TBG-Project Maria Nilsson and team

Comparative Genomics

Mobile Genetic Elements – novel treasures in unexplored genomes

Institution: Senckenberg Society for Nature Research

TBG group members

  • Dr. Maria Nilsson
  • Jordi de Raad (TBG funded PhD student)
  • Lennart Gries

TBG project summary

Our projects aim primarily at tracing the evolutionary history of genomes in a broad spectrum of species and systems. The research is focused on repetitive sequences (Transposable Elements, TEs) and investigation of the role they play in genome evolution. 

Ribbon worm genomics

The phylum Nemertea (ribbon worms) is so far only represented by one single short read genome assembly. We have established three high coverage long read assemblies of nemerteans that are in the process of being analysed and published. The project also investigates genome size dynamics and aim to shed light on the contribution of TE activity to ribbon worm genome composition as well as the evolution of nemertean-specific TEs. In a cross-TBG collaboration the genomes and transcriptomes are screened for natural products.

The evolution of food caching Nutcrackers across Eurasia

This project relates to the evolutionary history of nutcracker birds, with a focus on how species and sub-species evolved in a highly dispersive species complex. The genomes will subsequently be screened for TEs that have been active during the divergence processes of these species. In parallel, we study the phylogeny and evolution of the corvid lineage (nutcrackers, crows, magpies, jays). 

Fish genomics and venomics

Fish genomes are a hotspot of TE activity among vertebrates. We have established chromosome level genome assemblies as well as population level data set of the dragonet family. The genomic data will be screened with high throughput methods to elucidate the activity across and within different TE super-families. Additionally, as part of a TBG cross-cutting collaboration, the genome, transcriptome and proteome of the venomous greater weever fish are screened for natural products. TEs compose 40% of the greater weever genome and their suitability for biomedical use will be evaluated using experimental methods.

Activity of TEs in Ruminantia

Ruminant mammals (e.g. cow, sheep, antelopes) are one of the few mammalian groups that have two active autonomous TEs. Population-level data sets have been screened using high throughput methods to understand the interplay of different TEs across time.

Group expertise / Methods

  • Characterization and high throughput analysis of TEs using state of the art genome sequencing methods and bioinformatic approaches.
  • Phylogenomics of whole species complexes.
  • Long read sequencing methods
  • genome assembly and annotation
  • speciation and population genomics

Publications

von Reumont BM, Lüddecke T, Timm T, et al. Proteo-Transcriptomic Analysis Identifies Potential Novel Toxins Secreted by the Predatory, Prey-Piercing Ribbon Worm Amphiporus lactifloreus. Mar Drugs. 2020;18(8):E407. doi:10.3390/md18080407

Prost S, Winter S, De Raad J, et al. Education in the genomics era: Generating high-quality genome assemblies in university courses. Gigascience. 2020;9(6):giaa058. doi:10.1093/gigascience/giaa058

Chromosome-level genome assembly of a benthic associated Syngnathiformes species: the common dragonet, Callionymus lyra
Sven Winter, Stefan Prost, Jordi de Raad, Raphael T. F. Coimbra, Magnus Wolf, Marcel Nebenführ, Annika Held, Melina Kurzawe, Ramona Papapostolou, Jade Tessien, Julian Bludau, Andreas Kelch, Sarah Gronefeld, Yannis Schöneberg, Christian Zeitz, Konstantin Zapf, David Prochotta, Maximilian Murphy, Monica M. Sheffer, Moritz Sonnewald, Maria A. Nilsson, Axel Janke
bioRxiv 2020.09.08.287078; doi: https://doi.org/10.1101/2020.09.08.287078