Biology subjects

Van Dam, A. R.

Publications and source records attributed to Van Dam, A. R..

3 recordsLinked to original sources

bioRxiv2026

The genome of the coffee bean weevil (Araecerus fasciculatus) reveals a cytochrome P450 repertoire as a convergent candidate mechanism of insect-origin caffeine detoxification

The coffee bean weevil, Araecerus fasciculatus (Coleoptera, Curculionoidea, Anthribidae), is a cosmopolitan pest of over 100 stored agricultural commodities, with particular economic impact on coffee (Coffea arabica). Although two chromosome-level anthribid genomes have recently been released as part of the Darwin Tree of Life (DToL) project (Booth et al. 2024; Crowley et al. 2025), no functionally annotated genome has been available for the family. Here we present a draft genome assembly for A. fasciculatus, generated from PacBio HiFi long reads and processed through a three tiered metagenomic filtering pipeline to remove host plant (C. arabica) and microbial contamination. The final assembly spans 475 Mb across 3,617 scaffolds (N50 = 170 kb) with 88.5% BUSCO completeness (insecta_odb10) and only 3.1% duplication. Gene prediction with BRAKER2 identified 22,384 protein-coding genes, of which 11,783 received functional annotations through SwissProt similarity. Notably, we identified 92 cytochrome P450 (CYP) genes, including tandem gene clusters on two scaffolds (4 genes on ptg000464l, 5 genes on ptg001867l), suggestive of lineage-specific expansion through tandem duplication. Homology searches against Drosophila melanogaster caffeine-metabolizing P450s (CYP12D1, CYP6d5, CYP6a8) recovered strong matches (e-values 9.7 x 10-110 to 5.4 x 10-101, 33-38% identity). In stark contrast, comprehensive BLAST searches for bacterial caffeine N-demethylase genes (ndmA/B/C/D), which mediate caffeine degradation via horizontal gene transfer in the coffee berry borer Hypothenemus hampei (Scolytinae), returned zero hits across the A. fasciculatus genome, predicted proteome, and associated bacterial scaffolds. AlphaFold2 structure prediction of four top Araecerus P450 candidates produced high-confidence models (pLDDT 84.5-93.9, pTM 0.735-0.930) with conserved P450 catalytic motifs. Foldseek structural homology searches confirmed that all four candidates adopt cytochrome P450 folds (top hits: human CYP3A4, CYP3A7, CYP11A1; TM-scores 0.90-0.92; probability 1.000), with zero hits to bacterial Rieske-fold enzymes. Molecular docking of caffeine against these structures yielded binding affinities of -5.41 to -5.80 kcal/mol for the Araecerus candidates, comparable to or exceeding the -5.55 kcal/mol obtained for the experimentally validated Drosophila CYP6a8 and substantially stronger than the -3.70 kcal/mol for the bacterial NdmA structural outgroup (PDB: 6ICP). Phylogenetic analysis revealed that all four candidates have clear orthologs in two non-seed-feeding DToL anthribids (Pseudeuparius sepicola and Platystomos albinus), demonstrating that these P450 genes predate the dietary transition to caffeine-containing seeds. The Araecerus candidates predominantly belong to the CYP6 family (clan 3), whereas the primary Drosophila caffeine P450 CYP12D1 belongs to the mitochondrial clan, confirming convergent recruitment of different P450 subfamilies for caffeine metabolism. These results support the hypothesis that A. fasciculatus employs an insect-encoded, P450-mediated caffeine detoxification pathway fundamentally distinct from the bacterial horizontal gene transfer mechanism documented in Scolytinae. This represents convergent evolution of caffeine resistance via independent molecular strategies within Curculionoidea, and provides the first functionally annotated genomic resource for comparative studies across the Anthribidae.

genomics↗

bioRxiv2026

Descriptron-GBIF Annotator: A browser-based platform for crowdsourced morphological annotation of biodiversity images to help accelerate morphology based biodiversity data

The accelerating biodiversity crisis demands new approaches to taxonomic description that can scale beyond the capacity of professional taxonomists alone. We present the Descriptron-GBIF Annotator, a zero-installation, browser-based tool for morphological annotation of biodiversity specimen images retrieved directly from the Global Biodiversity Information Facility (GBIF). The application runs entirely client-side as a single HTML file, integrating SAM2 (Segment Anything Model 2) for AI-assisted segmentation, ontology-linked anatomical region templates covering 25 major taxonomic groups across 124 standardized views, 335 ontology Compact URI Expressions (CURIEs), with 745 possible ontology mentions, and structured trait attribute recording. The annotator supports multiple export formats including Darwin Core JSON, COCO JSON, traits CSV, and a novel JSON-LD knowledge graph linking specimens to anatomical regions and morphological traits via UBERON and domain-specific ontologies. A built-in Zenodo publishing pipeline enables users to deposit annotations as citable datasets with DOIs directly from the browser. Additionally users can also annotate images from Zenodo BioSysLit enabling annotation of taxonomic treatments directly. We position this public-facing tool as the first tier of a two-tier architecture complementing the Descriptron Portal, a GPU-accelerated professional workbench for taxonomists providing tools for fine-tuning AI models, geometric morphometrics, and automated species descriptions. Together, these tiers create a feedback loop where public annotations generate training data for expert AI models, while expert-validated outputs improve the public tool. This approach draws on the citizen science model pioneered by Notes from Nature and iNaturalist to engage diverse audiences in structured morphological data collection, addressing a critical gap in biodiversity informatics where specimen images exist in abundance but structured morphological annotations remain scarce. To learn more go here: https://descriptrongbifannotator.org

bioinformatics↗

bioRxiv2019

Title - Taxonomic survey of Anadenobolus monilicornis gut microbiota via shotgun nanopore sequencing

Millipedes constitute one of many soil-inhabiting organisms that act as important components of litter decomposition and nutrient recycling in terrestrial ecosystems. This is thanks in part to the microbial diversity that they contain in their gut compartments. However, millipedes and their gut microbiota are understudied, compared to other arthropods. For this reason, we partook in a metagenomic analysis of the gut of Anadenobolus monilicornis. We collected specimens of A. monilicornis, which were starved for a varying amount of time, from different municipalities of Puerto Rico. Once the DNA from their guts was extracted and sequenced using the MinION nanopore sequencer, we proceeded to analyze and compile the data obtained from the sequencer using programs such as Phylosift and MEGAN6 and the web-based MG-RAST. From our two best samples, we obtained a total of 87,110 and 99,749 reads, respectively. After comparing the data analyses and gene annotation done for both samples, we found that the bacterial phyla Proteobacteria, Bacteroidetes and Firmicutes were consistently well represented; one of our samples had much more Chlamydiae representation than the other, however. Sampled eukaryote phyla include Arthropoda, Chordata and Streptophyta. We would need a greater sample size to better determine differences in microbial diversity between millipede populations across the island; considering our small sample size, however, we were able to broadly reveal the diversity within the microenvironment of A. monilicorniss gut.

genomics↗