title: Evolution of the F-box gene family in Euarchontoglires: gene number variation and selection patterns.
abstract: F-box proteins are substrate adaptors used by the SKP1-CUL1-F-box protein (SCF) complex, a type of E3 ubiquitin ligase complex in the ubiquitin proteasome system (UPS). SCF-mediated ubiquitylation regulates proteolysis of hundreds of cellular proteins involved in key signaling and disease systems. However, our knowledge of the evolution of the F-box gene family in Euarchontoglires is limited. In the present study, 559 F-box genes and nine related pseudogenes were identified in eight genomes. Lineage-specific gene gain and loss events occurred during the evolution of Euarchontoglires, resulting in varying F-box gene numbers ranging from 66 to 81 among the eight species. Both tandem duplication and retrotransposition were found to have contributed to the increase of F-box gene number, whereas mutation in the F-box domain was the main mechanism responsible for reduction in the number of F-box genes, resulting in a balance of expansion and contraction in the F-box gene family. Thus, the Euarchontoglire F-box gene family evolved under a birth-and-death model. Signatures of positive selection were detected in substrate-recognizing domains of multiple F-box proteins, and adaptive changes played a role in evolution of the Euarchontoglire F-box gene family. In addition, single nucleotide polymorphism (SNP) distributions were found to be highly non-random among different regions of F-box genes in 1092 human individuals, with domain regions having a significantly lower number of non-synonymous SNPs.
authors.affiliation: State Key Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China; Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, China.
authors.forename: Ailan
authors.initials: A
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China; Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, China.
authors.forename: Mingchuan
authors.initials: M
authors.lastname: Fu
authors.affiliation: State Key Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China; Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, China.
authors.forename: Xiaoqian
authors.initials: X
authors.lastname: Jiang
authors.affiliation: State Key Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China; Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, China.
authors.forename: Yuanhui
authors.initials: Y
authors.lastname: Mao
authors.affiliation: State Key Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China; Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, China.
authors.forename: Xiangchen
authors.initials: X
authors.lastname: Li
authors.affiliation: State Key Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China; Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, China.
authors.forename: Shiheng
authors.initials: S
authors.lastname: Tao
mesh_terms: D000220:Adaptation, Biological; D000818:Animals; D002874:Chromosome Mapping; D016000:Cluster Analysis; D019143:Evolution, Molecular; D044783:F-Box Proteins / Q000737:chemistry / Q000235:genetics*; D023061:Gene Order; D056426:Genetic Loci; D014644:Genetic Variation; D016678:Genome; D055106:Genome-Wide Association Study; D006801:Humans; D008958:Models, Molecular; D005810:Multigene Family; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D011487:Protein Conformation; D054730:Protein Interaction Domains and Motifs; D012641:Selection, Genetic
chemical_list: D044783:F-Box Proteins
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