Network-based genomics


Network-based genomics
Photo: Photo Pixabay

We develop network-based methods for comparative regulomics, systems genetics, evolutionary studies, and analysis of host-microbiota interactions. 


EVOTREE: What makes a tree a tree? 

Forests are the world’s largest terrestrial carbon sink, with trees representing a sustainable and renewable source of ligno-cellulose raw material for traditional and future industries. Despite the vital importance of forests to life on earth, and their vast future potential, we still cannot answer the most fundamental question: What makes a tree a tree?

We aim to understand the process of wood formation in angiosperm and gymnosperm tree species by modelling the regulatory networks orchestrating the differentiation of stem cells into woody tissues. We are integrating multi-omics data to infer regulatory networks for each species and comparing these networks across species to identify regulatory mechanisms explaining the evolution of trees. In addition, we will test experimentally some of the predicted regulatory mechanisms.

To study the evolution of gene regulation in trees, we will align regulatory networks from three gymnosperm (conifers) and three angiosperm tree species. While each regulatory network will describe co-regulation within a species, their multiple alignment will reveal conserved and diverged regulation across species. We will then study various network properties including individual genes, simple topologies containing several genes (i.e. network motifs), subnetworks (i.e. gene modules), and regulatory mechanisms (i.e. one or more regulators targeting a cis-regulatory module (CRM) of co-expressed genes).

Network properties that align across all or most species are conserved and will reveal core regulatory mechanisms underlying wood formation, while those aligning in only subsets of species have diverged and can be used to explain the evolution of plant diversity. In this project, we are particularly interested in properties with high conservation within gymnosperms and angiosperm trees, but that differ between gymnosperms and angiosperms, since these can explain differences between the two tree lineages. We are also interested in properties conserved across all trees, but that are different in non-tree species such as arabidopsis, since these can answer the question: What makes a tree a tree?

Collaboration with:

Nathaniel Strees

Umeå University

Totte Niittylä

Umeå University

Hannele Tuominen

Umeå University

Klaas Vandepoele

VIB/Ghent University

Regulatory evolution after whole genome duplication in salmonids

We aim to understand how gene regulation evolves after whole genome duplication and to reveal whether whole genome duplicaitons spark new regulatory innovations. We are also developing phylogenetic methods for comparative transcriptomics in multiple species.

To understand the regulatory mechansims underlying change in gene regulation after whole genome duplication, we are also integrating multi-omics data to regulatory annotate Atlantic salmon.

Collaboration with:

Rori Rohls

San Francisco State University

Comparative transcriptomics in temperate grass

We are developing methods for comparative transcriptomics to sheed light on the evolution of traits characteristic to the temperate grass subfamily Pooideae - such as cold tolerance.

Collaboration with:

Host-microbial interactions and holo-genomics

We are developing network-based methods for unraveling the genetic interactions between hosts and their microbial communities (holo-genomics) in both fish and cow.

Collaboration with:

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