To function normally, organisms must ensure that genes are switched on and off at the right times and locations. Gene expression control is a complex process that requires the coordinated action of many regulatory biological molecules. Defects in the process can lead to many diseases, such as cancer. The Genomics and Regulatory Systems Unit combines computational and experimental methods to study principles of gene regulation during early organismal development, using Oikopleura dioica as a model organism.
We wish to understand the population, life cycle, and gene regulatory mecahnisms of zooplanktons in marine ecosystems using the globally distributed larvacean Oikopleura dioica. We achieve this by studying oceanic specimens and in-house animal cultures. Specifically, we will answer the following questions:
- What is the population structure of larvaceans across the world’s oceans and how do they evolve?
- In what ways do the genomes of larvaceans affect their developmental, morphological and behavioural characteristics?
- What is the interplay between the population genomic and phenotypic properties of larvaceans with the marine ecosystem?
Our unit applies computational and statistical methods to analyse genome-scale measurements. By taking a genomic perspective, we uncover global principles that encompass many biological conditions. We apply this knowledge to understand features unique to individual systems or organisms within a broader context. Ultimately, we wish to achieve quantitative explanations to the questions above in order to identify specific biological interventions that can help maintain or rebuild healthy marine ecosystems.
RESEARCH PROJECTS
Introduction
Oikopleura dioica is a globally prolific tunicate with the smallest chordate genome, measuring under 70MB. This tiny genome supports a complex organism featuring a notochord and tail, making it a non-model model organism for evo-devo studies. The loss of the canonical DNA repair pathway and significant gene losses further highlight its evolutionary adaptability. O. dioica's genomic simplicity, paired with its complex biology, makes it a captivating model for genomic studies.
Comparative genetic analysis of Oikopleura dioca among populations.
Our analysis has shown that morphologically identical populations of O. dioica spread across the globe show notable genomic differences, suggesting cryptic speciation. These differences even include gene order that is typically conserved across chordates. This unprecedented genomic flexibility highlights the species as a prime model for investigating the dynamics of gene order evolution and synteny conservation, offering insights into the balance between genomic structure and phenotypic stability.
Functional genomics of Oikopleura dioca.
It is unknown how geographically different populations with identical morphology but strikingly distinct genomes maintain their gene expression. Using advanced sequencing techniques to sequence epigenetic modifications and transcriptional patterns, we aim to uncover the mechanisms of gene regulation that make up for these differences in the genome structure.
Population genomics of Oikopleura dioca.
What is the population structure of larvaceans across the world’s oceans and how do they evolve? While we have shown significant genetic diversity among populations spanning large geographic distances, limited information exists regarding the structure and genetic diversity in local populations. We focus to address this gap by examining genotypes of the populations around the Ryukyu Islands, spanning from Kume to Amami.
Development of a new de novo genome assembly algorithm
We are developing a novel targeted assembly algorithm that excels in creating haplotype-resolved assemblies with exceptional accuracy, initially for short, simple human genomic regions but now also for a complete Oikopleura dioica genome. This method outperforms current methods by not needing trio binning or Hi-C data, aiming for broader application in small genome assembly. The goal is to assemble multiple Oikopleura genomes to explore genetic diversity within the species.
Marine climate change adaptation.
Oikopleura dioica is a globally ubiquitous plankton. How do they adapt to exceptionally diverse marine environments? By performing stress experiments (change in temperature, pH, salinity), and employing genomic and epigenomic sequencing techniques, we aim to elucidate the gene regulation mechanisms that enable them to thrive in different water conditions.
