Biology subjects

Cancio, I.

Publications and source records attributed to Cancio, I..

4 recordsLinked to original sources

bioRxiv2026

Enhancing Transcriptional Data Reliability in Fish Oogenesis Using cDNA-Based Normalization

Transcriptomic analyses are widely used to elucidate the molecular mechanisms driving gametogenesis and reproduction in fish, yet their accuracy depends heavily on appropriate normalization of gene expression data. Conventional approaches that rely on single or multiple reference genes are problematic during teleost oogenesis, as profound structural and physiological remodeling of the ovary challenges the assumption that commonly used reference transcripts remain stable. In this study, we assessed by qPCR the transcriptional variability of four widely used reference genes (actb, ef-1, gapdh, and 18S rRNA) throughout the oogenic cycle of the thicklip grey mullet (Chelon labrosus), using geNorm and NormFinder analyses, and we additionally evaluated total cDNA concentration as an alternative normalization factor. To examine the performance and interpretive consequences of each normalization strategy, we compared expression patterns of key steroidogenic genes (star, cyp19a1a, and cyp11b) normalized by individual reference genes, combinations of reference genes, or total cDNA concentration. All evaluated reference genes displayed notable transcriptional variability across oogenesis, confirming their limited suitability as sole internal controls. In contrast, normalization approaches integrating multiple reference genes and/or total cDNA concentration consistently provided greater stability and more reliable biological interpretation. These results support a refined and more robust normalization framework for transcriptional analyses in fish ovaries, particularly during stages of extensive tissue remodeling. Our findings demonstrate cDNA-based normalization is straightforward, rapid, and easy to implement across laboratories, providing a practical alternative for achieving accurate, reproducible transcript quantification in fish ovary studies.

pharmacology and toxicology↗

bioRxiv2024

A long-term ecological research data set from the marine genetic monitoring programme ARMS-MBON 2018-2020

Molecular methods such as DNA/eDNA metabarcoding have emerged as useful tools to document biodiversity of complex communities over large spatio-temporal scales. We established an international Marine Biodiversity Observation Network (ARMS-MBON) combining standardised sampling using autonomous reef monitoring structures (ARMS) with metabarcoding for genetic monitoring of marine hard-bottom benthic communities. Here, we present the data of our first sampling campaign comprising 56 ARMS units deployed in 2018-2019 and retrieved in 2018-2020 across 15 observatories along the coasts of Europe and adjacent regions. We describe the open-access data set (image, genetic, and metadata) and explore the genetic data to show its potential for marine biodiversity monitoring and ecological research. Our analysis shows that ARMS recovered more than 60 eukaryotic phyla capturing diversity of up to [~]5,500 amplicon sequence variants and [~]1,800 operational taxonomic units, and up to [~]250 and [~]50 species per observatory using the cytochrome c oxidase subunit I (COI) and 18S rRNA marker genes, respectively. Further, ARMS detected threatened, vulnerable and non-indigenous species often targeted in biological monitoring. We show that while deployment duration does not drive diversity estimates, sampling effort and sequencing depth across observatories do. We recommend that ARMS should be deployed for at least three to six months during the main growth season to use resources as efficiently as possible and that post-sequencing curation is applied to enable statistical comparison of spatio-temporal entities. We suggest that ARMS should be used in biological monitoring programmes and long-term ecological research and encourage the adoption of our ARMS-MBON protocols.

ecology↗

bioRxiv2021

Myth-busting the provider-user relationship for digital sequence information

The United Nations Convention on Biological Diversity (CBD) formally recognized the sovereign rights of nations over their biological diversity. Implicit within the treaty is the idea that mega-biodiverse countries will provide genetic resources and grant access to them and scientists in high-income countries will use these resources and share back benefits. However, little research has been conducted on how this framework is reflected in real-life scientific practice. Currently, parties to the CBD) are debating whether or not digital sequence information (DSI) should be regulated under a new benefit-sharing framework. At this critical time point in the upcoming international negotiations, we test the fundamental hypothesis of provision and use by looking at the global patterns of access and use in scientific publications. Our data reject the provider-user relationship and suggest far more complex information flow for digital sequence information. Therefore, any new policy decisions on digital sequence information should be aware of the high level of use of DSI across low- and middle-income countries and seek to preserve open access to this crucial common good.

scientific communication and education↗

bioRxiv2019

Replicated anthropogenic hybridisations reveal parallel patterns of admixture in marine mussels.

Human-mediated transport creates secondary contacts between genetically differentiated lineages, bringing new opportunities for gene exchange. When similar introductions occur in different places, they provide informally replicated experiments for studying hybridisation. We here examined 4279 Mytilus mussels, sampled in Europe and genotyped with 77 ancestry informative markers. We identified a type of introduced mussels, called dock mussels, associated with port habitats and displaying a particular genetic signal of admixture between M. edulis and the Mediterranean lineage of M. galloprovincialis. These mussels exhibit similarities in their ancestry compositions, regardless of the local native genetic backgrounds and the distance separating colonised ports. We observed fine-scale genetic shifts at the port entrance, at scales below natural dispersal distance. Such sharp clines do not fit with migration-selection tension zone models, and instead suggest habitat choice and early stage adaptation to the port environment, possibly coupled with connectivity barriers. Variations in the spread and admixture patterns of dock mussels seem to be influenced by the local native genetic backgrounds encountered. We next examined departures from the average admixture rate at different loci, and compared human-mediated admixture events, to naturally admixed populations and experimental crosses. When the same M. galloprovincialis background was involved, positive correlations in the departures of loci across locations were found; but when different backgrounds were involved, no or negative correlations were observed. While some observed positive correlations might be best explained by a shared history and saltatory colonisation, others are likely produced by parallel selective events. Altogether, genome-wide effect of admixture seems repeatable, and more dependent on genetic background than environmental context. Our results pave the way towards further genomic analyses of admixture, and monitoring of the spread of dock mussels both at large and fine spacial scales.

evolutionary biology↗