Biology subjects

Khost, D.

Publications and source records attributed to Khost, D..

4 recordsLinked to original sources

bioRxiv2026

An improved Stentor coeruleus genome and time-resolved transcriptomics link cyclic nucleotide-dependent kinase signaling to single-cell habituation

The giant ciliate Stentor coeruleus is a single cell capable of modifying its behavior through experience. When repeatedly disturbed, it undergoes habituation, a simple and widely conserved form of non-associative learning, despite lacking a nervous system. How a single cell achieves such behavioral plasticity at the molecular level remains poorly understood. Here, we report a compact, contiguous macronuclear reference genome for S. coeruleus, substantially improving genome continuity and annotation quality while resolving two successive rounds of whole-genome duplication and extensive lineage-specific gene-family expansion. Anchoring time-resolved transcriptomics to this reference, we profiled pooled RNA from behaviorally tracked cells collected at defined points during a mechanical stimulation paradigm and identified 341 genes with significant temporal expression dynamics during habituation. The dominant transcriptional signature of habituation was the coordinated, sustained up-regulation of a conserved cyclic nucleotide, calcium, and phosphatase signaling module centered on five cGMP-dependent protein kinase (PKG) paralogs together with a voltage-gated calcium channel and a protein phosphatase 2A regulatory subunit, representing conserved intracellular components of the neuronal long-term depression (LTD) pathway. By integrating an improved genome with time-resolved transcriptomics of habituation, this work provides a community resource for Stentor and identifies a conserved signaling program as a candidate molecular framework underlying single-cell habituation.

molecular biology↗

bioRxiv2025

Combining population genomics with ancient DNA to understand island colonization history of the Madagascar turtle dove

The Mascarene archipelago (Mauritius, Reunion and Rodrigues), characterized by first human arrival being recent, offers a unique setting to study species colonization. Here we use a combination of modern and ancient DNA data as a case study to investigate the recent colonization history of a species of concern in relation to conservation programs - the Madagascar turtle dove (Nesoenas picturata) on Mauritius and Reunion. We generated a reference genome and re-sequenced genomes from contemporary N. picturata populations, as well as genome-wide data from relevant subfossils. A combination of model-free inferences, site frequency spectrum (SFS) based demographic modelling, and analyses of population structure including that of subfossils indicate that N. picturata colonized both islands independently and naturally from Madagascar, long before human arrival. Summary statistics and SFS-based modeling reveal large effective population sizes (Ne) and high genetic diversity in island populations, conflicting with historical accounts of human-induced demographic collapse. Based on goodness-of-fit, genetic structure and diversity indices do not discriminate between two solutions, one of which posits large recent Ne and negligible translocation rates, while the other supports recent severe bottlenecks followed by high post-human translocation from Madagascar. Nonetheless, linkage disequilibrium provides stronger evidence for the latter scenario, which may also explain high genetic diversity. Both modern and ancient DNA data sources independently support the classification of N. picturata as native to both islands. Our findings highlight the importance of validating demographic models with multiple summary statistics, and potential of using a combination of different data sources to resolve colonization history in recent time.

evolutionary biology↗

bioRxiv2025

Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants

Structural variants (SVs) are widespread in vertebrate genomes, yet their evolutionary dynamics remain poorly understood. Using 45 long-read de novo genome assemblies and pangenome tools, we analyze SVs within three closely related species of North American jays (Aphelocoma, scrub-jays) displaying a 60-fold range in effective population size. We find rapid evolution of genome architecture, including [~]100 Mb variation in genome size driven by dynamic satellite landscapes with unexpectedly long (> 10 kb) repeat units and widespread variation in gene content, influencing gene expression. SVs exhibit slightly deleterious dynamics modulated by variant length and population size, with strong evidence of adaptive fixation only in large populations. Our results demonstrate how population size shapes the distribution of SVs and the importance of pangenomes to characterizing genomic diversity.

evolutionary biology↗

bioRxiv2020

Evolution of genome structure in the Drosophila simulans species complex

The rapid evolution of repetitive DNA sequences, including satellite DNA, tandem duplications, and transposable elements, underlies phenotypic evolution and contributes to hybrid incompatibilities between species. However, repetitive genomic regions are fragmented and misassembled in most contemporary genome assemblies. We generated highly contiguous de novo reference genomes for the Drosophila simulans species complex (D. simulans, D. mauritiana, and D. sechellia), which speciated [~]250,000 years ago. Our assemblies are comparable in contiguity and accuracy to the current D. melanogaster genome, allowing us to directly compare repetitive sequences between these four species. We find that at least 15% of the D. simulans complex species genomes fail to align uniquely to D. melanogaster due to structural divergence--twice the number of single-nucleotide substitutions. We also find rapid turnover of satellite DNA and extensive structural divergence in heterochromatic regions, while the euchromatic gene content is mostly conserved. Despite the overall preservation of gene synteny, euchromatin in each species has been shaped by clade and species-specific inversions, transposable elements, expansions and contractions of satellite and tRNA tandem arrays, and gene duplications. We also find rapid divergence among Y-linked genes, including copy number variation and recent gene duplications from autosomes. Our assemblies provide a valuable resource for studying genome evolution and its consequences for phenotypic evolution in these genetic model species.

genomics↗