Biology subjects

Luthringer, R.

Publications and source records attributed to Luthringer, R..

11 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

Life-cycle plasticity enables conditional asexual reproduction in a kelp

Many organisms alternate between distinct life stages and can reproduce either sexually or asexually, yet the mechanisms coordinating these developmental and reproductive transitions remain poorly understood. Here, we investigate the molecular basis of life stage identity and reproductive mode in the kelp Laminaria pallida, a multicellular organism with a complex life cycle. By combining gene expression analyses with developmental experiments and natural population-level approaches, we identify the genetic networks that govern developmental state transitions in both sexual and asexual contexts. We show that the capacity for asexual reproduction is broadly retained but rarely expressed in natural populations and is associated with reduced fitness. Moreover, we find that the presence of potential mating partners suppresses asexual development, revealing that reproductive mode is actively adjusted in response to reproductive opportunities. Together, these findings suggest that asexual reproduction functions as a conditional alternative to sex, promoting persistence when sexual reproduction is constrained while preserving the long-term benefits of sexual reproduction when mates are available. More broadly, our results reveal how organisms integrate developmental, environmental, and reproductive cues to balance alternative reproductive strategies across complex life cycles.

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↗

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↗

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

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↗

bioRxiv2023

Role of transcription and translation during the early development of the brown alga Ectocarpus

Background and aimsParthenogenesis, the embryonal development of an unfused gamete, is a widespread trait within the brown algae (Phaeophyceae). We hypothesized that the parthenogenetic development of male gametes of the model brown alga Ectocarpus species 7 would rapidly be dependent on de novo transcription and translation because of the small size of the gamete cell. MethodsWe followed the development of male Ectocarpus gametes to parthenosporophytes in the presence of either the transcription inhibitor thiolutin or the translation inhibitor emetine. Responses in morphology and growth were compared to development in inhibitor-free control conditions at three time points over 12 days. Potentially persistent inhibitor effects were then investigated by growing parthenosporophytes in an inhibitor-free post-culture for 14 days. Key resultsThiolutin did not affect gamete germination, but growth of parthenosporophytes was significantly delayed. While almost all control parthenosporophytes had grown larger than 10 cells over 12 days, thiolutin inhibited growth beyond a size of 5-10 cells. The effects of thiolutin were reversible in the post-culture. Consequences of the emetine treatment were more severe, germination was already strongly inhibited by day 5, and on average only 27.5% of emetine-treated gametes had completed the first cell division on day 12. Emetine fully inhibited development beyond the 5-cell stage during the treatment, and induced morphological abnormalities (i.e., round cell shape and abnormal cell division planes) which persisted throughout the post-culture. ConclusionsThese results imply that Ectocarpus gametes contain sufficient proteins to germinate, and that the first cell cycles of parthenogenetic gamete development presumably utilize mRNA already present in the gametes. We discuss that storing mRNA and proteins in the developing gametes before release may be an adaptive trait in Ectocarpus to ensure quick development after fertilization, or alternatively the vegetative completion of the life cycle in the absence of mates.

developmental biology↗

bioRxiv2019

Evolution of life cycles and reproductive traits: insights from 1 the brown algae

Brown algae are characterized by a remarkable diversity of life cycles, sexual systems, and reproductive modes, and these traits seem to be very labile across the whole group. This diversity makes them ideal models to test existing theories on the evolution of alternation between generations, and to examine correlations between life cycle and reproductive life history traits. In this study, we investigate the dynamics of trait evolution for four life-history traits: life cycle, sexual system, level of gamete dimorphism and gamete parthenogenetic capacity. We assign states to up to 70 species in a multi-gene phylogeny of brown algae, and use maximum likelihood and Bayesian analyses of correlated evolution, taking phylogeny into account, to test for correlations between life history traits and sexual systems, and to investigate the sequence of trait acquisition. Our analyses are consistent with the prediction that diploid growth may evolve because it allows the complementation of deleterious mutations, and that haploid sex determination is ancestral in relation to diploid sex determination. However, the idea that increased zygotic and diploid growth is associated with increased sexual dimorphism is not supported by our analysis. Finally, it appears that in the brown algae isogamous species evolved from anisogamous ancestors.

evolutionary biology↗

bioRxiv2018

A key role for UV sex chromosomes in the regulation of parthenogenesis in the brown alga Ectocarpus

AO_SCPLOWBSTRACTC_SCPLOWAlthough evolutionary transitions from sexual to asexual reproduction are frequent in eukaryotes, the genetic bases of these shifts remain largely elusive. Here, we used classic quantitative trait analysis, combined with genomic and transcriptomic information to dissect the genetic basis of asexual, parthenogenetic reproduction in the brown alga Ectocarpus. We found that parthenogenesis is controlled by the sex locus, together with two additional autosomal loci, highlight the key role of the sex chromosome as a major regulator of asexual reproduction. Importantly, we identify several negative effects of parthenogenesis on male fitness, but also different fitness effects between parthenogenesis and life cycle generations, supporting the idea that parthenogenesis may be under both sexual selection and generation/ploidally-antagonistic selection. Overall, our data provide the first empirical illustration, to our knowledge, of a trade-off between the haploid and diploid stages of the life cycle, where distinct parthenogenesis alleles have opposing effects on sexual and asexual reproduction and may contribute to the maintenance of genetic variation. These types of fitness trade-offs have profound evolutionary implications in natural populations and may structure life history evolution in organisms with haploid-diploid life cycles.

evolutionary biology↗