Diverse Evolution in 111 Plant Genomes Reveals Purifying and Dosage Balancing Selection Models for <i>F-Box</i> Genes
The F-box proteins function as substrate receptors to determine the specificity of Skp1-Cul1-F-box ubiquitin ligases. Genomic studies revealed large and diverse sizes of the <i>F-box</i> gene superfamily across plant species. Our previous studies suggested that the plant <i>F-box&l...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-01-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/22/2/871 |
| Summary: | The F-box proteins function as substrate receptors to determine the specificity of Skp1-Cul1-F-box ubiquitin ligases. Genomic studies revealed large and diverse sizes of the <i>F-box</i> gene superfamily across plant species. Our previous studies suggested that the plant <i>F-box</i> gene superfamily is under genomic drift evolution promoted by epigenomic programming. However, how the size of the superfamily drifts across plant genomes is currently unknown. Through a large-scale genomic and phylogenetic comparison of the <i>F-box</i> gene superfamily covering 110 green plants and one red algal species, I discovered four distinct groups of plant <i>F-box</i> genes with diverse evolutionary processes. While the members in Clusters 1 and 2 are species/lineage-specific, those in Clusters 3 and 4 are present in over 46 plant genomes. Statistical modeling suggests that <i>F-box</i> genes from the former two groups are skewed toward fewer species and more paralogs compared to those of the latter two groups whose presence frequency and sizes in plant genomes follow a random statistical model. The enrichment of known Arabidopsis <i>F-box</i> genes in Clusters 3 and 4, along with comprehensive biochemical evidence showing that Arabidopsis members in Cluster 4 interact with the Arabidopsis Skp1-like 1 (ASK1), demonstrates over-representation of active <i>F-box</i> genes in these two groups. Collectively, I propose purifying and dosage balancing selection models to explain the lineage/species-specific duplications and expansions of <i>F-box</i> genes in plant genomes. The purifying selection model suggests that most, if not all, lineage/species-specific <i>F-box</i> genes are detrimental and are thus kept at low frequencies in plant genomes. |
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| ISSN: | 1661-6596 1422-0067 |