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Complete plastid genome of Eriobotrya japonica (Thunb.) Lindl and comparative analysis in Rosaceae.

ABSTRACT: Eriobotrya japonica (Thunb.) Lindl (loquat) is an evergreen Rosaceae fruit tree widely distributed in subtropical regions. Its leaves are considered as traditional Chinese medicine and are of high medical value especially for cough and emesis. Thus, we sequenced the complete plastid genome of E. japonica to better utilize this important species. The complete plastid genome of E. japonica is 159,137 bp in length, which contains a typical quadripartite structure with a pair of inverted repeats (IR, 26,326 bp) separated by large (LSC, 89,202 bp) and small (SSC, 19,283 bp) single-copy regions. The E. japonica plastid genome encodes 112 unique genes which consist of 78 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Gene structure and content of E. japonica plastid genome are quite conserved and show similarity among Rosaceous species. Five large indels are unique to E. japonica in comparison with Pyrus pyrifolia and Prunus persica, which could be utilized as molecular markers. A total of 72 simple sequence repeats (SSRs) were detected and most of them are mononucleotide repeats composed of A or T, indicating a strong A or T bias for base composition. The Ka and Ks ratios of most genes are lower than 1, which suggests that most genes are under purifying selection. The phylogenetic analysis described the evolutionary relationship within Rosaceae and fully supported a close relationship between E. japonica and P. pyrifolia.

SUBMITTER: Shen L

PROVIDER: S-EPMC5127920 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Complete plastid genome of Eriobotrya japonica (Thunb.) Lindl and comparative analysis in Rosaceae.

Shen Liqun L Guan Qijie Q Amin Awais A Zhu Wei W Li Mengzhu M Li Ximin X Zhang Lin L Tian Jingkui J

SpringerPlus 20161129 1

Eriobotrya japonica (Thunb.) Lindl (loquat) is an evergreen Rosaceae fruit tree widely distributed in subtropical regions. Its leaves are considered as traditional Chinese medicine and are of high medical value especially for cough and emesis. Thus, we sequenced the complete plastid genome of E. japonica to better utilize this important species. The complete plastid genome of E. japonica is 159,137 bp in length, which contains a typical quadripartite structure with a pair of ...[more]

PMID: 27995013

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Project description:Background: The phytochemical composition, antioxidant, cytotoxic, and antimicrobial activities of a methanol extract from Glycyrrhiza glabra L. (Ge), a 50% ethanol (in water) extract from Paeonia lactiflora Pall. (Pe), and a 96% ethanol extract from Eriobotrya japonica (Thunb.) Lindl. (Ue) were investigated. Methods: The phytochemical profiles of the extracts were analyzed by LC-MS/MS. Antioxidant activity was evaluated by scavenging 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) radicals and reducing ferric complexes, and the total phenolic content was tested with the Folin?Ciocalteu method. Cytotoxicity was determined with a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay in murine macrophage RAW 264.7 cells. Antimicrobial activity of the three plant extracts was investigated against six bacterial strains with the broth microdilution method. Results: Only Pe showed high antioxidant activities compared to the positive controls ascorbic acid and (-)-epigallocatechin gallate (EGCG) in DPPH assay; and generally the antioxidant activity order was ascorbic acid or EGCG > Pe > Ue > Ge. The three plant extracts did not show strong cytotoxicity against RAW 264.7 cells after 24 h treatment with IC50 values above 60.53 ± 4.03 ?g/mL. Ue was not toxic against the six tested bacterial strains, with minimal inhibitory concentration (MIC) values above 5 mg/mL. Ge showed medium antibacterial activity against Acinetobacter bohemicus, Kocuria kristinae, Micrococcus luteus, Staphylococcus auricularis, and Bacillus megaterium with MICs between 0.31 and 1.25 mg/mL. Pe inhibited the growth of Acinetobacter bohemicus, Micrococcus luteus, and Bacillus megaterium at a MIC of 0.08 mg/mL. Conclusions: The three extracts were low-cytotoxic, but Pe exhibited effective DPPH radical scavenging ability and good antibacterial activity; Ue did not show antioxidant or antibacterial activity; Ge had no antioxidant potential, but medium antibacterial ability against five bacteria strains. Pe and Ge could be further studied for their potential to be developed as antioxidant or antibacterial candidates.

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.

Dataset Information

Complete plastid genome of Eriobotrya japonica (Thunb.) Lindl and comparative analysis in Rosaceae.

Publications

Complete plastid genome of <i>Eriobotrya japonica</i> (Thunb.) Lindl and comparative analysis in Rosaceae.

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