Marked Neurospora crassa Strains for Competition Experiments and Bayesian Methods for Fitness Estimates
Kronholm, I., Ormsby, T., McNaught, K. J., Selker, E. U., & Ketola, T. (2020). Marked Neurospora crassa Strains for Competition Experiments and Bayesian Methods for Fitness Estimates. G3: Genes, Genomes, Genetics, 10(4), 1261-1270. https://doi.org/10.1534/g3.119.400632
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G3: Genes, Genomes, GeneticsDate
2020Discipline
Ekologia ja evoluutiobiologiaBiologisten vuorovaikutusten huippututkimusyksikköEcology and Evolutionary BiologyCentre of Excellence in Biological Interactions ResearchCopyright
© 2020 Kronholm et al.
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.
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Genetics Society of AmericaISSN Search the Publication Forum
2160-1836Keywords
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https://converis.jyu.fi/converis/portal/detail/Publication/34504383
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Research Council of FinlandFunding program(s)
Postdoctoral Researcher, AoF; Academy Research Fellow, AoFAdditional information about funding
This study was supported by the Academy of Finland grant no. 274769 to IK and no. 278751 to TK. KJM was supported by National Institutes of Health Training Grant: T32 HD007348. EUS was supported by NIH grants GM093061 and GM127142.License
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