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Background F-box proteins represent a diverse class of adaptor proteins of the ubiquitin-proteasome system (UPS) that play critical roles in the cell cycle, signal transduction, and immune response by removing or modifying cellular regulators. Among closely related organisms of the  Caenorhabditis  genus, remarkable divergence in F-box gene copy numbers was caused by sizeable species-specific expansion and contraction. Although F-box gene number expansion plays a vital role in shaping genomic diversity, little is known about molecular evolutionary mechanisms responsible for substantial differences in gene number of F-box genes and their functional diversification in  Caenorhabditis . Here, we performed a comprehensive evolution and underlying mechanism analysis of F-box genes in five species of  Caenorhabditis  genus ,  including  C. brenneri ,  C. briggsae ,  C. elegans ,  C. japonica , and  C. remanei . Results Herein, we identified and characterized 594, 192, 377, 39, 1426 F-box homologs encoding putative F-box proteins in the genome of  C. brenneri ,  C. briggsae ,  C. elegans ,  C. japonica , and  C. remanei,  respectively. Our work suggested that extensive species-specific tandem duplication followed by a small amount of gene loss was the primary mechanism responsible for F-box gene number divergence in  Caenorhabditis  genus. After F-box gene duplication events occurred, multiple mechanisms have contributed to gene structure divergence, including exon/intron gain/loss, exonization/pseudoexonization, exon/intron boundaries alteration, exon splits, and intron elongation by tandem repeats. Based on high-throughput RNA sequencing data analysis, we proposed that F-box gene functions have diversified by sub-functionalization through highly divergent stage-specific expression patterns in  Caenorhabditis  species. Conclusions Massive species-specific tandem duplications and occasional gene loss drove the rapid evolution of the F-box gene family in  Caenorhabditis , leading to complex gene structural variation and diversified functions affecting growth and development within and among  Caenorhabditis  species .  In summary, our findings outline the evolution of F-box genes in the  Caenorhabditis  genome and lay the foundation for future functional studies.

Genome-wide characterization, evolution, structure, and expression analysis of the F-box genes in Caenorhabditis