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      Synchronised monitoring of plant and insect diversity: a case study using automated Malaise traps and DNA-based methods

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          Abstract

          The occurrence and distribution of insects and their possible associations with plant species are largely unknown in Germany and baseline data to monitor future trends are urgently needed. Using newly-designed automated Malaise trap multi-samplers, the occurrence of insect species and their potential associations with plants was monitored synchronously at two contrasting field sites in Germany: an urban botanical garden and a forest research station. Taxa were identified by metabarcoding of the insects and the plant traces present in the preservative ethanol of the Malaise trap samples. For comparison, a botanical survey was conducted in the vicinity of the traps. Across both sites, we identified a total of 1290 exact sequence variants (ESVs) assigned to Insecta , of which 205 are known to be pollinators. In the botanical garden, we detected the occurrence of 128 plant taxa, of which 41 also had one of their known insect pollinator species detected. Insect species richness was highest in May, mainly attributed to an increase in Diptera . These results present a case study of the applicability of automated sampling and DNA-based methods to monitor the timings of flowering and corresponding activity of plant-visiting insects.

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          DADA2: High resolution sample inference from Illumina amplicon data

          We present DADA2, a software package that models and corrects Illumina-sequenced amplicon errors. DADA2 infers sample sequences exactly, without coarse-graining into OTUs, and resolves differences of as little as one nucleotide. In several mock communities DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.
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            Cutadapt removes adapter sequences from high-throughput sequencing reads

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              BLAST+: architecture and applications

              Background Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings in the user-interface of the current command-line applications. Results We describe features and improvements of rewritten BLAST software and introduce new command-line applications. Long query sequences are broken into chunks for processing, in some cases leading to dramatically shorter run times. For long database sequences, it is possible to retrieve only the relevant parts of the sequence, reducing CPU time and memory usage for searches of short queries against databases of contigs or chromosomes. The program can now retrieve masking information for database sequences from the BLAST databases. A new modular software library can now access subject sequence data from arbitrary data sources. We introduce several new features, including strategy files that allow a user to save and reuse their favorite set of options. The strategy files can be uploaded to and downloaded from the NCBI BLAST web site. Conclusion The new BLAST command-line applications, compared to the current BLAST tools, demonstrate substantial speed improvements for long queries as well as chromosome length database sequences. We have also improved the user interface of the command-line applications.

                Author and article information

                Contributors
                Role: Writing - review and editingRole: Formal analysisRole: InvestigationRole: Visualization
                Role: Writing - original draftRole: Writing - review and editingRole: Project administrationRole: ResourcesRole: Visualization
                Role: ConceptualizationRole: Writing - review and editingRole: Funding acquisitionRole: Project administrationRole: Supervision
                Role: ConceptualizationRole: Writing - original draftRole: Writing - review and editingRole: Data curationRole: MethodologyRole: SupervisionRole: Validation
                Journal
                Biodivers Data J
                Biodivers Data J
                1
                urn:lsid:arphahub.com:pub:F9B2E808-C883-5F47-B276-6D62129E4FF4
                urn:lsid:zoobank.org:pub:245B00E9-BFE5-4B4F-B76E-15C30BA74C02
                Biodiversity Data Journal
                Pensoft Publishers
                1314-2836
                1314-2828
                2024
                30 July 2024
                : 12
                : e127669
                Affiliations
                [1 ] Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn Germany
                [2 ] University of Kassel, Kassel, Germany University of Kassel Kassel Germany
                Author notes
                Corresponding authors: Leighton J Thomas ( l.thomas@ 123456leibniz-lib.de ), Sarah J Bourlat ( S.Bourlat@ 123456leibniz-zfmk.de ).

                Academic editor: Paolo Biella

                Author information
                https://orcid.org/0000-0002-9145-9284
                https://orcid.org/0000-0003-0218-0298
                Article
                127669 24235
                10.3897/BDJ.12.e127669
                11303846
                39114129
                38e436aa-0a75-47b9-beb4-819b2d92f6eb
                Leighton J Thomas, Ameli Kirse, Hanna Raus, Kathrin Langen, Björn Nümann, Georg F. Tschan, Birgit Gemeinholzer, J. Wolfgang Wägele, Sarah J Bourlat

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 16 May 2024
                : 04 July 2024
                Page count
                Figures: 4, Tables: 2, References: 48
                Funding
                The project was funded by the German Federal Ministry of Education and Research (Bundesministerium für Bildung und Forschung), project number 16LC1903.
                Categories
                Research Article
                Coleoptera
                Diptera
                Hymenoptera
                Lepidoptera
                Mecoptera
                Biodiversity & Conservation
                Genetics
                Pollination ecology
                Central Europe
                Europe
                Germany

                metabarcoding,plant traces,plant-insect interaction,automated sampling,malaise trap,biomonitoring,phenology

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