The chromosome-level quality genome provides insights into the evolution of the biosynthesis genes for aroma compounds of Osmanthus fragrans

Abstract

Sweet osmanthus (<i>Osmanthus fragrans</i>) is a very popular ornamental tree species throughout Southeast Asia and USA particularly for its extremely fragrant aroma. We constructed a chromosome-level reference genome of <i>O</i>. <i>fragrans</i> to assist in studies of the evolution, genetic diversity, and molecular mechanism of aroma development. A total of over 118 Gb of polished reads was produced from HiSeq (45.1 Gb) and PacBio Sequel (73.35 Gb), giving 100× depth coverage for long reads. The combination of Illumina-short reads, PacBio-long reads, and Hi-C data produced the final chromosome quality genome of <i>O</i>. <i>fragrans</i> with a genome size of 727 Mb and a heterozygosity of 1.45 %. The genome was annotated using de novo and homology comparison and further refined with transcriptome data. The genome of <i>O</i>. <i>fragrans</i> was predicted to have 45,542 genes, of which 95.68 % were functionally annotated. Genome annotation found 49.35 % as the repetitive sequences, with long terminal repeats (LTR) being the richest (28.94 %). Genome evolution analysis indicated the evidence of whole-genome duplication 15 million years ago, which contributed to the current content of 45,242 genes. Metabolic analysis revealed that linalool, a monoterpene is the main aroma compound. Based on the genome and transcriptome, we further demonstrated the direct connection between terpene synthases (TPSs) and the rich aromatic molecules in <i>O</i>. <i>fragrans</i>. We identified three new flower-specific <i>TPS</i> genes, of which the expression coincided with the production of linalool. Our results suggest that the high number of <i>TPS</i> genes and the flower tissue- and stage-specific <i>TPS</i> genes expressions might drive the strong unique aroma production of <i>O</i>. <i>fragrans</i>.