Short read assembly and gene annotation of the first genome of the extinct Indian Javan subspecies, Rhinoceros sondaicus inermis

The Javan rhino ( Rhinoceros sondaicus ) is a critically endangered species in which approximately 50 individuals survive in the Ujung Kulon National Park in Southwest Java, Indonesia. There is limited genetic data of this rhino species in which only mitochondrial DNA sequences are available in the GenBank database. Here, the whole genome of the Javan rhino was sequenced, and the draft genome was assembled and annotated. The whole genome sequencing was performed using a tooth of the ancient Indian Javan rhino dated approximately 100 years before present collected from the rhino skeleton collection room in Khao Sam Roi Yot National Park, Prachuap Kiri Khan Province, Thailand. A total of 221 million reads were generated, and 51 million reads were mapped to black rhino ( Diceros bicornis ) sequences. Then, the total length of 195 Mb was assembled into 234,360 contigs and 343 scaffolds. The genome annotation was performed by comparing to the NCBI annotation of black rhino sequences which resulted in more than 6,000 annotated genes. This genomic data could gain insight into physiological characteristics, and it would be useful for evolutionary studies and conservation efforts of the critically endangered rhino species.