Strong Purifying Selection in Haploid Tissue–Specific Genes of Scots Pine Supports the Masking Theory

Molecular Biology and Evolution · 6 authors, 8 centres

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TL;DR

This study tested the masking theory in the gymnosperm Scots pine by analyzing genes with tissue-specific expression. The central result was that purifying selection is stronger for genes expressed in the haploid megagametophyte tissue compared to genes expressed in diploid tissues.

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The study used targeted resequencing data from 20 Scots pine megagametophytes to test the masking theory, which predicts stronger selection efficacy in haploid genomes. Researchers compared genetic diversity, site frequency spectra, and the distribution of fitness effects of new mutations between genes specifically expressed in the haploid megagametophyte and four diploid tissues. Results demonstrated that purifying selection is stronger for haploid tissue-specific genes, and this signal is robust to confounding factors like expression level and breadth. While no striking difference in overall genetic diversity was found, the haploid tissue-specific genes showed an excess of invariant sites consistent with very strong selection. The findings provide evidence for effective selection in a long-lived haploid plant tissue, free from confounding sexual selection effects.

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other

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preclinical research

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ORIGINAL PAPER

PMC10457172

Strong Purifying Selection in Haploid Tissue–Specific Genes of Scots Pine Supports the Masking Theory

Molecular Biology and Evolution

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ABSTRACT

Abstract The masking theory states that genes expressed in a haploid stage will be under more efficient selection. In contrast, selection will be less efficient in genes expressed in a diploid stage, where the fitness effects of recessive deleterious or beneficial mutations can be hidden from selection in heterozygous form. This difference can influence several evolutionary processes such as the maintenance of genetic variation, adaptation rate, and genetic load. Masking theory expectations have been confirmed in single-cell haploid and diploid organisms. However, in multicellular organisms, such as plants, the effects of haploid selection are not clear-cut. In plants, the great majority of studies indicating haploid selection have been carried out using male haploid tissues in angiosperms. Hence, evidence in these systems is confounded with the effects of sexual selection and intraspecific competition. Evidence from other plant groups is scarce, and results show no support for the masking theory. Here, we have used a gymnosperm Scots pine megagametophyte, a maternally derived seed haploid tissue, and four diploid tissues to test the strength of purifying selection on a set of genes with tissue-specific expression. By using targeted resequencing data of those genes, we obtained estimates of genetic diversity, the site frequency spectrum of 0-fold and 4-fold sites, and inferred the distribution of fitness effects of new mutations in haploid and diploid tissue–specific genes. Our results show that purifying selection is stronger for tissue-specific genes expressed in the haploid megagametophyte tissue and that this signal of strong selection is not an artifact driven by high expression levels.

CITATION EXPORT

Sandra Cervantes, Robert Kesälahti, Timo A Kumpula et al.. Strong Purifying Selection in Haploid Tissue–Specific Genes of Scots Pine Supports the Masking Theory. Molecular Biology and Evolution. (2023). https://doi.org/10.1093/molbev/msad183

AUTHORS

6 · 8 CENTRES

Sandra Cervantes, Robert Kesälahti, Timo A Kumpula, Tiina M Mattila, Heikki Helanterä, Tanja Pyhäjärvi

Department of Ecology and Genetics, University of Oulu, Oulu, Finland
Biocenter Oulu, University of Oulu, Oulu, Finland
Department of Ecology and Genetics, University of Oulu, Oulu, Finland
Biocenter Oulu, University of Oulu, Oulu, Finland
Laboratory of Cancer Genetics and Tumor Biology, Research Unit of Translational Medicine, University of Oulu, Oulu, Finland
Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
Department of Ecology and Genetics, University of Oulu, Oulu, Finland
Department of Forest Sciences, University of Helsinki, Helsinki, Finland

EDITOR / REVIEWER

John Parsch