The disclosure provides for methods of constructing synthetic chromosomes including the steps of providing host cells with an endogenous
chromosome, transforming a
cloning vector and a
cloning cassette into the host cells, excising target genomic nucleic acids from the endogenous
chromosome, recombining the excised target genomic nucleic acids with the
cloning cassette via
homologous recombination to form
heterologous vectors comprising cloned sequences, extracting the
heterologous vectors containing the cloned sequences from the host cells, digesting the
heterologous vectors with a restriction
endonuclease to release the cloned sequences from the heterologous vectors to provide released cloned sequences, and introducing the released cloned sequences, a
centromere cassette, and a
yeast artificial chromosomes or bacterial artificial chromosomes into a second host
cell, such that the released cloned sequences, the
centromere cassette, and the YAC or BAC recombine with one another via
homologous recombination to produce the synthetic
chromosome.