Biology subjects

Bogaert, K. A.

Publications and source records attributed to Bogaert, K. A..

5 recordsLinked to original sources

bioRxiv2026

Regulatory innovation and transcriptome turnover drive the evolution of multicellularity in brown algae

How complex multicellularity evolved repeatedly across eukaryotes remains a central unresolved question in biology. Whether principles inferred largely from animals and plants reflect universal features of multicellular evolution or lineage-specific outcomes is unknown. Here, using a stage- and tissue-resolved transcriptomic atlas spanning the full life cycles of 15 species across the brown algal radiation, comprising 639 RNA-seq libraries, we uncover general principles governing the evolution of developmental programs in an independently evolved multicellular lineage. Despite broad conservation of genome architecture and synteny, developmental and morphological diversification is accompanied by pervasive rewiring of gene expression and rapid turnover of co-expression networks, identifying regulatory evolution as a major driver of multicellular innovation. We show that evolutionarily young genes, including genes of giant viral origin, are repeatedly recruited into developmental programs, particularly in motile unicellular stages, revealing a broader role for these stages as hotspots of evolutionary novelty. We further identify lineage-specific cis-regulatory innovation linked to active chromatin and large-scale transcriptional rewiring, providing a mechanistic basis for transcriptome turnover. Together, these findings show that brown algae reinvented complex multicellularity through distinct molecular routes shaped by rapid regulatory innovation, while revealing organizational principles conserved across independent multicellular lineages.

evolutionary biology↗

bioRxiv2026

Fast zygotic genome activation in brown algae

The maternal-to-zygotic transition (MZT), during which developmental control shifts from maternal products to the zygotic genome, is a fundamental feature of embryogenesis. The prevailing model, established from animal systems, holds that maternal provisioning and nuclear-to-cytoplasmic (N/C) ratio determine the timing of zygotic genome activation (ZGA). Whether this developmental logic is conserved across multicellular eukaryotes remains unknown. Using brown algae, an independently evolved multicellular lineage spanning broad natural variation in maternal provisioning, we generated comparative embryonic transcriptomes across three species and resolved parental contributions through reciprocal crosses and allele-specific expression. Contrary to canonical animal models, all species activated their zygotic genomes immediately after fertilisation, including highly provisioned species with low N/C ratios, and showed no evidence of stable parental imprinting. These findings reveal that timing and regulation of MZT during embryogenesis is evolutionarily flexible and independently shaped across the tree of life.

developmental biology↗

bioRxiv2024

Cell wall-mediated maternal control of apical-basal patterning of the kelp Undaria pinnatifida

The role of maternal tissue in the control of embryogenesis remains enigmatic in many complex organisms. Here, we investigate the contribution of maternal tissue to apical-basal patterning in the kelp embryo. Using a modified kelp fertilisation protocol which yields synchronously developing kelp embryos, we show that detachment from maternal tissue leads to compromised robustness of apical-basal patterning. Detached embryos are rounder and often show aberrant morphologies. Furthermore, absence of contact with maternal tissue increases parthenogenesis, highlighting the critical role of maternal signals in the initial stages of kelp development. When zygotes are detached from the female gametophyte while part of the oogonial cell wall still remains attached to the egg, the proper apical-basal patterning is rescued showing a key role for the connection to the maternal cell wall in developmental patterning in kelps. This observation is reminiscent of another brown alga, Fucus, where the cell wall has been shown to play a key role in cell fate determination. In the case of kelps, the maternal oogonium mediates basal cell fate determination by providing an extrinsic patterning cue in its extracellular matrix to the future embryo. Our findings suggest a conserved mechanism across phylogenetically distant oogamous brown algal lineages, where localised secretion of sulphated F2 fucans mediate establishment of the apical-basal polarity.

developmental biology↗

bioRxiv2020

Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium

The green alga Ostreobium is an important coral holobiont member, playing key roles in skeletal decalcification and providing photosynthate to bleached corals that have lost their dinoflagellate endosymbionts. Ostreobium lives in the corals skeleton, a low-light environment with variable pH and O{square} availability. We present the Ostreobium nuclear genome and a metatranscriptomic analysis of healthy and bleached corals to improve our understanding of Ostreobiums adaptations to its extreme environment and its roles as a coral holobiont member. The Ostreobium genome has 10,663 predicted protein-coding genes and shows adaptations for life in low and variable light conditions and other stressors in the endolithic environment. This alga presents a rich repertoire of light-harvesting complex proteins but lacks many genes for photoprotection and photoreceptors. It also has a large arsenal of genes for oxidative stress response. An expansion of extracellular peptidases suggests that Ostreobium may supplement its energy needs by feeding on the organic skeletal matrix, and a diverse set of fermentation pathways allow it to live in the anoxic skeleton at night. Ostreobium depends on other holobiont members for vitamin B12, and our metatranscriptomes identify potential bacterial sources. Metatranscriptomes showed Ostreobium becoming a dominant agent of photosynthesis in bleached corals and provided evidence for variable responses among coral samples and different Ostreobium genotypes. Our work provides a comprehensive understanding of the adaptations of Ostreobium to its extreme environment and an important genomic resource to improve our comprehension of coral holobiont resilience, bleaching and recovery.

genomics↗

bioRxiv2017

The Plastid Genome In Cladophorales Green Algae Is Encoded By Hairpin Plasmids

Virtually all plastid (chloroplast) genomes are circular double-stranded DNA molecules, typically between 100-200 kb in size and encoding circa 80-250 genes. Exceptions to this universal plastid genome architecture are very few and include the dinoflagellates where genes are located on DNA minicircles. Here we report on the highly deviant chloroplast genome of Cladophorales green algae, which is entirely fragmented into hairpin plasmids. Short and long read high-throughput sequencing of DNA and RNA demonstrated that the chloroplast genes of Boodlea composita are encoded on 1-7 kb DNA contigs with an exceptionally high GC-content, each containing a long inverted repeat with one or two protein-coding genes and conserved non-coding regions putatively involved in replication and/or expression. We propose that these contigs correspond to linear single-stranded DNA molecules that fold onto themselves to form hairpin plasmids. The Boodlea chloroplast genes are highly divergent from their corresponding orthologs. The origin of this highly deviant chloroplast genome likely occurred before the emergence of the Cladophorales, and coincided with an elevated transfer of chloroplast genes to the nucleus. A chloroplast genome that is composed only of linear DNA molecules is unprecedented among eukaryotes and highlights unexpected variation in the plastid genome architecture.

genomics↗