title: 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.
authors.affiliation: State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: He
authors.affiliation: School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China.|Department of Pharmacy, Hospital of the University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu 610072, China.
authors.forename: Hongtao
authors.initials: H
authors.lastname: Xiao
authors.affiliation: DNA Stories Bioinformatics Center, Chengdu 610065, China.
authors.forename: Cao
authors.initials: C
authors.lastname: Deng
authors.affiliation: State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China.
authors.forename: Liang
authors.initials: L
authors.lastname: Xiong
authors.affiliation: DNA Stories Bioinformatics Center, Chengdu 610065, China.
authors.forename: Hu
authors.initials: H
authors.lastname: Nie
authors.affiliation: State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China.
authors.forename: Cheng
authors.initials: C
authors.lastname: Peng
mesh_terms: D053898:Biosynthetic Pathways; D019143:Evolution, Molecular; D018740:Genetic Heterogeneity; D059646:Genome Size; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D019686:Lamiaceae / Q000235:genetics; D009822:Oils, Volatile / Q000378:metabolism; D010802:Phylogeny; D000070177:Pogostemon / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA / Q000379:methods; D012717:Sesquiterpenes / Q000378:metabolism*
chemical_list: D009822:Oils, Volatile; D012717:Sesquiterpenes