Protecting the Arabian oryx by genome sequencing

Background and Objective: The Arabian oryx (Oryx leucoryx) was hunted to near extinction in from the 1950s to the 1970s. Thus, the oryx ranks among the rarest mammals in the world. Qatar currently has ~800 oryx and has donated numerous oryx to breeding programs around the world. As such, Qatar may be a significant source of genetic diversity to the worldwide oryx population. The primary purpose of this project was to provide a genome sequence and Single Nucleotide Polymorphism (SNP) data in hopes it can be used for improving breading strategies by maintaining as much genetic diversity as possible. Methods: A DNA sample was provided from an oryx male in the Wabra Wildlife Preservation in Qatar. The animal's whole genome was sequenced using next-generation sequencing approach. After assembling the contigs, we utilized a 67bp kmer and ~2.4B paired 100bp (~80X coverage) reads from the Illumina HiSeq. These reads were distributed across libraries ranging in size from 300-1200bp for paired-end and 2000-5000bp for mate-pair libraries. Genome physical coverage by mate-pair libraries was approximately 15X. De novo gene prediction was conducted on scaffolds >500bp. SNPs were also detected. Results: Predicted genome size of ~3Gb (similar to other Mammals), a scaffold N50 of ~300kb, an assembly spanning ~2.5Gb of the genome which is likely >90% of euchromatic sequence. The sequence is distributed across 36,964 scaffolds greater than 500bp. We detected ~1M SNPs between parental alleles, which is significantly fewer than in other "rare" animals such as the giant panda. Conclusion: The initial analysis of polymorphisms suggests a relatively high level of inbreeding, and further study will be needed to clarify whether this is only in certain herds or a worldwide issue.