The genome sequence of the Common Carder Bee, Bombus pascuorum (Scopoli, 1763)

Crowley, Liam M.; Sivell, Olga; Sivell, Duncan

doi:10.12688/wellcomeopenres.19251.1

Cited by 5 publications

(3 citation statements)

References 22 publications

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“…Read data were aligned using PALEOMIX v1.2.14 (Schubert et al 2014) to BomLapEIv1 (https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_936014575.1/) and BomPasc1.1 (Crowley et al 2023) after using AdapterRemoval/2.3.1 (Schubert et al 2016) and the mem algorithm as implemented in BWA/0.7.17 (Li 2013). Only reads with a minimum MapQ value of 15 were retained and considered endogenous.…”

Section: Methodsmentioning

confidence: 99%

A fast and inexpensive plate-based NGS library preparation method for insect genomics

Cobb,

de Muinck,

Kollias

et al. 2023

Preprint

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Entomological sampling and storage conditions often prioritise efficiency, practicality and conservation of morphological characteristics, and may therefore be suboptimal for DNA preservation. This practice can impact downstream molecular applications, such as the generation of high-throughput genomic libraries, which often requires substantial DNA input amounts. Here, we investigate a fast and economical Tn5 transposase tagmentation-based library preparation method optimised for 96-well plates and low yield DNA extracts from insect legs stored under different conditions. Using a standardised input of 6ng DNA, library preparation costs were significantly reduced through the 6-fold dilution of a commercially available tagmentation enzyme. Costs were further suppressed by direct post-amplification pooling, skipping quality assessment of individual libraries. We find that reduced DNA yields associated with ethanol-based storage do not impede overall sequencing success. Furthermore, we find that the efficiency of tagmentation-based library preparation can be improved by thorough post-amplification bead clean-up which selects against both short and large DNA fragments. By lowering data generation costs, broadening the scope of whole genome studies to include low yield DNA extracts and increasing throughput, we expect this protocol to be of significant value for a range of applications in the field of insect genomics.

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Section: Methodsmentioning

confidence: 99%

A fast and inexpensive plate-based NGS library preparation method for insect genomics

Cobb,

de Muinck,

Kollias

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…Read data were aligned using PALEOMIX v1.2.14 [33] to BomLapEIv1 (https://www.ncbi. nlm.nih.gov/datasets/genome/GCA_936014575.1/) and BomPasc1.1 [34] after using Adapter-Removal/2.3.1 [35] and the mem algorithm as implemented in BWA/0.7.17 [36]. Only reads with a minimum MapQ value of 15 were retained and considered endogenous.…”

Section: Post-amplification Clean-up and Sequencingmentioning

confidence: 99%

High-throughput sequencing of insect specimens with sub-optimal DNA preservation using a practical, plate-based Illumina-compatible Tn5 transposase library preparation method

Cobb,

de Muinck,

Kollias

et al. 2024

PLoS ONE

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Entomological sampling and storage conditions often prioritise efficiency, practicality and conservation of morphological characteristics, and may therefore be suboptimal for DNA preservation. This practice can impact downstream molecular applications, such as the generation of high-throughput genomic libraries, which often requires substantial DNA input amounts. Here, we use a practical Tn5 transposase tagmentation-based library preparation method optimised for 96-well plates and low yield DNA extracts from insect legs that were stored under sub-optimal conditions for DNA preservation. The samples were kept in field vehicles for extended periods of time, before long-term storage in ethanol in the freezer, or dry at room temperature. By reducing DNA input to 6ng, more samples with sub-optimal DNA yields could be processed. We matched this low DNA input with a 6-fold dilution of a commercially available tagmentation enzyme, significantly reducing library preparation costs. Costs and workload were further suppressed by direct post-amplification pooling of individual libraries. We generated medium coverage (>3-fold) genomes for 88 out of 90 specimens, with an average of approximately 10-fold coverage. While samples stored in ethanol yielded significantly less DNA compared to those which were stored dry, these samples had superior sequencing statistics, with longer sequencing reads and higher rates of endogenous DNA. Furthermore, we find that the efficiency of tagmentation-based library preparation can be improved by a thorough post-amplification bead clean-up which selects against both short and large DNA fragments. By opening opportunities for the use of sub-optimally preserved, low yield DNA extracts, we broaden the scope of whole genome studies of insect specimens. We therefore expect these results and this protocol to be valuable for a range of applications in the field of entomology.

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“…The genome of the honeybee was among the first genomes available for any insect (Honeybee Genome Sequencing Consortium 2006). Since then, most of the genomes of bees have been generated with a focus on the evolution of sociality (e.g., (Elsik et al 2014;Sadd et al 2015;Jones et al 2023;Kapheim et al 2015;Kocher et al 2013;Rehan et al 2016;Crowley et al 2023)). Only recently additional solitary species became available (e.g.…”

Section: Introductionmentioning

confidence: 99%

Reference genome sequence of the solitary beeCamptopoeum frieseiMocsáry, 1894 (Hymenoptera, Andrenidae)

Stolle,

Guiglielmoni,

Kirangwa

et al. 2023

Preprint

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Bees are major pollinators of flowering plants and thus are important ecosystem service providers for natural habitats and crops. Evolution led to a wide range of adaptations in behaviors, morphology and ecological traits. Many plants rely on specialized bee species for pollination events, and so this interdependence can make them increasingly vulnerable to ongoing threats of habitat loss and pesticide exposure. Studying the genomes of bee species across different life histories and ecological specializations can help understand the evolution of these traits more generally, but also inform conservation efforts forCamptopoeum frieseispecifically.Here, we present the reference genome of the solitary beeCamptopoeum friesei(Arthropoda; Insecta; Hymenoptera; Andrenidae).C. frieseiis highly dependent on steppe habitats where it nests in saline soils. Further, it is highly specialized (oligolectic) on a few Asteraceae:CentaureaandCirsium, in particular onCentaurea stoebe. As a consequence of its high specialization level, it is of its ecological niche with an extremely scattered and rare habitat,C. frieseiis highly threatened in central Europe, albeit local aggregations can be rich in individuals.The high-quality genome assembly for the colourful beeCamptopoeum frieseiwas generated using long-read PacBio HiFi in combination with chromatin conformation capture (Hi-C) sequencing. The genome spans 367.7 megabases (Mb), N50 of 25.2 Mb. The majority of the assembly is scaffolded into 10 chromosomes and harbours ∼40% repeats.Species taxonomyEukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Anthophila; Andrenidae; Panurginae; Panurgini;Camptopoeum frieseiMocsáry, 1894 (NCBI:txid2918745)

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The genome sequence of the Common Carder Bee, Bombus pascuorum (Scopoli, 1763)

Cited by 5 publications

References 22 publications

A fast and inexpensive plate-based NGS library preparation method for insect genomics

A fast and inexpensive plate-based NGS library preparation method for insect genomics

High-throughput sequencing of insect specimens with sub-optimal DNA preservation using a practical, plate-based Illumina-compatible Tn5 transposase library preparation method

Reference genome sequence of the solitary beeCamptopoeum frieseiMocsáry, 1894 (Hymenoptera, Andrenidae)

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