Background: Panax species are important herbal medicinal plants in the Araliaceae family. Recently, we reported the complete chloroplast genomes and 45S nuclear ribosomal DNA sequences from seven ...Panax species, two (P. quinquefolius and P. trifolius) from North America and five (P. ginseng, P. notoginseng, P. japonicus, P. vietnamensis, and P. stipuleanatus) from Asia. Methods: We conducted phylogenetic analysis of these chloroplast sequences with 12 other Araliaceae species and comprehensive comparative analysis among the seven Panax whole chloroplast genomes. Results: We identified 1,128 single nucleotide polymorphisms (SNP) in coding gene sequences, distributed among 72 of the 79 protein-coding genes in the chloroplast genomes of the seven Panax species. The other seven genes (including psaJ, psbN, rpl23, psbF, psbL, rps18, and rps7) were identical among the Panax species. We also discovered that 12 large chloroplast genome fragments were transferred into the mitochondrial genome based on sharing of more than 90% sequence similarity. The total size of transferred fragments was 60,331 bp, corresponding to approximately 38.6% of chloroplast genome. We developed 18 SNP markers from the chloroplast genic coding sequence regions that were not similar to regions in the mitochondrial genome. These markers included two or three species-specific markers for each species and can be used to authenticate all the seven Panax species from the others. Conclusion: The comparative analysis of chloroplast genomes from seven Panax species elucidated their genetic diversity and evolutionary relationships, and 18 species-specific markers were able to discriminate among these species, thereby furthering efforts to protect the ginseng industry from economically motivated adulteration.
The complete chloroplast genome sequence of Panax quinquefolius, an important medicinal herb, was generated by de novo assembly with low-coverage whole-genome sequence data and manual correction. A ...circular 156 088-bp chloroplast genome showed typical chloroplast genome structure comprising a large single copy region of 86 095 bp, a small single copy region of 17 993 bp, and a pair of inverted repeats of 26 000 bp. The chloroplast genome had 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis with the chloroplast genome revealed that P. quinquefolius is much closer to P. ginseng than P. notoginseng.
Cynanchum auriculatum is a climbing vine belonging to the Apocynaceae family and shows very similar morphology to Cynanchum wilfordii, a medicinal plant. The complete chloroplast genome of C. ...auriculatum was generated by de novo assembly using the small amount of whole genome sequencing data. The chloroplast genome of C. auriculatum was 160 840 bp in length and consisted of four distinct regions, such as large single copy region (91 973 bp), small single copy region (19 667 bp), and a pair of inverted repeat regions (24 600 bp). The overall GC contents of the chloroplast genome were 37.8%. A total of 114 genes were predicted and included 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed that C. auriculatum is most closely related to Cynanchum wilfordii, a medicinal plant.
Ledebouriella seseloides (Hoffm.) H.Wolff is a traditional medicinal herb belonging to Apiaceae family, whose dried roots and rhizomes have been used as traditional medicine in East Asian countries. ...The complete chloroplast genome of L. seseloides was obtained by de novo assembly using the small amount of whole genome sequencing data. The chloroplast genome of L. seseloides was 147 880 bp in length, which consisted of large single copy region (93 222 bp), small single copy region (17 324 bp), and a pair of inverted repeat regions (18 667 bp). The overall GC contents of the chloroplast genome were 37.5%. A total of 113 genes were annotated, which included 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed that L. seseloides is most closely related to Petroselinum crispum (parsley), an herb widely used in cooking.
Cynanchum wilfordii (Maxim.) Hemsl. is a traditional medicinal herb belonging to the Asclepiadoideae subfamily, whose dried roots have been used as traditional medicine in Asia. The complete ...chloroplast genome of C. wilfordii was generated by de novo assembly using the small amount of whole genome sequencing data. The chloroplast genome of C. wilfordii was 161 241 bp long, composed of large single copy region (91 995 bp), small single copy region (19 930 bp) and a pair of inverted repeat regions (24 658 bp). The overall GC contents of the chloroplast genome was 37.8%. A total of 114 genes were annotated, which included 80 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed that C. wilfordii is most closely related to Asclepias nivea (Caribbean milkweed) and Asclepias syriaca (common milkweed) within the Asclepiadoideae subfamily.
Gene and genome duplication events have long been accepted as driving forces in the evolution of angiosperms. Panax ginseng C. A. Meyer and Panax quinquefolius L., which inhabit eastern Asia and ...eastern North America, respectively, are famous medicinal herbs and are similar in growth condition, morphological and genetic characteristics. However, no molecular data regarding their evolution has been available. In this study, expressed sequence tags (ESTs) were generated from a cDNA library of P. ginseng and comparative analyses were conducted to reveal genome-level duplication and speciation of P. ginseng and P. quinquefolius by in-depth comparison of paralog and orthlog ESTs. Sequencing and assembly of 5,760 clones from the cDNA library resulted in 4,552 uniESTs of P. ginseng and these were subjected to initial annotation steps. Comparative analysis was conducted with the uniESTs and transcriptome data of P. quinquefolius retrieved from the public database. Paralog pairing and analysis of the distribution of synonymous substitutions per synonymous site (Ks) showed two coincident peaks in both Panax species, implying two rounds of genome duplication in their common ancestor. Comparison of orthologs revealed one Ks peak that is younger than the two peaks identified from the analysis of paralogs. However, absolute dating of genome duplication and speciation events is needed to address caveats related to their long generation times, speculated to be more than 8–10 years in the wild. This is the first report regarding the evolutionary relationship of Panax species at the genome-wide level, and will provide a foundation to unravel the genome structure of the enigmatic genus Panax and the family Araliaceae.
Background: Panax ginseng Meyer (Asian ginseng) has a large nuclear genome size of > 3.5 Gbp in haploid genome equivalent of 24 chromosomes. Tandem repeats (TRs) occupy significant portions of the ...genome in many plants and are often found in specific genomic loci, making them a valuable molecular cytogenetic tool in discriminating chromosomes. In an effort to understand the P. ginseng genome structure, we characterized an ultrahigh copy 167-bp TR (Pg167TR) and explored its chromosomal distribution as well as its utility for chromosome identification. Methods: Polymerase chain reaction amplicons of Pg167TR were labeled, along with 5S and 45S rDNA amplicons, using a direct nick-translation method. Direct fluorescence in situ hybridization (FISH) was used to analyze the chromosomal distribution of Pg167TR. Results: Recently, we reported a method of karyotyping the 24 chromosome pairs of P. ginseng using rDNA and DAPI (4',6-diamidino-2-phenylindole) bands. Here, a unique distribution of Pg167TR in all 24 P. ginseng chromosomes was observed, allowing easy identification of individual homologous chromosomes. Additionally, direct labeling of 5S and 45S rDNA probes allowed the identification of two additional 5S rDNA loci not previously reported, enabling the refinement of the P. ginseng karyotype. Conclusion: Identification of individual P. ginseng chromosomes was achieved using Pg167TR-FISH. Chromosome identification is important in understanding the P. ginseng genome structure, and our method will be useful for future integration of genetic linkage maps and genome scaffold anchoring. Additionally, it is a good tool for comparative studies with related species in efforts to understand the evolution of P. ginseng.
The complete chloroplast genome sequence of Panax vietnamensis, a medicinal herb belonging to Araliaceae family, was generated by de novo assembly using whole genome next-generation sequences. The ...chloroplast genome was a circular form of 155 992 bp long and showed typical chloroplast genome structure consisting of a large single-copy region of 86 177 bp, a small single copy region of 17 935 bp and a pair of inverted repeats of 25 940 bp. The chloroplast genome had 79 protein-coding genes, 29 tRNA genes and 4 rRNA genes. The phylogenetic analysis with the reported chloroplast genomes revealed that four Panax species were grouped in the same clade and P. vietnamensis is more closely related to P. notoginseng than P. ginseng and P. quinquefolius.
Eleutherococcus gracilistylus is a plant species that is close to E. senticosus, a famous medicinal plant called Siberian ginseng. The complete chloroplast genome sequence of the E. gracilistylus was ...determined by de novo assembly using whole genome next generation sequences. The chloroplast genome of E. gracilistylus was 156 770 bp long and showed distinct four partite structures such as a large single copy region of 86 729 bp, a small single copy region of 18 175 bp, and a pair of inverted repeat regions of 25 933 bp. The overall GC contents of the genome sequence were 36.8%. The chloroplast genome of E. gracilistylus contains 79 protein-coding sequences, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis with the reported chloroplast genomes confirmed close taxonomical relationship of E. gracilistylus with E. senticosus.
PDF
