The plastid genome and its implications in barcoding specific-chemotypes of the medicinal herb Pogostemon cablin in China

Abstract

Pogostemon cablin (Blanco) Benth. (Patchouli) is not only an important essential oil plant, but also a valuable medicinal plant in China. P . cablin in China can be divided into three cultivars (Shipai, Gaoyao, and Hainan) and two chemotypes (pogostone-type and patchoulol-type). The pogostone-type and patchoulol-type are, respectively, used for medicinals and perfumes. In this study, we sequenced and characterized the plastid genomes for all three Chinese cultivars and aimed to develop a chemotype-specific barcode for future quality control. The plastid genomes of P . cablin cultivars ranged from 152,461 to 152,462 bp in length and comprise 114 genes including 80 protein coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analyses suggested that P . cablin cultivars clustered with the other two Pogostemon species with strong support. Although extremely conserved in P . cablin plastid genomes, 58 cpSSRs were filtered out among the three cultivars. One single variable locus, cpSSR, was discovered. The cpSSR genotypes successfully matched the chemotypes of Chinese patchouli, which was further supported by PCR-based Sanger sequences in more Chinese patchouli samples. The barcode developed in this study is thought to be a simple and reliable quality control method for Chinese P . cablin on the market.

Comparative Analyses of the Chloroplast Genomes of Patchouli Plants and Their Relatives in Pogostemon (Lamiaceae)

“…In this study, we detected six highly variable loci in Pogostemon cp genomes, all of which are located within the eight top-ranking regions identified in 25 angiosperm lineages by Shaw et al [17], consistent with previous findings in Pogostemon [9]. The phylogenetic utility of protein-coding sequences in Pogostemon was also evaluated by a comparison of the number of PICs.…”

“…The overall GC content of the cp genome is 38.3% for P. plectranthoides and 38.2% for P. septentrionalis. The newly generated cp genomes of the two P. cablin cultivars ("Indonesia" and "Vietnam") were effectively identical to those of other P. cablin cultivars, with only one base difference [9]. We therefore arbitrarily chose the cp genome of the cultivar "Gaoyao" (GenBank no.…”

“…Chloroplast (cp) genomes have been considered as "ultra-barcode" for species/cultivar identification [7][8][9] and phylogenomic analyses [10][11][12]. Recently, obtaining hundreds to thousands of organelle loci has become routine because of rapid improvements in high-throughput sequencing (HTS) technology in the past decade [13,14].…”

“…However, there is still a lack of cp genome data for the genus Pogostemon (especially for patchouli species). So far, only nine cp genome sequences derived from three Pogostemon species are publicly available, of which only the P. cablin cp genomes have been well studied [9]. It is necessary to sequence and characterize more cp genomes for analyzing the infrageneric phylogeny and species identification of Pogostemon, especially for the economically important patchouli plants.…”

The First Plastid Genome of the Holoparasitic Genus Prosopanche (Hydnoraceae)

“…The sequence for trnW-CCA (Trp) is predicted by tRNAscan to have an ACA anticodon instead of a CCA anticodon. No tRNA with an ACA anticodon is known from Piperales plastomes but was found, for example, in Asterales (e.g., Pogostemon cablin MF287373 [48]). Sequence similarity strongly suggests that said Asterales tRNA with ACA anticodon is known as the intron-containing trnV-UAC in Piperales.…”