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The mangrove  Kandelia obovata  (Rhizophoraceae) is an important coastal shelterbelt and landscape tree distributed in tropical and subtropical areas across East Asia and Southeast Asia. Herein, a chromosome-level reference genome of  K. obovata  based on PacBio, Illumina, and Hi-C data is reported. The high-quality assembled genome size is 177.99 Mb, with a contig N50 value of 5.74 Mb. A large number of contracted gene families and a small number of expanded gene families, as well as a small number of repeated sequences, may account for the small  K. obovata  genome. We found that  K. obovata  experienced two whole-genome polyploidization events: one whole-genome duplication shared with other Rhizophoreae and one shared with most eudicots (γ event). We confidently annotated 19,138 protein-coding genes in  K. obovata  and identified the MADS-box gene class and the  RPW8  gene class, which might be related to flowering and resistance to powdery mildew in  K. obovata  and  Rhizophora apiculata , respectively. The reference  K. obovata  genome described here will be very useful for further molecular elucidation of various traits, the breeding of this coastal shelterbelt species, and evolutionary studies with related taxa.

Chromosome-scale assembly of the Kandelia obovata genome