Chromosomal-scale genome assembly of Eleutherococcus senticosus provides insights into chromosome evolution in Araliaceae.

Abstract

Siberian ginseng (Eleutherococcus senticosus, also known as ciwujia) belongs to the Araliaceae family, which contains more than 1,500 species in 41 genera with diverse chromosome numbers and genome sizes. General consensus posits that ancient whole-genome duplication events and rapid evolutionary radiation are the driving forces for this variation in genome properties. In an attempt to generate more genomic information for the Araliaceae family, we report a 1.30Gb high-quality draft genome assembly (contig N50=309.43kb) of E.senticosus via PacBio long reads and Hi-C chromatin interaction maps. We found that transposable elements accounted for 72.82% of the genome and a total of 36,372 protein-coding genes were predicted. Comparative analyses of the E.senticosus, Panax notoginseng and Daucus carota genomes revealed a burst expansion of Tekay chromoviral elements in Araliaceae after its divergence with Apiaceae. We also found that E.senticosus underwent a lineage-specific whole-genome duplication event Es-α and a whole-genome duplication event Araliaceae-β that was probably shared by all Araliaceae species. Even though the rediploidization of the E.senticosus genome is evident, pathway analyses show that these two whole-genome duplication events may have contributed to the adaptation of E.senticosus to a cold environment. Taken together, the high-quality genome assembly of E.senticosus provides a valuable genomic resource for future research on the evolution of Araliaceae.