Complete chloroplast genome sequence of a medicinal landrace citrus Jinkyool (Citrus sunki Hort. ex Tanaka) in Jeju Island, Korea.
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ABSTRACT:
SUBMITTER: Yoo YH
PROVIDER: S-EPMC7655064 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundThis study aims to analyze and record orally transmitted knowledge of medicinal plants from the indigenous people living in Hallasan National Park of Korea.MethodsData was collected through the participatory rural appraisal method involving interviews, informal meetings, open and group discussions, and overt observations with semi-structured questionnaires.ResultsIn this study, a total of 68 families, 141 genera, and 171 species of plants that showed 777 ways of usage were recorded. Looking into the distribution of the families, 14 species of Asteraceae occupied 11.1% of the total followed by 13 species of Rosaceae, 10 species of Rutaceae, and nine species of Apiaceae which occupied 5.0%, 7.1% and 3.0% of the whole, respectively. 32 kinds of plant-parts were used for 47 various medicinal purposes. Values for the informant consensus factor regarding the ailment categories were for birth related disorders (0.92), followed by respiratory system disorders (0.90), skin disease and disorders (0.89), genitourinary system disorders (0.87), physical pain (0.87), and other conditions. According to fidelity levels, 36 plant species resulted in fidelity levels of 100%.ConclusionConsequently, results of this study will legally utilize to provide preparatory measures against the Nagoya Protocol (2010) about benefit-sharing for traditional knowledge of genetic resources.
| S-EPMC3716930 | biostudies-literature
Project description:Polymethoxyflavones (PMFs) are flavonoids exclusively found in certain citrus fruits and have been reported to be beneficial to human health. Most studies have been conducted with PMFs isolated from citrus peels, while there is no study on PMFs isolated from leaves. In this study, we prepared PMF-rich fraction (PRF) from leaf of Citrus sunki Hort ex. Tanaka (Jinkyool) and investigated whether PRF can improve metabolic decline in obese mice induced by high-fat diet (HFD) for five weeks. HFD induced obese mice were assigned into HFD, OR (HFD + orlistat 15.6 mg/kg of body weight/day), and PRF (HFD + 50, 100, 200 mg/kg of body weight/day) groups. Orlistat and PRE were orally administrated for 5 weeks. At the end of experiment, serum biochemical parameters, histology and protein expression profiles were investigated in the tissues of each group. The body weight gain of obese mice was significantly reduced after orlistat and PRF administration for five weeks. PRE effectively improved HFD-induced insulin resistance and dyslipidemia. Histological analysis in liver demonstrated that PRF potentially improved the liver function as it inhibited the incidence of fatty liver. Moreover, PRF increased the phosphorylation of activated AMP-activated protein kinase (AMPK), acetyl-CoA carboxylase (ACC), and hormone-sensitive lipase (HSL) in HFD-induced obese mice. Moreover, the liver transcriptome analysis revealed that PRE administration enriched the genes, which were mainly fatty acid metabolism. Overall, these results indicated that PRF exert anti-obesity effect by modulation of lipid metabolism.
2022-03-02 | GSE193785 | GEO
Project description:The enchytraeid fauna of three areas in Jeju Island (Korea) was studied, and comparative morphological and molecular taxonomic examinations (based on CO1, ITS and H3 sequences) were performed on nine samples collected in 2016. Twenty-two enchytraeid species were recorded and identified. The descriptions of two new species (Achaetamultisacculata sp. n. and Fridericiafloriformis sp. n.) are presented in this paper. The main diagnostic features of A.multisacculata sp. n. are: three pairs of pyriform glands per segment, clitellum with two "baguette-like" packages of glands, dorsal blood vessel from VII, secondary pharyngeal glands absent, oesophageal appendages well developed, two pairs of preclitellar nephridia, the reproductive organs (except the spermathecae in V) shifted one segment forward. The main features of F.floriformis sp. n. are that they are large worms, have up to 2-4 chaetae in bundles, strong body wall, thick cuticle, five pairs of preclitellar nephridia, c-type coelomo-mucocytes sometimes with some refractile vesicles, chylus cells in XII-XV, sperm funnels approximately twice as long than wide, spermathecae with long ectal duct without glands, ampullae surrounded distally by about 9-12 sessile diverticula of varying size. Molecular phylogenetic analyses supported the morphological results and confirmed the status of the two new species.
| S-EPMC6384282 | biostudies-literature
Project description:A new eusirid amphipod, Eusirus bulbodigitussp. n., from Jeju Island, Korea is described with a detailed description and illustrations. Eusirus bulbodigitussp. n. shows common features with the five known eusirid amphipods Eusirus abyssi Stephensen, 1944, Eusirus columbianus Bousfield & Hendrycks, 1995, Eusirus hirayamae Bousfield & Hendrycks, 1995, Eusirus laticarpus Chevreux, 1906, and Eusirus parvus Pirlot, 1934, such as the mandibular palp article 3 bearing a group of setae laterally. However, this new species is differentiated by the combination of the following characteristics: the eyes are poorly developed, the propodus on pereopod 4 is slightly shorter, the inner margin of dactylus on pereopod 4 is swollen, the length of pereopods 5-7 is moderate, the urosomite 1 has a dorsal protrusion distally, and the telson is shallowly cleft. This is the first record of the genus Eusirus Krøyer, 1845 from Korean waters.
| S-EPMC5240363 | biostudies-other
Project description:A survey on the harpacticoid copepods from an intertidal zone in Hyeopjae sandy beach, Jeju Island, Korea, resulted in the discovery of an unusual laophontid, Jejulaophontehyeopjaeensis sp. n., which cannot be placed in any extant genus within the family. To accommodate the species, a new genus of the family Laophontidae T. Scott, 1905 is proposed and fully described here. The new species is closely related to the lineage of the five primitive genera, Carraroenia McCormack, 2006, Coullia Hamond, 1973, Hemilaophonte Jakubisiak 1933, Psammoplatypus Lee & Huys, 1999, and Robustunguis Fiers, 1992 (the CCHPR-lineage) by the reduced P2 endopod, ovate shape of the female P5 exopod and sexual dimorphism in the P3 endopod. However, it displays discrepancies from the species of the CCHPR-lineage in the presence of an inner seta on P3 and P4 exp-2, four setae on P4 enp-2, and an inner seta on P3 and P4 enp-2 in the female. Furthermore, no other species within the family Laophontidae has three setae on P2 exp-3 and a seta on P2 enp-2 at the same time. The new species has sexual dimorphism in the antennule, genital segmentation and the legs from P2 to P5. The terminal seta on the second endopodal segment of P2 in the male is longer than that in the female. The endopod of P3 is 3-segmented and displays a short inner apophysis on the second segment in the male. The outer setae on the exopod of P3 and P4 are distinctly thicker and stronger in the male than in the female. Mitochondrial cytochrome oxidase subunit I (mtCOI) sequencing of the new species has been realized in order to be used in future phylogenetic analysis.
| S-EPMC4205746 | biostudies-literature
Project description:During a survey of intertidal zones at beaches on Jeju Island, two species belonging to the family Thoracostomopsidae were discovered. One new species, Enoploides koreanus sp. nov. and one known species, Epacanthion hirsutum Shi & Xu, 2016 are reported. Along with morphological analysis, mitochondrial cytochrome oxidase c subunit 1 (mtCOI) sequences and 18S rRNA sequences of the species were also obtained and used to check relative p-distance and phylogenetic positions. While most species of Enoploides have long spicules, the new species belongs to a group of Enoploides with short spicules < 150 µm). Of the seven species with short spicules, the new species is most closely related to E. disparilis Sergeeva, 1974. They both have similar body length, fairly similar sized and shaped spicules with small gubernaculum running parallel to distal end of spicule, and an index value of b. The new species can be distinguished from E. disparilis by having pre-anal supplementary organ with short conical tail, while E. disparilis lacks pre-anal supplementary organ and has a long conico-cylindrical tail. Along with the description of the new species, the genus Enoploides Ssaweljev, 1912 is bibliographically reviewed and revised. Of 45 species described to date, 27 are now considered valid, 16 species inquirendae due to inadequate descriptions and ambiguity of the material examined, along with two cases of nomen nudum. With this review, we provide an updated diagnosis and list of valid species, a tabular key comparing diagnostic characters of all valid species, and a new complete key to species. One known species, Epacanthion hirsutum Shi & Xu, 2016, is reported in Korea for the first time. The morphology agrees well with the original description provided by Shi & Xu, 2016. As they had already reviewed the genus at the time of reporting four Epacanthion species, we provide only a description, depiction, and measurements for comparison purposes.
| S-EPMC7194091 | biostudies-literature
Project description:BACKGROUND:Bud mutation is a vital method of citrus. 'Wuzi Ougan' (mutant type, MT) as a bud variant of 'Ougan' (wild type, WT) was first found in 1996 and has become popular because of its male sterility and seedless character. Previous analysis of its cytological sections and transcriptome revealed that the abnormal microsporogenesis that occurs before the tetrad stage of anther development might be the result of down-regulated oxidation-reduction biological processes in MT. To reveal the mechanism behind the male sterility in MT at the post-transcriptional stage, proteome profiling and integrative analysis on previously obtained transcriptome and proteome data were performed in two strains. RESULTS:The proteome profiling was performed by iTRAQ (isobaric Tags for relative and absolute quantitation) analysis and 6201 high-confidence proteins were identified, among which there were 487 differentially expressed proteins (DEPs) in one or more developmental stages of anthers between MT and WT. The main functional subcategories associated with the main category biological process into which the DEPs were classified were sporopollenin biosynthesis process and pollen exine formation. The enriched pathways were phenylpropanoid biosynthesis, flavonoid biosynthesis, and phenylalanine metabolism. Moreover, there were eight pathways linked in terms of being related to phenylpropanoid metabolism. Eighteen important genes related to phenylpropanoid metabolism were also analysized by qRT-PCR (quantitative real time PCR). An integrative analysis of the fold change at the transcript (log2 FPKM ratios) and protein (log1.2 iTRAQ ratios) levels was performed to reveal the consistency of gene expression at transcriptional and proteomic level. In general, the expression of genes and proteins tended to be positively correlated, in which the correlation coefficients were 0.3414 (all genes and all proteins) and 0.5686 (DEPs and according genes). CONCLUSION:This study is the first to offer a comprehensive understanding of the gene regulation in 'Wuzi Ougan' and its wild type, especially during the microsporocyte to meiosis stage. Specifically, the involved genes include those in phenylpropanoid biosynthesis, flavonoid biosynthesis, and phenylalanine metabolism, as determined by integrative transcriptome and proteome analysis.
| S-EPMC6245639 | biostudies-literature
Project description:A fungal internal transcribed spacer region was used to identify the mycorrhizae of Cymbidium kanran. The family Russulaceae was found to be the most frequently occurring group in both root and soil samples. In phylogenetic analyses, the majority of the Russulaceae clones were clustered with Russula brevipes and R. cyanoxantha. Therefore, C. kanran may form symbiotic relationships with the genus Russula.
| S-EPMC4731653 | biostudies-literature
Project description:BackgroundMost modern citrus cultivars have an interspecific origin. As a foundational step towards deciphering the interspecific genome structures, a reference whole genome sequence was produced by the International Citrus Genome Consortium from a haploid derived from Clementine mandarin. The availability of a saturated genetic map of Clementine was identified as an essential prerequisite to assist the whole genome sequence assembly. Clementine is believed to be a 'Mediterranean' mandarin × sweet orange hybrid, and sweet orange likely arose from interspecific hybridizations between mandarin and pummelo gene pools. The primary goals of the present study were to establish a Clementine reference map using codominant markers, and to perform comparative mapping of pummelo, sweet orange, and Clementine.ResultsFive parental genetic maps were established from three segregating populations, which were genotyped with Single Nucleotide Polymorphism (SNP), Simple Sequence Repeats (SSR) and Insertion-Deletion (Indel) markers. An initial medium density reference map (961 markers for 1084.1 cM) of the Clementine was established by combining male and female Clementine segregation data. This Clementine map was compared with two pummelo maps and a sweet orange map. The linear order of markers was highly conserved in the different species. However, significant differences in map size were observed, which suggests a variation in the recombination rates. Skewed segregations were much higher in the male than female Clementine mapping data. The mapping data confirmed that Clementine arose from hybridization between 'Mediterranean' mandarin and sweet orange. The results identified nine recombination break points for the sweet orange gamete that contributed to the Clementine genome.ConclusionsA reference genetic map of citrus, used to facilitate the chromosome assembly of the first citrus reference genome sequence, was established. The high conservation of marker order observed at the interspecific level should allow reasonable inferences of most citrus genome sequences by mapping next-generation sequencing (NGS) data in the reference genome sequence. The genome of the haploid Clementine used to establish the citrus reference genome sequence appears to have been inherited primarily from the 'Mediterranean' mandarin. The high frequency of skewed allelic segregations in the male Clementine data underline the probable extent of deviation from Mendelian segregation for characters controlled by heterozygous loci in male parents.
| S-EPMC3546309 | biostudies-literature
Project description:The Gibberellic Acid Stimulated Arabidopsis (GASA) proteins were investigated in the study to help understand their possible roles in fruit trees, particularly in Citrus. A total of 18 CcGASA proteins were identified and characterized in Citrus clementina via a genome-wide approach. It was shown that the CcGASA proteins structurally shared a conserved GASA domain but varied considerably in primary sequences and motif compositions. Thus, they could be classified into three major phylogenetic groups, G1~G3, and two groups, G1 and G3 could be further classified into subgroups. The cis- elements on all CcGASA promoters were identified and categorized, and the associated transcription factors were predicted. In addition, the possible interactions between the CcGASA proteins and other proteins were predicted. All the clues suggested that these genes should be involved in defense against biotic and abiotic stresses and in growth and development. The notion was further supported by gene expression analysis that showed these genes were more or less responsive to the treatments of plant hormones (GA3, SA, ABA and IAA), and infections of citrus canker pathogen Xanthomonas citri. It was noted that both the segmental and the tandem duplications had played a role in the expansion of the CcGASA gene family in Citrus. Our results showed that the members of the CcGASA gene family should have structurally and functionally diverged to different degrees, and hence, the representative group members should be individually investigated to dissect their specific roles.
| S-EPMC8638133 | biostudies-literature