Survey of the genome of Pogostemon cablin provides insights into its evolutionary history and sesquiterpenoid biosynthesis

Abstract

Pogostemon cablin (Blanco) Benth. (Patchouli) is an important traditional Chinese medicinal plant that has both essential oil value and a broad range of therapeutic effects. Here we report the first de novo assembled 1.15-Gb draft genome sequence for P. cablin from next-generation sequencing technology. Our assembly, with a misassembly rate of <4 bp per 100 kb, is ~73% of the predicted genome size (1.57 Gb). Analysis of whole-genome sequences identified 3,147,333 heterozygous single-nucleotide polymorphisms and 490,407 insertions and deletions, giving an estimated heterozygosity rate of 0.274%. A comprehensive annotation pipeline indicated that repetitive sequences make up 58.55% of the assemblies, and that there are estimated 45,020 genes. Comparative genomics analysis showed that the Phrymaceae and Lamiaceae family split ~62.80 Mya, and the divergence between patchouli and sesame occurred ~52.42 Mya, implying a potentially shared recent whole-genome duplication event. Analysis of gene homologs involved in sesquiterpenoid biosynthesis showed that patchouli contains key genes involved in more sesquiterpenoid types and has more copies of genes for each sesquiterpenoid type than several other related plant species. The patchouli genome will facilitate future research on secondary metabolic pathways and their regulation as well as potential selective breeding of patchouli.

Bioactivities of patchoulol and phloroacetophenone from Pogostemon cablin essential oil against three insects

“…[31] There are some researchers investigated the underlying reasons at genetic aspect. He et al [32] surveyed the genome of P. cablin. Their analysis showed that P. cablin contains key genes involved in more sesquiterpenoid types and has more copies of genes for each sesquiterpenoid types than several other related plant species.…”

Building an octaploid genome and transcriptome of the medicinal plant Pogostemon cablin from Lamiales

“…Lamiales (eudicots/Asterids I clade), one of the largest orders of flowering plants, has more than 23,000 species in at least 23 families 1 and representatives are found all over the world. Well-known, economically or medicinally important members of this order include lavender, olive 2 , the ash tree 3 , sesame 4 , bladderwort 5 , mint 6 and patchouli 7 . Lamiales species present highly specialized life strategies, such as carnivory, parasitism, epiphytism, and desiccation tolerance 8 .…”

“…Patchouli, Pogostemon cablin (Blanco) Benth., is one of species from the Lamiaceae (mint family), and has been widely cultivated in tropical and subtropical areas of Asia owing to high demand for its essential oil 11 . Chemical and pharmacological studies of patchouli over the last few decades indicated that the patchouli oil contains >40 major components 7 . These compounds play an essential role in plant reproduction, defence, and signalling, and are also precious important industrial ingredient for perfumes, incense, soaps and cosmetic products 12 , 13 .…”

Genome Survey Sequencing of Acer truncatum Bunge to Identify Genomic Information, Simple Sequence Repeat (SSR) Markers and Complete Chloroplast Genome

“…Recently, genome survey sequencing by next generation sequencing (NGS) has emerged as an important and cost-effective strategy for generating a wide range of genetic and genomic information for different plant species [11][12][13][14][15][16][17][18]. It can also identify a large number of molecular markers for breeding [19].…”