Comparative studies of chromosome content and organization are providing insight into
fundamental questions of genome evolution and speciation. BAC library has tremendous potential
to facilitate such studies to shed light on the temporal relationships of extant species by comparative
sequence analysis and cytogenetic mapping of genome rearrangement, expansion, and loss (Gomyoet al. 1999; Srinivasan et al. 2002 ). In addition to decipher genome evolution, BAC resources could be used to address specific questions pertaining to centromeric and pericentromeric evolution, and the mechanisms of karyotypic change between closely related species. The Indian muntjac
(Muntiacus muntjac vaginalis) has the lowest chromosome number in mammalian species with 6
chromosomes in female and 7 in male. Recent molecular cytogenetic studies landed support to the hypothesis that the karyotype of the Indian muntjac could evolve from an ancient deer species with a karyotype 2n=70 through extensive tandem fusions and several centric fusions (Li et al. 2000b).Moreover, the centromere of X+3 chromosome of the species is compound and unique. Therefore, it
is an ideal species for studying chromosome rearrangement,comparative genomic and karyotype evolution. In an attempt to explore the centromeric evolution and function, and to elucidate the fusion orientations of conserved chromosome segments and the underlying mechanism of tandem
