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The complete chloroplast genome of Korean Pyrus ussuriensis Maxim. (Rosaceae): providing genetic background of two types of P. ussuriensis.

ABSTRACT: Pyrus ussuriensis Maxim. is one of the most important pear species cultivated in Asia, grown in northern China, far-east Russia, Korea, and Japan. Here we completed the chloroplast genome of wild P. ussuriensis collected in Bonghwa-gun, Korea, which was 159,986?bp in length consisting of four subregions: 87,947?bp of large single copy (LSC) and 19,255?bp of small single copy (SSC) regions are separated by 26,392?bp of inverted repeat (IR) regions. The genome contained a total of 130 genes including 85 protein-coding genes, eight rRNAs, and 37 tRNAs. The overall GC content was 36.5% and those in the LSC, SSC, and IR regions were 34.2%, 30.4%, and 42.6%, respectively. Phylogenetic analysis of 14 Pyrus chloroplast genomes provided the diverse genetic background for wild P. ussuriensis populations in Korea by confirming that wild P. ussuriensis sequenced in this study contained Pyrus pyrifolia type plastome. It revealed substantial sequence variations up to 121 single nucleotide polymorphisms and 781 insertions and deletions against another wild accession of P. ussuriensis (P. ussuriensis type) collected in Mt. Hambaek, Korea.

SUBMITTER: Cho MS

PROVIDER: S-EPMC7687443 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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The complete chloroplast genome of Korean Pyrus ussuriensis Maxim. (Rosaceae): providing genetic background of two types of P. ussuriensis.

Cho Myong-Suk MS Kim Yongsung Y Kim Seung-Chul SC Park Jongsun J

Mitochondrial DNA. Part B, Resources 20190712 2

Pyrus ussuriensis Maxim. is one of the most important pear species cultivated in Asia, grown in northern China, far-east Russia, Korea, and Japan. Here we completed the chloroplast genome of wild P. ussuriensis collected in Bonghwa-gun, Korea, which was 159,986 bp in length consisting of four subregions: 87,947 bp of large single copy (LSC) and 19,255 bp of small single copy (SSC) regions are separated by 26,392 bp of inverted repeat (IR) regions. The genome contained a total of 13 ...[more]

PMID: 33365570

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Project description:Pyrus ussuriensis Maxim (Korean pear) has been used for hundreds of years as a traditional herbal medicine for asthma, cough, and atopic dermatitis in Korea and China. Although it was originally shown to possess anti-inflammatory, antioxidant, and antiatopic properties, its gastroprotective effects have not been investigated. In the present study, we evaluated the protective effects of Pyrus ussuriensis Maxim extract (PUE) against ethanol-induced gastritis in rats. The bioactive compound profile of PUE was determined by gas chromatography mass spectroscopy (GC-MS) and high-performance liquid chromatography (HPLC). The gastroprotection of PUE at different doses (250 and 500 mg/kg body weight) prior to ethanol ingestion was evaluated using an in vivo gastritis rat model. Several endpoints were evaluated, including gastric mucosal lesions, cellular degeneration, intracellular damage, and immunohistochemical localization of leucocyte common antigen. The gastric mucosal injury and ulcer score were determined by evaluating the inflamed gastric mucosa and by histological examination. To identify the mechanisms of gastroprotection by PUE, antisecretory action and plasma prostaglandin E2 (PGE2), gastric mucosal cyclic adenosine monophosphate (cAMP), and histamine levels were measured. PUE exhibited significant antioxidant effects with IC50 values of 56.18 and 22.49 µg/mL for 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'- azino-di-(3-ethylbenzothiazoline)-6-sulfonic acid (ABTS) inhibition (%), respectively. In addition, GC/MS and HPLC analyses revealed several bioactive compounds of PUE. Pretreatment with PUE significantly (p < 0.05) decreased the ulcer index by preventing gastric mucosal lesions, erosion, and cellular degeneration. An immunohistochemical analysis revealed that PUE markedly attenuated leucocyte infiltration in a dose-dependent manner. The enhancement of PGE2 levels and attenuation of cAMP levels along with the inhibition of histamine release following PUE pretreatment was associated with the cytoprotective and healing effects of PUE. In contrast, the downregulation of the H+/K+ ATPase pathway as well as muscarinic receptor (M3R) and histamine receptor (H2R) inhibition was also involved in the gastroprotective effects of PUE; however, the expression of cholecystokinin-2 receptors (CCK2R) was unchanged. Finally, no signs of toxicity were observed following PUE treatment. Based on our results, we conclude that PUE represents an effective therapeutic option to reduce the risk of gastritis and warrants further study.

Project description:Purpose: The goals of this study was to obtain transcriptome data from five developmental stages of adventitious roots of Pyrus ussuriensis Maxim using transcriptome analysis (RNA-Seq) and qRT-PCR analysis. Mathods: The mRNA profiles of the adventitious root development of Pyrus ussuriensis on day 0, day 3, day 6, day 9, and day 12 were examined by deep sequencing, in triplicate, using Illumina HiSeq 2000. Ultra™ RNA LibraryPrep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and indexcodes were added to attribute sequences to each sample. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: The transcriptome regulation analysis of the Pyrus ussuriensis adventitious root formation was performed on this study. And a total of 19,470 DEGs (Differentially Expressed Gene), which were mainly enriched in hormone synthesis and signaling pathways, energy metabolism, synthesis and metabolism of secondary products, were detected. the key regulatory genes of adventitious root formation were screened, mainly including the gene family WOX, LBD and SRS. Auxin, plays a key role in the induction and development of root primordium, its signal transduction pathway-related genes were up-regulated during the induction period of root primordium, and down-regulated during the development of root primordia. Carotenoids is the precursor substance of abscisic acid synthetize. And for the reasons that the genes of carotenoid synthesis and signal transduction pathway of abscisic acid were down-regulated during the period of stable development and the root primordium induction, and up-regulated during the period of root primordium development of adventitious root, it was supposed that abscisic acid was a control substance, that regulated the metabolic network of development of adventitious roots. Conclusions: Our results provide a comprehensive high-resolution characterization of gene expression profiles during the pear root transition process.A number of DEGs were detected from the root primordium to adventitious root growth stages, and these belonged to hormone metabolism pathways.These results provide a valuable resource for studies in other closely related species with similar agricultural and productive value. The differentially expressed genes dataset will also provide useful candidate genes for functional analysis of pear rooting.

Project description:BackgroundFritillaria ussuriensis is an endangered medicinal plant known for its notable therapeutic properties. Unfortunately, its population has drastically declined due to the destruction of forest habitats. Thus, effectively protecting F. ussuriensis from extinction poses a significant challenge. A profound understanding of its genetic foundation is crucial. To date, research on the complete mitochondrial genome of F. ussuriensis has not yet been reported.ResultsThe complete mitochondrial genome of F. ussuriensis was sequenced and assembled by integrating PacBio and Illumina sequencing technologies, revealing 13 circular chromosomes totaling 737,569 bp with an average GC content of 45.41%. A total of 55 genes were annotated in this mitogenome, including 2 rRNA genes, 12 tRNA genes, and 41 PCGs. The mitochondrial genome of F. ussuriensis contained 192 SSRs and 4,027 dispersed repeats. In the PCGs of F. ussuriensis mitogenome, 90.00% of the RSCU values exceeding 1 exhibited a preference for A-ended or U-ended codons. In addition, 505 RNA editing sites were predicted across these PCGs. Selective pressure analysis suggested negative selection on most PCGs to preserve mitochondrial functionality, as the notable exception of the gene nad3 showed positive selection. Comparison between the mitochondrial and chloroplast genomes of F. ussuriensis revealed 20 homologous fragments totaling 8,954 bp. Nucleotide diversity analysis revealed the variation among genes, and gene atp9 was the most notable. Despite the conservation of GC content, mitogenome sizes varied significantly among six closely related species, and colinear analysis confirmed the lack of conservation in their genomic structures. Phylogenetic analysis indicated a close relationship between F. ussuriensis and Lilium tsingtauense.ConclusionsIn this study, we sequenced and annotated the mitogenome of F. ussuriensis and compared it with the mitogenomes of other closely related species. In addition to genomic features and evolutionary position, this study also provides valuable genomic resources to further understand and utilize this medicinal plant.

Dataset Information

The complete chloroplast genome of Korean Pyrus ussuriensis Maxim. (Rosaceae): providing genetic background of two types of P. ussuriensis.

Publications

The complete chloroplast genome of Korean <i>Pyrus ussuriensis</i> Maxim. (<i>Rosaceae</i>): providing genetic background of two types of <i>P. ussuriensis</i>.

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