Genome sequences are key resources to understand functional processes and divergent trait evolution within and between different species. Within CEPLAS, many high-quality genome assemblies of closely related species of the Brassicaceae and other plant families are being generated. This makes it possible, in principle, to reveal intra-family similarities and structural variations from pairwise whole-genome alignments (WGA) as a major step towards family pangenome representations. However, even though efficient whole-genome alignment solutions exist there are no computational approaches that would annotate all genomic differences including the obvious hierarchy ranging from small single nucleotide changes to large complex rearrangements. The project will therefore extend SyRI, an existing algorithm for genome-wide structural rearrangement identification to solve this efficiently.
Qualifications needed: good algorithmic background, programming skills, basic knowledge in bioinformatics , Plus: experience with genomic data and/or plant genomics
Contact person: Gunnar Klau, Korbinian Schneeberger
Within CEPLAS genome variation will be exploited across a wide area of species and within a complementary project (see above), a genome comparison pipeline based on co-linear blocks is being developed. Within this project, we will complete our Mercator4 and MapMan framework (Schwacke et al., Mol Plant 2019) for functional annotation to allow complete classification of plant genes. We will leverage the underlying protein sub-family information to directly identify plant gene sub-families in the genome, without prior gene calling to enable studying evolutionary aspects and fast full genome comparisons using machine learning.
Qualifications needed: programming skills. Understanding of plants and background in machine learning are a plus.
Contact person: Björn Usadel
This project will functionally analyze gene regulatory networks (GRNs) that act in plant shoot meristems to control the switch to flowering. We have defined an intricate network involving transcription factors and microRNAs that controls this developmental transition in Arabidopsis and its perennial relatives. The project will address how the activity of these GRNs are controlled by environmental cues, such as day length, and internal cues, such as phytohormones and metabolites, to initiate the earliest stages of the floral transition. The project involves constructing transgenic plants to control the temporal and quantitative expression of network components, testing regulatory connections in orthogonal systems, imaging the transition by confocal microscopy and collaboration with computational biologists modelling GRN activity. References: Hyun et al (2019) Science 363, 409-412; Hyun et al (2016) Developmental Cell 37, 254-266.
Qualifications needed: Molecular biology, confocal imaging, computational capability
Contact person: George Coupland
The number of grains per spike is among the most variable and important traits determining final yield in cereal crops. Grain number is controlled by complex developmental processes including the regulation of meristem size, of branching and floret fertility. Grass mutants affecting inflorescence architecture have provided insights into the genes and gene networks regulating inflorescence architecture and seed number. This project uses the important cereal crop barley with a vast collection of developmental mutants to understand how the interplay between hormonal signalling and nutrient allocation to meristems controls yield in crop plants. The project will be carried out in close collaboration with a second Postdoc (project 3) across three research groups with expertise in developmental genetics, imaging, transport and signaling.
Qualifications needed: molecular plant biology, grass genetics, plant development, imaging
Contact persons: Maria von Korff-Schmising, Rüdiger Simon
We have previously characterized process underlying diversity in leaf form between and within species and have identified genetic pathways influencing this trait. Here we propose to investigate the possible physiological significance of this variation as well as possible feedbacks between physiology, metabolism and leaf form. The project will involve comparative studies of Cardamine hirsuta and Arabidopsis thaliana. References: Kierzkowski D, Runions A, et al., (2019) A growth-based framework for leaf shape development and diversity. Cell, 177:1405-1418 Vuolo F, et al., (2016) Genes Dev. 30, 2370-75. 2. Gan X, et al., (2016) Nat Plants 2, 16167. 3. Rast-Somssich, M.I et al., (2015). Genes Dev 29, 2391-2404 Cartolano, M., et al., 4. 2015 PNAS 112, 10539-44. 5. Vlad D, et al., (2014) Science 343, 780-3.
Qualifications needed: Plant Physiology skills particularly on gas exchange or hydraulics, Plant Molecular/Developmental Genetics (especially in Arabidopsis), NGS data analysis
Contact persons: Miltos Tsiantis, Ismene Karakasilioti