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Characterization of the chloroplast genome of a rare species Polygonatum sp. in China (Asparagaceae, Asparagales).

ABSTRACT: Polygonatum (Asparagaceae) is a medicinal and food plant that is naturally distributed in most of countries throughout the temperate Northern Hemisphere. Here we report on the complete chloroplast (cp) genome sequence of a rare species Polygonatum sp. without defoliation in late autumn or winter. The cp genome is 157,696 bp in size and includes two inverted repeat regions of 52,821bp, which is separated by a large single-copy region of 84,359 bp and a small single copy region of 20,516 bp. A total of 132 genes were predicted, including 38 tRNA, 8 rRNA, and 86 protein-coding genes. Phylogenetic analysis placed Polygonatum sp. under the subfamily Nolinoideae of the family Asparagaceae.

SUBMITTER: Zhong C

PROVIDER: S-EPMC7748811 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Polygonatum Miller belongs to the tribe Polygonateae of Asparagaceae. The horizontal creeping fleshy roots of several species in this genus serve as traditional Chinese medicine. Previous studies have mainly reported the size and gene contents of the plastomes, with little information on the comparative analysis of the plastid genomes of this genus. Additionally, there are still some species whose chloroplast genome information has not been reported. In this study, the complete plastomes of six Polygonatum were sequenced and assembled, among them, the chloroplast genome of P. campanulatum was reported for the first time. Comparative and phylogenetic analyses were then conducted with the published plastomes of three related species. Results indicated that the whole plastome length of the Polygonatum species ranged from 154,564 bp (P. multiflorum) to 156,028 bp (P. stenophyllum) having a quadripartite structure of LSC and SSC separated by two IR regions. A total of 113 unique genes were detected in each of the species. Comparative analysis revealed that gene content and total GC content in these species were highly identical. No significant contraction or expansion was observed in the IR boundaries among all the species except P. sibiricum1, in which the rps19 gene was pseudogenized owing to incomplete duplication. Abundant long dispersed repeats and SSRs were detected in each genome. There were five remarkably variable regions and 14 positively selected genes were identified among Polygonatum and Heteropolygonatum. Phylogenetic results based on chloroplast genome strongly supported the placement of P. campanulatum with alternate leaves in sect. Verticillata, a group characterized by whorled leaves. Moreover, P. verticillatum and P. cyrtonema were displayed as paraphyletic. This study revealed that the characters of plastomes in Polygonatum and Heteropolygonatum maintained a high degree of similarity. Five highly variable regions were found to be potential specific DNA barcodes in Polygonatum. Phylogenetic results suggested that leaf arrangement was not suitable as a basis for delimitation of subgeneric groups in Polygonatum and the definitions of P. cyrtonema and P. verticillatum require further study.

Project description:BackgroundPolygonatum kingianum has been widely used as a traditional Chinese medicine as well as a healthy food. Because of its highly variable morphology, this medicinal plant is often difficult to distinguish from other related verticillate leaf types of the Polygonatum species. The contaminants in P. kingianum products not only decrease the products' quality but also threaten consumer safety, seriously inhibiting the industrial application of P. kingianum.MethodsNine complete chloroplast (cp) genomes of six verticillate leaf types of the Polygonatum species were de novo assembled and systematically analyzed.ResultsThe total lengths of newly sequenced cp genomes ranged from 155,437 to 155,977 bp, including 86/87 protein-coding, 38 tRNA, and 8 rRNA genes, which all exhibited well-conserved genomic structures and gene orders. The differences in the IR/SC (inverted repeats/single-copy) boundary regions and simple sequence repeats were detected among the verticillate leaf types of the Polygonatum cp genomes. Comparative cp genomes analyses revealed that a higher similarity was conserved in the IR regions than in the SC regions. In addition, 11 divergent hotspot regions were selected, providing potential molecular markers for the identification of the Polygonatum species with verticillate leaf types. Phylogenetic analysis indicated that, as a super barcode, plastids realized a fast and efficient identification that clearly characterized the relationships within the verticillate leaf types of the Polygonatum species. In brief, our results not only enrich the data on the cp genomes of the genus Polygonatum but also provide references for the P. kingianum germplasm resource protection, herbal cultivation, and drug production.ConclusionThis study not only accurately identifies P. kingianum species, but also provides valuable information for the development of molecular markers and phylogenetic analyses of the Polygonatum species with verticillate leaf types.

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Characterization of the chloroplast genome of a rare species Polygonatum sp. in China (Asparagaceae, Asparagales).

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