This study generated genetic 'metabarcode' data using high-throughput sequencing to characterize pollen foraging behavior of the endangered rusty-patched bumblebee, Bombus affinis. Pollen samples were collected primarily from forest meadow habitats in the Appalachian piedmont of the eastern United States, specifically within the states of Virginia and West Virginia. Three additional samples from the upper Midwest were also included for comparison.
This data release consists of three tab-delimited files and a file of DNA sequences: 1) sample.metadata.txt includes sample identifiers and the accessions they have been 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.nlm.nih.gov. Alternatively, the BioProject accession PRJNA1235776 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 herein. 2) ITS1.raw.pollen.counts.txt includes the inferred taxon counts at the internal transcribed spacer 1 (ITS1) genetic locus, i.e. number of ITS1 sequences in a sample 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. 3) ITS2.raw.pollen.counts.txt includes the inferred taxon counts at the internal transcribed spacer 2 (ITS2) genetic locus, i.e. number of ITS2 sequences in a sample attributable to each identified taxon in each sample. The file is identical in structure to the ITS1 file. 4) reference.db.fas contains the plant reference DNA sequences used for taxonomic assignment of the pollen sample sequences.