Biology subjects

Madrigal, G.

Publications and source records attributed to Madrigal, G..

5 recordsLinked to original sources

bioRxiv2026

Transcriptomic differences underlying fin sexual dichromatism and male color polymorphism in bluefin killifish (Lucania goodei)

Color polymorphisms offer a powerful lens for examining how selection shapes genetic and phenotypic variation. Genomic analyses of color variation provide deeper insight into how genetic differences and phenotypic plasticity contribute to trait variation. Here, we use the bluefin killifish (Lucania goodei) to study this relationship. Male fins can display either red or yellow coloration based on pigments (pterins) or blue structural coloration (iridophores) often induced in UV-depauperate environments. Female fins lack pigmentation. To characterize the molecular basis of this variation, we assembled a high-quality genome and examined gene expression in the anal fins of male and female bluefin killifish to identify the molecular mechanisms underlying color variation. Our gene expression analysis found sex differences driven by male-biased upregulation of melanin synthesis and canonical pigment pathway genes. We additionally identified that the progesterone sex receptor was upregulated in females. Among male color morphs, several genes involved in xanthophore and iridophore formation differed between blue and non-blue males, including the transcription factor tfec, and iridophore-patterning genes atic, pnp4a, and sox10. Extraocular opsins, which are involved in non-image-forming light perception, were expressed at low levels across all fins, but showed population- and morph-specific patterns; notably, rgrb (retinal G protein coupled receptor b) was upregulated in blue males. To the best of our knowledge, this is the first report of an extraocular opsin varying as a function of population and color morph. Together, these results identify the pigment pathways underlying male-limited color polymorphisms and reveal candidate genes likely involved in light-sensitive phenotypic plasticity.

evolutionary biology↗

bioRxiv2026

Synolog: A Scalable Synteny-Based Framework for Genome Architecture Characterization

Detailing the genomic architecture across multiple organisms has been a task performed for decades. The continuing growth of genomic datasets not only serves as a resource for studying genome evolution but warrants the availability of scalable and user-friendly software for processing these datasets. Here, we present Synolog, a bioinformatic toolkit that can automatically identify orthologs for both protein-coding and non-coding genes, synteny clusters across two or more genomes, as well as retrogenes, and segmental duplications. Applying Synolog, we illustrate cases of local gene expansions in ecologically disparate turtle species, identify synteny clusters across hundreds of millions of years of metazoan evolution, and reconstruct chromosome-level assemblies in teleosts using the inferred synteny clusters; all using its integrated visual features. In parallel, we compare our orthogroup method to that of commonly used software and note the tradeoffs of making inferences solely based on sequence similarity versus a synteny-based approach.

bioinformatics↗

bioRxiv2026

Molecular and biophysical requirements for B cell receptor dependent enhancement of dengue virus infection

Dengue virus (DENV) is the causative agent of dengue, a mosquito-borne disease that represents a significant and growing public health burden around the world. A unique pathophysiological feature of dengue is immune-mediated enhancement, wherein preexisting immunity elicited by a primary infection can enhance the severity of a subsequent infection by a heterologous DENV serotype. A leading mechanistic explanation for this phenomenon is antibody dependent enhancement (ADE), where sub-neutralizing concentrations of DENV-specific IgG antibodies facilitate entry of DENV into Fc{gamma}R expressing cells. Accordingly, this model posits that phagocytic mononuclear cells are the primary reservoir of DENV. However, multiple independent groups have shown that B cells are the largest reservoir of virally infected cells in circulation during acute dengue, representing a disconnect in our understanding of immune-mediated DENV tropism. In response to this persistent knowledge gap, our team has previously identified a novel mechanism of immune-mediated enhancement we have termed BCR-dependent enhancement (BDE) of DENV infection. In this study, we show that DENV infection of DENV-reactive B cells is highly sensitive to BCR/DENV envelope (E) protein interactions. DENV entry into this subset of B cells is dynamin-mediated and requires proximal BCR signaling. Finally, we show that DENV-reactive B cells are productively infected by live DENV, capable of supporting active viral replication and dissemination. We propose that BDE provides an additional layer of pathogen-specific immune-mediated infection risk that complements existing models of ADE and offers additional insight into potential mechanisms of DENV immunopathogenesis.

immunology↗

bioRxiv2024

Klumpy: A tool to evaluate the integrity of long-read genome assemblies and illusive sequence motifs

The improvement and decreasing costs of third-generation sequencing technologies has widened the scope of biological questions researchers can address with de novo genome assemblies. With the increasing number of reference genomes, validating their integrity with minimal overhead is vital for establishing confident results in their applications. Here, we present Klumpy, a tool for detecting and visualizing both misassembled regions in a genome assembly and genetic elements (e.g., genes, promotors, or transposable elements) of interest in a set of sequences. By leveraging the initial raw reads in combination with their respective genome assembly, we illustrate Klumpys utility by investigating antifreeze glycoprotein (afgp) loci across two icefishes, by searching for a reported absent gene in the northern snakehead fish, and by scanning the reference genomes of a mudskipper and bumblebee for misassembled regions. In the two former cases, we were able to provide support for the noncanonical placement of an afgp locus in the icefishes and locate the missing snakehead gene. Furthermore, our genome scans were able to identify an cryptic locus in the mudskipper reference genome, and identify a putative repetitive element shared amongst several species of bees.

bioinformatics↗

bioRxiv2022

Genomics of secondarily temperate adaptation in the only non-Antarctic icefish

AO_SCPLOWBSTRACTC_SCPLOWWhite-blooded Antarctic icefishes, a family within the adaptive radiation of Antarctic notothenioid fishes, are an example of extreme biological specialization to both the chronic cold of the Southern Ocean and life without hemoglobin. As a result, icefishes display derived physiology that limits them to the cold and highly oxygenated Antarctic waters. Against these constraints, remarkably one species, the pike icefish Champsocephalus esox, successfully colonized temperate South American waters. To study the genetic mechanisms underlying secondarily temperate adaptation in icefishes, we generated chromosome-level genome assemblies of both C. esox and its Antarctic sister species, Champsocephalus gunnari. The C. esox genome is similar in structure and organization to that of its Antarctic congener; however, we observe evidence of chromosomal rearrangements coinciding with regions of elevated genetic divergence in pike icefish populations. We also find several key biological pathways under selection, including genes related to mitochondria and vision, highlighting candidates behind temperate adaptation in C. esox. Substantial antifreeze glycoprotein (AFGP) pseudogenization has occurred in the pike icefish, likely due to relaxed selection following ancestral escape from Antarctica. The canonical AFGP locus organization is conserved in C. esox and C. gunnari, but both show a translocation of two AFGP copies to a separate locus, previously unobserved in cryonotothenioids. Altogether, the study of this secondarily temperate species provides an insight into the mechanisms underlying adaptation to ecologically disparate environments in this otherwise highly specialized group.

genomics↗