Biology subjects

Lipinska, A.

Publications and source records attributed to Lipinska, A..

5 recordsLinked to original sources

bioRxiv2026

Chromosome-level genome assemblies of the red algae Porphyra dioica and Porphyra linearis

As one of the earliest-diverging multicellular eukaryotic lineages, the bladed Bangiales (Rhodophyta) possess a deep evolutionary history with a central role in the multi-billion-dollar global seaweed aquaculture industry. Although North Atlantic representatives are emerging candidates for regional mariculture, the scarcity of high-quality genomic resources for these taxa hinders both fundamental research and commercial optimization. To address this, we present the first chromosome-level genome assemblies for two native European species: Porphyra dioica (150.44 Mbp) and Porphyra linearis (95.22 Mbp). By integrating Oxford Nanopore Technologies (ONT) long-read sequencing with Hi-C proximity ligation, we generated highly contiguous nuclear genomes resolved into five chromosomes. Structural gene models were predicted through the BRAKER3 pipeline, identifying 12,548 and 10,382 protein-coding genes for P. dioica and P. linearis, respectively. Subsequent homology-based functional annotation characterized 57.4% and 59.8% of these predicted proteins. Supplemented by circularized organellar genomes, these reference genomes provide a critical framework for future research, enabling comparative studies of Atlantic-Pacific divergence and facilitating the development of selective breeding programs for sustainable European aquaculture.

genomics↗

bioRxiv2026

The Two Lives of Visual Working Memory: Evidence for Distinct Conscious and Unconscious Representations.

Visual working memory (vWM) is often linked to conscious experience and visual imagery, but it is typically described as a system that stores separate, independent items. These assumptions are difficult to reconcile, given the unified nature of conscious experience. Here, we test the hypothesis that vWM relies on at least two distinct representations: an underlying, unconscious memory trace and a consciously accessible, integrated representation. A total of 216 participants performed a change-detection task, in which they rated their perceptual awareness of the memory display during the maintenance interval. Critically, we manipulated the statistical properties of the displays (average item size and size variability) to probe sensitivity to unified ensemble-level structure. Results revealed a dissociation between subjective and objective measures. Perceptual awareness increased for displays with larger, more variable items, whereas objective performance improved for displays with smaller, less variable items. Despite this difference, subjective awareness still predicted performance, and even incorrect responses showed consistent biases rather than random guesses. Importantly, individual differences in imagery vividness (VVIQ) were selectively associated with subjective awareness and estimation bias, but not with objective correctness. These precision biases were further shaped by display statistics, suggesting that multiple representations can guide behavior. Together, our findings support a reinterpretation of vWM performance in which task responses can draw on both unconscious and consciously accessible representations. One possible explanation for these behavioral patterns is that subjective experience reflects integrated, ensemble-like representations, while objective performance depends more strongly on item-specific information. Public significance statementsWorking memory allows us to temporarily hold and use information, and differences in this ability are closely linked to broader cognitive skills such as intelligence. This study shows that these differences may not depend only on how much information people can store, but also on how they experience it: some individuals appear to rely more on consciously accessible, image-like representations, especially when memory is uncertain or prone to error. By demonstrating that subjective experience and the vividness of imagery can shape behavior independently of objective accuracy, these findings suggest that how we use memory may be as important as how much we can store, with implications for understanding individual differences in cognition.

neuroscience↗

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↗

bioRxiv2021

A partially sex-reversed giant kelp sheds light into the mechanisms of sexual differentiation in a UV sexual system

In UV sexual systems, sex is determined during the haploid phase of the life cycle and males have a V chromosome whereas females have a U chromosome. Previous work in the brown algal model Ectocarpus revealed that the V chromosome has a dominant role in male sex determination and suggested that the female developmental program may occur by default, triggered in the absence of the male master sex determination gene(s). Here, we describe the identification of a genetically male giant kelp strain presenting phenotypic features typical of a female, despite lacking the U-specific region. The conversion to the female developmental program is however incomplete, because gametes of this feminised male are unable to produce the sperm-attracting pheromone lamoxirene. We identify the transcriptomic patterns underlying the male and female specific developmental programs, and reveal the faster evolutionary rates of male-biased genes compared to female-biased and unbiased genes. Moreover, we show that the phenotypic feminisation of the variant strain is associated with both feminisation and de-masculinisation of gene expression patterns. Importantly, the feminisation phenotype was associated with the dramatic downregulation of two V-specific genes including a candidate sex-determining gene on the V-specific region. Our results reveal the transcriptional changes associated with sexual differentiation in a UV system with marked sexual dimorphism, and contribute to disentangling the role of sex-linked genes and autosomal gene expression in the initiation of the male and female developmental programs. Overall, the data presented here imply that the U-specific region in the giant kelp is not required to initiate the female developmental program, but is critical to produce fully functional eggs, arguing against the idea that female is the default sex in this species.

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↗