Genome sequence and salinity adaptation of the desert shrub Nitraria sibirica (Nitrariaceae, Sapindales)

Abstract The genetic bases of halophytes for salinity tolerance are crucial for genetically breeding salt-tolerant crops. All natural Nitrariaceae species that exclusively occur in arid environments are highly tolerant to salt stress, but the underlying genomic bases to this adaptation remain unknown. Here we present a high-quality, chromosome-level genome sequence of Nitraria sibirica, with an assembled size of 456.66 Mb and 23,365 annotated genes. Phylogenomic analyses confirmed N. sibirica as the sister to all other sampled representatives from other families in Sapindales, and no lineage-specific whole-genome duplication was found except the gamma triplication event. Still, we found that the genes involved in K+ retention, energy supply, and Fe absorption expanded greatly in N. sibirica. Deep transcriptome analyses showed that leaf photosynthesis and cuticular wax formation in roots were enhanced under salt treatments. Furthermore, many transcription factors involved in salt tolerance changed their expressions significantly and displayed tissue- and concentration-dependent signalling in response to salt stress. Additionally, we found vacuolar Na+ compartmentalization is an ongoing process under salt treatment, while Na+ exclusion tends to function at high salt concentrations. These genomic and transcriptomic changes conferred salt tolerance in N. sibirica and pave the way for the future breeding of salt-tolerant crops.