Biology subjects

Avdievich, E.

Publications and source records attributed to Avdievich, E..

4 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↗

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↗

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

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↗