Oleg Simakov

Genome reorganisation and expansion shape 3D genome architecture and define a distinct regulatory landscape in coleoid cephalopods

The paper investigates how genomic changes in coleoid cephalopods shape 3D genome architecture and regulatory landscapes, revealing species-specific chromatin loops and their role in neural development.

Topological mixing and irreversibility in animal chromosome evolution

The paper analyzes chromosomal evolution across 3,631 animal genomes to show that karyotype contraction and expansion drive genome evolution, with subchromosomal mixing and irreversibility shaping clade-specific trajectories.

A Chromosome-Scale Genome of Nanomia septata Reveals Extensive Rearrangement But No Clear Driver of the Unique Colony-Level Organization of Siphonophores

The paper sequenced the chromosome-scale genome of Nanomia septata, revealing genome rearrangements and expansion but no clear genomic drivers for siphonophore colony-level organization.

Chromosome-scale genome assembly of the European common cuttlefish Sepia officinalis

The paper presents a chromosome-scale genome assembly of the common cuttlefish Sepia officinalis, revealing its true karyotype and identifying cephalopod-specific gene expansions.

Genome expansions and regulatory contact entanglement help preserve ancestral metazoan synteny

The paper investigates how genome expansion in Hydra vulgaris affects chromatin loops and regulatory interactions, finding that it preserves ancestral synteny through entangled long-range regulatory configurations.

Histo-anatomical atlas and thermal tolerance of Garra rufa: A novel small teleost model adaptable to human body temperature

This paper provides a histo-anatomical atlas of Garra rufa, highlighting its unique morphological features and thermal tolerance, establishing it as a potential novel experimental model.

Giant genome of the vampire squid reveals the derived state of modern octopod karyotypes

The paper presents a draft genome of the vampire squid, revealing ancestral chromosomal features and evolutionary changes in octopod karyotypes.

The dynamic genomes of Hydra and the anciently active repeat complement of animal chromosomes

This study investigates the dynamic genomes of Hydra, revealing active transposable elements (TEs) that contribute to genome size variation and structural changes, with evolutionary implications for eukaryotic genomes.

Chromosome-level genome assembly of the doctor fish (Garra rufa)

This paper presents a chromosome-level genome assembly of Garra rufa, identifies heat shock-related genes, and highlights its evolutionary relationship to other cyprinid species.

Expansion of a single Helitron subfamily in Hydractinia symbiolongicarpus suggests a shared mechanism of cnidarian chromosomal extension

The paper identifies a Helitron subfamily expansion in Hydractinia symbiolongicarpus that contributes to genome size increase through subtelomeric amplification, suggesting a shared cnidarian mechanism.

A genome resource for the marine annelid Platynereis dumerilii

The paper presents genome assemblies for three Platynereis species to support comparative genomic studies and explore their biology.

Acceleration of genome rearrangement in clitellate annelids

The paper compares 12 clitellate genomes and 11 outgroup representatives to show that genome rearrangements in Clitellata began at their base and significantly shaped the Hox cluster evolution.

The genome of the colonial hydroid Hydractinia reveals their stem cells use a toolkit of genes shared with all animals

This study characterizes the genome and single-cell transcriptome of Hydractinia, revealing that its stem cells use a conserved gene toolkit shared with all animals.

The hagfish genome and the evolution of vertebrates

This study analyzes the hagfish genome to understand vertebrate evolution, identifying ancient genome duplications and their functional roles in vertebrate innovations.

Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny

The paper reports chromosome-level genome assemblies of two sea anemones and finds conserved chromosomal blocks across cnidarians and bilaterians, but loss of microsynteny in Hox and NK clusters.

A chromosome-level reference genome for the common octopus, Octopus vulgaris (Cuvier, 1797)

The paper presents a chromosome-level genome assembly for the common octopus, O. vulgaris, which spans 2.8 billion basepairs and supports a karyotype of 1n=30 chromosomes.

An ancient split of germline and somatic stem cell lineages in Hydra

The paper identifies two distinct stem cell lineages in Hydra, germline and somatic, and finds shared stemness genes with origins in unicellular eukaryotes.

Using a handful of transcriptomes to detect sex-linked markers in a lizard with homomorphic sex chromosomes

The paper identifies sex-linked markers in a lizard with homomorphic sex chromosomes using transcriptomes from 3 males and 3 females, enabling PCR-based sexing and comparative analysis of sex determination systems.

New Hydra Genomes Reveal Conserved Principles of Hydrozoan Transcriptional Regulation

This study generates new Hydra genomes and transcriptomic resources to uncover conserved transcriptional regulatory mechanisms in cnidarians.

Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain

The paper identifies LINE retrotransposons and long non-coding RNAs in octopus brains, suggesting their role in cognitive evolution through germline and somatic activity.

Microchromosomes are building blocks of bird, reptile and mammal chromosomes

The paper traces the origin and evolution of microchromosomes across birds, reptiles, and mammals, finding they are conserved and functionally coherent, with mammals being atypical in losing them.

The Crown Pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

The paper presents the first draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera using Illumina sequencing technologies.

Signatures of selection in the coral holobiont reveal complex adaptations to inshore environments driven by Holocene climate change

The paper identifies genetic adaptations in coral holobionts from the Great Barrier Reef's inshore regions linked to Holocene climate change.

The quagga mussel genome and the evolution of freshwater tolerance

The paper sequenced the quagga mussel genome to identify evolutionary adaptations for freshwater tolerance, finding expanded aquaporin genes and osmoregulatory structures involved in embryonic osmoregulation.