Syringa oblata Genome sequencing and assembly

Lilac (Syringa oblata Lindl.), a member of family Oleaceae, is a well-known woody ornamental and important Chinese medicinal plant which is originated in China and widely cultivated in the world. Here, we reported the first Syringa genus chromosome-scale reference genome of Syringa oblata using a combination of Nanopore long reads, DNBseq short reads and Hi-C data to research the molecular mechanism of floral pigment biosynthesis. The final genome assembly was 1.05 Gb, with a contig N50 size of 3.96 Mb and a BUSCO complete gene percentage of 93.5%. Scaffolds covering 93.50% of the assembled genome were anchored on 23 chromosomes, resulting in a scaffold N50 of 46.33 Mb. The genome was predicted to contain 35,313 protein-coding genes, and 54.30% of the assembled sequences are repetitive sequences, with long terminal repeats (LTR) retrotransposons being the most abundant (37.79%). We also confirmed a WGD event shared with Oleaceae. Further, combining with genome, transcriptome and metabolome, the flavonols and anthocyanins biosynthesis pathways and related regulatory networks were reconstructed through time-ordered gene co-expression network analysis. In addition to MYB, bHLH, and WD40 transcription factors that play a vital role synergistically in flower coloring, WRKY also plays an essential role in the early stage of flowering, while ERF is more important in the color transition period. The data from this study will be beneficial for flower pigmentation and further molecular elucidation of other traits, and could accelerate rare flower color development and directed breeding in lilac.