Marked neurospora crassa strains for competition experiments and Bayesian methods for fitness estimates

Ilkka Kronholm, Tereza Ormsby, Kevin J. McNaught, Eric U. Selker, Tarmo Ketola

Research output: Contribution to journalArticlepeer-review

7 Scopus citations

Abstract

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.

Original languageEnglish
Pages (from-to)1261-1270
Number of pages10
JournalG3: Genes, Genomes, Genetics
Volume10
Issue number4
DOIs
StatePublished - Apr 1 2020
Externally publishedYes

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. We thank Matthieu Bruneaux, Roghaieh Ashrafi, and Neda Moghadam for comments on the manuscript. We also thank two anonymous reviewers for their constructive comments that improved the manuscript.

Keywords

  • Competitive
  • Evolution
  • Experimental
  • Fitness
  • Fungi
  • High resolution
  • Melting

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