Very Low Rates of Spontaneous Gene Deletions and Gene Duplications in Dictyostelium discoideum

The study of spontaneous mutation rates has revealed a wide range of heritable point mutation rates across species, but there are comparatively few estimates for large-scale deletion and duplication rates. The handful of studies that have directly calculated spontaneous rates of deletion and duplica...

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Bibliographic Details
Published in:	Journal of molecular evolution Vol. 91; no. 1; pp. 24 - 32
Main Authors:	Gill, Shelbi E., Chain, Frédéric J. J.
Format:	Journal Article
Language:	English
Published:	New York Springer US 01-02-2023 Springer Nature B.V
Subjects:	Accumulation Animal Genetics and Genomics Biomedical and Life Sciences Cell Biology Copy number Dictyostelium - genetics Dictyostelium discoideum Eukaryota - genetics Eukaryotes Evolutionary Biology Gene Deletion Gene Duplication Gene sequencing Genome Genomes Life Sciences Mathematical analysis Microbiology Molecular machines Mutation Mutation rates Original Original Article Plant Genetics and Genomics Plant Sciences Point mutation Reproduction (copying) Whole genome sequencing GC content Mutation rate Copy number variation Mutation Mutation accumulation experiment Dictyostelium discoideum
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Summary:	The study of spontaneous mutation rates has revealed a wide range of heritable point mutation rates across species, but there are comparatively few estimates for large-scale deletion and duplication rates. The handful of studies that have directly calculated spontaneous rates of deletion and duplication using mutation accumulation lines have estimated that genes are duplicated and deleted at orders of magnitude greater rates than the spontaneous point mutation rate . In our study, we tested whether spontaneous gene deletion and gene duplication rates are also high in Dictyostelium discoideum , a eukaryote with among the lowest point mutation rates (2.5 × 10 –11 per site per generation) and an AT-rich genome (GC content of 22%) . We calculated mutation rates of gene deletions and duplications using whole-genome sequencing data originating from a mutation accumulation experiment and determined the association between the copy number mutations and GC content. Overall, we estimated an average of 3.93 × 10 –8 gene deletions and 1.18 × 10 –8 gene duplications per gene per generation. While orders of magnitude greater than their point mutation rate, these rates are much lower compared to gene deletion and duplication rates estimated from mutation accumulation lines in other organisms (that are on the order of ~ 10 –6 per gene/generation). The deletions and duplications were enriched in regions that were AT-rich even compared to the genomic background, in contrast to our expectations if low GC content was contributing to low mutation rates. The low deletion and duplication mutation rates in D. discoideum compared to other eukaryotes mirror their low point mutation rates, supporting previous work suggesting that this organism has high replication fidelity and effective molecular machinery to avoid the accumulation of mutations in their genome.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Handling editor: David Liberles.
ISSN:	0022-2844 1432-1432
DOI:	10.1007/s00239-022-10081-1