Genome assembly provides insights into the genome evolution of Baccaurea ramiflora Lour.

Baccaurea ramiflora Lour., an evergreen tree of the Baccaurea genus of the Phyllanthaceae family, is mainly distributed in South Asia, Southeast Asia, and southern China, including southern Yunnan Province. It is a wild or semicultivated tree species of ornamental, edible, and medicinal value, with important development potential. Here, we report the whole-genome sequencing of B. ramiflora through the combination of PacBio SMRT and Illumina HiSeq 2500 sequencing techniques. The size of the assembled genome is 975.8 Mb, with a contig N50 of 509.33 kb and a longest contig of 7.74 Mb. Highly repetitive sequences make up 73.47% of the genome, of which 52.1% are long terminal repeat–retrotransposon sequences. A total of 29,172 protein-coding genes are predicted, of which 25,980 (89.06%) have been annotated, while 3,452 noncoding RNAs are found. Comparative genomic analysis indicates that B. ramiflora is closely related to the family Euphorbiaceae, being sister groups to each other that diverged approximately 59.9 Mya. During the evolutionary process, B. ramiflora has 278 candidate genes under positive selection. The synonymous substitution rate and collinearity analysis show that B. ramiflora only underwent one ancient genome-wide triploidization event and no recent genome-wide duplication event. This high-quality B. ramiflora genome provides a valuable resource for basic research and tree improvement programs of the Phyllanthaceae family.