Biology subjects

Coffing, G. C.

Publications and source records attributed to Coffing, G. C..

5 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↗

bioRxiv2024

Cephalopod Sex Determination and its AncientEvolutionary Origin Revealed by Chromosome-levelAssembly of the California two-spot Octopus

Octopuses, squids, and cuttlefishes - the coleoid cephalopods - are a remarkable branch in the tree of life whose members exhibit a repertoire of sophisticated behaviors (Hanlon and Messenger, 2018). As a clade, coleoids harbor an incredible variety of novel traits including the most complex nervous system among invertebrates, derived camera-type eyes, and rapid adaptive camouflage abilities (Young, 1971; Hanlon, 2007). The burst of evolutionary novelty that distinguishes cephalopods is even more striking in a phylogenetic context; cephalopods are a deeply diverged lineage that last share a common ancestor with other extant molluscs in the Cambrian period, roughly 550 million years ago (Ponder and Lindberg, 2008; Huang et al., 2022). With recent advances in genome sequencing technologies, we have the capability to explore the genomic foundations of cephalopod novelties. Here, using PacBio long-read sequencing of genomic DNA and IsoSeq full-length mRNA sequencing, we provide a novel chromosome-scale reference genome and annotation for a female California two-spot octopus (O. bimaculoides). Our assembly reveals that the female octopus has just one sex chromosome, consistent with a ZO karyotype, while the male has two (ZZ), providing the first evidence of genetic sex determination in cephalopods. We use our assembly and annotation in combination with existing genomic information from other cephalopods to create the first whole genome alignments from this group and demonstrate that the sex chromosome is of an ancient origin, before the radiation of extant cephalopods approximately 480 million years ago (Huang et al., 2022), and has been conserved to the present day in all cephalopod genomes available.

evolutionary biology↗

bioRxiv2022

Cell types and molecular architecture of the octopus visual system

Cephalopods have a remarkable visual system, with a camera-type eye, high acuity vision, and a wide range of sophisticated visual behaviors. However, the cephalopod brain is organized dramatically differently from that of vertebrates, as well as other invertebrates, and little is known regarding the cell types and molecular determinants of their visual system organization beyond neuroanatomical descriptions. Here we present a comprehensive single-cell molecular atlas of the octopus optic lobe, which is the primary visual processing structure in the cephalopod brain. We combined single-cell RNA sequencing with RNA fluorescence in situ hybridization to both identify putative molecular cell types and determine their anatomical and spatial organization within the optic lobe. Our results reveal six major neuronal cell classes identified by neurotransmitter/neuropeptide usage, in addition to non-neuronal and immature neuronal populations. Moreover, we find that additional markers divide these neuronal classes into subtypes with distinct anatomical localizations, revealing cell type diversity and a detailed laminar organization within the optic lobe. We also delineate the immature neurons within this continuously growing tissue into subtypes defined by evolutionarily conserved fate specification genes as well as novel cephalopod- and octopus-specific genes. Together, these findings outline the organizational logic of the octopus visual system, based on functional determinants, laminar identity, and developmental markers/pathways. The resulting atlas presented here delineates the "parts list" of the neural circuits used for vision in octopus, providing a platform for investigations into the development and function of the octopus visual system as well as the evolution of visual processing. HighlightsO_LISingle-cell RNA sequencing coupled with RNA fluorescence in situ hybridization produces a molecular taxonomy of cell types in the octopus visual system. C_LIO_LISix major neuronal cell classes are delineated based on neurotransmitters/neuropeptides, and are further subdivided based on laminar organization and additional marker genes. C_LIO_LIImmature neurons are divided into multiple transcriptional subgroups that correspond to mature cell types, delineated by expression of genes known for their developmental roles in other organisms as well as apparent novel genes. C_LIO_LIThis atlas provides the foundation for future studies of the function, development, and comparative evolution of visual processing in cephalopods. C_LI

neuroscience↗

bioRxiv2020

Visualizing Population Structure with Variational Autoencoders

Dimensionality reduction is a common tool for visualization and inference of population structure from genotypes, but popular methods either return too many dimensions for easy plotting (PCA) or fail to preserve global geometry (t-SNE and UMAP). Here we explore the utility of variational autoencoders (VAEs) - generative machine learning models in which a pair of neural networks seek to first compress and then recreate the input data - for visualizing population genetic variation. VAEs incorporate non-linear relationships, allow users to define the dimensionality of the latent space, and in our tests preserve global geometry better than t-SNE and UMAP. Our implementation, which we call popvae, is available as a command-line python program at github.com/kr-colab/popvae. The approach yields latent embeddings that capture subtle aspects of population structure in humans and Anopheles mosquitoes, and can generate artificial genotypes characteristic of a given sample or population.

genetics↗