Biology subjects

Choi, S.-W.

Publications and source records attributed to Choi, S.-W..

4 recordsLinked to original sources

bioRxiv2026

Evolution of multicellularity and reproductive strategies in yellow-green algae (Xanthophyceae, Heterokontophyta)

The evolution of multicellularity has long been linked to reproductive strategies. A long-standing debate concerns whether multicellular organisms are primarily stabilized by small single-cell propagules that minimize genetic heterogeneity or by larger multicellular and multinucleate propagules that may improve developmental success and survival of individuals. the Xanthophyceae provides an excellent model for investigating these questions, exhibiting transitions between unicellular to multicellular filamentous and coenocytic forms together with diverse reproductive modes, including single-cell zoospores and autospores, and multinucleate monospores and akinetes. However, a robust phylogenetic framework and systematic analyses of character evolution have remained lacking in this lineage. Here, we present a phylogenomic framework based on a nuclear dataset of 680 genes from 18 species, including 17 newly generated transcriptomes. Nuclear phylogenies robustly resolve all sampled inter-ordinal and inter-familial relationships with full concordance between concatenation and coalescent analyses, while plastid (141 genes) and mitochondrial (31 genes) datasets from 33 species recover identical topologies. Based on these results, we establish one new order (Pseudopleurochloridales), emend one order (Heterococcales), and propose five new families. Ancestral character reconstruction indicates at least four independent transitions from unicellular ancestors to simple multicellularity. Bayesian analyses of multicellularity and reproductive characters show that these transitions were consistently accompanied by shifts from multiple autospore-type propagules toward single monospore- and akinete-type propagules, whereas reversions to unicellularity were associated with the reappearance of autospore-based reproduction. These results provide a phylogenomic framework for understanding multicellular evolution in Xanthophyceae and shed light on the relationship between reproductive modes and the emergence of simple multicellularity.

evolutionary biology↗

bioRxiv2026

The genomic basis of evolutionary stasis in the 500-million-year-old red seaweed genus Ahnfeltia

The red seaweed genus Ahnfeltia is an ancient lineage that has persisted for over 500 million years with remarkably limited diversification despite a global distribution in cold-temperate intertidal habitats. Compared to the highly diverse sister lineage, Rhodymeniophycidae, Ahnfeltia provides a unique system for investigating long-term evolutionary persistence in marine macroalgae. Here, we generated chromosome-scale genomes from five populations across three species and combined population genomics with paleogeographic niche modelling. Our results reveal remarkable genomic conservation, strong geographic isolation with limited gene flow, high homozygosity, and evidence of purifying selection. Niche projections indicate long-term stability and spatial connectivity of suitable cold-temperate habitats. These findings suggest that Ahnfeltias persistence and limited diversification are linked to genomic constraints and stable ecological niches over geological timescales. This study provides new insights into the genomic basis of evolutionary stasis in ancient marine lineages and highlights potential vulnerability to ongoing climate change affecting cold-water coastal ecosystems.

evolutionary biology↗

bioRxiv2025

A computational framework for mapping isoform landscape and regulatory mechanisms from spatial transcriptomics data

Transcript diversity including splicing and alternative 3 end usage is crucial for cellular identity and adaptation, yet its spatial coordination remains poorly understood. Here, we present SPLISOSM (SpatiaL ISOform Statistical Modeling), a computational framework for detecting isoform-resolution patterns from spatial transcriptomics data. SPLISOSM leverages multivariate testing to account for spot- and isoform-level dependencies, demonstrating robust and theoretically grounded performance on sparse data. In the mouse brain, we identify over 1,000 spatially variable transcript diversity events, primarily in synaptic signaling pathways linked to neuropsychiatric disorders, and uncover both known and novel regulatory relationships with region-specific RNA binding proteins. We further show that these patterns are evolutionarily conserved between mouse and human prefrontal cortex. Analysis of human glioblastoma highlights pervasive transcript diversity in antigen presentation and adhesion genes associated with specific microenvironmental conditions. Together, we present a comprehensive spatial splicing analysis in the brain under normal and neoplastic conditions.

bioinformatics↗

bioRxiv2024

Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems

Brown seaweeds are keystone species of coastal ecosystems, often forming extensive underwater forests, that are under considerable threat from climate change. Despite their ecological and evolutionary importance, this phylogenetic group, which is very distantly related to animals and land plants, is still poorly characterised at the genome level. Here we analyse 60 new genomes that include species from all the major brown algal orders. Comparative analysis of these genomes indicated the occurrence of several major events coinciding approximately with the emergence of the brown algal lineage. These included marked gain of new orthologous gene families, enhanced protein domain rearrangement, horizontal gene transfer events and the acquisition of novel signalling molecules and metabolic pathways. The latter include enzymes implicated in processes emblematic of the brown algae such as biosynthesis of the alginate-based extracellular matrix, and halogen and phlorotannin biosynthesis. These early genomic innovations enabled the adaptation of brown algae to their intertidal habitats. The subsequent diversification of the brown algal orders tended to involve loss of gene families, and genomic features were identified that correlated with the emergence of differences in life cycle strategy, flagellar structure and halogen metabolism. Analysis of microevolutionary patterns within the genus Ectocarpus indicated that deep gene flow between species may be an important factor in genome evolution on more recent timescales. Finally, we show that integration of large viral genomes has had a significant impact on brown algal genome content and propose that this process has persisted throughout the evolutionary history of the lineage.

genomics↗