Biology subjects

Kocot, K. M.

Publications and source records attributed to Kocot, K. M..

6 recordsLinked to original sources

bioRxiv2026

Dynamic genomes uncover opposite sex determination in the invasive quagga and zebra mussels

Sex determination is a fundamental developmental switch, yet the genetic architectures that underlie transitions between sex-determining systems remain poorly understood, especially in non-model animals with homomorphic sex chromosomes. Here, we combine chromosome-scale genomes, whole-genome resequencing of 80 sexed individuals, sex-specific k-mer analyses, and developmental transcriptomics to resolve and compare sex determination in zebra and quagga mussels, two closely related and globally invasive freshwater bivalves. We find that these species have evolved sharply contrasting sex-determining architectures since their divergence. Zebra mussels show signatures of a polygenic ZZ/ZW system, with sex-linked regions on multiple chromosomes, including signal at the conserved ovarian regulator FoxL2. In contrast, quagga mussels possess a localized [~]800 kb XX/XY sex-determining region containing FoxL2-Y, a duplicated and structurally modified FoxL2 paralog and candidate male-determining locus. In quagga mussels, SNP-based differentiation, model-based inference, sex-biased read coverage, and male-specific k-mers independently converge on this Y-linked region, while diagnostic k-mer screening of staged embryonic transcriptomes reveals rare, early developmental expression of FoxL2-Y, consistent with a transient regulatory role. The quagga sex-determining region is enriched for C-type lectins and other genes implicated in reproductive interactions, suggesting that haploid selection may have contributed to the stabilization of this region. Together, these findings show that closely related species can rapidly evolve different genetic solutions to sex determination and identify gene duplication, genome dynamism, and reproductive selection as potential contributors to sex-determining system turnover. Because zebra and quagga mussels are major freshwater invaders, resolving their divergent reproductive architectures also provides essential genomic context for assessing the future feasibility of sex-ratio-based biocontrol strategies.

genomics↗

bioRxiv2025

Phylogenomics supports monophyly of marsupial crustaceans: a journey to direct development

Peracarida (marsupial crustaceans) represent one of the most diverse and ecologically important crustacean groups, yet their evolutionary relationships have long been debated. Here, we present the most comprehensive phylogenomic analysis of Peracarida to date, incorporating the relict taxa Thermosbaenacea, Mictacea, Ingolfiellida, and Spelaeogriphacea for the first time in a phylogenomic framework. Our results robustly confirm peracarid monophyly and recover a well-supported clade uniting Mancoida (Isopoda, Tanaidaca, Cumacea), Mictacea, and Spelaeogriphacea. We propose the new taxon Panmancoida to encompass this expanded lineage defined by shared developmental and morphological traits. The inferred phylogeny further suggests that peracarid evolution involved a transition from an intermediate "pseudodirect" developmental mode to the direct development seen in most lineages. We further show that the shift to extensive brood care within the marsupium, accompanied by the loss of a free-swimming larval stage, may have accelerated rates of molecular evolution across lineages. Together, these findings provide a robust evolutionary framework for this major malacostracan lineage and highlight how key reproductive innovations reshaped the genomic and life-history trajectories of the marsupial crustaceans.

evolutionary biology↗

bioRxiv2024

First chromosome-level genome assembly of a ribbon worm from the Hoplonemertea clade, Emplectonema gracile, and its structural annotation

Genome-wide information has so far been unavailable for ribbon worms of the clade Hoplonemertea, the most species-rich class within the phylum Nemertea. While species within Pilidiophora, the sister clade of Hoplonemertea, possess a pilidium larval stage and lack stylets on their proboscis, Hoplonemertea species have a planuliform larva and are armed with stylets employed for the injection of toxins into their prey. To further compare these developmental, physiological, and behavioral differences from a genomic perspective, the availability of a reference genome of a Hoplonemertea species is crucial. To this end, we herein present the annotated chromosome-level genome assembly for Emplectonema gracile (Nemertea; Hoplonemertea; Monostilifera; Emplectonematidae), an easily collected nemertean well-suited for laboratory experimentation. The genome is 157.9 Mbp in span. Hi-C scaffolding yielded 15 putative chromosomes with a scaffold N50 of 10.0 Mbp and a BUSCO completeness score of 95.3%. Structural annotation predicted 20,684 protein-coding genes. The high-quality reference genome reaches an Earth BioGenome standard level of 7.C.Q50. These data will be highly useful for future investigations towards a better understanding of the evolution, development, morphology, and toxicology of Nemertea. SignificanceThe genome of Emplectonema gracile is highly contiguous, well annotated, and shorter than those of the other two ribbon worm species sequenced to date. This genome is a valuable resource for studies on molecular ecology, venom evolution, and regeneration in marine invertebrates.

genomics↗

bioRxiv2023

A genome-scale Opisthokonta tree of life: toward phylogenomic resolution of ancient divergences

AbstractAncient divergences within Opisthokonta--a major lineage that includes organisms in the kingdoms Animalia, Fungi, and their unicellular relatives-- remain contentious, hindering investigations of the evolutionary processes that gave rise to two kingdoms and the repeated emergence of iconic phenotypes like multicellularity. Here, we use genome-scale amounts of data to reconstruct the most taxon-rich Opisthokonta tree of life to date (348 species) and place divergences in geologic time, suggesting a Mesoproterozoic origin ([~] 1.11 billion years ago). By dissecting multiple dimensions of phylogenomic error, such as the influence of taxon sampling and model complexity, we found that deep divergences within Holozoa remain unresolved and suggest Pluriformea is either sister to Ichthyosporea and Filozoa (Pluriformea-sister hypothesis) or is monophyletic to Ichthyosporea, forming the Teretosporea lineage (Teretosporea-sister hypothesis). A combination of information theory and sensitivity analyses revealed that the inferred unicellular Holozoa relationships are largely robust to common sources of analytical error, such as insufficient model complexity, and suggest that previous reports likely suffered from insufficient taxon sampling. Our study presents a robust Opisthokonta phylogenomic framework, highlights the challenges in resolving the relationships of unicellular Holozoa, and paves the way for illuminating ancient evolutionary episodes concerning the origin of two kingdoms.

evolutionary biology↗

bioRxiv2020

The iron-responsive genome of the chiton Acanthopleura granulata

Molluscs biomineralize structures that vary in composition, form, and function, prompting questions about the genetic mechanisms responsible for their production and the evolution of these mechanisms. Chitons (Mollusca, Polyplacophora) are a promising system for studies of biomineralization because they build a range of calcified structures including shell plates and spine- or scale-like sclerites. Chitons also harden the calcified teeth of their rasp-like radula with a coat of iron (as magnetite). Here we present the genome of the West Indian fuzzy chiton Acanthopleura granulata, the first from any aculiferan mollusc. The A. granulata genome contains homologs of many biomineralization genes identified previously in conchiferan molluscs. We expected chitons to lack genes previously identified from pathways conchiferans use to make biominerals like calcite and nacre because chitons do not use these materials in their shells. Surprisingly, the A. granulata genome has homologs of many of these genes, suggesting that the ancestral mollusc had a more diverse biomineralization toolkit than expected. The A. granulata genome has features that may be specialized for iron biomineralization, including a higher proportion of genes regulated directly by iron than other molluscs. A. granulata also produces two isoforms of soma-like ferritin: one is regulated by iron and similar in sequence to the soma-like ferritins of other molluscs, and the other is constitutively translated and is not found in other molluscs. The A. granulata genome is a resource for future studies of molluscan evolution and biomineralization. SIGNIFICANCE STATEMENTChitons are molluscs that make shell plates, spine- or scale-like sclerites, and iron-coated teeth. Currently, all molluscs with sequenced genomes lie within one major clade (Conchifera). Sequencing the genome of a representative from the other major clade (Aculifera) helps us learn about the origins and evolution of molluscan traits. The genome of the West Indian Fuzzy Chiton, Acanthopleura granulata, reveals chitons have homologs of many genes other molluscs use to make shells, suggesting all molluscs share some shell-making pathways. The genome of A. granulata has more genes that may be regulated directly by iron than other molluscs, and chitons produce a unique isoform of a major iron-transport protein (ferritin), suggesting that chitons have genomic specializations that contribute to their production of iron-coated teeth.

genomics↗

bioRxiv2017

Phylogenomics offers resolution of major tunicate relationships

Tunicata, a diverse clade of approximately 3,000 described species of marine, filter-feeding chordates, is of great interest to researchers because tunicates are the closest living relatives of vertebrates and they facilitate comparative studies of our own biology. The group also includes numerous invasive species that cause considerable economic damage and some species of tunicates are edible. Despite their diversity and importance, relationships among major lineages of Tunicata are not completely resolved. Here, we supplemented public data with transcriptomes from seven species spanning the diversity of Tunicata and conducted phylogenomic analyses on data sets of up to 798 genes. Sensitivity analyses were employed to examine the influences of reducing compositional heterogeneity and branch-length heterogeneity. All analyses maximally supported a monophyletic Tunicata within Olfactores (Vertebrata + Tunicata). Within Tunicata, all analyses recovered Appendicularia sister to the rest of Tunicata and confirmed (with maximal support) that Thaliacea is nested within Ascidiacea. Stolidobranchia is the sister taxon to all other tunicates except Appendicularia. In most analyses, phlebobranch tunicates were recovered paraphyletic with respect to Aplousobranchia. Support for this topology varied but was strong in some cases. However, when only the 50 best genes based on compositional heterogeneity were analysed, we recovered Phlebobranchia and Aplousobranchia reciprocally monophyletic with strong support, consistent with most traditional morphology-based hypotheses. Examination of internode certainty also cast doubt on results of phlebobranch paraphyly, which may be due to limited taxon sampling. Taken together, these results provide a higher-level phylogenetic framework for our closest living invertebrate relatives.

zoology↗