Dataset Information

A trnI_CAU triplication event in the complete chloroplast genome of Paris verticillata M.Bieb. (Melanthiaceae, Liliales).

ABSTRACT: The chloroplast is an essential plant organelle responsible for photosynthesis. Gene duplication, relocation, and loss in the chloroplast genome (cpDNA) are useful for exploring the evolution and phylogeny of plant species. In this study, the complete chloroplast genome of Paris verticillata was sequenced using the 454 sequencing system and Sanger sequencing method to trace the evolutionary pattern in the tribe Parideae of the family Melanthiaceae (Liliales). The circular double-stranded cpDNA of P. verticillata (157,379 bp) consists of two inverted repeat regions each of 28,373 bp, a large single copy of 82,726 bp, and a small single copy of 17,907 bp. Gene content and order are generally similar to the previously reported cpDNA sequences within the order Liliales. However, we found that trnI_CAU was triplicated in P. verticillata. In addition, cemA is suspected to be a pseudogene due to the presence of internal stop codons created by poly(A) insertion and single small CA repeats. Such changes were not found in previously examined cpDNAs of the Melanthiaceae or other families of the Liliales, suggesting that such features are unique to the tribe Parideae of Melanthiaceae. The characteristics of P. verticillata cpDNA will provide useful information for uncovering the evolution within Paris and for further research of plastid genome evolution and phylogenetic studies in Liliales.

SUBMITTER: Do HD

PROVIDER: S-EPMC4122936 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature

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A trnI_CAU triplication event in the complete chloroplast genome of Paris verticillata M.Bieb. (Melanthiaceae, Liliales).

Do Hoang Dang Khoa HD Kim Jung Sung JS Kim Joo-Hwan JH

Genome biology and evolution 20140619 7

The chloroplast is an essential plant organelle responsible for photosynthesis. Gene duplication, relocation, and loss in the chloroplast genome (cpDNA) are useful for exploring the evolution and phylogeny of plant species. In this study, the complete chloroplast genome of Paris verticillata was sequenced using the 454 sequencing system and Sanger sequencing method to trace the evolutionary pattern in the tribe Parideae of the family Melanthiaceae (Liliales). The circular double-stranded cpDNA o ...[more]

PMID: 24951560

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Project description:BackgroundParis yunnanensis (Melanthiaceae) is a traditional Chinese medicinal plant of significant pharmaceutical importance. Due to previous taxonomic confusion, a congeneric species, Paris liiana, has been mistaken for P. yunnanensis and cultivated on a large scale, leading to the mixing of commercial products (i.e., seedlings and processed rhizomes) of P. yunnanensis with those of P. liiana. This may have adverse effects on quality control in the standardization of P. yunnanensis productions. As the lack of PCR amplifiable genomic DNA within processed rhizomes is an intractable obstacle to the authentication of P. yunnanensis products using PCR-based diagnostic tools, this study aimed to develop a PCR-free method to authenticate commercial P. yunnanensis products, by applying genome skimming to generate complete plastomes and nrDNA arrays for use as the molecular tags.ResultsBased on a dense intraspecies sampling of P. liiana and P. yunnanensis, the robustness of the proposed authentication systems was evaluated by phylogenetic inferences and experimental authentication of commercial seedling and processed rhizome samples. The results indicate that the genetic criteria of both complete plastomes and nrDNA arrays were consistent with the species boundaries to achieve accurate discrimination of P. yunnanensis and P. liinna. Owing to its desirable accuracy and sensitivity, genome skimming can serve as an effective and sensitive tool for monitoring and controlling the trade of P. yunnanensis products.ConclusionThis study provides a new way to solve the long-standing problem of the molecular authentication of processed plant products due to the lack of PCR amplifiable genomic DNA. The proposed authentication system will support quality control in the standardization of P. yunnanensis products in cultivation and drug production. This study also provides molecular evidence to clarify the long-standing taxonomic confusion regarding the species delimitation of P. yunnanensis, which will contribute to the rational exploration and conservation of the species.

Dataset Information

A trnI_CAU triplication event in the complete chloroplast genome of Paris verticillata M.Bieb. (Melanthiaceae, Liliales).

Publications

A trnI_CAU triplication event in the complete chloroplast genome of Paris verticillata M.Bieb. (Melanthiaceae, Liliales).

Similar Datasets

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