The Solanaceae comprise many commercially important plants such as tomatoes, potatoes, eggplants, peppers or tobacco. However whilst modern, domesticated species often exhibit superior yield and/or quality, they often have lost beneficial abiotic and biotic stress tolerance/resistance traits. Luckily after their identification, these traits can be re-introduced into domesticated species, either using biotechnological or classical breeding technologies. In both cases however, knowledge about underlying genes is necessary. Here, recent updates in sequencing technology come to help as these have made it possible to tackle Solanaceous plant genomes with comparatively low laboratory effort using e.g. long read Oxford Nanopore sequencing data coupled to Hi-C or optical mapping technologies. To facilitate the subsequent genome comparisons, we have developed a new automated high throughput functional classification and annotation platform called Mercator4 based on the MapMan4 ontology. This ontology is specifically tailored to plants and redundancy reduced. These design choices were guided by the need to improve visualization capabilities and in order to facilitate guilt by association approaches in network driven data analysis and to be able to compare gene families based on their function across species. In the case of closely related species, it allows to rapidly detect changes in the size of gene families whereas a whole genome comparison for presence/absence variation of gene families can reveal evolutionary changes. We will demonstrate the versatility based on our latest genome assemblies and analysis data on Solanales genomes ranging from wild tomato species to the parasitic plant Cuscuta campestris and show how the controlled MapMan4 ontology can be used to infer insights into plant biology.
Björn Usadel studied Biochemistry at the Free University Berlin and conducted his MSc research on Drosophila at the Rockefeller University. Upon returning to Germany in 2001, he conducted his PhD studies in the lab of Dr. Markus Pauly at the Max Planck Institute of Molecular Plant Physiology, Potsdam on identifying and characterizing novel cell wall genes using bioinformatics approaches.
After a postdoc and group leader position with Prof Mark Stitt at the same institute, he became full professor and director at RWTH Aachen University and the Research Center Jülich in 2011. He has co-authored more than 120 publications and is an ISI highly cited researcher in Plant and Animal Sciences.