Marked Neurospora crassa Strains for Competition Experiments and Bayesian Methods for Fitness Estimates
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...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Oxford University Press
2020-04-01
|
| Series: | G3: Genes, Genomes, Genetics |
| Subjects: | |
| Online Access: | http://g3journal.org/lookup/doi/10.1534/g3.119.400632 |
| _version_ | 1819148157445996544 |
|---|---|
| author | Ilkka Kronholm Tereza Ormsby Kevin J. McNaught Eric U. Selker Tarmo Ketola |
| author_facet | Ilkka Kronholm Tereza Ormsby Kevin J. McNaught Eric U. Selker Tarmo Ketola |
| author_sort | Ilkka Kronholm |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-22T13:41:15Z |
| format | Article |
| id | doaj.art-13c1bdfc59b54934ba78747e50f10342 |
| institution | Directory Open Access Journal |
| issn | 2160-1836 |
| language | English |
| last_indexed | 2024-12-22T13:41:15Z |
| publishDate | 2020-04-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | G3: Genes, Genomes, Genetics |
| spelling | doaj.art-13c1bdfc59b54934ba78747e50f103422022-12-21T18:23:55ZengOxford University PressG3: Genes, Genomes, Genetics2160-18362020-04-011041261127010.1534/g3.119.40063211Marked Neurospora crassa Strains for Competition Experiments and Bayesian Methods for Fitness EstimatesIlkka KronholmTereza OrmsbyKevin J. McNaughtEric U. SelkerTarmo KetolaThe 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.http://g3journal.org/lookup/doi/10.1534/g3.119.400632fungihigh resolution meltingcompetitive fitnessexperimental evolution |
| spellingShingle | Ilkka Kronholm Tereza Ormsby Kevin J. McNaught Eric U. Selker Tarmo Ketola Marked Neurospora crassa Strains for Competition Experiments and Bayesian Methods for Fitness Estimates G3: Genes, Genomes, Genetics fungi high resolution melting competitive fitness experimental evolution |
| title | Marked Neurospora crassa Strains for Competition Experiments and Bayesian Methods for Fitness Estimates |
| title_full | Marked Neurospora crassa Strains for Competition Experiments and Bayesian Methods for Fitness Estimates |
| title_fullStr | Marked Neurospora crassa Strains for Competition Experiments and Bayesian Methods for Fitness Estimates |
| title_full_unstemmed | Marked Neurospora crassa Strains for Competition Experiments and Bayesian Methods for Fitness Estimates |
| title_short | Marked Neurospora crassa Strains for Competition Experiments and Bayesian Methods for Fitness Estimates |
| title_sort | marked neurospora crassa strains for competition experiments and bayesian methods for fitness estimates |
| topic | fungi high resolution melting competitive fitness experimental evolution |
| url | http://g3journal.org/lookup/doi/10.1534/g3.119.400632 |
| work_keys_str_mv | AT ilkkakronholm markedneurosporacrassastrainsforcompetitionexperimentsandbayesianmethodsforfitnessestimates AT terezaormsby markedneurosporacrassastrainsforcompetitionexperimentsandbayesianmethodsforfitnessestimates AT kevinjmcnaught markedneurosporacrassastrainsforcompetitionexperimentsandbayesianmethodsforfitnessestimates AT ericuselker markedneurosporacrassastrainsforcompetitionexperimentsandbayesianmethodsforfitnessestimates AT tarmoketola markedneurosporacrassastrainsforcompetitionexperimentsandbayesianmethodsforfitnessestimates |