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The complete chloroplast genome of Dryopteris crassirhizoma Nakai.

ABSTRACT: Dryopteris crassirhizoma Nakai is a fern plant with important evolutionary and medicinal values. Herein, we assembled the complete chloroplast genome of D. crassirhizoma by next-generation sequencing technology. The complete chloroplast genome of D. crassirhizoma was 153,355 bp in length, and the GC content was 42.86%; the genome consisted of a pair of inverted repeats (IRs, 23,470 bp), a small single copy region (SSC, 21,570 bp) and a large single copy region (LSC, 84,854 bp). The genome contained 111 genes, namely, 73 protein-coding genes, 34 tRNA genes and four rRNA genes. The phylogenetic analysis suggested that both D. crassirhizoma and D. decipiens from Dryopteridaceae were most closely related to Lepisorus clathratus from Polypodiaceae.

SUBMITTER: Wang Q

PROVIDER: S-EPMC8168769 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature

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The complete chloroplast genome of Dryopteris crassirhizoma Nakai.

Wang Qi Q Xu Wenting W Zhou Lirong L Mai Biwei B Zhu Naiyun N Zhao Xiaoli X Lei Zhixian Z

Mitochondrial DNA. Part B, Resources 20210527 6

Dryopteris crassirhizoma Nakai is a fern plant with important evolutionary and medicinal values. Herein, we assembled the complete chloroplast genome of D. crassirhizoma by next-generation sequencing technology. The complete chloroplast genome of D. crassirhizoma was 153,355 bp in length, and the GC content was 42.86%; the genome consisted of a pair of inverted repeats (IRs, 23,470 bp), a small single copy region (SSC, 21,570 bp) and a large single copy region (LSC, 84,854 b ...[more]

PMID: 34104772

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Project description:BackgroundDryopteris crassirhizoma Nakai and Osmunda japonica Thunb. are ferns that are popularly used for medicine, as recorded by the Chinese pharmacopoeia, and are distributed in different regions of China. However, O. japonica is not record in the Standards of Chinese Herbal Medicines in Hong Kong. Research on identification methods of D. crassirhizoma and O. japonica is necessary and the phylogenetic position of the two species should be identified. The plastid genome is structurally highly conserved, providing valuable sources of genetic markers for phylogenetic analyses and development of molecule makers for identification.MethodsThe plastid genome DNA was extracted from both fern species and then sequenced on the Illumina Hiseq 4000. Sequences were assembled into contigs by SOAPdenovo2.04, aligned to the reference genome using BLAST, and then manually corrected. Genome annotation was performed by the online DOGMA tool. General characteristics of the plastid genomes of the two species were analyzed and compared with closely related species. Additionally, phylogenetical trees were reconstructed by maximum likelihood methods. The content of dryocrassin of the two species were determined according to the Standards of Chinese Herbal Medicines in Hong Kong.ResultsThe genome structures of D. crassirhizoma and O. japonica have different characteristics including the genome size, the size of each area, gene location, and types. Moreover, the (simple sequence repeats) SSRs of the plastid genomes were more similar to other species in the same genera. Compared with D. fragrans, D. crassirhizoma shows an inversion (approximately 1.6 kb), and O. japonica shows two inversions (1.9 kb and 216 bp). The nucleotide diversity (polymorphism information, Pi) analysis showed that the psbK gene and rpl14-rpl16 region have the highest Pi value in Dryopteris, and the ycf2-CDS3 and rpl14-rpl16 regions show the highest Pi vale in O. japonica. Phylogenetic analyses showed that the two species were grouped in two separate clades from each other, with both individually located with other members of their genus. The marker content of dryocrassin is not found in O. japonica.ConclusionsThe study is the first to identify plastid genome features of D. crassirhizoma and O. japonica. The results may provide a theoretical basis for the identification and the application of the two medically important fern species.

Project description:Platelets are an important component of the initial response to vascular endothelial injury; however, platelet dysfunction induces the acute clinical symptoms of thrombotic disorders, which trigger severe cardiovascular diseases such as myocardial infarction, ischemia, and stroke. In this study, we investigated the Dryopteris crassirhizoma's antiplatelet activity. A water extract of D.crassirhizoma (WDC) was partitioned into dichloromethane (DCM), ethyl acetate, n-butyl alcohol, and water. Among these four fractions, the DCM fraction potently inhibited the collagen-stimulated platelet aggregation in a concentration-dependent manner. From this fraction, five different acylphloroglucinol compounds and one flavonoid were isolated by activity-guided column chromatography. They were identified by comparing their mass, 1H-, and 13C-NMR spectral data with those reported in the literature. Quantifying the six compounds in WDC and its DCM fraction by high-performance liquid chromatography (HPLC) revealed that butyryl-3-methylphloroglucinol (compound 4) was the most abundant in these samples. Additionally, butyryl-3-methylphloroglucinol showed the strongest inhibitory activity in the collagen- and arachidonic acid (AA)-induced platelet aggregation, with inhibition ratios of 92.36% and 89.51% in the collagen and AA-induced platelet aggregation, respectively, without cytotoxicity. On the active concentrations, butyryl-3-methylphloroglucinol significantly suppressed the convulxin-induced platelet activation. Regarding the structure-activity relationships for the five acylphloroglucinol compounds, our results demonstrated that the functional butanonyl, methoxy, and hydroxy groups in butyryl-3-methylphloroglucinol play important roles in antiplatelet activity. The findings indicate that acylphloroglucinols, including butyryl-3-methylphloroglucinol from D.crassirhizom, possess an antiplatelet activity, supporting the use of this species for antiplatelet remedies.

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The complete chloroplast genome of Dryopteris crassirhizoma Nakai.

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The complete chloroplast genome of <i>Dryopteris crassirhizoma</i> Nakai.

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