Dataset Information

Commercialized non-Camellia tea: traditional function and molecular identification.

ABSTRACT: Non-Camellia tea is a part of the colorful Chinese tea culture, and is also widely used as beverage and medicine in folk for disease prevention and treatment. In this study, 37 samples were collected, including 33 kinds of non-Camellia teas and 4 kinds of teas (Camellia). Traditional functions of non-Camellia teas were investigated. Furthermore, non-Camellia teas of original plants were characterized and identified by molecular methods. Four candidate regions (rbcL, matK, ITS2, psbA-trnH) were amplified by polymerase chain reaction. In addition, DNA barcodes were used for the first time to discriminate the commercial non-Camellia tea and their adulterants, and to evaluate their safety. This study showed that BLASTN and the relevant phylogenetic tree are efficient tools for identification of the commercial non-Camellia tea and their adulterants. However, some sequences from original plants have not been found and there is a limitation of sequence number of original plants in GenBank. Submitting more original plant sequences to the GenBank will be helpful for evaluating the safety of non-Camellia teas.

SUBMITTER: Long P

PROVIDER: S-EPMC4629065 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature

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Commercialized non-Camellia tea: traditional function and molecular identification.

Long Ping P Cui Zhanhu Z Wang Yingli Y Zhang Chunhong C Zhang Na N Li Minhui M Xiao Peigen P

Acta pharmaceutica Sinica. B 20140324 3

Non-Camellia tea is a part of the colorful Chinese tea culture, and is also widely used as beverage and medicine in folk for disease prevention and treatment. In this study, 37 samples were collected, including 33 kinds of non-Camellia teas and 4 kinds of teas (Camellia). Traditional functions of non-Camellia teas were investigated. Furthermore, non-Camellia teas of original plants were characterized and identified by molecular methods. Four candidate regions (rbcL, matK, ITS2, psbA-trnH) were a ...[more]

PMID: 26579387

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Project description:BACKGROUND: Medicinal plant trade is important for local livelihoods. However, many medicinal plants are difficult to identify when they are sold as roots, powders or bark. DNA barcoding involves using a short, agreed-upon region of a genome as a unique identifier for species- ideally, as a global standard. RESEARCH QUESTION: What is the functionality, efficacy and accuracy of the use of barcoding for identifying root material, using medicinal plant roots sold by herbalists in Marrakech, Morocco, as a test dataset. METHODOLOGY: In total, 111 root samples were sequenced for four proposed barcode regions rpoC1, psbA-trnH, matK and ITS. Sequences were searched against a tailored reference database of Moroccan medicinal plants and their closest relatives using BLAST and Blastclust, and through inference of RAxML phylograms of the aligned market and reference samples. PRINCIPAL FINDINGS: Sequencing success was high for rpoC1, psbA-trnH, and ITS, but low for matK. Searches using rpoC1 alone resulted in a number of ambiguous identifications, indicating insufficient DNA variation for accurate species-level identification. Combining rpoC1, psbA-trnH and ITS allowed the majority of the market samples to be identified to genus level. For a minority of the market samples, the barcoding identification differed significantly from previous hypotheses based on the vernacular names. CONCLUSIONS/SIGNIFICANCE: Endemic plant species are commercialized in Marrakech. Adulteration is common and this may indicate that the products are becoming locally endangered. Nevertheless the majority of the traded roots belong to species that are common and not known to be endangered. A significant conclusion from our results is that unknown samples are more difficult to identify than earlier suggested, especially if the reference sequences were obtained from different populations. A global barcoding database should therefore contain sequences from different populations of the same species to assure the reference sequences characterize the species throughout its distributional range.

Project description:The comparison of chloroplast genome (cpDNA) sequences among different plant species is an important source of plant molecular phylogenetic data. In this paper, the cpDNA sequences of 13 different oil-tea camellia samples were compared to identify an undetermined oil-tea camellia species from Hainan Province. The cpDNA of the samples was sequenced and resequenced, and divergence hotspots and simple sequence repeat (SSR) variations were analyzed. Bayesian inference (BI) and maximum-likelihood (ML) phylogenetic trees were constructed based on the full cpDNA sequences. The cpDNA sequences were 156512∼157089 bp in length and had the circular tetrad structure typical of angiosperms. The inverted repeats (IRs) of different species included varying contractions and expansions. The cpDNA sequences of the samples of the undetermined species of oil-tea camellia from Hainan Province and Camellia gauchowensis from Xuwen County were identical. In total, 136 genes were annotated, including 91 protein-coding genes (PCGs), 37 tRNA genes and 8 rRNA genes. The GC content of the cpDNA was 37.3%. The small single-copy (SSC)/IR boundary was rich in variation. Divergence hotspots were mainly located in the intergenic space (IGS) and coding sequences (CDSs), and there were obvious differences in divergence hotspots among species. The same divergence hotspots were found in Camellia vietnamensis, Camellia gauchowensis and the undetermined species of oil-tea camellia from Hainan Province. A total of 191∼198 SSR loci were detected. Most of the SSRs included A or T, and the distribution of SSRs in the cpDNA was uneven. Different species shared common SSRs and exhibited unique SSRs. Based on the full cpDNA sequences, the evolutionary relationships of different species of Camellia were well identified. The thirteen samples were classified into 2 clades and 6 subclades, and the different sections of Camellia clustered on the same branch in 2 clades and 2 subclades. Camellia vietnamensis was more closely related to the undetermined species of oil-tea camellia from Hainan Province and the sample of Camellia gauchowensis from Xuwen County than to the sample of Camellia gauchowensis from Luchuan County. Camellia osmantha was closely related to Camellia gauchowensis and Camellia vietnamensis. In conclusion, the cpDNA of different oil-tea camellia species has a conserved tetrad structure with certain length polymorphisms. SSRs are expected to be developed as "barcodes" or "identity cards" for species identification. SSR variations and other factors result in abundant divergence hotspots in the CDSs and IGS (one non-CDS region), indicating that full cpDNA sequences can be used for the species identification and phylogenetic analysis of Camellia. Accordingly, the undetermined species of oil-tea camellia from Hainan Province is likely Camellia vietnamensis, Camellia vietnamensis and Camellia gauchowensis may be the same species, and additional genetic evidence is needed to determine whether Camellia osmantha is a new independent species. The previous division of related sections of Camellia may need readjustment based on full cpDNA sequences.

Project description:Genes that have no homologous sequences with other species are called lineage-specific genes (LSGs), are common in living organisms, and have an important role in the generation of new functions, adaptive evolution and phenotypic alteration of species. Camellia sinensis var. sinensis (CSS) is one of the most widely distributed cultivars for quality green tea production. The rich catechins in tea have antioxidant, free radical elimination, fat loss and cancer prevention potential. To further understand the evolution and utilize the function of LSGs in tea, we performed a comparative genomics approach to identify Camellia-specific genes (CSGs). Our result reveals that 1701 CSGs were identified specific to CSS, accounting for 3.37% of all protein-coding genes. The majority of CSGs (57.08%) were generated by gene duplication, and the time of duplication occurrence coincide with the time of two genome-wide replication (WGD) events that happened in CSS genome. Gene structure analysis revealed that CSGs have shorter gene lengths, fewer exons, higher GC content and higher isoelectric point. Gene expression analysis showed that CSG had more tissue-specific expression compared to evolutionary conserved genes (ECs). Weighted gene co-expression network analysis (WGCNA) showed that 18 CSGs are mainly associated with catechin synthesis-related pathways, including phenylalanine biosynthesis, biosynthesis of amino acids, pentose phosphate pathway, photosynthesis and carbon metabolism. Besides, we found that the expression of three CSGs (CSS0030246, CSS0002298, and CSS0030939) was significantly down-regulated in response to both types of stresses (salt and drought). Our study first systematically identified LSGs in CSS, and comprehensively analyzed the features and potential functions of CSGs. We also identified key candidate genes, which will provide valuable assistance for further studies on catechin synthesis and provide a molecular basis for the excavation of excellent germplasm resources.

Project description:BackgroundDespite great advances in genomic technology observed in several crop species, the availability of molecular tools such as microsatellite markers has been limited in tea (Camellia sinensis L.). The development of microsatellite markers will have a major impact on genetic analysis, gene mapping and marker assisted breeding. Unigene derived microsatellite (UGMS) markers identified from publicly available sequence database have the advantage of assaying variation in the expressed component of the genome with unique identity and position. Therefore, they can serve as efficient and cost effective alternative markers in such species.ResultsConsidering the multiple advantages of UGMS markers, 1,223 unigenes were predicted from 2,181 expressed sequence tags (ESTs) of tea (Camellia sinensis L.). A total of 109 (8.9%) unigenes containing 120 SSRs were identified. SSR abundance was one in every 3.55 kb of EST sequences. The microsatellites mainly comprised of di (50.8%), tri (30.8%), tetra (6.6%), penta (7.5%) and few hexa (4.1%) nucleotide repeats. Among the dinucleotide repeats, (GA)n.(TC)n were most abundant (83.6%). Ninety six primer pairs could be designed form 83.5% of SSR containing unigenes. Of these, 61 (63.5%) primer pairs were experimentally validated and used to investigate the genetic diversity among the 34 accessions of different Camellia spp. Fifty one primer pairs (83.6%) were successfully cross transferred to the related species at various levels. Functional annotation of the unigenes containing SSRs was done through gene ontology (GO) characterization. Thirty six (60%) of them revealed significant sequence similarity with the known/putative proteins of Arabidopsis thaliana. Polymorphism information content (PIC) ranged from 0.018 to 0.972 with a mean value of 0.497. The average heterozygosity expected (HE) and observed (Ho) obtained was 0.654 and 0.413 respectively, thereby suggesting highly heterogeneous nature of tea. Further, test for IAM and SMM models for the UGMS loci showed excess heterozygosity and did not show any bottleneck operating in the tea population.ConclusionUGMS markers identified and characterized in this study provided insight about the abundance and distribution of SSR in the expressed genome of C. sinensis. The identification and validation of 61 new UGMS markers will not only help in intra and inter specific genetic diversity assessment but also be enriching limited microsatellite markers resource in tea. Further, the use of these markers would reduce the cost and facilitate the gene mapping and marker-aided selection in tea. Since, 36 of these UGMS markers correspond to the Arabidopsis protein sequence data with known functions will offer the opportunity to investigate the consequences of SSR polymorphism on gene functions.

Dataset Information

Commercialized non-Camellia tea: traditional function and molecular identification.

Publications

Commercialized non-Camellia tea: traditional function and molecular identification.

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