Horses, asses and zebras belong to the genus Equus and are the only extant species of the family Equidae in the order Perissodactyla. In a previous work (Carbone et al., Genomics 87: 777, 2006), we demonstrated that a key factor in the rapid karyotypic evolution of this genus was evolutionary centromere repositioning, that is the shift of the centromeric function to a new position without alteration of the order of markers along the chromosome. In search of previously undiscovered evolutionarily new centromeres, we traced the phylogeny of horse chromosome 5 analysing the order of BAC markers, derived from a horse genomic library, in seven Equus species (E. caballus, E. hemionus onager, E. kiang, E. asinus, E. grevyi, E. burchelli and E. zebra hartmannae). This analysis showed that repositioned centromeres are present in E. asinus (domestic donkey, EAS) chromosome 16 and in E.burchelli (Burchelli’s zebra, EBU) chromosome 17, confirming that centromere repositioning is a strikingly frequent phenomenon in this genus. The observation that the neocentromeres in EAS 16 and EBU 17 are in the same chromosomal position suggests that they may derive from the same event and therefore E. asinus and E.burchelli may be more closely related than previously proposed; alternatively, two centromere repositioning events, involving the same chromosomal region, may have occurred independently in different lineages, pointing to the possible existence of hot spots for neocentromere formation. Our comparative analysis also showed that, while E. caballus chromosome 5 seems to represent the ancestral configuration, centric fission followed by independent fusion events gave rise to three different submetacentric chromosomes in other Equus lineages.
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