High-throughput methods for identification of pollinator taxa are desirable to improve our understanding of pollinator distributions, population trends, and ecology. Genetic sequencing of taxonomically informative 'barcode' loci is one high-throughput strategy, which can be applied to individual specimens using Sanger technology and to complex mixtures using metabarcoding technology. This study generated Sanger sequencing data from morphologically identified specimens and metabarcoding data derived from pooled tissues. This data release consists of several files: 1. sample.metadata.txt, which contains sampling metadata and identifiers linking to sequence data that has been deposited in the Sequence Read Archive of the National Center for Biotechnology Information (NCBI). This database is authoritative and comprehensive for sharing high-throughput sequence data produced with public funds. All NCBI-derived accessions listed in the file can be searched at www.ncbi.nlm.nih.gov to retrieve sample and sequence information 2. raw.counts.txt, which is a tab-delimited table of counts of individual metabarcode sequences that are attributed to each detected bee genus. 3. BeeSangerSequencesFASTA.txt, which is a text document in FASTA format containing the DNA sequences obtained from the individual specimens using Sanger sequencing technology. 4. reference.sequences.fasta, which is a text document in FASTA format containing the DNA sequences obtained from public databases for taxonomic assignment of metabarcode sequences as described in the process steps.

,A native solitary bee to North America, the blue orchard bee (Osmia lignaria Say, Hymenoptera: Megachilidae) is a crucial pollinator for orchard crops such as apples, almonds, and cherries. Osmia lignaria is often managed commercially and sold to complement honey bee pollination services.,We collected data following an accidental drop of developing immature bees inside their cocoons. These bees were part of a larger experiment performed in 2020. On June 17, 2020, bees were dropped approximately one meter onto a linoleum floor at the USDA-ARS-PWA Pollinating Insect Research Unit in Logan, Utah, USA. Developing bees were in gelatin capsules and attached to a sticky board for X-ray imaging. Using a board from the same study that had not fallen, we compared survival, life stages, and bodily injuries to document the effects of dropping immature O. lignaria a short distance.,Our research highlights the risks of handling immature O. lignaria during metamorphosis. Our data provides valuable information for bee managers and researchers about the risks of physical disturbances during critical developmental stages, which could affect bee survival and pollination services in orchards.,Key findings include: (1) Near-complete mortality of developing bees before the adult molt stage, (2) Insights into the vulnerability of O. lignaria during immature developmental stages, even when inside cocoons, and (3) Documentation of how mechanical injury during immature development impacts survival.,The dataset provides counts of bees in different life stages and conditions, including: (1) Life status (alive or dead) at cocoon completion, pupation, and adult molt stages, (2) Sex determination for bees that reached adulthood (male or female), (3) Final life stage reached (prepupa, pupa, or adult), and (4) Body condition after the fall (malformed, melanized, no observable change, or partially melanized).,Additional variables in the dataset include: (1) Sample identifiers, treatment groups, and X-ray board identifiers from the original experiment and (2) Whether the board was dropped or not.,Abbreviations and acronyms in the dataset,,

This study generated genetic 'metabarcode' data using high-throughput sequencing to characterize pollen foraging behavior of pollinating bee species on managed field habitat within units of the National Park Service. Specimens were collected within parks of the National Capital Region from 2021-2023 and subsequently identified to species or genus. DNA was then extracted from specimens using leg samples if pollen was adherent to the corbiculae ("pollen baskets") of corbiculate bees, otherwise using whole-body samples. 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 PRJNA1236404 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) ITS2.raw.pollen.counts.txt includes the inferred taxon counts at the ITS2 locus, i.e. number of ITS2 sequences in a sample attributable to each identified taxon in each sample. 3. potential.contaminants.txt lists plant taxa that were over-represented in negative controls samples within a particular sequence run. Values for these plant taxa in these runs should either be zeroed-out or adjusted based on a statistical model to account for potential sample contamination. Censoring data based on results in negative controls is a standard practice in metabarcoding. Many samples in this study were very small and/or had no visible pollen, which increases the potential for contamination as the endogenous DNA concentration is expected to be very low in these cases. 3) reference.db.fas contains the plant reference DNA sequences used for taxonomic assignment of the pollen sample sequences.

,The blue orchard bee (Osmia lignaria Say, Hymenoptera: Megachilidae) is a native solitary bee in North America. This pollinator species is crucial for orchard pollination, primarily apples, almonds, and cherries. Osmia lignaria is an increasingly managed commercial species sold to supplement honey bee pollination services or used alone. Consistent protocols to rear O. lignaria and other above-ground nesting solitary bee species are lacking. This makes comparisons to social species, such as honey bees and bumble bees, difficult, and data comparisons between solitary bee species are incompatible.,We collected data from two study years, comprising three studies, where we followed O. lignaria’s development from grafting of eggs or first instars in the summer to adult emergence the following spring. The data presented were control bees that were fed sterilized sham inoculate treatments in a larger pathogen-pesticide study.,Adult O. lignaria were first released into an apple orchard in Logan, Utah, USA, where they were allowed to pollinate and mate, and females created nests with provisioned offspring. We then took completed nests to the laboratory, where they were opened to obtain O. lignaria-collected provisions (pollen+nectar) and eggs/first instars. We retained these provisions and eggs/first instars in our rearing studies and to evaluate our protocol methods. We then grafted eggs/first instars onto homogenized provisions on a graft date inside 3-D printed well plates. 3-D printed well plates were desired for our protocol to provide enough space to allow O. lignaria to complete their life cycle to adult emergence the following spring.,Our research proves that O. lignaria can be reared in 3-D-printed well plates and emerge as adults the following spring. This can allow researchers to evaluate the chronic effects of pathogen and/or pesticide exposure on immature solitary bees. Alterations to the protocol, including different kinds of treatment types, can allow researchers to evaluate synergisms, antagonisms, or additive effects that may influence the survival, development, or weight metrics of O. lignaria. The protocol is replicable and could be adapted for other above-ground nesting solitary bee species.,Our O. lignaria rearing protocol is provided in full detail at: dx.doi.org/10.17504/protocols.io.eq2lyj4qplx9/v2,Key findings include: (1) Determination of development in fine detail and near-exact dates for individual developing O. lignaria inside 3-D printed well plates, (2) a 3-D print file that can be altered for other species if desired, (3) Number of days between life stages and the total number of days to each life stage, (4) Life status at various immature and mature life stages, (5) Sex determination for bees that reached adulthood (male or female), (6) Final life stage reached (larva, prepupa, pupa, or live/dead adult), (7) Suggested weight metrics evaluate for O. lignaria, and (8) Different winter diapause durations may produce variable emergence and weight loss results from year-to-year or study-to-study.,Additional variables in the dataset include: (1) Study year, (2) Study name, (3) Sample identifier), (4) Provision batch, (5) Graft date, and (6) Various dates that reflect temperature and relative humidity (RH) durations.,Abbreviations and acronyms in the “RAWdata” dataset,Abbreviations and acronyms in the "Death_graft" dataset: The number of samples per year and study that did not survive past the first instar stage. The second instar stage was used to standardize survival and development since they begin to feed on provisions. Eggs and first instars were used as the initial grafting life stage because they are non-feeding stages of O. lignaria; therefore, they should be excluded from analyses unless desired.,,

,The small hive beetle (Aethina tumida, ATUMI) is an invasive parasite of bee colonies. ATUMI feeds on both fruits and bee nest products, facilitating its spread and increasing its impact on honey bees and other pollinators. The ATUMI genome has been sequenced and annotated, providing the first genomic resources for this species and for the Nitidulidae, a beetle family that is closely related to the extraordinarily species-rich clade of beetles known as the Phytophaga. ATUMI thus provides a contrasting view as a neighbor for one of the most successful known animal groups. A robust genome assembly and a gene set possessing 97.5% of the core proteins known from the holometabolous insects are presented. The ATUMI genome encodes fewer enzymes for plant digestion than the genomes of wood-feeding beetles, but nonetheless shows signs of broad metabolic plasticity. Gustatory receptors are few in number compared to other beetles, especially receptors with known sensitivity (in other beetles) to bitter substances. In contrast, several gene families implicated in detoxification of insecticides and adaptation to diverse dietary resources show increased copy numbers. The presence and diversity of homologs involved in detoxification differs substantially from the bee hosts of ATUMI. Results provide new insights into the genomic basis for local adaption and invasiveness in ATUMI, and a blueprint for control strategies that target this pest without harming their honey bee hosts. A minimal set of gustatory receptors is consistent with the observation that, once a host colony is invaded, food resources are predictable. Unique detoxification pathways and pathway members can help identify which treatments might control this species even in the presence of honey bees, which are notoriously sensitive to pesticides.,,

,A high-quality reference genome is an essential tool for applied and basic research on arthropods. Long-read sequencing technologies may be used to generate more complete and contiguous genome assemblies than alternate technologies, however, long-read methods have historically had greater input DNA requirements and higher costs than next generation sequencing, which are barriers to their use on many samples. Here, we present a 2.3 Gb de novo genome assembly of a field-collected adult female Spotted Lanternfly (Lycorma delicatula) using a single PacBio SMRT Cell. The Spotted Lanternfly is an invasive species recently discovered in the northeastern United States, threatening to damage economically important crop plants in the region. The DNA from one individual female specimen collected in Reading, Berks County, Pennsylvania was used to make one standard, size-selected library with an average DNA fragment size of ~20 kb. The library was run on one Sequel II SMRT Cell 8M, generating a total of 132 Gb of long-read sequences, of which 82 Gb were from unique library molecules, representing approximately 38x coverage of the genome. The assembly had high contiguity (contig N50 length = 1.5 Mb), completeness, and sequence level accuracy as estimated by conserved gene set analysis (96.8% of conserved genes both complete and without frame shift errors). Further, it was possible to segregate more than half of the diploid genome into the two separate haplotypes. The assembly also recovered two microbial symbiont genomes known to be associated with L. delicatula, each microbial genome being assembled into a single contig. We demonstrate that field-collected arthropods can be used for the rapid generation of high-quality genome assemblies, an attractive approach for projects on emerging invasive species, disease vectors, or conservation efforts of endangered species.,Supporting files for the manuscript "A High-Quality Genome Assembly from a Single, Field-collected Spotted Lanternfly (Lycorma delicatula) using the PacBio Sequel II System", include several intermediate versions of the assembly (raw output from Falcon, raw output from Falcon unzip, etc.) as well as the final assembly primary contigs and haplotigs (for the regions of the genome that were phased).,,

,These data represent V. destructor genomic annotations to be used for evolutionary comparison with other arthropods.,The ectoparasitic mite Varroa destructor has emerged as the primary pest of domestic honey bees (Apis mellifera). Here we present an initial survey of the V. destructor genome carried out to advance our understanding of Varroa biology and to identify new avenues for mite control. This sequence survey provides immediate resources for molecular and population-genetic analyses of Varroa-Apis interactions and defines the challenges ahead for a comprehensive Varroa genome project.,

,The Baylor College of Medicine recently sequenced and annotated the Homalodisca vitripennis genome as part of the i5k pilot project.,The Glassy-winged sharpshooter, GWSS, (Homalodisca vitripennis) [Hemiptera: Cicadellidae], occurs naturally within the southern United States. Once restricted to the southeastern states, it was accidentally spread across the south into California. The GWSS is a voracious feeder, and can fly long distances, preferring to feed upon cultivated crops, ie. Grapevine, fruit trees, and in the nymphal stages many weeds and grasses. The GWSS is a serious threat to the viticulture industry as the primary vector of the plant-infecting bacterium, Xylella fastidiosa, Xf. The GWSS feeds on a diverse number of plants, during which the bacteria can infect many tree fruit, nut, vine, and woody ornamental crops. Glassy-winged Sharpshooter adults are ½ inch (13mm) long being fairly large for the Sharpshooter leafhopper family of insects. Sharpshooters use an ovipositor to lay eggs inside of the underside of leaves. The Sharpshooter will lay its eggs on almost any plant including cactus. The egg masses are usually composed of 10-20 eggs, but can lay more or as few as 1. Most of the egg masses have a waxy coating of brocosomes around the eggs for protection. The nymphs (5 instars) do not have wings, but develop wing pads in the 5th instar and are generally smaller than the adults, ranging in size from .07 inches (2 mm) to nearly ½ inch (13mm) long. The nymphs have very distinct red eyes. The Sharpshooter can consume about 300 times its own weight in fluids from the xylem vessels of the plants upon which it feeds, thus producing copious amounts of excreta fluid.,This dataset presents the Homalodisca vitripennis genome v1.0. This assembly version is the pre-release version, prior to filtering and quality control by the National Center for Biotechnology Information's GenBank resource (https://www.ncbi.nlm.nih.gov/assembly/GCA_000696855.1). Assembly method details will be available in a forthcoming publication.,If you wish to use this dataset, please follow the Baylor College of Medicine's conditions for data use: https://www.hgsc.bcm.edu/bcm-hgsc-conditions-use,

The Melampsora lini genome was sequenced to improve its genome assembly. PacBio HiFi and Hi-C data was generated as well as RNA-seq data.

The data being released were part of a project funded by the Section 40804 Ecosystem Restoration of the Bipartisan Infrastructure Law (PL-117-58) in support of advancing a national revegetation effort. Data included are from a series of DNA degradation experiments targeting the mitochondrial 16S rRNA gene of the European honeybee (Apis mellifera). This study sought to determine how various environmental conditions may affect eDNA left behind on flowers by bee visitation and thus the impact that may have on monitoring bees via eDNA. The experiments occurred in the laboratory and in the natural environment in 2022 and 2023 using store-bought potted or natural flowers spiked with Apis mellifera DNA. Flower samples were processed to elute DNA, DNA was extracted, and Apis mellifera quantified by qPCR. More information about the individual degradation experiments can be found in the Supplemental Information section.