Conservation genomics reveals pesticide and pathogen exposure in the declining bumblebee Bombus terricola
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ABSTRACT:
PROVIDER: PRJNA730495 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14567204_1.fastq.gz | Fastqsanger.gz | |||
| SRR14567204_2.fastq.gz | Fastqsanger.gz | |||
| SRR14567205_1.fastq.gz | Fastqsanger.gz | |||
| SRR14567205_2.fastq.gz | Fastqsanger.gz | |||
| SRR14567206_1.fastq.gz | Fastqsanger.gz |
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Project description:We use high-thoughput RNA sequencing to investigate the stressors experienced by the vulnerable Bombus terricola near agricultural areas.
2021-06-25 | GSE174536 | GEO
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Project description:Pesticides pose a potential threat to bee health, especially in combination with other stressors, like parasites. However, pesticide risk assessment tests them in isolation from other stresses. We tested acute oral doses of three pesticides - glyphosate, Amistar and sulfoxaflor - on the bumblebee, Bombus terrestris, alongside the gut parasite Crithidia bombi. We found no impact of any pesticide on parasite intensity and no impact of sulfoxaflor or glyphosate on survival or weight change. Amistar caused weight loss and 19-41% mortality. Haemoproteome analysis showed various protein dysregulations. The major pathways dysregulated are those involved in insect defences and immune responses, with Amistar having the strongest impact on these. Our results show that while no response can be seen at a whole organism level, MALDI BeeTyping® can detect effects. Mass spectrometry analysis of bee haemolymph represent a pertinent tool to evaluate the stressor impacts on bee health, even at the individual scale.
2023-02-09 | PXD039916 | Pride
Project description:In recent years, many pollinators have experienced large population declines, which threaten food security and the stability of natural ecosystems. Bumble bees are particularly important because their ability to "buzz" pollinate and tolerate cooler conditions make them critical pollinators for certain plants and regions. Here, we apply a conservation genomics approach to study the vulnerable Bombus terricola. We sequenced RNA from 30 worker abdomens, 18 of which were collected from agricultural sites and 12 of which were collected from nonagricultural sites. We found transcriptional signatures associated with exposure to insecticides, with gene expression patterns suggesting that bumble bees were exposed to neonicotinoids and/or fipronil-two compounds known to negatively impact bees. We also found transcriptional signatures associated with pathogen infections. In addition to the transcriptomic analysis, we carried out a metatranscriptomic analysis and detected five pathogens in the abdomens of workers, three of which are common in managed honey bee and bumble bee colonies. Our conservation genomics study provides functional support for the role of pesticides and pathogen spillover in the decline of B. terricola. We demonstrate that conservation genomics is an invaluable tool which allows researchers to quantify the effects of multiple stressors that impact pollinator populations in the wild.
| S-EPMC8457087 | biostudies-literature
Project description:Bumblebees (Hymenoptera: Apidae) are important pollinating insects that play pivotal roles in crop production and natural ecosystem services. To achieve a comprehensive profile of accessible chromatin regions and provide clues for all possible regulatory elements in the bumblebee genome, we did ATAC-seq for Bombus terrestris samples derived from its four developmental stages: egg, larva, pupa, and adult, respectively. The sequencing reads of ATAC-seq were mapped to B. terrestris reference genome, and its accessible chromatin regions were identified and characterized using bioinformatic methods. Our study will provide important resources not only for uncovering regulatory elements in the bumblebee genome, but also for expanding our understanding of bumblebee biology.
2020-10-02 | GSE151858 | GEO
Project description:The yellow-banded bumblebee Bombus terricola was common in North America but has recently declined and is now on the IUCN Red List of threatened species. The causes of B. terricola's decline are not well understood. Our objectives were to create a partial genome and then use this to estimate population data of conservation interest, and to determine whether genes showing signs of recent selection suggest a specific cause of decline. First, we generated a draft partial genome (contig set) for B. terricola, sequenced using Pacific Biosciences RS II at an average depth of 35×. Second, we sequenced the individual genomes of 22 bumblebee gynes from Ontario and Quebec using Illumina HiSeq 2500, each at an average depth of 20×, which were used to improve the PacBio genome calls and for population genetic analyses. The latter revealed that several samples had long runs of homozygosity, and individuals had high inbreeding coefficient F, consistent with low effective population size. Our data suggest that B. terricola's effective population size has decreased orders of magnitude from pre-Holocene levels. We carried out tests of selection to identify genes that may have played a role in ameliorating environmental stressors underlying B. terricola's decline. Several immune-related genes have signatures of recent positive selection, which is consistent with the pathogen-spillover hypothesis for B. terricola's decline. The new B. terricola contig set can help solve the mystery of bumblebee decline by enabling functional genomics research to directly assess the health of pollinators and identify the stressors causing declines.
| S-EPMC6095975 | biostudies-literature
Project description:Our aims in this study were: 1) to identify the miRNAs of the bumble bees Bombus terrestris and B. impatiens; 2) to compare the total numbers of miRNAs between both bumble bee species and between them and the honey bee, Apis mellifera; and 3) to test whether the sequences and expression patterns of miRNAs were conserved between species. To investigate each of these aims we used miRNA-seq (deep sequencing of miRNA-enriched libraries) in B. terrestris, and bioinformatics prediction programs to identify miRNAs in both Bombus species. We identified 131 miRNAs in B. terrestris, and 114 in B. impatiens; of these, 17 were new miRNAs that had not previously been sequenced in any species. We found a striking level of difference in the miRNAs present between Bombus and A. mellifera, with 103 miRNAs in A. mellifera not being present in the genomes of the two bumble bees. miRNA profiles of Bombus terrestris at two developmental stages in larvae. This submission represents 'Bombus terrestris' component of study.
2015-03-06 | E-GEOD-64512 | biostudies-arrayexpress
Project description:Our aims in this study were: 1) to identify the miRNAs of the bumble bees Bombus terrestris and B. impatiens; 2) to compare the total numbers of miRNAs between both bumble bee species and between them and the honey bee, Apis mellifera; and 3) to test whether the sequences and expression patterns of miRNAs were conserved between species. To investigate each of these aims we used miRNA-seq (deep sequencing of miRNA-enriched libraries) in B. terrestris, and bioinformatics prediction programs to identify miRNAs in both Bombus species. We identified 131 miRNAs in B. terrestris, and 114 in B. impatiens; of these, 17 were new miRNAs that had not previously been sequenced in any species. We found a striking level of difference in the miRNAs present between Bombus and A. mellifera, with 103 miRNAs in A. mellifera not being present in the genomes of the two bumble bees.
2015-03-06 | GSE64512 | GEO
Project description:The biological samples analyzed in this study were honey samples from the bumblebee B. terrestris. Commercially available Tripol hives used for pollination consist of three complete bumblebee colonies (Koppert Biological Systems). Four Tripol hives (12 colonies overall) were placed in the Crop Research Institute (Prague-Ruzyne, Czechia) at the time of rapeseed Brassica napus and apple tree flowering. Honey stores were manually collected into 50-mL sterile centrifuge tubes. Honey samples per colony were pooled. These 12 honey samples were analyzed using label-free nano-LC-MS/MS.
In addition, 3 bands excised from 1D-E SDS-PAGE were analyzed using nano-LC-MS/MS. Note that modification for analysis the bands was carbamidomethyl instead of MethylThio.
Combined.txt and used databases are provided.
2022-03-03 | MSV000088979 | MassIVE