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

Abstract

Sweet osmanthus (Osmanthus fragrans) 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 O. fragrans 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 O. fragrans 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 O. fragrans 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 O. fragrans. We identified three new flower-specific TPS genes, of which the expression coincided with the production of linalool. Our results suggest that the high number of TPS genes and the flower tissue- and stage-specific TPS genes expressions might drive the strong unique aroma production of O. fragrans.

Chromosome-level genome assembly, annotation and evolutionary analysis of the ornamental plant Asparagus setaceus

“…BUSCO assessment revealed that 90.0% of the complete BUSCOs could be found in the current assembled A. setaceus genome. This percentage was lower than those in Osmanthus fragrans (96.1%) 24 and Brassica oleracea (96.77%) 25 , but higher than those in the genomes of some other species, such as Ginkgo biloba (73.95%) 26 and A. officinalis (88.2%) 11 . Considering the high level of heterozygosity and repetitiveness of the genome, the current version represents a high-quality genome assembly of A. setaceus.…”

Genome-Wide Identification, Classification, and Expression Profiling Reveals R2R3-MYB Transcription Factors Related to Monoterpenoid Biosynthesis in Osmanthus fragrans

“…In this study, four tissue types from sweet osmanthus ('RiXiangGui'), including roots, stems, leaves (young and mature), and flowers in initial, full, and final flowering stages, were collected. Fresh flowers in the different flowering stages were used to detect the scent compounds with the method of head space solid phase microextraction(HS-SPME) and gas chromatography/mass spectrometer (GC/MS); the detailed information was stated and the results presented in our previous work [15,30]. Altogether, 21 different samples were subjected to Illumina RNA-seq analysis [15].…”

“…Fresh flowers in the different flowering stages were used to detect the scent compounds with the method of head space solid phase microextraction(HS-SPME) and gas chromatography/mass spectrometer (GC/MS); the detailed information was stated and the results presented in our previous work [15,30]. Altogether, 21 different samples were subjected to Illumina RNA-seq analysis [15]. Reads per kilobase of exon per million reads mapped (RPKM) values were measured to the transcript abundance of each gene.…”

“…The largest number of fragrant compounds are released during the full flowering stages of the life cycle. The main floral volatile compounds released from sweet osmanthus are terpenoids, especially monoterpenes including β-ionone, cis-linalool oxide (furan), trans-linalool oxide (furan), linalool, and trans-β-ocimene [14,15].…”

The complete chloroplast genome of Osmanthus serrulatus rehd., a natural sweet olive endemic to China

“…(Oleaceae), usually known as Baoxing osmanthus, is one of the rare spring flowering endemic Osmanthus species of which narrowly and sporadically distributed under the evergreen broad-leaved forests at elevations of 1800-2400 m in west Sichuan Province, China (Xiang and Liu 2008). Although it occupies an important phylogenetic node in genus Osmanthus, and plays a crucial germplasm resource for genetic breeding of sweet osmanthus, the genetic information of O. serrulatus is still limited so far (Chen et al 2015), while most study always focus on O. fragrans (Mu et al 2014;Yang et al 2018;Duan et al 2019). So, it is necessary to develop genetic resources of O. serrulatus to provide basic intragenic information for the further study on phylogeny and biogeography in genus Osmanthus.…”