Porco, D. | Search bioRxiv

bioRxiv2026

Introducing the digital PCR data essentials standard to harmonize data structure for clinical and research use

Digital PCR (dPCR) is a powerful technology for absolute quantification of nucleic acids, valued for its accuracy, sensitivity, and repeatability. Yet, the commercialization of different instruments with proprietary software has introduced challenges to data analysis, interoperability, and comparability. Therefore, we present the Digital PCR Data Essentials Standard (DDES) - a lightweight, human- and machine-readable, and cross-platform data standard developed in collaboration with the dPCR community. The standard consists of three file types designed to enable both manual inspection and automated analysis: (i) a main file summarizing experiment and reaction-level (meta-)data; (ii) an assay file describing targets and detection chemistry, and (iii) intensity files capturing partition-level raw fluorescence data per reaction. DDES supports a wide range of current dPCR applications, including singleplex and multiplex assays, endpoint and real-time readouts, and will be curated to implement future dPCR developments. By harmonizing the data structure, DDES lays out the foundation for FAIR dPCR data practices and supports improved software compatibility, collaborative and reproducible research, and future dPCR data repositories.

bioinformatics↗

bioRxiv2022

Reproductive strategies in a complex of simultaneously hermaphroditic species, the Allolobophora chlorotica case study

An in-depth knowledge of reproductive strategies is essential to understand the evolutionary history of species and their resulting patterns of taxonomic diversity. In particular, the study of life history traits related to reproduction could help to resolve the speciation patterns in the cryptic species complexes recently found in earthworms. Here, we carried out a parentage analysis in such a complex, the Allolobophora chlorotica aggregate. Using four nuclear microsatellite markers and a fragment of the cytochrome c oxidase subunit I mitochondrial gene we investigated (i) the mating strategies between individuals belonging to two divergent mitochondrial lineages (L2 and L3) that cannot be distinguished with nuclear markers and (ii) the reproductive isolation between lineages that are differentiated both at the mitochondrial and nuclear level (L2/L3 and L1). Among the 157 field collected individuals, 66 adults were used in cross-breeding experiments to form 22 trios based on their assignment to a mitochondrial lineage, and 453 obtained juveniles were genotyped. We showed that adults that mated with both their potential mates in the trio produced significantly more juveniles. In L2 and L3 crosses, a sex-specific pattern of reproduction characteristic to each lineage was observed, suggesting a possible conflict of interest between mating partners. In L2/L3 and L1 crosses, a high production of cocoons was counterbalanced by a low hatching rate, suggesting a post-zygotic reproductive isolation. Reproductive strategies are thus likely to contributed to the diversification of this complex of species and we advocate further studies on sexual selection and sex allocation in earthworms.

evolutionary biology↗