Unintended Side Effects of Transformation Are Very Rare in Cryptococcus neoformans
Received wisdom in the field of fungal biology holds that the process of editing a genome by transformation and homologous recombination is inherently mutagenic. However, that belief is based on circumstantial evidence. We provide the first direct measurement of the effects of transformation on a fu...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Oxford University Press
2018-03-01
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| Series: | G3: Genes, Genomes, Genetics |
| Subjects: | |
| Online Access: | http://g3journal.org/lookup/doi/10.1534/g3.117.300357 |
| _version_ | 1818613727184814080 |
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| author | Ryan Z. Friedman Stacey R. Gish Holly Brown Lindsey Brier Nicole Howard Tamara L. Doering Michael R. Brent |
| author_facet | Ryan Z. Friedman Stacey R. Gish Holly Brown Lindsey Brier Nicole Howard Tamara L. Doering Michael R. Brent |
| author_sort | Ryan Z. Friedman |
| collection | DOAJ |
| description | Received wisdom in the field of fungal biology holds that the process of editing a genome by transformation and homologous recombination is inherently mutagenic. However, that belief is based on circumstantial evidence. We provide the first direct measurement of the effects of transformation on a fungal genome by sequencing the genomes of 29 transformants and 30 untransformed controls with high coverage. Contrary to the received wisdom, our results show that transformation of DNA segments flanked by long targeting sequences, followed by homologous recombination and selection for a drug marker, is extremely safe. If a transformation deletes a gene, that may create selective pressure for a few compensatory mutations, but even when we deleted a gene, we found fewer than two point mutations per deletion strain, on average. We also tested these strains for changes in gene expression and found only a few genes that were consistently differentially expressed between the wild type and strains modified by genomic insertion of a drug resistance marker. As part of our report, we provide the assembled genome sequence of the commonly used laboratory strain Cryptococcus neoformans var. grubii strain KN99α. |
| first_indexed | 2024-12-16T16:06:43Z |
| format | Article |
| id | doaj.art-7d068d646ee04403ba4cbfca5f838b36 |
| institution | Directory Open Access Journal |
| issn | 2160-1836 |
| language | English |
| last_indexed | 2024-12-16T16:06:43Z |
| publishDate | 2018-03-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | G3: Genes, Genomes, Genetics |
| spelling | doaj.art-7d068d646ee04403ba4cbfca5f838b362022-12-21T22:25:21ZengOxford University PressG3: Genes, Genomes, Genetics2160-18362018-03-018381582210.1534/g3.117.3003578Unintended Side Effects of Transformation Are Very Rare in Cryptococcus neoformansRyan Z. FriedmanStacey R. GishHolly BrownLindsey BrierNicole HowardTamara L. DoeringMichael R. BrentReceived wisdom in the field of fungal biology holds that the process of editing a genome by transformation and homologous recombination is inherently mutagenic. However, that belief is based on circumstantial evidence. We provide the first direct measurement of the effects of transformation on a fungal genome by sequencing the genomes of 29 transformants and 30 untransformed controls with high coverage. Contrary to the received wisdom, our results show that transformation of DNA segments flanked by long targeting sequences, followed by homologous recombination and selection for a drug marker, is extremely safe. If a transformation deletes a gene, that may create selective pressure for a few compensatory mutations, but even when we deleted a gene, we found fewer than two point mutations per deletion strain, on average. We also tested these strains for changes in gene expression and found only a few genes that were consistently differentially expressed between the wild type and strains modified by genomic insertion of a drug resistance marker. As part of our report, we provide the assembled genome sequence of the commonly used laboratory strain Cryptococcus neoformans var. grubii strain KN99α.http://g3journal.org/lookup/doi/10.1534/g3.117.300357Reverse geneticsgene deletionyeastsgenome sequenceCryptococcus neoformans strain KN99 |
| spellingShingle | Ryan Z. Friedman Stacey R. Gish Holly Brown Lindsey Brier Nicole Howard Tamara L. Doering Michael R. Brent Unintended Side Effects of Transformation Are Very Rare in Cryptococcus neoformans G3: Genes, Genomes, Genetics Reverse genetics gene deletion yeasts genome sequence Cryptococcus neoformans strain KN99 |
| title | Unintended Side Effects of Transformation Are Very Rare in Cryptococcus neoformans |
| title_full | Unintended Side Effects of Transformation Are Very Rare in Cryptococcus neoformans |
| title_fullStr | Unintended Side Effects of Transformation Are Very Rare in Cryptococcus neoformans |
| title_full_unstemmed | Unintended Side Effects of Transformation Are Very Rare in Cryptococcus neoformans |
| title_short | Unintended Side Effects of Transformation Are Very Rare in Cryptococcus neoformans |
| title_sort | unintended side effects of transformation are very rare in cryptococcus neoformans |
| topic | Reverse genetics gene deletion yeasts genome sequence Cryptococcus neoformans strain KN99 |
| url | http://g3journal.org/lookup/doi/10.1534/g3.117.300357 |
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