15
End Date
2020-08-10
Citation
Cornman, R.S., Iwanowicz, D., and Otto, C.R., 2024, Amplicon sequencing of pollen foraged by Bombus affinis for compositional analysis: U.S. Geological Survey data release, https://doi.org/10.5066/P14UMYJM.
Summary
This study generated genetic 'barcode' data using high-throughput sequencing to characterize pollen collected by the endangered rusty-patched bumblebee, Bombus affinis. Pollen samples were associated with a single Bombus affinis colony within a structure in Red Wing, Minnesota, USA, as previously described by Boone et al. (2022). This data release consists of two tab-delimited files: 1) sample.metadata.txt includes sample identifiers and accessions assigned by the National Center for Biotechnology Information (NCBI), the authoritative repository for publicly funded genetic data in the United States. These accessions can be used individually to obtain raw sequencing data or sample information at www.ncbi.nih.nlm.gov. Alternatively, [...]
Summary
This study generated genetic 'barcode' data using high-throughput sequencing to characterize pollen collected by the endangered rusty-patched bumblebee, Bombus affinis. Pollen samples were associated with a single Bombus affinis colony within a structure in Red Wing, Minnesota, USA, as previously described by Boone et al. (2022).
This data release consists of two tab-delimited files:
1) sample.metadata.txt includes sample identifiers and accessions assigned by the National Center for Biotechnology Information (NCBI), the authoritative repository for publicly funded genetic data in the United States. These accessions can be used individually to obtain raw sequencing data or sample information at www.ncbi.nih.nlm.gov. Alternatively, the BioProject accession PRJNA1045705 can be searched to retrieve the full set of data and sample accessions listed in the file. Entity and attribute metadata are provided for this file.
2) taxon.counts.txt includes the inferred counts, or number of sequences, attributable to each identified taxon in each sample. Taxa are in rows and sequencing libraries are in columns. Taxa are listed by scientific name and the taxonomic rank of that scientific name. A numeric taxonomic identifier used by NCBI for each taxon is also provided, as the taxonomic identifier is unique in the NCBI databases whereas scientific names may not be. Entity and attribute data are not provided for this file due to its size and repetitive content.
Click on title to download individual files attached to this item.
Bombus.pollen.forage.xml Original FGDC Metadata
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21.99 KB
application/fgdc+xml
sample.metadata.txt
2.14 KB
text/plain
taxon.counts.txt
17.56 KB
text/plain
Purpose
The data were generated to assess the composition of pollen collected by worker Bombus affinis, to better understand species ecology. The data can be used to characterize the plant diversity in these environmental samples.
