Biology subjects

Coelho, S. M.

Publications and source records attributed to Coelho, S. M..

At least 19 recordsLinked to original sources

bioRxiv2026

Endogenous gene tagging in the model brown alga Ectocarpus using a simplified CRISPR/Cas method

Brown algae represent one of the few eukaryotic lineages to have independently evolved complex multicellularity, providing a powerful comparative system for investigating the molecular and evolutionary principles underlying multicellular development. Ectocarpus has emerged as the principal model for this lineage, supported by extensive genomic and transcriptomic resources. However, mechanistic and functional studies have remained limited by the available reverse-genetic tools. While recent CRISPR-Cas developments have enabled targeted gene knock-outs, the lack of knock-in (KI) approaches for endogenous protein tagging and precise genomic insertion remains a major experimental bottleneck. Here, we establish a comprehensive CRISPR-Cas genome-engineering framework for Ectocarpus that enables both targeted gene disruption and precise genomic insertion. We demonstrate efficient knock-in of multiple peptide tags at endogenous loci, enabling direct analysis of native proteins. By combining robust gene knock-out with endogenous protein tagging, this framework substantially expands the experimental possibilities for brown algal research and establishes Ectocarpus as a genetically tractable system for functional genomics, providing a foundation for genome engineering across stramenopiles.

developmental biology↗

bioRxiv2026

Haplotype tagging sheds light on speciation between two divergent cryptic species of the brown algae Ectocarpus

Understanding how genome-wide divergence translates to barriers to gene flow is a central question in speciation research, particularly in marine environments where interconnected habitats frequently accommodate cryptic diversity. Using linked-read whole-genome data from the brown alga Ectocarpus, we investigated genome-wide reproductive isolation between two cryptic brown algal species E. siliculosus and E. crouaniorum across replicated hybrid zones in Europe and Chile. We first uncover deep genetic structure within E. crouaniorum, revealing a more intricate species complex than previously recognized. Despite this complexity, we found parallel patterns of asymmetric introgression that emerged independently in Europe and Chile, where we detected both, F1 and low-level introgressed individuals. However, the specific lineage pairs involved in hybridization depended on local demographic history. Demographic modeling further indicated that reproductive isolation strengthens gradually with divergence time and differs markedly between geographic regions, with ongoing asymmetric gene flow even between lineage pairs where hybrids were not detected in the field. In all cases, the genomic landscape of hybridization is consistent with a polygenic, genome-wide barrier to gene flow rather than a few large-effect regions. Our results show that cryptic speciation in brown algae is driven by repeatable, regionally parallel architectures of genome-wide reproductive isolation which is shaped by ecological and demographic context.

evolutionary biology↗

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↗

bioRxiv2026

Ribosome profiling reveals widespread translational control across developmental stages in the brown alga Ectocarpus

Translation represents a central regulatory layer of gene expression, enabling rapid and dynamic modulation of protein output. While its importance in development is well established, it remains poorly characterized outside animals and land plants. Brown algae, and in particular Ectocarpus, offer a compelling system to investigate translational regulation in development, having evolved multicellularity independently of other major eukaryotic lineages and exhibiting a complex life cycle with distinct haploid and diploid developmental programs. Although transcriptional regulation contributes to Ectocarpus development, the striking similarity of transcriptomes across life cycle stages indicates that transcription alone is insufficient to explain their distinct developmental identities, pointing to a major role for post-transcriptional regulation. Here, we establish ribosome profiling in Ectocarpus and define its translatome across key developmental stages. We uncover widespread stage- and sex-specific translational regulation, with post-transcriptional buffering emerging as the predominant mode of control. Genes subject to translational regulation exhibit optimized codon usage, broader transcriptional profiles and shorter 3' UTRs. These genomic features are associated with variation in translation efficiency. Collectively, these results provide the first comprehensive characterization of the Ectocarpus translatome and highlight a major role for translational regulation in developmental gene expression in an independently evolved multicellular lineage.

developmental biology↗

bioRxiv2026

PKN is a sex- and species-specific fertilization factor in brown algae

Fertilization, the union of male and female gametes, is central to sexual reproduction, yet the molecular mechanisms that ensure partner recognition and enforce species specificity remain elusive. Here we identify PKN, a previously uncharacterized transmembrane protein expressed exclusively in female gametes of brown algae, as an essential determinant of fertilization. Loss of PKN abolishes fertilization without affecting earlier mating steps, including gamete attraction, placing its function as a key mediator of male-female recognition. PKN contains extracellular {beta}-propeller and mucin-like domains that are enriched in predicted glycosylation sites and rapidly evolving, consistent with a role in species-specific cell-cell recognition. Notably, PKN enforces reproductive isolation within the genus Scytosiphon by preventing interspecific fertilization. Together, these findings uncover a female-encoded recognition mechanism in brown algae and reveal protein-glycan interfaces as a conserved strategy for enforcing sex- and species-specific fertilization across Eukaryotes.

developmental biology↗

bioRxiv2025

Lineage-wide evolution of 3D genome organisation and centromeres in brown algae

Although 3D genome architecture has been described for an increasing number of plant and algal species, comparative analyses across closely related lineages remain scarce. Consequently, fundamental questions persist about how chromatin organization is maintained or reshaped over deep evolutionary time, and how such changes relate to life-history traits, genome size, and linear genome features. Here, we present a comprehensive analysis of 3D chromatin architecture across six brown algae species and one outgroup, spanning the phylogenetic breadth and biological complexity of this key photosynthetic lineage. We show that compact genomes lack chromatin domains whereas larger, transposable element-rich genomes of morphologically complex taxa tend to exhibit structured organization including TAD-like domains. We investigate chromatin folding patterns and gene expression over evolutionary time and uncover 3D chromatin features associated with transitions in sexual systems. Moreover, we reconstruct the ancestral brown algal karyotype, revealing deeply conserved macrosynteny and providing a new framework for interpreting chromosome-scale genome dynamics. Finally, we uncover an ancient and highly conserved association between centromeres and chromodomain-encoding retrotransposons, revealing a remarkable example of convergence in centromere-transposon co-evolution between brown algae and angio-sperms, and one of the most stable examples of centromere-linked transposable elements known in eukaryotes. Together, our findings elucidate the evolutionary history of 3D chromatin and linear genome architectures across an entire eukaryotic lineage and highlight extreme centromere stability in brown algae, providing a powerful point of comparison with land plants and deepening our understanding of genome evolution in independent multicellular lineages. One sentence summaryWe present a lineage-wide evolutionary analysis of 3D genome architecture and organization across brown algae, revealing conserved chromosomal features, lineage-specific rearrangements, and long-term co-evolution of centromeres and retrotransposons that together illuminate how nuclear architecture evolves over hundreds of millions of years.

genomics↗

bioRxiv2025

Rewiring of chromatin regulation underlies the evolution of brown algal multicellularity

Chromatin structure plays a central role in regulating transcription, genome stability, and epigenetic inheritance in eukaryotes. Much of our understanding of chromatin architecture and histone post-translational modifications (hPTMs) comes from a narrow set of animal and plant models, but emerging data from non-model lineages are challenging canonical views of how chromatin functions across the tree of life. Brown algae are complex multicellular eukaryotes that provide a unique perspective on chromatin evolution given their independent origin of complex multicellularity. Here, we compile the chromatin toolkit of brown algae and show that canonical silencing systems involving DNA cytosine methylation and PRC2-mediated H3K27 methylation were lost early in their evolution. By generating hPTM profiles from diverse brown algal clades, we resolve the nature and regulatory roles of chromatin states in this lineage and show how H3K79 methylation emerged and diversified as a repressive system. We further uncover sex-specific reconfigurations in species with varying degrees of sexual dimorphism and reconstruct the ancestral regulatory landscape that likely preceded the emergence of brown algae. Together, our findings illuminate the dynamic evolution of chromatin regulation in a distinct multicellular lineage and challenge assumptions about the universality of chromatin-based mechanisms across eukaryotes.

evolutionary biology↗

bioRxiv2025

Latent endogenous viral elements drive active infection and inheritance in a multicellular host

Endogenous viral elements (EVEs) inserted in host genomes are often regarded as inert relics of past infections. Whether they can retain infective potential and contribute to active viral cycles has remained unresolved. Here, we demonstrate that EVEs in the brown alga Ectocarpus can reactivate and drive productive viral infections. Using long-read sequencing and transcriptomics, we identify full-length, transcriptionally active giant viruses integrated within the host genome. Reactivation of these elements is specific to reproductive cells, transforming gametangia into virus-producing structures, and viral symptoms strictly correlate to the presence of active EVEs. Genetic analyses show that these elements are stably inherited, while their activation is precisely regulated by developmental and environmental cues. By resolving the genomic integration sites, we propose a mechanism for Phaeovirus integration and replication. This work provides the first direct evidence that giant EVEs can reactivate, replicate, and transmit both horizontally and vertically in a multicellular eukaryote, establishing a new model to explore latency, inheritance and the evolutionary impact of large dsDNA viruses.

genetics↗

bioRxiv2025

Efficient CRISPR Cas genome editing in brown algae

Brown algae represent the third most complex lineage to evolve multicellularity, independently from plants and animals. However, functional studies of their development, evolution, and biology have been constrained by the lack of efficient and scalable genome editing tools. Here, we report a robust, high-efficiency, and transgene-free CRISPR-Cas12-based genome editing method applicable across four ecologically and biotechnologically important brown algal species. Using Ectocarpus as a model, we optimized a PEG-mediated RNP delivery system employing a temperature-tolerant Cas12 variant, achieving reproducible, high-efficiency editing across multiple loci without the need for cloning or specialized equipment. As proof of concept, we precisely recapitulated the hallmark imm mutant phenotype by editing the IMMEDIATE UPRIGHT (IMM) locus, a phenotype previously described only from a rare spontaneous mutation. APT/2-FA-based selection further improved specificity with minimal false positives. The protocol was readily transferrable to other species, including kelps long considered recalcitrant to transformation. This platform now makes functional genomics accessible in brown algae, enabling mechanistic dissection of developmental processes, life cycle transitions, and the independent origins of complex multicellularity. Our work enables the broader adoption of brown algae as experimental models and provides a valuable platform for marine biotechnology and evolutionary research. MotivationAlthough most of biodiversity on Earth lives in oceans, a significant proportion of its organisms remain largely uncharacterized. Brown algae represent one of such understudied group of marine photosynthetic eukaryotes. Despite their importance as emerging models for developmental evolution and blue biotechnology, functional genomics in brown algae has remained largely inaccessible due to a lack of efficient and scalable genome editing tools. Our aim is to democratize genome editing in brown algae by developing a high-efficiency, transgene-free protocol that works across multiple species, without the need for specialized equipment. This high-efficiency method fully enables the field of functional genomics in an unexplored multicellular lineage. HighlightsO_LIHigh-efficiency, low-cost genome editing in brown algae without specialized equipment. C_LIO_LI{middle dot}Applicable to non-model species, including those of economic importance. C_LI

molecular biology↗

bioRxiv2025

The expanded Bostrychia moritziana genome unveils evolution in the most diverse and complex order of red algae

Red seaweeds form part of an ancient lineage of eukaryotes that were one of the first to evolve multicellularity. Although they share a common evolutionary origin with modern-day plants and display complex multicellular development, we still lack comprehensive genome data from the most highly-evolved groups of red algae. Here, we present a chromosome-level genome assembly of Bostrychia moritziana, a species that is classified into the Rhodomelaceae family of the Ceramiales order, both of which constitute the largest and most diverse family and order of red algae, respectively. Contrary to the commonly held view that red algae generally have small genomes, we report significant genome size expansion in Bostrychia and other Ceramiales species, which we posit as one of at least three independent genome expansion events that occurred during red algal evolution. Our analyses suggest that these expansions do not involve polyploidy or ancient whole genome duplications, but in the case of Bostrychia appear to be largely driven by the dramatic proliferation of a single lineage of giant Plavaka DNA transposons. Consistent with increased genome size, we identify a substantial increase in gene content in Bostrychia that was shaped both by de novo gene emergence and by the amplification of gene families in common with other Ceramiales seaweeds, providing key insight into the genetic adaptations underpinning the evolutionary success of this species-rich order. Finally, our sex-specific assemblies enabled us to resolve the UV sex chromosomes in Bostrychia, which feature expanded gene-rich sex-linked regions. Notably, these sex-linked regions each harbour a distinct TALE-HD transcription factor orthologous to ancient regulators of haploid-diploid transitions in other multicellular lineages. Together, our findings offer a unique perspective of the genomic adaptations driving red algal diversity and demonstrate how this highly successful group of red seaweeds can provide insight into the evolutionary origins and universal principles of complex multicellular plant life.

genomics↗

bioRxiv2024

Exploring Meiosis in Brown Algae: Meiotic Axis Proteins in the model brown alga Ectocarpus

Most extant eukaryotic systems share core meiosis-specific genes, suggesting meiosis evolved only once in the last eukaryotic common ancestor (LECA). These genes have been characterized as master regulators of meiotic recombination, ensuring genetically diverse lineages. However, our understanding is limited as eukaryotic organisms beyond the animal, plant, and yeast lineages remain poorly understood. Recently, core meiotic genes have been identified in the genome of the model brown alga Ectocarpus, but currently lack proper characterization. Here, we combine bioinformatic, structural, and biochemical approaches to characterise the axial element orthologs, meiotic Ectocarpus HORMA domain protein (ecHOP1) and its interactor, reductional division protein 1 (ecRED1), in order to elucidate the molecular mechanisms of synaptonemal complex (SC) and double strand break (DSB) formation in brown algae. We highlight novel domain architecture within ecHOP1 and ecRED1 that support HORMA domain conformational switches and quantify the thermodynamic parameters of these interactions. Together, our data suggests that brown algae may employ alternative HORMA domain regulation mechanisms compared with animal, plant and yeast systems, and provide clues for future studies on the evolutionary constraints and adaptation of meiosis across the tree of life.

biochemistry↗

bioRxiv2024

Structural and evolutionary features of red algal UV sex chromosomes

BackgroundSex chromosomes in red algae have remained relatively understudied, despite their fundamental role in understanding the evolution of sex determination across eukaryotes. In this study, we investigate the structure, gene composition, and evolutionary history of the U and V sex chromosomes in four Gracilaria species, which diverged approximately 100 million years ago (MYA). ResultsOur findings reveal that UV sex chromosomes, previously identified in green and brown algae as well as bryophytes, have also evolved in red algae, contributing to the diversity of sex determination systems across eukaryotes. The shared orthology of conserved sex-determining region (SDR) genes between Gracilaria and distantly related red algae suggests that this system may have originated approximately 390 MYA, making it one of the oldest known sex chromosome systems. The SDR in Gracilaria is relatively small but contains conserved gametologs and V-specific genes involved in transcriptional regulation and signaling, suggesting their essential role in sexual differentiation. Unlike the conserved V-specific genes, U-specific genes appear absent, pointing to a dominant role of the V chromosome in sex determination. The evolution of Gracilaria sex chromosomes involved recombination suppression, gene relocations, duplications, and potential gene loss. Despite their ancient origin, the sex chromosomes show low levels of degeneration, likely due to haploid purifying selection during the gametophytic phase of the life cycle. ConclusionThis study provides the first detailed characterization of the U and V sex chromosomes in red algae, preparing the ground for future studies on reproductive life cycles and speciation in this understudied group of eukaryotes.

evolutionary biology↗

bioRxiv2024

3D chromatin maps of a brown alga reveal U/V sex chromosome spatial organisation

Sex chromosomes are unique genomic regions displaying structural and evolutionary features that distinguish them markedly from autosomes. Although nuclear three dimensional (3D) folding of chromatin structure is im-portant for gene expression regulation and correct developmental programs, very little is known about the 3D architecture of sex chromosomes within the nucleus, and how that impacts their function in sex determination. Here, we determine the sex-specific 3D organization of the model brown alga Ectocarpus chromosomes at 2 kb resolution, by comprehensively mapping long-range chromosomal interactions using Hi-C coupled with Oxford Nanopore long reads. We report that Ectocarpus interphase chromatin exhibits a non-Rabl conformation, with strong contacts among telomeres and among centromeres, which feature centromere-specific LTR retrotranspos-ons. The Ectocarpus chromosomes do not contain large local interactive domains that resemble TADs described in animals, but their 3D genome organization is largely shaped by post-translational modifications of histone pro-teins that regulate chromatin compaction and mediate transcriptional regulation. We describe the spatial confor-mation and sub-nuclear positioning of the sex determining region (SDR) within the U and V chromosomes and show that these regions are very insulated and span the centromeres. Moreover, we link sex-specific chromatin dynamics and gene expression levels to the 3D chromatin structure of U and V chromosomes. Finally, we uncover the unique conformation of a large genomic region on chromosome 6 harboring an endogenous viral element (EVE), providing insights regarding the functional significance of the chromatin organisation of latent giant dsDNA virus.

genomics↗

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↗

bioRxiv2024

A Transcriptomic Hourglass In Brown Algae

Complex multicellularity has emerged independently across a few eukaryotic lineages and is often associated with the rise of elaborate, tightly coordinated developmental processes. How multicellularity and development are interconnected in evolution is a major question in biology. The hourglass model of embryonic evolution depicts how developmental processes are conserved during evolution, predicting morphological and molecular divergence in early and late embryo stages, bridged by a conserved mid-embryonic (phylotypic) period linked to the formation of the basic body plan. Initially found in animal embryos, molecular hourglass patterns have recently been proposed for land plants and fungi. However, whether the hourglass pattern is an intrinsic feature of all developmentally complex eukaryotic lineages remains elusive. Here, we tested the prevalence of a (molecular) hourglass in the brown algae, the third most developmentally complex lineage on earth that has evolved multicellularity independently from animals, fungi, and plants. By exploring the evolutionary transcriptome of brown algae with distinct morphological complexities, we uncovered an hourglass pattern during embryogenesis in developmentally complex species. Filamentous algae without a canonical embryogenesis display an evolutionary transcriptome that is most conserved in multicellular stages of the life cycle, whereas unicellular stages are more rapidly evolving. Our findings suggest that transcriptome conservation in brown algae is associated with cell differentiation stages, but not necessarily linked to embryogenesis. Together with previous work in animals, plants and fungi, we provide further evidence for the generality of a developmental hourglass pattern across complex multicellular eukaryotes.

evolutionary biology↗

bioRxiv2024

Developmental pathways underlying sexual differentiation in a U/V sex chromosome system

In many multicellular organisms, sexual development is not determined by XX/XY or ZW/ZZ systems but by U/V sex chromosomes. In U/V systems, sex determination occurs in the haploid phase, with U chromosomes in females and V chromosomes in males. Here, we explore several male, female and partially sex-reversed male lines of giant kelp to decipher how U/V sex chromosomes and autosomes initiate male versus female development. We identify a key set of genes on the sex chromosomes involved in triggering sexual development, and characterise autosomal effector genes underlying sexual differentiation. We show that male, but not female, development involves large-scale transcriptome reorganisation with pervasive enrichment in regulatory genes, faster evolutionary rates, and high species specificity of male-biased genes. Our observations imply that a female-like phenotype is the "ground state", which is complemented by the presence of a U-chromosome, but overridden by a dominant male developmental program in the presence of a V-chromosome.

developmental biology↗

bioRxiv2024

Origin and evolutionary trajectories of brown algal sex chromosomes

Sex chromosomes fall into three classes: XX/XY, ZW/ZZ and U/V systems. The rise, evolution and demise of U/V systems has remained an evolutionary enigma. Here, we analyse genomes spanning the entire brown algal phylogeny to decipher their sex-determination evolutionary history. U/V sex chromosomes emerged between 450 and 224 million years ago, when a region containing the pivotal male-determinant MIN located in a discrete region in proto-U and proto-V chromosomes ceased recombining. Over time, nested inversions led to step-wise expansions of the sex locus, accompanying increasing morphological complexity and sexual differentiation of brown seaweeds. Unlike XX/XY and ZW/ZZ, brown algal U/V evolve mainly by gene gain, showing minimal degeneration. They are structurally dynamic and act as genomic cradles fostering the birth of new genes, potentially from ancestrally non coding sequences. Our analyses demonstrate that hermaphroditism arose from ancestral males that acquired U-specific genes by ectopic recombination, and that in the transition from a U/V to an XX/XY system, V-specific genes moved down the genetic hierarchy of sex determination. Both events lead to the demise of U and V and erosion of their specific genomic characteristics. Taken together, our findings offer a comprehensive model of U/V sex chromosome evolution.

evolutionary biology↗