A method for cloning a donor genome comprising: obtaining a donor genome from a bacterial, cyanobacterial, or microalgal donor cell as one or more fragments; and introducing the donor genome and a yeast host vector into a yeast host cell, wherein the donor genome and the yeast host vector are joined prior to or after introduction of the donor genome and yeast host vector into the yeast host cell, thereby generating a yeast host cell comprising the donor genome comprising the yeast host vector, and further wherein the donor genome is at least a minimal genome, and is greater than 300 kb in length; propagating the donor genome in the yeast host cell; preparing a bacterial, cyanobacterial or microalgal recipient cell and/or donor genome for transplantation of the donor genome into the recipient cell; and recovering the donor genome comprising the yeast host vector from the host cell and introducing the recovered donor genome comprising the yeast host vector into the recipient cell, wherein; the recovered donor genome is methylated prior to introduction into the recipient cell; or wherein the recipient cell's restriction endonuclease function is absent, removed or inactivated; or wherein the endogenous genome of the recipient cell is degraded or removed, wherein the recipient cell supports gene expression from the donor genome, thereby cloning the donor genome and producing a self-replicating recipient cell controlled only by the donor genome; wherein the donor genome is sufficient to sustain viability and continuous self-replication of the recipient cell, and wherein the yeast host vector is a centromeric plasmid. obtaining a donor genome from a bacterial, cyanobacterial, or microalgal donor cell as one or more fragments; and introducing the donor genome and a yeast host vector into a yeast host cell, wherein the donor genome and the yeast host vector are joined prior to or after introduction of the donor genome and yeast host vector into the yeast host cell, thereby generating a yeast host cell comprising the donor genome comprising the yeast host vector, and further wherein the donor genome is at least a minimal genome, and is greater than 300 kb in length; propagating the donor genome in the yeast host cell; preparing a bacterial, cyanobacterial or microalgal recipient cell and/or donor genome for transplantation of the donor genome into the recipient cell; and recovering the donor genome comprising the yeast host vector from the host cell and introducing the recovered donor genome comprising the yeast host vector into the recipient cell, wherein; the recovered donor genome is methylated prior to introduction into the recipient cell; or wherein the recipient cell's restriction endonuclease function is absent, removed or inactivated; or wherein the endogenous genome of the recipient cell is degraded or removed, wherein the recipient cell supports gene expression from the donor genome, thereby cloning the donor genome and producing a self-replicating recipient cell controlled only by the donor genome; wherein the donor genome is sufficient to sustain viability and continuous self-replication of the recipient cell, and wherein the yeast host vector is a centromeric plasmid.