De novo assembly of the Haloxylon persicum genome as a part of the KSA Native Genome Project

Abstract

Haloxylon persicum is a xerophytic desert tree that grows mostly in deserts in West and Central Asia. This tree is very tolerant to the harsh conditions of deserts, mainly drought and heat. As a part of the Kingdom of Saudi Arabia Native Genome Project, a voucher specimen was identified, and the genome of this plant was sequenced, assembled, and annotated. The chromosome level assembly was performed using the integration of PacBio Hifi reads and Bionano optical maps, resulting in 9 chromosome-sized molecules that only exhibit 3 gaps located in highly repetitive regions. The annotation of the transposable elements in the genome shows that more than 55% of the genome consists of transposable elements. Moreover, genes were predicted using Iso-seq and RNA-seq and annotated using publicly available protein databases, resulting in the identification of more than 45,000 predicted genes, of which ≈ 10,000 have RNA evidence. The genome assembly and annotation of Haloxylon persicum will: provide valuable insight on the evolutionary history of desert plants, aid in discovering the mechanisms developed by this species to cope with the extreme desert conditions and unveil the possibilities and opportunities of neo-domesticating this plant. Furthermore, this assembly can serve as a reference for assembling other plant species in the KSA Native genome project or any other project worldwide.