Evolutionary divergence constrains the potential of Christmas Island rat de-extinction through genome resurrection

Three principal methods are under discussion as possible pathways to “true” deextinction, i.e. where the genomes of reconstructed species closely resemble those lost: targeted back-breeding, cloning through interspecific somatic cell nuclear transfer (iSCNT), and genome resurrection by genetic engineering of the genomes of extant species to resemble as closely as possible the genome of extinct relatives. Of these, while the latter approach is most likely to be applicable to the largest number of extinct species, ultimately its potential is constrained by the degree to which the sequence of the extinct species genome can be reconstructed. We elected to computationally explore this question using the extinct Christmas Island rat (Rattus macleari , also known as Maclear's rat) as a model. As one of two endemic rat species found on Christmas Island in the Indian Ocean, it was driven extinct between 1898 and 1908, potentially as a result of the introduction of pathogenic trypanosomes from black rats (R. rattus ) arriving on visiting ships. First we resequenced the Christmas Island rat genome to an average of >60x coverage, and mapped it to the reference genomes of different Rattus species. We then explored how evolutionary divergence from the extant reference genome affected the fraction of the Christmas Island rat genome that could be recovered. Our analyses show that even when the extremely high quality Norway brown rat (R. norvegicus ) is used as a reference, nearly 5% of the genome sequence is unrecoverable, with 1661 genes recovered at lower than 90% completeness, and 26 completely absent. Furthermore, we find the distribution of regions affected is not random, but for example if 90% completeness is used as the cutoff, GO/KEGG annotation related to immune response and olfaction are excessively affected. Ultimately our approach demonstrates the importance of applying similar analyses to candidates for de-extinction through genome editing, in order to provide critical baseline information about how representative the edited form would be of the extinct species.