We are a newly established research group with expertise in genomics and bioinformatics, and we are conducting our research in close collaboration with a number of national and international research groups in ecology, molecular biology, and genomics.

Our work can be summarised under the three main topics “Genomic adaptation to environmental change”, “Host – microbiome interactions” and “Biodiversity monitoring using eDNA technology”.

PROJECTS

Adaptation to warming in natural phytoplankton populations

Global warming imposes rapid environmental shifts on all species and it is therefore important to investigate the capacity of biological systems to adapt to changed conditions. In this project we study adaptation of phytoplankton populations revived from sediment cores from an area affected by cooling water discharges from a nuclear power plant. Resting stages of the diatom Skeletonema marinoi, from before and after the thermal perturbation began, have be germinated. Each strain has then been phenotyped in a lab-experiment at 18°C (low) and 23°C (high temperature conditions), to recreate the temperature regimes of pre- and post-power plant summer conditions. We have found that under high temperature conditions, post-power plant populations have higher fitness than pre-power plant populations and vice versa, indicating that adaptation to warmer water conditions has occurred. We are now analysing whole genome sequence data from these adapted strains to identify genomic changes that can explain the differences in phenotype. The sequence reads are beeing aligned to the reference genome of S. marinoi and the degree of polymorphism and large-scale structural rearrangements are beeing identified. By comparing the frequency of warm water genotypes in pre- versus post-power plant populations we can determine if the changes is due to selection on standing genetic variation or if the changes are due to a new mutation favored by selection under thermal stress.

Funding: Formas 2017 - 00466

Survivors of the Sea: How diatom resting stages remain alive 100 years embedded in sediment

Diatoms are important primary producers and responsible for 20% of the global CO2 fixation. Resting stages produced during adverse conditions in the water column serve to anchor populations in their native areas, and hence sinking and survival in the sediment are important features of the life history. It is believed that dormant stages turn-off the exchange with the environment and survive on their storage of nutrients. However, this approach can sustain them for only a few months, but intriguingly resting stages has been germinated after a century embedded in sediments. Preliminary results indicate that resting stages are not as dormant as formerly believed. This assumption is based on data which shows that diatom resting stages assimilate nitrogen during long dark and anoxic storage. In this project we investigate the cellular processes of resting cells from the common planktonic coastal diatom Skeletonema marinoi, which readily forms resting stages that are buried in marine sediment. We incubate resting cells with isotope labeled elements and analyse these with SIMS and GC-IRMS/EA-IRMS to reveal assimilatory and dissimilatory processes and combine this with differential gene expression through RNAseq analysis. We aim to reveal functional pathways to elucidate the interexchange between the diatom resting stage and the microhabitat, and we hope the information gained will shed light on diatom dark survival strategies and the processes necessary for a durable interexchange with the surrounding environment.

This project is conducted in collaboration with Helle Ploug and Volker Brüchert.

Funding: VR 2018 - 04555

Skeletonema marinoi RO5AC reference genome

As part of CeMEB’s Infrastructure for MArine Genetic model Organisms (IMAGO) initiative, the chain-forming centric diatom Skeletonema marinoi is being developed into a model organism for marine evolutionary biology. In addition to being easy to collect and maintain, this species possesses the ability to survive as a resting stage in the sediment for at least a century, a state from which it can be revived and cultured. This means that it can serve as a time capsule, allowing us to compare the phenotype and genotype of these older populations with their contemporary counterparts. Many projects are currently underway to investigate S. marinoi, such as comparing different strains’ responses to a changing environment, generation of a mutant library, and investigation of the diatom microbiome. Genome and transcriptome sequencing of several strains is also being performed, allowing for investigation of genomic and phenomic differences between strains adapted to various environmental conditions.

The genome of strain RO5AC has been sequences using 19 PacBio SMRTcell’s and assembled using FALCON and annotated with MAKER. The resulting assembly consists of 601 contigs (XXX primary and XXX associated) and harbours approximately 22000 genes, of which 80% are of unknown function.

Funding by CeMEB

MEMBERS

Mats Töpel

Researcher in genomics and bioinformatics. My research focus is Skeletonema marinoi genomics and analysis of features that can explain the ecological success of this and other diatoms. I teach phylogenomics, bioinformatics and programming at MSc and PhD level courses and occationally build computer clusters.

mats.topel@marine.gu.se

Matthew Pinder

Research assistant in bioinformatics, with a background in genetics and genomics. For the past three years I have worked primarily with genomic data from the diatom Skeletonema marinoi and its microbiome, including genome assembly and annotation of the bacteria in this holobiont. More recently I have been working on pipelines for the automation of bioinformatic analyses.

matt.pinder@gu.se

Vilma Canfjorden

I have a background in molecular biology, systems biology and I have years of experience selling tomato plants as a part-time job. I have always been interested in computers and science, which made bioinformatics a perfect subject for my masters thesies. In this project I have been developing a bioinformatics pipeline in Python focusing on population genomics.

OPEN POSITIONS

PostDoc position

Loss of function (LoF) gene mutation is a phenomenon often considered to be detrimental. However, recent studies in humans have shown that they can be beneficial, such as in lipid metabolism. Our aim is to investigate whether beneficial LoF mutations play a role in the adaptation of species to climate change, using the marine diatom Skeletonema marinoi as a model. This organism is well-suited to such a study as it has a short generation time and can enter a resting stage in sediments for at least 100 years, allowing us to compare samples in the same population from before and after an anthropogenic-driven temperature increase.

We have sampled S. marinoi from a location where nuclear power plant cooling water discharge has increased local water temperature, and establish cultures of both pre- and post-power plant populations revived from sediment cores. These cultures have been sequenced and in this project we are looking for a PostDoc candidate interested in using bioinformatic techniques to identify LoF mutations appearing either exclusively or more frequently under post-warming conditions. The knockout/knockdown mutations will be confirmed using RNAseq, and further examined in phenotyping studies in order to identify signatures of adaptation to warming, and also identify genes of unknown function, important in this process.

The project involves bioinformatic method development and programming in python and is suitable for someone interested in using massive amounts of sequence data to investigate evolutionary processes in phytoplankton. If this sounds interesting, please send a message to mats.topel@marine.gu.se to discuss your ideas and interests.

Two years duration

Funding: Carl Tryggers CTS 18:397

PUBLICATIONS

Ling Q, Broad W, Trösch R, Töpel M, Sert TD, Lymperopoulos P, Baldwin A. Jarvis P. (2019) Ubiquitin-dependent chloroplast-associated protein degradation in plants. Science, Vol. 363, Issue 6429, DOI:10.1126/science.aav4467