MinION2FixID: fast and reliable legume root nodule bacteria identification using nanopore sequencing technology
MinION2FixID: rasche Identifikation von Knöllchenbakterien mit nanopore-basierter Sequenzierungstechnologie
Auf einen Blick
- Co-Projektleiter/in : Dr. Joël Pothier, Dr. Fabio Rezzonico
- Projektvolumen : CHF 40'000
- Projektstatus : abgeschlossen
- Drittmittelgeber : Interne Förderung
- Projektpartner : Université de Genève / Unité de Microbiologie, MALDI-ID, Mabritec AG, Murdoch University
- Kontaktperson : Fabio Rezzonico
Beschreibung
Rhizobia are bacterial symbionts associated with legumes that
are of paramount importance for the fixation of atmospheric
nitrogen in the soil. The success of this process (and ultimately
the performance of the plant) depends on the type of root nodule
bacteria, which should be adequate to each plant species. The
objective of this project is to establish a quick and effective
identification tool for rhizobial symbionts within the most
important grain legumes. Our approach combines next generation
sequencing (NGS) data and MALDI-TOF MS protein markers to identify
the different inoculant strains based on their unique fingerprints.
During this project we will introduce the nanopore-based MinION
device as routine tool for genomic and amplicon sequencing in our
laboratory, testing various protocols and establishing the
associated bioinformatics infrastructure and data analysis
pipeline. Together with the gain of expertise, this will enable us
to refine and expand the available genomic data on rhizobia, which
will allow the precise identification of individual protein signals
obtained with MALDI-TOF MS, thus enabling the selection of the best
discriminatory markers for the different bacterial species and
improving the accuracy of the proteomics approach.
Publikationen
-
Fossou, Romain K.; Pothier, Joël F.; Zézé, Adolphe; Perret, Xavier,
2020.
International Journal of Systematic and Evolutionary Microbiology.
70(2), S. 1421-1430.
Verfügbar unter: https://doi.org/10.1099/ijsem.0.003931