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PubMed2026

"Not flying solo": phylogenetic identification and life-cycle insights of larval cestodes in the European flying squid Todarodes sagittatus (Cephalopoda: Ommastrephidae).

The European flying squid Todarodes sagittatus Lamarck is a widely distributed ommastrephid cephalopod in the Northeast Atlantic and Mediterranean Sea, yet its parasite fauna remains poorly documented in the Mediterranean Sea. In this study, two cestode larvae species infecting T. sagittatus from the Algerian coast (Western Mediterranean) were investigated using an integrative approach combining morphological observations and molecular analyses. A total of 63 squids were examined for parasitic infection. Cestodes in plerocercoid stage were detected in 31 individuals (prevalence of 46%), primarily located within the gastrointestinal tract, including the stomach, intestine, and caecum. Morphological features of the larvae were consistent with members of the order Phyllobothriidea but did not allow identification to the species level. Molecular analysis of the D1-D3 region of the 28S rDNA revealed two distinct larval lineages belonging to the genus Crossobothrium Linton, 1889. One lineage showed 100% sequence identity with the adult cestode Crossobothrium dohrnii (Oerley, 1885), a parasite of hexanchid sharks, confirming the identity of these larvae as plerocercoids of C. dohrnii. The second lineage clustered within the Crossobothrium clade but could not be assigned to a known species and is therefore referred to as Crossobothrium sp. The occurrence of these larvae in T. sagittatus, together with ecological data on squid diet and predator-prey relationships, suggests that this cephalopod acts as an intermediate or paratenic host in the life cycle of hexanchid cestodes. Infection likely occurs through predation on crustaceans acting as first intermediate hosts, while transmission to definitive hosts occurs when infected squids are consumed by sharks. These findings provide the first molecular identification of cestode larvae from T. sagittatus in the Mediterranean and highlight the important role of ommastrephid squids in the trophic transmission of elasmobranch parasites in pelagic ecosystems.

Crossobothrium↗

PubMed2025

Common to rare transfer learning (CORAL) enables inference and prediction for a quarter million rare Malagasy arthropods.

DNA-based biodiversity surveys result in massive-scale data, including up to millions of species-of which, most are rare. Making the most of such data for inference and prediction requires modeling approaches that can relate species occurrences to environmental and spatial predictors, while incorporating information about their taxonomic or phylogenetic placement. Even if the scalability of joint species distribution models to large communities has greatly advanced, incorporating hundreds of thousands of species has not been feasible to date, leading to compromised analyses. Here we present a 'common to rare transfer learning' (CORAL) approach, based on borrowing information from the common species to enable statistically and computationally efficient modeling of both common and rare species. We illustrate that CORAL leads to much improved prediction and inference in the context of DNA metabarcoding data from Madagascar, comprising 255,188 arthropod species detected in 2,874 samples.

Animals↗

PubMed2025

NanoASV: a snakemake workflow for reproducible field-based Nanopore full-length 16S metabarcoding amplicon data analysis.

SUMMARY: NanoASV is a conda environment and snakemake-based workflow using state-of-the-art bioinformatics software to process full-length SSU rRNA (16S/18S) amplicons acquired with Oxford Nanopore Sequencing technology. Its strength lies in reproducibility, portability, and the possibility to run offline, allowing in-field analysis. It can be installed on the Nanopore MK1C sequencing device and process data locally. AVAILABILITY AND IMPLEMENTATION: Source code and documentation are freely available at https://github.com/ImagoXV/NanoASV and Zenodo archive at https://doi.org/10.5281/zenodo.14730742.

Software↗

PubMed2025

Predicting coarse-grained representations of biogeochemical cycles from metabarcoding data.

MOTIVATION: Taxonomic analysis of environmental microbial communities is now routinely performed thanks to advances in DNA sequencing. Determining the role of these communities in global biogeochemical cycles requires the identification of their metabolic functions, such as hydrogen oxidation, sulfur reduction, and carbon fixation. These functions can be directly inferred from metagenomics data, but in many environmental applications metabarcoding is still the method of choice. The reconstruction of metabolic functions from metabarcoding data and their integration into coarse-grained representations of biogeochemical cycles remains a difficult bioinformatics problem today. RESULTS: We developed a pipeline, called Tabigecy, which exploits taxonomic affiliations to predict metabolic functions constituting biogeochemical cycles. In a first step, Tabigecy uses the tool EsMeCaTa to predict consensus proteomes from input affiliations. To optimize this process, we generated a precomputed database containing information about 2404 taxa from UniProt. The consensus proteomes are searched using bigecyhmm, a newly developed Python package relying on Hidden Markov Models to identify key enzymes involved in metabolic function of biogeochemical cycles. The metabolic functions are then projected on coarse-grained representation of the cycles. We applied Tabigecy to two salt cavern datasets and validated its predictions with microbial activity and hydrochemistry measurements performed on the samples. The results highlight the utility of the approach to investigate the impact of microbial communities on biogeochemical processes. AVAILABILITY AND IMPLEMENTATION: The Tabigecy pipeline is available at https://github.com/ArnaudBelcour/tabigecy. The Python package bigecyhmm and the precomputed EsMeCaTa database are also separately available at https://github.com/ArnaudBelcour/bigecyhmm and https://doi.org/10.5281/zenodo.13354073, respectively.

Metagenomics↗

PubMed2026

Bycatch in a bottle: what taxa are recoverable from metabarcoding DNA in historical invertebrate collection preservative fluid?

Natural history museum collections are invaluable repositories of biodiversity, offering insights into life on Earth. Genomic approaches provide powerful tools to characterize biodiversity in these collections. However using these collections for genomics without damaging specimens is a challenge. Here, we develop and test non-destructive DNA metabarcoding methods to capture biodiversity from the preservative fluids of archived insect collections ('Bycatch'). We optimized workflows for extracting and amplifying the partial CO1 locus (CO1) and fungal ITS1 locus from ethanol-based preservative fluids, validating ethanol preparation methods, comparing DNA extraction kits, and refining PCR protocols. Our results demonstrate that from museum collections with low DNA yields, CO1 and fungal ITS1 loci can often be recovered from preservative fluids, and we present detailed methodology and workflows. We test metabarcoding success to recover taxa in several museum collections ranging in age and storage condition. This is to support the State of California's effort to catalog and sequence all insects and fungi, building baselines of California biodiversity with help from museum collections. Lastly, we investigate the complementarity of metabarcoding water versus ethanol and morphological identifications aimed to capture benthic macroinvertebrate biodiversity in streams. Our findings highlight that DNA metabarcoding of the preservative fluid is a non-destructive tool for capturing biodiversity in historical specimens, but there are limitations on the overlaps between DNA results and physical contents, where morphological identification still reigns in taxon counts, but metabarcoding sometimes provides more taxonomic resolution, and can be used to track DNA from other organisms such as fungi beyond the directly surveyed specimens.

Animals↗

PubMed2025

The role of stochasticity in fungal community assembly: explaining apparent stochasticity with field experiments.

Stochasticity is a main process in community assembly. However, experimental studies rarely target stochasticity in natural communities, and hence experimental validation of stochasticity estimates in observational studies is lacking. Here, we combine experimental and observational data to unravel the role of stochasticity in the assembly of wood-inhabiting fungi. We carried out a replicated field experiment where the natural colonization of a focal fungal species was simulated through inoculation, and the local fungal communities were monitored through DNA metabarcoding before and after the inoculations. The amount of stochasticity in fungal colonization was less pronounced than expected from the amount of unpredictability in observational data, suggesting that stochasticity may play a smaller role in fungal occurrence than previously anticipated, or that it may be a stronger influence in the dispersal and establishment phases than in colonization per se. Stochasticity was more prominent in the initial phase of community succession, with the earliest successional stage involving a higher level of stochasticity than the later stage after 2 years. We conclude that experimentally measuring the role of stochasticity in community assembly is feasible for species-rich communities under natural conditions and highlight the importance of experimentally testing the accuracy of stochasticity estimates based on observational data.

Stochastic Processes↗

PubMed2026

Getting to the Core of the Matter-Assessing the Role of Replication in Metabarcoding-Based sedaDNA.

Replication is central to most experimental and sampling designs, increasing inferential power and capturing fine-scale data heterogeneity. However, its importance remains poorly evaluated in some ecological and evolutionary settings. This is the case of metabarcoding studies using DNA recovered from sedimentary archives, in which biological signals integrate ecological information through depositional and burial processes, yet are commonly inferred from a single sediment core per site. Here, we evaluated the effect of different types of replication using sedimentary DNA metabarcoding data from two genetic markers (mitochondrial COI and nuclear 18S) using a nested sampling design. The design included three intertidal sites, three spatially separated sediment cores per site (biological replicates), two sediment horizons per core, and eight PCR (technical) replicates per sediment sample. Variance partitioning showed that site identity and sediment age group together explained > 70% of the variation in beta diversity, indicating that among-site spatial and stratigraphic differences were the dominant drivers of community composition. PERMANOVA likewise identified non-significant effects of biological replication. Among PCR replicates from the same sediment sample, richness varied substantially, whereas Shannon diversity was more consistent. Despite this variability, differences in community composition among technical replicates remained smaller than those associated with biological replication or site identity, indicating a limited influence on broader ecological patterns. Community composition was highly similar among replicate cores within sites, consistent with stratigraphic coherence. These results indicate limited within-site heterogeneity and suggest that, under stratigraphically coherent conditions, increasing biological replication may provide little additional information, whereas enhancing technical replication and stratigraphic resolution can improve ecological inference from sedimentary DNA metabarcoding datasets.

DNA Barcoding, Taxonomic↗

PubMed2021

The genome sequence of the common green lacewing, Chrysoperla carnea (Stephens, 1836).

We present a genome assembly from an individual female Chrysoperla carnea (a common green lacewing; Arthropoda; Insecta; Neuroptera; Chrysopidae). The genome sequence is 560 megabases in span. The majority of the assembly (95.70%) is scaffolded into six chromosomal pseudomolecules, with the X sex chromosome assembled. Gene annotation of this assembly by the NCBI Eukaryotic Genome Annotation Pipeline has identified 12,985 protein coding genes.

Chrysoperla carnea↗

PubMed2022

The genome sequence of the plain-faced dronefly, Eristalis arbustorum (Linnaeus, 1758).

We present a genome assembly from an individual female Eristalis arbustorum (the plain-faced dronefly; Arthropoda; Insecta; Diptera; Syriphidae). The genome sequence is 451 megabases in span. The majority of the assembly (94.71%) is scaffolded into 6 chromosomal pseudomolecules, with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 16.0 kilobases in length.

Diptera↗

PubMed2025

The genome sequence of the bronze furrow bee, Seladonia tumulorum (Linnaeus, 1758).

We present the haploid genome assembly of an individual male Seladonia tumulorum (the bronze furrow bee; Arthropoda; Insecta; Hymenoptera; Halictidae). The genome sequence is 479 megabases in span. Most of the assembly (84.28%) is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial genome was also assembled and is 17.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,308 protein-coding genes. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.

Hymenoptera↗

PubMed2023

The genome sequence of the Red-green Carpet, Chloroclysta siterata (Hufnagel, 1767).

We present a genome assembly from an individual male Chloroclysta siterata (the Red-green Carpet; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 437.9 megabases in span. Most of the assembly is scaffolded into 21 chromosomal pseudomolecules including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,814 protein coding genes.

Chloroclysta siterata↗

PubMed2026

The genome sequence of the Tufted Button, Acleris cristana (Denis & Schiffermüller, 1775).

We present a genome assembly from an individual female Acleris cristana (the Tufted Button; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 562.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 16.1 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,598 protein coding genes.

Acleris cristana↗

PubMed2023

The genome sequence of the small wasp-sawfly, Tenthredo distinguenda (R. Stein, 1885).

We present a genome assembly from an individual male Tenthredo distinguenda (the small wasp-sawfly; Arthropoda; Insecta; Hymenoptera; Tenthredinidae). The genome sequence is 229.4 megabases in span. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 31.6 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,332 protein coding genes.

Hymenoptera↗

PubMed2023

The genome sequence of the Locust Fly, Stomorhina lunata (Fabricius, 1805).

We present a genome assembly from an individual female Stomorhina lunata (the Locust Fly; Arthropoda; Insecta; Diptera; Rhiniidae). The genome sequence is 728.1 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.49 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,358 protein coding genes.

Diptera↗

PubMed2023

The genome sequence of the Coxcomb Prominent, Ptilodon capucinus (Linnaeus, 1758).

We present a genome assembly from an individual male Ptilodon capucinus (the Coxcomb Prominent; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 348.7 megabases in span. The assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.38 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,968 protein coding genes.

Coxcomb Prominent↗

PubMed2023

The genome sequence of the Scarce Umber, Agriopis aurantiaria (Hübner, 1799).

We present a genome assembly from an individual male Agriopis aurantiaria (the Scarce Umber; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 485.4 megabases in span. The whole assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.44 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,963 protein coding genes.

Agriopis aurantiaria↗

PubMed2023

The genome sequence of the Autumnal Rustic, Eugnorisma glareosa (Esper, 1788).

We present a genome assembly from an individual male Eugnorisma glareosa (the Autumnal Rustic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 631.0 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,768 protein coding genes.

Autumnal Rustic↗

PubMed2023

The genome sequence of the Six-striped Rustic, Xestia sexstrigata (Haworth, 1809).

We present a genome assembly from an individual female Xestia sexstrigata (the Six-striped Rustic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 638.3 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 15,104 protein coding genes.

Lepidoptera↗