Biology subjects

Rubino, F. A.

Publications and source records attributed to Rubino, F. A..

3 recordsLinked to original sources

bioRxiv2026

Protocol for genotyping cephalopod sex using a skin swab and quantitative PCR

The coleoid cephalopods (octopus, cuttlefish, and squid) are emerging model organisms for neuroscience, development, and evolutionary biology. Determining their sex early in life is critical for population management and controlled experiments. Here, we present a protocol to non-invasively determine the sex of multiple cephalopod species as young as 3 hours post-hatching using a skin swab and quantitative PCR (qPCR). We describe steps for designing qPCR primers, swabbing live animals, extracting DNA, running the qPCR, and analyzing the results. For complete details on the use and execution of this protocol, please refer to Rubino et al.1 HighlightsO_LISwab live cephalopods as early as 3 hours post-hatching C_LIO_LIExtract DNA from cephalopod skin swabs C_LIO_LIPerform qPCR-based sex determination C_LIO_LIDesign and validate qPCR primers for new species C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=190 SRC="FIGDIR/small/715692v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@10797f5org.highwire.dtl.DTLVardef@18961a2org.highwire.dtl.DTLVardef@690df0org.highwire.dtl.DTLVardef@1122899_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

A non-invasive method to genotype cephalopod sex by quantitative PCR

Coleoid cephalopods (cuttlefish, octopus, and squid) are emerging model organisms in neuroscience, development, and evolutionary biology, and are of major economic importance in global fisheries. However, they are notoriously difficult and expensive to culture. The ability to determine sex early in development would enable more efficient and sustainable population management in both laboratory and wild settings. Here, we present a non-invasive method to genotype the sex of dwarf cuttlefish (Ascarosepion bandense) as young as three hours post-hatching using a skin swab and quantitative PCR assay, which detects a two-fold dosage difference between ZZ and Z0 sex chromosomes of males and females, respectively. Furthermore, we designed and validated primers for four additional cephalopod research species with assembled genomes (Octopus bimaculoides, Sepia officinalis, Euprymna berryi, Doryteuthis pealeii), and for a wild-caught species of economic value (Illex illecebrosus) using low-coverage whole genome sequencing data. This method enables accurate sex determination from hatchlings to adults across cephalopods, independent of genome quality or availability. HighlightsO_LIThe Z sex chromosome was identified in multiple cuttlefish, squid, and octopus species. C_LIO_LIA sensitive quantitative PCR assay can genotype ZZ/Z0 sex in each species. C_LIO_LILow-coverage short-read sequencing data is sufficient to design effective primers. C_LIO_LIqPCR on non-invasive skin swabs enables genotyping of living animals. C_LI

genetics↗

bioRxiv2022

A brain atlas of the camouflaging dwarf cuttlefish, Sepia bandensis

The coleoid cephalopods (cuttlefish, octopus, and squid) are a group of soft-bodied marine mollusks that exhibit an array of interesting biological phenomena, including dynamic camouflage, complex social behaviors, prehensile regenerating arms, and large brains capable of learning, memory, and problem-solving [1-10]. The dwarf cuttlefish, Sepia bandensis, is a promising model cephalopod species due to its small size, substantial egg production, short generation time, and dynamic social and camouflage behaviors [11]. Cuttlefish dynamically camouflage to their surroundings by changing the color, pattern and texture of their skin. Camouflage is optically-driven, and is achieved by expanding and contracting hundreds of thousands of pigment-filled saccules (chromatophores) in the skin, which are controlled by motor neurons emanating from the brain. We generated a dwarf cuttlefish brain atlas using magnetic resonance imaging (MRI), deep learning, and histology, and we built an interactive web tool (cuttlebase.org) to host the data. Guided by observations in other cephalopods [12-20], we identified 32 brain lobes, including two large optic lobes (75% the total volume of the brain), chromatophore lobes whose motor neurons directly innervate the chromatophores of the color-changing skin, and a vertical lobe that has been implicated in learning and memory. This brain atlas provides a valuable tool for exploring the neural basis of cuttlefish behavior.

neuroscience↗