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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:Loquat is a widely grown subtropic fruit because of its unique ripening season, nutrient content, and smooth texture of its fruits. However, loquat is not well-received because the fruits contain many large seeds. Therefore, the development of seedless or few-seed loquat varieties is the main objective of loquat breeding. Polyploidization is an effective approach for few-seed loquat breeding, but the resource is rare. The few-seed loquat line H30-6 was derived from a seedy variety. Additionally, H30-6 was systematically studied for its fruit characteristics, gamete fertility, pollen mother cell (PMC) meiosis, stigma receptivity, in situ pollen germination, fruit set, and karyotype. The results were as follows. (1) H30-6 produced only 1.54 seeds per fruit and the fruit edible rate was 70.77%. The fruit setting rate was 14.44% under open pollination, and the other qualities were equivalent to those of two other seedy varieties. (2) The in vitro pollen germination rate was only 4.04 and 77.46% of the H30-6 embryo sacs were abnormal. Stigma receptivity and self-compatibility in H30-6 were verified by in situ pollen germination and artificial pollination. Furthermore, the seed numbers in the fruits of H30-6 did not significantly differ among any of the pollination treatments (from 1.59 ±0.14 to 2 ± 0.17). (3) The chromosome configuration at meiotic diakinesis of H30-6 was 6.87I + 9.99II + 1.07III +0.69IV +0.24V (H30-6), and a total of 89.55% of H30-6 PMCs presented univalent chromosomes. Furthermore, chromosome lagging was the main abnormal phenomenon. Karyotype analysis showed that chromosomes of H30-6 had no recognizable karyotype abnormalities leading to unusual synapsis on the large scale above. (4) The abnormal embryo sacs of H30-6 could be divided into three main types: those remaining in the tetrad stage (13.38%), those remaining in the binucleate embryo sac stage (1.41%), and those without embryo sacs (52.82%). Therefore, we conclude that the loquat line H30-6 is a potential few-seed loquat resource. The diploid loquat line H30-6 was with low gametophyte fertility, which may be driven by abnormal meiotic synapses. The low female gamete fertility was the main reason for the few seeds. This diploid loquat line provides a new possibility for breeding a few-seed loquat at the diploid level.

Project description:Loquat (Eriobotrya japonica Lindl. ) is one of the most economically important evergreen fruit crops in China, while it often suffered the injury of cold stress in winter and earlier spring, and the annual yield loss of loquat fruits caused by cold or freezing stress was immeasurable. However, knowledge about the physiological response and molecular mechanism under cold stress is still limited. To investigate the potential regulation mechanism pre- and post-cold stress in loquat and the changes in physiological indicators, a comparative transcriptome analysis was performed against a cold-resistant cv. "Huoju" and a cold-sensitive cv. "Ninghaibai". The results of physiological indicators related to cold resistance indicated that rachis was most sensitive to cold stress and was considered as the representative organ to directly evaluate cold resistance of loquat based on subordinate function analysis. Here, we compared the transcriptome profiles of rachis pre- and under cold stress in "Huoju" and "Ninghaibai". A total of 4,347 and 3,513 differentially expressed genes (DEGs) were detected in "Ninghaibai" and "Huoju", among which 223 and 166 were newly identified genes, respectively, most of them were functionally enriched in plant hormone signal transduction (Huoju: 142; Ninghaibai: 200), and there were higher plant hormone content and related DEG expression levels in "Huoju" than that of "Ninghaibai". Moreover, a total of 3,309 differentially expressed transcription factors (DETFs) were identified, and some DEGs and DETFs were screened to be subjected to co-expression network analysis based on the gene expression profile data. Some candidate DEGs, including UDP-glycosyltransferase (UGT), glycosyltransferase (GT), sugar phosphate/phosphate translocator (SPT), sugar transport protein (STP), proline-rich receptor-like protein kinase (PERK), and peroxidise (POD), were significantly affected by cold stress, and the expression level of these genes obtained from real-time quantitative RT-PCR was consistent with the pattern of transcriptome profile, which suggested that these genes might play the vital roles in cold resistance of loquat. Our results provide an invaluable resource for the identification of specific genes and TFs and help to clarify gene transcription during the cold stress response of loquat.

Project description:Prunus subgenus Cerasus (cherry) is an economically important group that distributed in temperate regions of the northern hemisphere. However, shared interspecific morphological traits and variability across taxa of Cerasus are among the impediments to taxonomic efforts to correctly delimit taxa. This is further complicated by a lack of genetic information on these taxa, with no focused genomic or phylogenetic studies being done on Cerasus. In this study, we conducted comparative analysis on the complete plastid genomes (plastomes) of 20 Cerasus species to gain a greater understanding of the attributes of the plastome of these taxa while helping resolve their phylogenetic placement in Prunus sensu lato and interspecific relationships within the subgenus. Our results displayed that (1) the plastomes of the 20 Cerasus species studied exhibited a typical quadripartite structure with conversed genome arrangement, structure, and moderate divergence. (2) The average size of complete plastomes for the Cerasus taxa studied was 157,861 bp, ranging from 157,458 to 158,024 bp. A total of 134 genes were annotated, including 86 protein-coding genes, 40 tRNAs, and 8 rRNAs across all species. In simple sequence repeat analysis, we found Cerasus had a comparable number of dispersed and tandem repeats to those identified in other angiosperm taxa, with only P. pseudocerasus found to contain trinucleotide repeats. Nucleotide diversity analysis revealed that the trnG-GCC gene and rpl32-trnL region had the highest Pi value showing potential as phylogenetic markers. (3) Two phylogenetic trees of the plastomes verified the monophyletic relationship of Cerasus and provided a more resolved species-level phylogeny. Our study provides detailed plastome information for exploring the phylogeny of subg. Cerasus taxa. We identified various types of repeats and nucleotide diversity hotspots, which can be a reference for species identification and reconstruction of phylogenetic relationships.

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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