Marked Neurospora crassa Strains for Competition Experiments and Bayesian Methods for Fitness Estimates

0524148 - ÚOCHB 2021 RIV US eng J - Článek v odborném periodiku
Kronholm, I. - Ormsby, Tereza - McNaught, K. J. - Selker, E. U. - Ketola, T.
Marked Neurospora crassa Strains for Competition Experiments and Bayesian Methods for Fitness Estimates.
G3-Genes, Genomes, Genetics. Roč. 10, č. 4 (2020), s. 1261-1270. ISSN 2160-1836. E-ISSN 2160-1836
Institucionální podpora: RVO:61388963
Klíčová slova: fungi * high resolution melting * competitive fitness * experimental evolution
Obor OECD: Biochemistry and molecular biology
Impakt faktor: 3.154, rok: 2020
Způsob publikování: Open access
https://www.g3journal.org/content/10/4/1261

The filamentous fungus Neurospora crassa, a model microbial eukaryote, has a life cycle with many features that make it suitable for studying experimental evolution. However, it has lacked a general tool for estimating relative fitness of different strains in competition experiments. To remedy this need, we constructed N. crassa strains that contain a modified csr-1 locus and developed an assay for detecting the proportion of the marked strain using a post PCR high resolution melting assay. DNA extraction from spore samples can be performed on 96-well plates, followed by a PCR step, which allows many samples to be processed with ease. Furthermore, we suggest a Bayesian approach for estimating relative fitness from competition experiments that takes into account the uncertainty in measured strain proportions. We show that there is a fitness effect of the mating type locus, as mating type mat a has a higher competitive fitness than mat A. The csr-1* marker also has a small fitness effect, but is still a suitable marker for competition experiments. As a proof of concept, we estimate the fitness effect of the qde-2 mutation, a gene in the RNA interference pathway, and show that its competitive fitness is lower than what would be expected from its mycelial growth rate alone.
Trvalý link: http://hdl.handle.net/11104/0308515