Optimized sequencing depth and de novo assembler for deeply reconstructing the transcriptome of the tea plant, an economically important plant species.

BACKGROUND: Tea is the oldest and among the world's most popular non-alcoholic beverages, which has important economic, health and cultural values. Tea is commonly produced from the leaves of tea plants (Camellia sinensis), which belong to the genus Camellia of family Theaceae. In the last decade, many studies have generated the transcriptomes of tea plants at different developmental stages or under abiotic and/or biotic stresses to investigate the genetic basis of secondary metabolites that determine tea quality. However, these results exhibited large differences, particularly in the total number of reconstructed transcripts and the quality of the assembled transcriptomes. These differences largely result from limited knowledge regarding the optimized sequencing depth and assembler for transcriptome assembly of structurally complex plant species genomes. RESULTS: We employed different amounts of RNA-sequencing data, ranging from 4 to 84 Gb, to assemble the tea plant transcriptome using five well-known and representative transcript assemblers. Although the total number of assembled transcripts increased with increasing sequencing data, the proportion of unassembled transcripts became saturated as revealed by plant BUSCO datasets. Among the five representative assemblers, the Bridger package shows the best performance in both assembly completeness and accuracy as evaluated by the BUSCO datasets and genome alignment. In addition, we showed that Bridger and BinPacker harbored the shortest runtimes followed by SOAPdenovo and Trans-ABySS. CONCLUSIONS: The present study compares the performance of five representative transcript assemblers and investigates the key factors that affect the assembly quality of the transcriptome of the tea plants. This study will be of significance in helping the tea research community obtain better sequencing and assembly of tea plant transcriptomes under conditions of interest and may thus help to answer major biological questions currently facing the tea industry.

Tea Plant Information Archive: a comprehensive genomics and bioinformatics platform for tea plant.

Tea is the world's widely consumed nonalcohol beverage with essential economic and health benefits. Confronted with the increasing large-scale omics-data set particularly the genome sequence released in tea plant, the construction of a comprehensive knowledgebase is urgently needed to facilitate the utilization of these data sets towards molecular breeding. We hereby present the first integrative and specially designed web-accessible database, Tea Plant Information Archive (TPIA; http://tpia.teaplant.org). The current release of TPIA employs the comprehensively annotated tea plant genome as framework and incorporates with abundant well-organized transcriptomes, gene expressions (across species, tissues and stresses), orthologs and characteristic metabolites determining tea quality. It also hosts massive transcription factors, polymorphic simple sequence repeats, single nucleotide polymorphisms, correlations, manually curated functional genes and globally collected germplasm information. A variety of versatile analytic tools (e.g. JBrowse, blast, enrichment analysis, etc.) are established helping users to perform further comparative, evolutionary and functional analysis. We show a case application of TPIA that provides novel and interesting insights into the phytochemical content variation of section Thea of genus Camellia under a well-resolved phylogenetic framework. The constructed knowledgebase of tea plant will serve as a central gateway for global tea community to better understand the tea plant biology that largely benefits the whole tea industry.

Long term epidemiological effects of vaccination on hemorrhagical fever with renal syndrome (HFRS) in Shaanxi provincial HFRS epidemic areas / 中华流行病学杂志

Objective To evaluate the protective rate and the variation of HFRS-IgG on hemorrhagical fever with renal syndrome (HFRS) vaccine.Methods Cluster,random sampling and cross-sectional study were used to assess the protective rate of HFRS vaccination.Level of HFRS-IgG was detected with ELISA in epidemic and non-epidemic areas of HFRS.Results Curve equation was obtained as Yprocective rate=(0.863+0.283/Xvaccination term) × 100％ by protective rate with vaccination term.Protective rates showed a reducing trend,90％ after 7-8 years of vaccination,88％ after 10 years,and 94％ on average.Absorbance (A) value of HFRS-IgG was 4 times higher in persons with vaccination than those without,in the epidemic area.Higher antibody level could be obtained after primary vaccination,but the level of antibody had a 50％ reduction after 5-10 years of vaccination,and a 60％ reduction after 10 years of vaccination.Conclusion HFRS antibody had a 50％ reduction after 5-10 years of vaccination.The protective rate of HFRS vaccination had a 90％ loss,after 7-8 years of vaccination.Booster dose was necessary after 7 years of vaccination.

Antibiotic prescribing patterns for upper respiratory tract infections in rural Western China / 西安交通大学学报·英文版

Objective: To explore the prescribing patterns of outpatients receiving antibiotics for upper respiratory tract infections (URTIs) in rural Western China and to identify the correlation in terms of doctors and patients characteristics. Methods: Totally 7 678 prescriptions for URTIs were collected from 680 primary health village clinics of 40 counties across 10 provinces of Western China. Two outcome variables were used in the analysis: the occurrence of prescribing at least one antibiotic drug for an URTI and the occurrence of prescribing two or more antibiotics for an URTI. GEE logistic regression models were used to examine the socioeconomic and demographic determinants of the above two outcome variables. Results: The percentage of prescribing at least one antibiotic for URTIs was 48.6% while the percentage of prescribing antibiotic combination (two or more antibiotics) was 4.6%. The two measurements of antibiotic utilization differed remarkably among the 10 provinces. Patients diagnosed with tonsillitis and faucitis had higher odds (OR = 8.86 for tonsillitis and OR = 4.64 for faucitis) of antibiotic prescription than patients with other diagnosis of URTIs. Patients with tonsillitis and faucitis also had higher odds (OR = 3.82 for tonsillitis and OR = 2.71 for faucitis) of multiple antibiotic prescription than those with other diagnosis of URTIs. The number of drugs per prescription and injection in prescriptions were also significant predictors of antibiotic and multiple antibiotic utilization for URTIs. Conclusion: It is concluded that the percentage of antibiotic prescription for URTIs is higher in rural Western China than in most of other countries with available data and that prescriptions of antibiotics for URTIs are associated with residence regions of patients, URTI diagnosis and background information on drug prescription.