RESEARCH

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Nature is full of diversity. Understanding of this natural diversity is important to not only answer how different organisms evolve to be what they are, but also to improve future conservation and growth. With this aim in mind, we work in different facets of genomics. Our research can be broadly divided into three categories:

1) Creating genomics resources

This involves the comprehensive and systematic process of gathering, sequencing, annotating, and organizing genetic information from various organisms.

2) Developing methods for performing comparative genomic analysis

This involves creating sophisticated techniques and approaches to study the genetic information of different organisms in a comparative context. The aims is to identify similarities, differences, patterns, and evolutionary relationships within genomes, shedding light on the processes that have shaped the diversity of life.

3) Analysis available data to get biological insights to genomics diversity

This refers to the process of examining existing genetic information and using it to uncover valuable knowledge about the range of genetic variations and differences present in different species or populations. This analysis aims to reveal patterns, trends, and relationships within the genomes of various organisms, providing a deeper understanding of how diversity has evolved and how it functions at a genetic level.

OUR PROJECTS

1.) Computational methods for comparative genomics.

Latest genome assembly advancements now allow the generation of full genome assemblies at relatively low costs. Soon the common way of analyzing genomes will turn away from read-alignment-based approaches to analyzing the complete genomic sequences. We develop methods that leverage the complement of genomic differences from SNPs to large chromosomal rearrangements (like SyRI or SHOREmap) and add tools to visualize them (like plotsr).

2.) How genomes change over time 

We are interested in the way how genomes change over time, including spontaneous, uncontrolled mutations and controlled pathways like recombination. From short (mutation accumulation) to long (within and between species) timescales. And how these changs influence biological processes downstream, like gene expression and meiotic recombination landscapes.

3.)  Potato genome assemblies

a. Cultivated European potato

    Otava reference: In 2022 our lab was the first to produce … 

    i. Solanum tuberosum (tuberosum) became the crop it is today through a series of bottlenecks: first via ships from South America, and then through the European potato failure…

    ii. We are now assembling further tetraploid potato genomes to understand the diversity of haplotypes within this unique  population

    iii. Wild/Native potato 

b. Wild/Native potatoes exist at many different ploidy levels…

c. Inference of evolutionary history of domestication by means of comparative genomics

The potato´s puzzling genome

4.) Single cell sequencing for haplotype phasing, inference of recombination and prediction of genomic incompatibilities

      a. We use single-cell sequencing technologies to assist the assembly of complex genomes, and are currently pushing the boundaries of …

      b. We can measure meiotic recombination in single gametes to infer patterns of recombination across the genome.

      c. We study genetic incompatibilities between genetic groups or species and the extent these incompatibilities restrict recombination and gene flow at the population level.

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Our TOOL&RESEARCH section gives you a perfect overview about different NGS-appliance we are using to answer different questions about the whole plant genome.

We develop methods to reconstruct genomes, find differences between them and try to understand what their contribution to phenotypic differences is.

Our group´s major focus is to advanced NGS-based analyses by addressing questions that could not be resolved previously. Whole-genome sequencing-based methods were used to accelerate forward genetics by directly linking mutant phenotypes to the genetic changes and to understand how genomes change over time (e.g. due to controlled mechanisms like recombination during meiosis).

a   Extraction of gamete nuclei

b   Single-cell genome sequencing of haploid gametes and haplotype phasing

c   Genetic map construction based on the recombination patterns in the gamete genomes

d   Long-read sequencing of somatic material

e   Separation if long reads based on genetic linkage groups using phased alleles

f   Independent assembly of each haplotype of each linkage group

g   Scaffolding assemblies to chromosome-level using gamete-derived genetic map

2.) How genomes change over time 

We are interested in the way how genomes change over time, including spontaneous, uncontrolled mutations and controlled pathways like recombination. From short (mutation accumulation) to long (within and between species) timescales. And how these changs influence biological processes downstream, like gene expression and meiotic recombination landscapes.