Biology subjects

Dru, P.

Publications and source records attributed to Dru, P..

4 recordsLinked to original sources

bioRxiv2024

Chromosome-scale genome assembly and gene annotation of the hydrothermal vent annelid Alvinella pompejana yield insight into animal evolution in extreme environments

The types of genomic change needed for environmental adaptation are of great interest. Annelid worms are a large phylum found in a rich diversity of habitats, giving opportunities to explore this issue. We report the chromosome level genome sequence of the Pompeii worm, the annelid Alvinella pompejana, an inhabitant of an extreme deep-sea hydrothermal vent environment. We find strong but heterogeneously distributed genetic divergence between populations taken from either side of the equator. Using transcript data, we produced a set of gene models and analysed the predicted protein set in the light of past hypotheses about the thermotolerance of Alvinella, and compared it to other recently sequenced annelid vent worms. We do not find evidence of a more extreme genome wide amino acid composition than other species, neither do we find evidence for rapid genome evolution in the form of disrupted synteny. We discount the hypothesis of loss of amino acid biosynthesis genes associated with obligate symbioses reported in siboglinid annelids. We do find evidence of a parallel increase in the number of globin encoding genes and loss of light sensitive opsins and cryptochromes. Alvinella encodes several respiratory enzymes unusual for bilaterian animals, suggesting an ability to better tolerate hypoxic environments.

genomics↗

bioRxiv2024

First chromosome-level genome assembly of the colonial tunicate Botryllus schlosseri

Botryllus schlosseri (Tunicata) is a colonial chordate that has long been studied for its multiple developmental pathways and regenerative abilities and its genetically determined allorecognition system based on a polymorphic locus that controls chimerism and cell parasitism. We present the first chromosome-level genome assembly from an isogenic colony of B. schlosseri clade A1 using a mix of long and short reads scaf-folded using Hi-C. This haploid assembly spans 533 Mb, of which 96% are found in 16 chromosome-scale scaffolds. With a BUSCO completeness of 91.2%, this complete and contiguous B. schlosseri genome assembly provides a valuable genomic resource for the scientific community and lays the foundation for future investigations into the molecular mechanisms underlying coloniality, regeneration, histocompatibility, and the immune system in tunicates.

genomics↗

bioRxiv2023

The Mediterranean mussel, Mytilus galloprovincialis, a novel model for developmental studies of mollusks

A model organism in developmental biology is defined by its experimental amenability as well as by resources created for the model system by the scientific community. For the most powerful models, the combination of both has already yielded a thorough understanding of development. However, the number of developmental model systems is still very limited, and their phylogenetic distribution is heavily biased. Members of one of the largest animal phyla, the mollusks, for example, have long been neglected as developmental model organisms. To remedy this shortcoming, we produced a detailed developmental transcriptome for the Mediterranean mussel Mytilus galloprovincialis, a bivalve mollusk, and expanded the list of experimental protocols available for this species. Our high-quality transcriptome allowed us to identify transcriptomic signatures of developmental transitions and to perform a first comparison with the Pacific oyster Crassostrea gigas that can be used in future multi-species analyses. To allow co-labelling studies, we optimized protocols for immunohistochemistry and hybridization chain reaction and combined both techniques to create high-resolution co-expression maps of developmental genes. The resources and protocols we describe here thus represent an enormous boost for the establishment of the Mediterranean mussel as a laboratory model in developmental biology. Summary statementResources and techniques are described for the Mediterranean mussel Mytilus galloprovincialis, which, together, establish a novel model system for studying mollusk development and animal evolution.

developmental biology↗

bioRxiv2018

The genome of the jellyfish Clytia hemisphaerica and the evolution of the cnidarian life-cycle

Jellyfish (medusae) are a distinctive life-cycle stage of medusozoan cnidarians. They are major marine predators, with integrated neurosensory, muscular and organ systems. The genetic foundations of this complex form are largely unknown. We report the draft genome of the hydrozoan jellyfish Clytia hemisphaerica and use multiple transcriptomes to determine gene use across life-cycle stages. Medusa, planula larva and polyp are each characterised by distinct transcriptome signatures reflecting abrupt life cycle transitions, and all deploy a mixture of phylogenetically old and new genes. Medusa specific transcription factors, including many with bilaterian orthologs, associate with diverse neurosensory structures. Compared to Clytia, the polyp-only hydrozoan Hydra has lost many of the medusa-expressed transcription factors, despite similar overall rates of gene content and sequence evolution. Absence of expression and gene loss among Clytia orthologs of genes patterning the anthozoan aboral pole, secondary axis and endomesoderm support simplification of planulae and polyps in Hydrozoa, including loss of bilateral symmetry. Consequently, although the polyp and planula are generally considered the ancestral cnidarian forms, in Clytia the medusa maximally deploys ancestral cnidarian-bilaterian transcription factor gene complexity.

evolutionary biology↗