Join the first ERGA BioGenome Analysis & Applications Seminar of 2025! This month featuring talks by Martin Mascher and Marina Pupke Marone from the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK). More details below.
🕚 Monday, February 24th 2025 - 11:00 AM CET
Join us live on YouTube:
Structural variation in the pangenome of wild and domesticated barley
Abstract
Pangenomes, which are collections of annotated genome sequences from multiple individuals of a species, provide valuable insights into structural variants that enhance genetic analysis in crop plants. This study presents a barley pangenome comprising long-read assemblies from 76 wild and domesticated genomes, supplemented by short-read data from 1,315 genotypes. The expanded variation catalog reveals structurally complex loci enriched in gene copy number variation. The utility of the pangenome is demonstrated through analysis of selected loci related to disease resistance, plant architecture, nutrient release, and trichome development. Novel allelic variations were identified, including a powdery mildew resistance locus and population-specific copy number gains in a vegetative branching regulator. Additionally, an expanded enzyme family in elite malting barley varieties was linked to altered enzymatic activity in micro-malting trials, and the deletion of an enhancer motif was associated with changes in the development of hairy appendages on barley grains. These findings suggest that allelic diversity at structurally complex loci has facilitated crop adaptation to selective pressures in agricultural environments.
Speaker
Martin Mascher leads the ‘Domestication Genomics’ research group at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben. His lab investigates crop evolution and adaptation, focusing on how these processes shape genetic diversity in domesticated plants and their wild ancestors. His research centers on temperate cereals—barley, wheat, rye, and oats—leveraging the extensive collections of these crops and their wild relatives housed in the German national genebank.
How to assemble plant genomes with TRITEX
Abstract
TRITEX is a computational pipeline for chromosome-scale assembly of plant genomes. TRITEX uses an input contig assembly (using HiFi long-reads, for example), Hi-C reads and a guide map (or reference genome) to assemble the genomes within a short time frame. Manual curation of contig placements is done intuitively with user-editable tables and plots. The pipeline is available at https://tritexassembly.bitbucket.io/ and the related publication at https://plantmethods.biomedcentral.com/articles/10.1186/s13007-022-00964-1
Speaker
Marina Pupke Marone is a biologist with a degree from the University of São Paulo, Brazil, who started working with plant bioinformatics in 2016 during her master’s at the University of Campinas, Brazil. During her PhD in the same University, she completed a 9-month internship in the Domestication Genomics group at IPK in Germany, where she gained experience with the TRITEX pipeline and barley genomics. In 2023, she started her postdoc in the same group to start working in the barley pangenome.
Related publications
Marone, M.P., Singh, H.C., Pozniak, C.J. et al. A technical guide to TRITEX, a computational pipeline for chromosome-scale sequence assembly of plant genomes. Plant Methods 18, 128 (2022). https://doi.org/10.1186/s13007-022-00964-1
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