Biology subjects

Gillard, G.

Publications and source records attributed to Gillard, G..

6 recordsLinked to original sources

bioRxiv2025

Salmonids reveal principles of regulatory evolution following autotetraploidization

Early vertebrate autotetraploidization events may have enabled major innovations by expanding the genetic material for functional diversification, yet their ancient timing obscures how genome doubling reshaped gene regulatory evolution. Salmonids provide a unique window to these mechanisms, because they experienced a comparatively recent autotetraploidization and are earlier in the rediploidization process - which creates new genes and regulatory elements during evolution. Here, using large-scale multiomics spanning embryonic and adult tissues in two salmonids, we investigate gene regulatory evolution following genome doubling and rediploidization, which we show is governed by developmental and tissue-specific context, with a period of maximal constraint at advanced stages of embryogenesis. This work advances understanding of vertebrate genome evolution, while providing an open resource supporting salmonid aquaculture and conservation.

evolutionary biology↗

bioRxiv2024

Empowering bioinformatics communities with Nextflow and nf-core

Standardised analysis pipelines are an important part of FAIR bioinformatics research. Over the last decade, there has been a notable shift from point-and-click pipeline solutions such as Galaxy towards command-line solutions such as Nextflow and Snakemake. We report on recent developments in the nf-core and Nextflow frameworks that have led to widespread adoption across many scientific communities. We describe how adopting nf-core standards enables faster development, improved interoperability, and collaboration with the >8,000 members of the nf-core community. The recent development of Nextflow Domain-Specific Language 2 (DSL2) allows pipeline components to be shared and combined across projects. The nf-core community has harnessed this with a library of modules and subworkflows that can be integrated into any Nextflow pipeline, enabling research communities to progressively transition to nf-core best practices. We present a case study of nf-core adoption by six European research consortia, grouped under the EuroFAANG umbrella and dedicated to farmed animal genomics. We believe that the process outlined in this report can inspire many large consortia to seek harmonisation of their data analysis procedures.

bioinformatics↗

bioRxiv2023

β-H-Spectrin is a key component of an apical-medial hub of proteins during cell wedging in tube morphogenesis

Coordinated cell shape changes are a major driver of tissue morphogenesis during development, with apical constriction or wedging of groups of epithelial cells for instance leading to tissue bending in folding or budding processes. During the budding of the tubes of the salivary glands in the Drosophila embryo we previously identified a key interplay between the apical-medial actomyosin that drives apical constriction with the underlying longitudinal microtubule array. At this microtubule-actomyosin interface a hub of proteins accumulates: in addition to the microtubule-actin crosslinker Shot and the minus-end-binder Patronin, we identified two actin-crosslinkers, {beta}-H-Spectrin and Filamin, and the multi-PDZ protein Big bang as components of this apical-medial hub. Tissue-specific degradation of {beta}-H-Spectrin led to reduction of apical-medial Big bang, F-actin, Shot and Patronin and concomittant defects in apical constriction and tube morphogenesis. Residual Patronin still present in the apical-medial position was sufficient to assist microtubule reorganisation into the longitudinal array. In contrast to Patronin and Shot, neither {beta}-H-Spectrin nor Big bang required microtubules for their localisation. {beta}-H-Spectrin instead appeared to be recruited to the apical-medial domain via binding to phosphoinositides that accumulated here. Overexpression of a {beta}-H-Spectrin fragment containing its PH domain displaced endogenous {beta}-H-Spectrin from the apical-medial domain and led to strong morphogenetic defects. The interconnected hub therefore required the synergy of membrane-associated {beta}-H-Spectrin and microtubules and their respective interactors for its assembly and function in sustaining the apical constriction during tube invagination.

cell biology↗

bioRxiv2020

A release-and-capture mechanism generates an essential non-centrosomal microtubule array during tube budding

Non-centrosomal microtubule arrays serve crucial functions in cells, yet the mechanisms of their generation are poorly understood. During budding of the epithelial tubes of the salivary glands in the Drosophila embryo, we previously demonstrated that the activity of pulsatile apical-medial actomyosin depends on a longitudinal non-centrosomal microtubule array. Here we uncover that the exit from the last embryonic division cycle of the epidermal cells of the salivary gland placode leads to the mother centrosome in the cells losing all microtubule-nucleation capacity. This restriction of nucleation activity to the daughter centrosome is key for proper morphogenesis. Furthermore, the microtubule-severing protein Katanin and the minus-end-binding protein Patronin accumulate in an apical-medial position only in placodal cells. Loss of either in the placode prevents formation of the longitudinal microtubule array and leads to loss of apical-medial actomyosin and apical constriction. We thus propose a mechanism whereby Katanin-severing at the single active centrosome releases microtubule minus-ends that are then anchored by apical-medial Patronin to promote formation of the longitudinal microtubule array crucial for apical constriction and tube formation.

developmental biology↗

bioRxiv2017

Coordinated morphogenesis through tension-induced planar polarity

Tissues from different developmental origins must interact to achieve coordinated morphogenesis at the level of a whole organism. C. elegans embryonic elongation is controlled by actomyosin dynamics which trigger cell shape changes in the epidermis and by muscle contractions, but how the two processes are coordinated is not known. We found that a tissue-wide tension generated by muscle contractions and relayed by tendon-like hemidesmosomes in the dorso-ventral epidermis is required to establish a planar polarity of the apical PAR module in the lateral epidermis. This planar polarized PAR module then controls actin planar organization, thus determining the orientation of cell shape changes and the elongation axis of the whole embryo. This trans-tissular mechanotransduction pathway thus contributes to coordinate the morphogenesis of three embryonic tissues.

developmental biology↗

bioRxiv2017

Diet And Life Stage Associated Remodeling Of Lipid Metabolism Regulation In The Duplicated Atlantic Salmon Genome

Atlantic salmon migrates from rivers to sea to feed, grow and develop gonads before returning to spawn in freshwater. These habitat shifts require great phenotypic plasticity. To address the unresolved question of how the shift in diet between fresh and saltwater affects the regulation of metabolic function, we fed salmon contrasting diets in each of the two life stages. Combining transcriptomics with comparative genomics, we found that lipid metabolism undergoes a concerted shift between fresh- and saltwater stages. Lipogenesis and lipid transport become less active in liver after transition to saltwater, while genes for lipid uptake in gut are more expressed in lipid-rich seawater environments. We assess how the whole-genome duplication that gave rise to the salmonids has impacted the evolution of lipid metabolism, and find signatures of pathway-specific selection pressure on gene duplicates, as well as a limited number of cases of increased gene dosage.

evolutionary biology↗