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.
Highlights
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
To obtain sufficient quantities of nuclear DNA for the sequencing libraries, nuclear DNA was isolated from leaves of P. cablin
To determine whether there were sequences from other species in the clean data, 10,000 clean reads were randomly selected to align to the National Center for Biotechnology Information (NCBI) nucleotide (NT) database
Summary
This is expected because of the abundant repetitive sequences in the patchouli genome, as it has been demonstrated that assembled genome size can be inflated when there is high repeat content and/or heterozygosity[27] This percentage is quite similar in the Lamiales relative sesame (Sesamum indicum L., 274 Mb relative to an estimated 357 Mb)[28], the assembled patchouli genome is much larger. Improving the sequencing depth and assembly quality of the patchouli genome and constructing a prediction model based on full-length cDNA sequences obtained from RNA sequencing will improve the quality of gene annotation With this assembly we could explore patchouli genes at the exon and intron level (Fig. 2B,C). A total of 4,243 gene families are shared by all the five species (Fig. 3A,B), and within these gene families, Species Patchouli Sesame Monkey flower Tomato Arabidopsis
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