Prof. Dr. Björn Usadel

Research focus

Figure 1: The results of a comparative analysis from the website for gene copy numer variation between different genomes focussed on terpenoids.

We are interested in the comparative analyses of plant omics data including wild crop relatives to identify mechanisms and underlying genes that confer abiotic stress tolerance or valuable/healthy compound accumulation.

To this aim we draw extensively on our cutting edge nanopore platform for pangenomics and rely on our ‘Mercator’ platform (https://www.plabipd.de/mercator_main.html) to automatically classify and annotate plant proteins (or transcripts).

The classification relies on hand-curated and tuned hidden Markov models describing the underlying sequences underlying each of the more than  6000 functional processes and categories (Figure 1) which is complemented by the AI structural annotator HELIXER.

 

To support these analyses and the plant community, a database was established to track protein annotation across the more than 1000 sequenced plant genomes (Figure 2), these resources are part of the German ELIXIR plant nodes.

To also analyze such data sets in a sustainable way, FAIR data management is necessary. Here the group is participating in both the fundamental plant science and agricultural plant sciences. At the same time, the group has built a Plant Knowledge Hub where not raw but derived data is stored and made accessible to users relying on interactive web technology allowing to plot and analyse data within a web browser.

Figure 2: An automated genome annotation platform using machine learning to enable interpretation and visualization of plant genomes and transcriptomes

Most important publications

  1. Serra Mari R, Schrinner S, Finkers R, Ziegler FMR, Arens P, Schmidt MH, Usadel B, Klau GW, Marschall T (2024) Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data. Genome Biol 25(1):26. doi: 10.1186/s13059-023-03160-z.
  2. Jayakodi M, Golicz AA, Kreplak J, Fechete LI, Angra D, Bednar P, Bornhofen E, Zhang H, Boussageon R, Kaur S, Cheung K, Cizkova J, Gundlach H, Hallab A, Imbert B, Keeble-Gagnere G, Koblizkova A, Kobrlova L, Krejci P, Mouritzen TW, Neumann P, Nadzieja M, Nielsen LK, Novak P, Orabi J, Padmarasu S, Robertson-Shersby-Harvie T, Robledillo LA, Schiemann A, Tanskanen J, Toronen P, Warsame AO, Wittenberg AHJ, Himmelbach A, Aubert G, Courty PE, Dolezel J, Holm LU, Janss LL, Khazaei H, Macas J, Mascher M, Smykal P, Snowdon RJ, Stein N, Stoddard FL, Stougaard J, Tayeh N, Torres AM, Usadel B, Schubert I, O'Sullivan DM, Schulman AH, Andersen SU (2023) The giant diploid faba genome unlocks variation in a global protein crop. Nature 615(7953):652-659. doi: 10.1038/s41586-023-05791-5.
  3. van Rengs WMJ, Schmidt MH, Effgen S, Le DB, Wang Y, Zaidan M, Huettel B, Schouten HJ, Usadel B, Underwood CJ (2022) A chromosome scale tomato genome built from complementary PacBio and Nanopore sequences alone reveals extensive linkage drag during breeding. Plant J 110(2):572-588. doi: 10.1111/tpj.15690.
  4. Powell AF, Feder A, Li J, Schmidt MH, Courtney L, Alseekh S, Jobson EM, Vogel A, Xu Y, Lyon D, Dumschott K, McHale M, Sulpice R, Bao K, Lal R, Duhan A, Hallab A, Denton AK, Bolger ME, Fernie AR, Hind SR, Mueller LA, Martin GB, Fei Z, Martin C, Giovannoni JJ, Strickler SR, Usadel B (2022) A Solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity. Plant J 110(6):1791-1810. doi: 10.1111/tpj.15770.
  5. Hoopes G, Meng X, Hamilton JP, Achakkagari SR, de Alves Freitas Guesdes F, Bolger ME, Coombs JJ, Esselink D, Kaiser NR, Kodde L, Kyriakidou M, Lavrijssen B, van Lieshout N, Shereda R, Tuttle HK, Vaillancourt B, Wood JC, de Boer JM, Bornowski N, Bourke P, Douches D, van Eck HJ, Ellis D, Feldman MJ, Gardner KM, Hopman JCP, Jiang J, De Jong WS, Kuhl JC, Novy RG, Oome S, Sathuvalli V, Tan EH, Ursum RA, Vales MI, Vining K, Visser RGF, Vossen J, Yencho GC, Anglin NL, Bachem CWB, Endelman JB, Shannon LM, Stromvik MV, Tai HH, Usadel B, Buell CR, Finkers R (2022) Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity. Mol Plant 15(3):520-536. doi: 10.1016/j.molp.2022.01.003.
  6. Zhang W, Zhang Y, Qiu H, Guo Y, Wan H, Zhang X, Scossa F, Alseekh S, Zhang Q, Wang P, Xu L, Schmidt MH, Jia X, Li D, Zhu A, Guo F, Chen W, Ni D, Usadel B, Fernie AR, Wen W (2020) Genome assembly of wild tea tree DASZ reveals pedigree and selection history of tea varieties. Nat Commun 11(1):3719. doi: 10.1038/s41467-020-17498-6.
  7. Schwacke R, Ponce-Soto GY, Krause K, Bolger AM, Arsova B, Hallab A, Gruden K, Stitt M, Bolger ME, Usadel B (2019) MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis. Mol Plant 12(6):879-892. doi: 10.1016/j.molp.2019.01.003.
  8. Vogel A, Schwacke R, Denton AK, Usadel B, Hollmann J, Fischer K, Bolger A, Schmidt MH, Bolger ME, Gundlach H, Mayer KFX, Weiss-Schneeweiss H, Temsch EM, Krause K (2018) Footprints of parasitism in the genome of the parasitic flowering plant Cuscuta campestris. Nat Commun 9(1):2515. doi: 10.1038/s41467-018-04344-z.
  9. Schmidt MH, Vogel A, Denton AK, Istace B, Wormit A, van de Geest H, Bolger ME, Alseekh S, Mass J, Pfaff C, Schurr U, Chetelat R, Maumus F, Aury JM, Koren S, Fernie AR, Zamir D, Bolger AM, Usadel B (2017) De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing. Plant Cell 29(10):2336-2348. doi: 10.1105/tpc.17.00521.
  10. Bolger A, Scossa F, Bolger ME, Lanz C, Maumus F, Tohge T, Quesneville H, Alseekh S, Sorensen I, Lichtenstein G, Fich EA, Conte M, Keller H, Schneeberger K, Schwacke R, Ofner I, Vrebalov J, Xu Y, Osorio S, Aflitos SA, Schijlen E, Jimenez-Gomez JM, Ryngajllo M, Kimura S, Kumar R, Koenig D, Headland LR, Maloof JN, Sinha N, van Ham RC, Lankhorst RK, Mao L, Vogel A, Arsova B, Panstruga R, Fei Z, Rose JK, Zamir D, Carrari F, Giovannoni JJ, Weigel D, Usadel B, Fernie AR (2014) The genome of the stress-tolerant wild tomato species Solanum pennellii. Nat Genet 46(9):1034-1038. doi: 10.1038/ng.3046.