Biodiv Sci ›› 2011, Vol. 19 ›› Issue (1): 3-16.DOI: 10.3724/SP.J.1003.2011.14256

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Mechanisms underlying copy number variation in F-box genes: evidence from comparison of 12 Drosophila species

An Li1,2, Guixia Xu1, Hongzhi Kong1,*()   

  1. 1 State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093
    2 Graduate University of the Chinese Academy of Sciences, Beijing 100049
  • Received:2010-10-26 Accepted:2010-12-30 Online:2011-01-20 Published:2011-04-01
  • Contact: Hongzhi Kong


Copy number variation (CNV) is a special type of mutational change that plays important roles in phenotypic variation and organismal evolution. To explore the mechanisms underlying copy number variation and to understand its biological significance, we analyzed the phylogenetic relationships, evolutionary patterns and chromosomal locations of F-box genes in 12 closely-related Drosophila species. A total of 541 F-box genes were identified and phylogenetic analyses suggested that they are members of 48 gene clusters (or orthologous groups). Although we observed no drastic changes in the total numbers of F-box genes among the 12 extant Drosophila species (42-47), we found many gene gain and loss events that have caused copy number variation. These results demonstrated that the similarity in the total numbers of F-box genes among different species has, to a certain degree, masked the frequent and independent gain and loss events. Comparisons of the chromosomal locations of orthologous genes showed that extensive microsynteny could be detected only between very closely-related sibling species. We also found that the main mechanisms that caused the increase in gene number were dispersed duplication and tandem duplication, while retroposition and de novo origination from non-coding sequences were two other noteworthy mechanisms. Mutations that caused shifts in exon-intron boundaries and/or losses of exons seemed to be the main mechanisms that underlie decreases in copy number. Although the most recent common ancestor (MRCA) of the 12 Drosophila species had a similar number of genes as the extant species we studied, gains of new genes and losses of existing ones have caused changes in the makeup of F-box genes in descendent species. Our study suggested that variations in the numbers of gene copies is a reflection of “birth-and-death” evolution at the genomic level and have provided raw materials for phenotypic and physiological diversification.

Key words: copy number variation, F-box gene, Drosophila, orthologs