Dedifferentiation-like reprogramming of degenerative nucleus pulposus cells into notochordal-like cells by defined factors.

The extensive degeneration of functional somatic cells and the depletion of endogenous stem/progenitor populations present significant challenges to tissue regeneration in degenerative diseases. Currently, a cellular reprogramming approach enabling directly generating corresponding progenitor populations from degenerative somatic cells remains elusive. The present study focused on intervertebral disc degeneration (IVDD) and identified a three-factor combination (OCT4, FOXA2, TBXT (OFT)) that could induce the dedifferentiation-like reprogramming of degenerative nucleus pulposus cells (dNPCs) toward induced notochordal-like cells (iNCs). Single-cell transcriptomics dissected the transitions of cell identity during reprogramming. Further, OCT4 was found to directly interact with bromodomain PHD-finger transcription factor (BPTF) to remodel the chromatin during the early phases, which was crucial for initiating this dedifferentiation-like reprogramming. In rat models, intradiscal injection of adeno-associated virus carrying OFT generated iNCs from in situ dNPCs and reversed IVDD. These results collectively present a proof-of-concept for dedifferentiation-like reprogramming of degenerated somatic cells into corresponding progenitors through the development of a factor-based strategy, providing a promising approach for regeneration in degenerative disc diseases.

Long-term effect of extreme temperature on cognitive function of middle-aged and older adults in China.

BACKGROUND: Several studies have explored the association between temperature and cognitive function. However, few studies have examined the effect of extreme temperature on cognitive function. In this study, we aimed to quantify the long-term effect of extreme temperature (e.g., heat waves, cold spells, and hot night excess (HNE)) on cognitive performance in middle-aged and older people in China. METHOD: We investigated 7915 aged >45 years people from the China Health and Retirement Longitudinal Study (CHARLS), surveyed in 2011 and 2015. A structured questionnaire was utilized to assess cognitive function, including four dimensions: episodic memory, attention, orientation, and visuo-construction. Hourly ambient temperature from the ERA5-Land datasets were used to calculate variables indicating extreme temperature. We performed difference-in-difference (DID) models to assess the potential causal relationship between extreme temperature and cognitive function. RESULTS: Non-linear analyses suggested that both sustained increases in temperature and excessive variability in temperature increased the risk of cognitive decline. Meanwhile, we observed the extra risk of global cognitive function decline was 2.3% (95% Confidence interval (95% CI): 0.2%, 4.4%) for heat waves (one unit increase) and 5.9% (95% CI: 0.6%, 11.6%) for HNE (one unit increase), while the association for cold spells was insignificant. Two cognitive dimensions, episodic memory and visuo-construction, were sensitive to these two heat-related factors. CONCLUSION: Extreme temperature was inversely related to cognitive performance in middle-aged and older adults, which was substantial for heat waves and HNE particularly. The effect size varied by cognitive dimensions.

Outcomes Following Total Hip Arthroplasty in Patients Who Have Charcot Neuroarthropathy of the Hip.

BACKGROUND: Historically, Charcot neuroarthropathy hip (CNH) was deemed a contraindication for total hip arthroplasty (THA). However, as implant design and surgical techniques advance, THA for CNH has been performed and documented in literature. Information regarding the outcomes of THA for CNH is limited. The objective of the study was to assess outcomes following THA in patients who have CNH. METHODS: Patients who have CNH underwent primary THA and had at least 2 years of follow-up were identified in a national insurance database. For comparison, a 1:10 matched control cohort of patients who did not have CNH was created based on age, sex, and relevant comorbidities. Eight hundred and ninety-five CNH patients who underwent primary THA were compared to 8,785 controls. Medical outcomes, emergency department visits, hospital readmissions, and surgical outcomes including revisions between cohorts were evaluated using multivariate logistic regressions. RESULTS: The CNH patients were found to have higher risks of 90-day wound complications (P = .014), periprosthetic joint infection (P = .013) (P = .021), dislocation (P < .001) (P < .001), aseptic loosening (P = .040) (P = .002), periprosthetic fracture (P = .003) (P < .001), and revision (P < .001) (P < .001) at 1-year and 2-year follow-up, respectively. CONCLUSION: While patients who have CNH are at a higher risk of wound and implant-related complications, they are comparatively lower than previously reported in literature. Orthopaedic surgeons should be cognizant of the increased risk in this population to provide appropriate preoperative counseling and enhanced perioperative medical management.

PCV2 infection aggravates OTA-induced immunotoxicity in vivo and in vitro.

Ochratoxin A (OTA), frequently existing in the food and feeds, could induce immunotoxicity. Porcine circovirus type 2 (PCV2), as a primary causative agent of porcine circovirus-associated disease, also could induce immunosuppression. However, it is still unknown whether PCV2 infection impacts OTA-induced immunotoxicity. The pigs and porcine alveolar macrophages (PAMs) were used as the model in the present experiment. The results in vivo indicated that PCV2 infection exacerbated OTA-induced immunotoxicity, NF-κB p65 phosphorylation, and TLR4 and MyD88 mRNA and protein expression in spleen. The results in vitro showed that OTA at 7.0 and 9.0 µM decreased cell viability and increased LDH release of PAMs without PCV2 infection. However, with PCV2 infection, OTA at 5.0, 7.0 and 9.0 µM significantly decreased cell viability and increased LDH release compared with absence of PCV2 infection. In addition, OTA at 5.0 and 7.0 µM significantly increased Annexin V/PI-positive rate, apoptosis of nuclear, γ-H2AX foci, IL-1α and TNF-α expression in PAMs with PCV2 infection compared with absence of PCV2 infection. In addition, PCV2 infection enhanced OTA-induced TLR4 and MyD88 mRNA and protein expression and NF-κB p65 phosphorylation. Knockdown of TLR4 alleviated the exacerbating effects of PCV2 infection on OTA-induced cytotoxicity, apoptosis and DNA damage in PAMs. These results indicated that PCV2 infection aggravated OTA-induced immunotoxicity and reduced the dose of OTA-induced immunotoxicity via TLR4/NF-κB p65 signaling pathway, which could provide basis for establishing limits for OTA.

Rea regulates microglial polarization and attenuates neuronal apoptosis via inhibition of the NF-κB and MAPK signalings for spinal cord injury repair.

Inflammation and neuronal apoptosis aggravate the secondary damage after spinal cord injury (SCI). Rehmannioside A (Rea) is a bioactive herbal extract isolated from Rehmanniae radix with low toxicity and neuroprotection effects. Rea treatment inhibited the release of pro-inflammatory mediators from microglial cells, and promoted M2 polarization in vitro, which in turn protected the co-cultured neurons from apoptosis via suppression of the NF-κB and MAPK signalling pathways. Furthermore, daily intraperitoneal injections of 80 mg/kg Rea into a rat model of SCI significantly improved the behavioural and histological indices, promoted M2 microglial polarization, alleviated neuronal apoptosis, and increased motor function recovery. Therefore, Rea is a promising therapeutic option for SCI and should be clinically explored.

Injectable exosome-functionalized extracellular matrix hydrogel for metabolism balance and pyroptosis regulation in intervertebral disc degeneration.

Exosome therapy is a promising therapeutic approach for intervertebral disc degeneration (IVDD) and achieves its therapeutic effects by regulating metabolic disorders, the microenvironment and cell homeostasis with the sustained release of microRNAs, proteins, and transcription factors. However, the rapid clearance and disruption of exosomes are the two major challenges for the application of exosome therapy in IVDD. Herein, a thermosensitive acellular extracellular matrix (ECM) hydrogel coupled with adipose-derived mesenchymal stem cell (ADSC) exosomes (dECM@exo) that inherits the superior properties of nucleus pulposus tissue and ADSCs was fabricated to ameliorate IVDD. This thermosensitive dECM@exo hydrogel system can provide not only in situ gelation to replenish ECM leakage in nucleus pulposus cells (NPCs) but also an environment for the growth of NPCs. In addition, sustained release of ADSC-derived exosomes from this system regulates matrix synthesis and degradation by regulating matrix metalloproteinases (MMPs) and inhibits pyroptosis by mitigating the inflammatory response in vitro. Animal results demonstrated that the dECM@exo hydrogel system maintained early IVD microenvironment homeostasis and ameliorated IVDD. This functional system can serve as a powerful platform for IVD drug delivery and biotherapy and an alternative therapy for IVDD.

[Clinical features of very preterm small-for-gestational-age infants born due to severe preeclampsia].

OBJECTIVE: To study the clinical features of very preterm small-for-gestational-age infants born by cesarean section due to severe preeclampsia. METHODS: Forty-two small-for-gestational-age infants who were admitted from August 2017 to July 2018 and were born due to severe preeclampsia were enrolled as the observation group. Forty very preterm infants who were born to healthy mothers since uterine contractions could not be suppressed were enrolled as the control group. Perinatal features, clinical manifestations of infection, complications, and clinical outcomes were analyzed for the two groups. RESULTS: Within 6 hours and 2-3 days after birth, the observation group had significantly lower white blood cell count (WBC), absolute neutrophil count (ANC), and platelet count (PLT) than the control group (P < 0.05). At 5-7 days after birth, there was no significant difference in WBC between the two groups (P > 0.05), while the observation group still had significantly lower ANC and PLT than the control group (P < 0.05). The observation group had a significantly higher C-reactive protein (CRP) level than the control group at 2-3 days and 5-7 days after birth (P < 0.05). The observation group had a significantly higher proportion of infants with severe infections than the control group (P < 0.05). The observation group had a significantly higher hemoglobin level than the control group within 6 hours after birth (P < 0.05). The observation group had a significantly higher incidence rate of bronchopulmonary dysplasia than the control group (P < 0.05). There was no significant difference between the two groups in the rate of pulmonary hemorrhage, intracranial hemorrhage, neonatal necrotizing enterocolitis, retinopathy of prematurity, and the rate of use of invasive ventilation, and clinical outcomes (P > 0.05). CONCLUSIONS: Very preterm small-for-gestational-age infants born due to severe preeclampsia have a high incidence rate of infection and severe conditions. Early manifestations include reductions in the infection indicators WBC, ANC, and PLT, and CRP does not increase significantly in the early stage and gradually increases at 2-3 days after birth. Most of these infants require invasive ventilation after birth, with bronchopulmonary dysplasia as the main complication. Clinical changes should be closely observed and inflammatory indicators should be monitored for early identification of infection, timely diagnosis, and timely adjustment of antibiotic treatment, so as to improve the outcome.

A Atractylodes lancea polysaccharide inhibits metastasis of human osteosarcoma U-2 OS cells by blocking sialyl Lewis X (sLex )/E-selectin binding.

In this study, a new water and alkaline-soluble polysaccharide (ALP), with an average molecular weight of 6.63 × 104  Da, was successfully purified from the rhizomes of Atractylodes lancea. GC analysis demonstrated that ALP was a kind of glucan. The effect of the ALP on the interaction between E-selectin and sialyl Lewis X (sLex ) was examined in human osteosarcoma U-2 OS cells. It was obvious that the expression of sLex antigen on the surface of U-2 OS cells was visible under fluorescence microscopy. The addition of ALP (0.5, 1 and 2 mg/mL) resulted in a marked inhibition on the adhesion, migration and invasion of U-2 OS cells to human umbilical vein endothelial cells (HUVECs), which was achieved by the decreased sLex expression on U-2 OS cells. Additionally, the induction of apoptosis can be observed in U-2 OS cells following ALP treatment using TUNEL staining and Annexin V-FITC/PI double-staining analysis on flow cytometry. In conclusion, these results indicated that ALP exerted anti-metastatic activity towards osteosarcoma cells via inhibition of sLex /E-selectin binding, which suggested that ALP could be a potent agent for human osteosarcoma intervention.

First report of feline morbillivirus in mainland China.

Feline morbillivirus (FeMV) is an emerging member of the family Paramyxoviridae that is suspected to be involved in chronic kidney disease (CKD). FeMV was first discovered in Hong Kong in 2012 and has subsequently been detected in many countries. However, the prevalence of FeMV in mainland China is still unclear. To clarify the present status and examine the genetic diversity of FeMV in mainland China, in this study, we collected cat urine samples in veterinary hospitals in Guangdong Province in 2017 and 2018. Using reverse transcription (RT)-PCR, we found that the urine of six out of 64 cats tested positive for FeMV RNA. Sequencing and genetic analysis of the FeMV L gene showed that FeMV in mainland China is genetically diverse, and phylogenetic analysis showed that the viruses segregated into two clusters. Two isolates, GD5 and GD6, grouped in a branch that was separate from the one containing other previously reported FeMV isolates. These results will contribute to a better understanding of the evolution of FeMV in China.

Genome Sequence and Comparative Analysis of Colletotrichum gloeosporioides Isolated from Liriodendron Leaves.

Colletotrichum gloeosporioides is a hemibiotrophic pathogen causing significant losses to economically important crops and forest trees, including Liriodendron. To explore the interaction between C. gloeosporioides and Liriodendron and to identify the candidate genes determining the pathogenesis, we sequenced and assembled the whole genome of C. gloeosporioides Lc1 (CgLc1) using PacBio and Illumina next generation sequencing and performed a comparative genomic analysis between CgLc1 and Cg01, the latter being a described endophytic species of the C. gloeosporioides complex. Gene structure prediction identified 15,744 protein-coding genes and 837 noncoding RNAs. Species-specific genes were characterized using an ortholog analysis followed by a pathway enrichment analysis, which showed that genes specific to CgLc1 were enriched for the arginine biosynthetic process. Furthermore, genome synteny analysis revealed that most of the protein-coding genes fell into collinear blocks. However, two clusters of polyketide synthase genes were identified to be specific for CgLc1, suggesting that they might have an important role in virulence control. Transcriptional regulators coexpressed with polyketide synthase genes were detected through a Weighted Correlation Network Analysis. Taken together, this work provides new insight into the virulence- and pathogenesis-associated genes present in C. gloeosporioides and its possible lifestyle.

Effects of Marital Status on Prognosis in Women with Infiltrating Ductal Carcinoma of the Breast: A Real-World 1: 1 Propensity-Matched Study.

BACKGROUND The effects of marital status on infiltrating ductal carcinoma of breast cancer (IDC) have not been studied in detail. This study investigated the impact of marital status on IDC patients. MATERIAL AND METHODS SEER databases were searched from 2010 to 2015 for subjects who were married, divorced, single, and widowed. The influence of marital status on breast cancer-specific survival (BCSS) and overall survival (OS) of IDC patients was investigated through multivariate Cox regression analysis and Kaplan-Meier analysis. To prevent bias, propensity score matching (PSM) analysis was performed. RESULTS The 5-year OS was 89.6%in married patients, 84.9% in divorced patients, 83.5% in single patients, and 71.3% in widowed patients (p<0.001). The 5-year BCSS were 92.9%, 90.2%, 87.6%, and 86.4%, respectively (p<0.001). Multivariate Cox regression analysis revealed that marriage was a protective factor for patients with IDC in terms of OS (divorced: HR, 1.27; 95% CI, 1.21-1.32; p<0.001; single: HR, 1.36; 95% CI, 1.31-1.42; p<0.001; widowed: HR, 1.42; 95% CI, 1.36-1.48; p<0.001) and BCSS (divorced: HR, 1.15; 95% CI, 1.09-1.21; p<0.001; single: HR, 1.27; 95% CI, 1.21-1.33; p<0.001; widowed: HR, 1.32; 95% CI, 1.25-1.40; p<0.001). Following subgroup and PSM analysis, married patients were shown to have better OS and BCSS as opposed to divorced, single, or widowed patients. CONCLUSIONS We identify marital status as a predictor of survival in those with IDC. Widowed patients showed the highest mortality risk.

A High-Quality Draft Genome Sequence of Colletotrichum gloeosporioides sensu stricto SMCG1#C, a Causal Agent of Anthracnose on Cunninghamia lanceolata in China.

Colletotrichum has a broad host range and causes major yield losses of crops. The fungus Colletotrichum gloeosporioides is associated with anthracnose on Chinese fir. In this study, we present a high-quality draft genome sequence of C. gloeosporioides sensu stricto SMCG1#C, providing a reference genomic data for further research on anthracnose of Chinese fir and other hosts.

Correction to: Molecular characterization of a genetically divergent equine pegivirus strain identified in China.

Unfortunately, the corresponding author name was incorrectly published in the original article and the same is corrected here. The original article was corrected.

Molecular characterization of a genetically divergent equine pegivirus strain identified in China.

Equine pegivirus (EPgV) is a newly discovered equine virus, which is taxonomically classified in the Pegivirus genus of the Flaviviridae family. Until now, only the complete genome sequence of the first reported EPgV strain, from the USA (strain name: C0035) is available on online databases. Considering this, horse serum samples were collected from horses in China and screened for EPgV RNA by RT-PCR. One EPgV strain, LW/2016, was obtained and its near-complete genome sequence was acquired by standard PCR. Further analysis of its nucleotide sequence indicates LW/2016 is genetically divergent from C0035, with a nucleotide identity of 89.02%. These two viruses clustered into two independent branches following phylogenetic analysis of on the NS3 and NS5B genes. To our knowledge, this is the first report of genetic divergence in the EPgV genome.

Estimated assessment of cumulative dietary exposure to organophosphorus residues from tea infusion in China.

BACKGROUND: China has the world's largest tea plantation area in the world. To sustain high yields of the tea, multiple pesticides are used on tea crops to control pests. Organophosphorus (OP) pesticides are among the most widely used types of agricultural pesticides in China. As tea is a significant potential source of exposure to pesticide residues, the public concern has increased in relation to pesticide residues found in tea in China. The aim of the study was to estimate cumulative dietary exposure to OP residues from tea infusion for Chinese tea consumers to determine whether exposure to OP residues from tea infusion is a cause of health concern for tea consumers in China. METHODS: OP residue data were obtained from the China National Monitoring Program on Food Safety (2013-2014), encompassing 1687 tea samples from 12 provinces. Tea consumption data were obtained from the China National Nutrient and Health Survey (2002), comprising 506 tea consumers aged 15-82 years. The transfer rates of residues from tea leaves into tea infusions were obtained from the literature. The relative potency factor (RPF) approach was used to estimate acute cumulative exposure to 20 OP residues from tea infusion using methamidophos as the index compound. Dietary exposure was calculated in a probabilistic way. RESULTS: For tea consumers, the mean and the 99.9th percentile (P99.9) of cumulative dietary exposure to OP residues from tea infusion equalled 0.08 and 1.08 µg/kg bw/d. When compared with the acute reference dose (ARfD), 10 µg/kg bw/d for methamidophos, this accounts for 0.8 and 10.8% of the ARfD. CONCLUSIONS: Even when considering OP residues from vegetables, fruits and other foods, there are no health concerns based on acute dietary exposure to OP residues from tea infusion. However, it is necessary to strengthen the management of the OP pesticides used on tea in China to reduce the risk of chronic dietary exposure to OPs from tea infusion.

Development of oligonucleotides and multiplex probes for quick and accurate identification of wheat and Thinopyrum bessarabicum chromosomes.

In comparison with general FISH for preparing probes in terms of time and cost, synthesized oligonucleotide (oligo hereafter) probes for FISH have many advantages such as ease of design, synthesis, and labeling. Low cost and high sensitivity and resolution of oligo probes greatly simplify the FISH procedure as a simple, fast, and efficient method of chromosome identification. In this study, we developed new oligo and oligo multiplex probes to accurately and efficiently distinguish wheat (Triticum aestivum, 2n = 6x, AABBDD) and Thinopyrum bessarabicum (2n = 2x = 14, JJ) chromosomes. The oligo probes contained more nucleotides or more repeat units that produced stronger signals for more efficient chromosome painting. Four Th. bessarabicum-specific oligo probes were developed based on genomic DNA sequences of Th. bessarabicum chromosome arm 4JL, and one of them (oligo DP4J27982) was pooled with the oligo multiplex #1 to simultaneously detect wheat and Th. bessarabicum chromosomes for quick and accurate identification of Chinese Spring (CS) - Th. bessarabicum alien chromosome introgression lines. Oligo multiplex #4 revealed chromosome variations among CS and eight wheat cultivars by a single round of FISH analysis. This research demonstrated the high efficiency of using oligos and oligo multiplexes in chromosome identification and manipulation.

[Animal experiment of recombinant human lactoferrin based on the 28 days repeated oral toxicity].

OBJECTIVE: To evaluate the food safety of recombinant human lactoferrin( rhLF) and its iron nutrition. METHODS: 100 SPF grade weanling SD rats with half male and female, were randomly divided into five groups and they were control group, 100 and200 g/kg bLF group, 100 and 200 g/kg rhLF group. Rates in control group were feed with AIN-93 laboratory rodent pure fodder, while bLF and rhLF group were feed with sample protein part and all alternative formulations existed casein component respectively. All Rates were free of water consumption and observed in 28 days. Body weight, food consumption, food utilization and organ coefficient were recorded, while hematology, iron nutrition index [serum iron( SI), total iron binding capacity( TIBC), Transferringsaturation( TS), Soluble transferrin receptor( s TfR) ] and clinical biochemistry were measured. RESULTS: There was no significant difference in body weight between 200 g/kg bLF group and 200 g/kg rhLF groups neither for male nor female animals, while both significantly lower than the control group( P < 0. 05). No significant change in clinical biochemistry hematology, anatomy and histopathology results were observed for 100 g/kg and 200 g/kg rhLF group. There was no significant difference in serum iron level and transferrin saturation between bLF group and rhLF group, but the serum iron level and transferrin saturation of both bLF group and rhLF group were higher than the control group. CONCLUSION: No significant difference were observed in food safety indicators and iron nutrition improvement between 28-day rhLF and bLF in the present study.

Genome-wide identification of phenolic acid biosynthetic genes in Salvia miltiorrhiza.

MAIN CONCLUSION: Twenty-nine genes related to phenolic acid biosynthesis were identified in the Salvia miltiorrhiza genome. Nineteen of these are described for the first time, with ten genes experimentally correlating to phenolic acid biosynthesis. Vast stores of secondary metabolites exist in plants, many of which possess biological activities related to human health. Phenolic acid derivatives are a class of valuable bioactive pharmaceuticals abundant in the widely used Chinese medicinal herb, Salvia miltiorrhiza. The biosynthetic pathway for phenolic acids differs in this species from that of other investigated plants. However, the molecular basis for this is unknown, with systematic analysis of the genes involved not yet performed. As the first step towards unraveling this complex biosynthetic pathway in S. miltiorrhiza, the current genome assembly was searched for putatively involved genes. Twenty-nine genes were revealed, 19 of which are described here for the first time. These include 15 genes predicted in the phenylpropanoid pathway; seven genes in the tyrosine-derived pathway; six genes encoding putative hydroxycinnamoyltransferases, and one CYP98A, namely CYP98A78. The promoter regions, gene structures and expression patterns of these genes were examined. Furthermore, conserved domains and phylogenetic relationships with homologous proteins in other species were revealed. Most of the key enzymes, including 4-coumarate: CoA ligase, 4-hydroxyphenylpyruvate reductase and hydroxycinnamoyltransferase, were found in multiple copies, each exhibiting different characteristics. Ten genes putatively involved in rosmarinic acid biosynthesis are also described. These findings provide a foundation for further analysis of this complex and diverse pathway, with potential to enhance the synthesis of water-soluble medicinal compounds in S. miltiorrhiza.

[Agricultural biotechnology safety assessment].

Genetically modified (GM) crops were first introduced to farmers in 1995 with the intent to provide better crop yield and meet the increasing demand for food and feed. GM crops have evolved to include a thorough safety evaluation for their use in human food and animal feed. Safety considerations begin at the level of DNA whereby the inserted GM DNA is evaluated for its content, position and stability once placed into the crop genome. The safety of the proteins coded by the inserted DNA and potential effects on the crop are considered, and the purpose is to ensure that the transgenic novel proteins are safe from a toxicity, allergy, and environmental perspective. In addition, the grain that provides the processed food or animal feed is also tested to evaluate its nutritional content and identify unintended effects to the plant composition when warranted. To provide a platform for the safety assessment, the GM crop is compared to non-GM comparators in what is typically referred to as composition equivalence testing. New technologies, such as mass spectrometry and well-designed antibody-based methods, allow better analytical measurements of crop composition, including endogenous allergens. Many of the analytical methods and their intended uses are based on regulatory guidance documents, some of which are outlined in globally recognized documents such as Codex Alimentarius. In certain cases, animal models are recommended by some regulatory agencies in specific countries, but there is typically no hypothesis or justification of their use in testing the safety of GM crops. The quality and standardization of testing methods can be supported, in some cases, by employing good laboratory practices (GLP) and is recognized in China as important to ensure quality data. Although the number of recommended, in some cases, required methods for safety testing are increasing in some regulatory agencies, it should be noted that GM crops registered to date have been shown to be comparable to their nontransgenic counterparts and safe . The crops upon which GM development are based are generally considered safe.

High-accuracy de novo assembly and SNP detection of chloroplast genomes using a SMRT circular consensus sequencing strategy.

A circular consensus sequencing (CCS) strategy involving single molecule, real-time (SMRT) DNA sequencing technology was applied to de novo assembly and single nucleotide polymorphism (SNP) detection of chloroplast genomes. Chloroplast DNA was purified from enriched chloroplasts of pooled individuals to construct a shotgun library for each species. The sequencing reactions were performed on a PacBio RS platform. CCS sub-reads were generated from polymerase reads that passed the native dumbbell-shaped DNA templates multiple times. The complete chloroplast genome sequence was generated by mapping all reads to the draft sequence constructed in a step-by-step manner. The full-chain, PCR-free approach eliminates the possible context-specific biases in library construction and sequencing reaction. The chloroplast genome was easily and completely assembled using the data generated from one SMRT Cell without requiring a reference genome. Comparisons of the three assembled Fritillaria genomes to 34.1 kb of validation Sanger sequences revealed 100% concordance, and the detected intraspecies SNPs at a minimum variant frequency of 15% were all confirmed. This simple approach with potential for parallel sequencing yields high-quality chloroplast genomes for sensitive SNP detection and comparative analyses. We recommend this approach for its powerful applicability for evolutionary genetics and genomics studies in plants based on the sequences of chloroplast genomes.