Biology subjects

Simakov, O.

Publications and source records attributed to Simakov, O..

3 recordsLinked to original sources

bioRxiv2020

Whole-body integration of gene expression and single-cell morphology

Animal bodies are composed of hundreds of cell types that differ in location, morphology, cytoarchitecture, and physiology. This is reflected by cell type-specific transcription factors and downstream effector genes implementing functional specialisation. Here, we establish and explore the link between cell type-specific gene expression and subcellular morphology for the entire body of the marine annelid Platynereis dumerilii. For this, we registered a whole-body cellular expression atlas to a high-resolution electron microscopy dataset, automatically segmented all cell somata and nuclei, and clustered the cells according to gene expression or morphological parameters. We show that collective gene expression most efficiently identifies spatially coherent groups of cells that match anatomical boundaries, which indicates that combinations of regionally expressed transcription factors specify tissue identity. We provide an integrated browser as a Fiji plugin to readily explore, analyse and visualise multimodal datasets with remote on-demand access to all available datasets.

cell biology↗

bioRxiv2020

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

Climate change at the Pleistocene/Holocene boundary reshaped many coastal landscapes, and provides an opportunity to study recent adaptive processes in marine species and ecosystems including coral reefs. On the Great Barrier Reef (GBR) sea level rise flooded a vast shelf creating a distinct inshore region which now harbours extensive coral assemblages despite being subject to relatively high turbidity, freshwater input and thermal fluctuations. To investigate how the coral holobiont has adapted to these conditions we first generated a highly contiguous genome assembly for Acropora tenuis based on long-read sequencing, and then used shallow whole-genome resequencing of 148 Acropora tenuis colonies from five inshore locations to model demographic history, identify signatures of selection and profile symbiont communities. We show that corals from Magnetic Island, located in the central inshore region of the GBR, are genetically distinct from those 50-500km further north, reflecting a Pleistocene (250-600Kya) split, whereas photosymbiont genotypes differ between reefs in a pattern more likely to reflect contemporary (Holocene) conditions. We also identified loci in the coral host genome with signatures of positive selection in the northern population and used coalescent simulations to show that these are unlikely to be accounted for by demographic history. Genes at these loci have roles in a diverse range of processes that includes heterotrophic nutrition, osmotic regulation, skeletal development and the establishment and maintenance of symbiosis. Our results show that, in the case of A. tenuis holobionts from the inshore GBR, the genomes of both the coral host and the primary photosymbiont of have been significantly shaped by their environment and illustrate the complexity of adaptations that have occurred in response to past climate change.

genomics↗

bioRxiv2018

The quagga mussel genome and the evolution of freshwater tolerance

European freshwater dreissenid mussels evolved from marine ancestors during the Miocene approximately 30 million years ago and today include some of the most successful and destructive invasive invertebrate species of temperate freshwater environments. Here we sequenced the genome of the quagga mussel Dreissena rostriformis to identify evolutionary adaptations involved in embryonic osmoregulation. We found high gene expression levels of a novel subfamily of lophotrochozoan-specific aquaporin water channel, a vacuolar ATPase and a sodium/hydrogen exchanger during early cleavage, a period defined by the formation of inter-cellular fluid-filled cleavage cavities. Independent expansions of the lophotrochoaquaporin clade that coincide with at least five independent colonisation events of freshwater environments confirm their central role in freshwater adaptation. The pattern of repeated aquaporin expansion and the evolution of membrane-bound fluid-filled osmoregulatory structures in diverse taxa points to a fundamental principle guiding the evolution of freshwater tolerance that may provide a framework for future efforts towards invasive species control.

genomics↗