Evolution And Population Genetics Study Of F-box Genes In Animals

Degradation of unique protein through the ubiquitin-proteasome system(UPS) is an important mechanism that underlies numerous cellular and organismal processes. The specific of substrate depends on E3 ubiquitin ligase, among which SCF(SKP1–CUL1–F-box) complex is best understood. F-box proteins containing a F-box domain function as substrate adaptor in SCF complex.F-box gene numbers vary greatly among different species, from tens to thousands. In this study, we investigated F-box gene number variation and underlying mechanisms, gene structural and functional divergence during evolution of Euarchontoglires and Caenorhabditis, all of which are benefit to deeply understand genome evolution and figure out F-box protein function. In addition, SNPs included in human E3 genes and cattle FBXO32 and their population genetics character were investigated. The main results are as follows:Part I: By phylogenetic analysis and selection pressure detection methods, we investigated F-box gene number variation and the underlying mechanisms as well as selection patterns during the evolution of Euarchontoglires. The results showed that(1) 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 extant species;(2) 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;(3) Signatures of positive selection were detected in substrate-recognizing domains of multiple F-box proteins. Conclusions:(1) F-box genes evolved under a birth-and-death model;(2)Lineage-specific adaptive changes in amino acid played a role in evolution of the F-box genes.Part II: By comparative genomics and transcriptome sequencing data analysis, we investigated F-box gene number variation among five species of Caenorhabditis, and gene structural and functional divergence of duplicated F-box genes. The results showed that(1) The number of F-box genes in five species of Caenorhabditis vary greatly from tens to thousands, which was caused mainly by a series of tandem duplication events;(2) Many of duplicated F-box genes diverged strikingly at their F-box domain regions;(3) Mechanisms involved in gene structure divergence are exon/intron gain/loss, mutation, exonization/pseudoexonization, insertion/deletion, and intron sequence elongation;(4) In Caenorhabditis elegans(C. elegans) and Caenorhabditis briggsae(C. briggsae), all of paralogous groups differentiated at developmental stage-specific expression patterns. Conclusions:(1) A couple of mechanisms have contributed to structure divergence of duplicated F-box genes;(2) F-box gene duplications have diverged in function through different developmental stage-specific expression patterns.Part III: Using the human 1000 Genomes Project data, we investigated SNPs of E3 genes, and selective pressures on E3 genes especially on substrate-recognizing domains. The results showed that(1)Africa human populations is richer in SNP of E3 genes than that of populations from other continents;(2) Substrate-recognizing domains of E3 genes have underwent strong purifying selection. Conclusions: substrate-recognizing domains of E3 genes have underwent the strongest purifying selection than that of other regions.Part IV: By DNA sequencing and restricted fragment length polymorphisms experimental techniques, we investigated the polymorphism of FBXO32 gene in 1, 313 cattle from seven bovine breeds, and association study of identified SNPs with growth traits. The results showed that(1) Four novel SNPs were identified and were deposited in the Gen Bank database(ss411628932, ss411628934 ss411628935 and ss411628936);(2) Sites ss411628932 and ss411628936 were shown to be significantly associated with body length of 24-month-old Nan Yang cattle(P-value ﹤ 0.05);(3) The phylogenetic distance between seven bovine populations is positive correlation with their geographical distance. Conclusions:(1) A recombination hot may be located between exon 3 and intron 10 of FBXO32 gene;(2) FBXO32 gene is predictive of genetic potential for body length phenotype, and sites ss411628932 and ss411628936 may be genomic selection marker for bovine breeding;(3) Geographical distance was essential to gene flow among seven cattle breeds.Taken together, we studied F-box gene number variation and underlying mechanims, selection patterns, gene structure and functional divergence of F-box genes in Euarchontoglires and Caenorhabditis using approaches statistic, comparative genomics, phylogenetic analysis and natural selection. In addition, by experimental techniques of molecular biology, we investigated SNPs in FBXO32 and performed association study of identified SNPs with growth traits. These studies provide fundamental knowledge to reveal the origin, evolution and function of F-box genes, and what’s more intriguing significant is that studies give us a new insight to investigate the evolution of other gene families.