The chromosome-level reference genome assembly for Dendrobium officinale and its utility of functional genomics research and molecular breeding study

Abstract

Dendrobium officinale , an important medicinal plant of the genus Dendrobium in Orchidaceae family, has been used as traditional Chinese medicine (TCM) for nearly thousands of years. Here, we report the first chromosome-level reference genome of D . officinale , based on PacBio long-reads, Illumina short-reads and Hi-C data. The high-quality assembled genome is 1.23 Gb long, with contig N50 of 1.44 Mb. A total of 93.53% genome sequences were assembled into 19 pseudochromosomes with a super scaffold N50 of 63.07 Mb. Through comparative genomic analysis, we explored the expanded gene families of D . officinale , and also their impact on environmental adaptation and biosynthesis of secondary metabolites. We further performed detailed transcriptional analysis of D. officinale , and identified the candidate genes involved in the biosynthesis of three main active ingredients, including polysaccharides, alkaloids and flavonoids. In addition, the MODIFYING WALL LIGNIN-1 ( MWL1 ) gene, which inferred from Genome-Wide Association Studies (GWAS) based on the resequencing date from D. officinale and five related species and their morphologic features, may contribute to the plant production (yield of stems) of D. officinale . Therefore, the high-quality reference genome reported in this study could benefits functional genomics research and molecular breeding of D. officinale .

Effects of Various Processing Methods on the Metabolic Profile and Antioxidant Activity of Dendrobium catenatum Lindley Leaves

“…It has been widely used as a tonic in China and other Southeast Asian countries for thousands of years. The importance of this species is highlighted by its high economic value, as the market price of wild D. catenatum is around $16,000 per kilogram [2,3]. However, wild D. catenatum is on the verge of extinction due to the destructive harvest, the destruction of the living environment, and its low reproduction ability.…”

Research Advances in Multi-Omics on the Traditional Chinese Herb Dendrobium officinale

“…Genome data can provide basic and comprehensive information on genetic backgrounds and bridge gaps between genetic bases and active compounds in medicinal plants. To date, three versions of D. officinale genomic data (2n = 38) have been reported, with the genome size varying from 1.01 to 1.36 Gb and heterozygosity of 0.48–1.27% ( Yan et al, 2015 ; Zhang G. Q. et al, 2016 ; Niu et al, 2021 ). A comparison between them is listed in Table 1 .…”

“…A comparison between them is listed in Table 1 . The first two versions were assembled at the scaffold level, while the third version was assembled onto 19 chromosomes with third-generation and Hi-C sequencing platforms ( Niu et al, 2021 ). The number of protein-coding genes varied from 27631 to 35567, with 629–1462 gene families specific to D. officinale .…”

“…There are differences in genomic data between three versions, which could result from the sequencing platform, assembly strategies and genome annotation methods. The genome of D. officinale characteristically features abundant repetitive sequences and two rounds of whole-genome duplication (WGD; Zhang G. Q. et al, 2016 ; Niu et al, 2021 ). In the future, with the aid of genetic and physical maps and more transcriptomic data, genome quality and annotation integrity can be further improved.…”

“…According to the earlier two versions, some key enzyme genes involved in the biosynthesis of active compounds were identified ( Yan et al, 2015 ; Zhang G. Q. et al, 2016 ). Based on the third version, the researchers comprehensively identified the genes in the biosynthetic pathways of polysaccharides, alkaloids, and flavonoids, including 418 genes ( Niu et al, 2021 ; Figures 1 – 3 ). For the biosynthesis of polysaccharides, a total of 268 genes encoding 56 enzymes were identified ( Niu et al, 2021 ).…”