Distraction-aware hierarchical learning for vascular structure segmentation in intravascular ultrasound images.

Vascular structure segmentation in intravascular ultrasound (IVUS) images plays an important role in pre-procedural evaluation of percutaneous coronary intervention (PCI). However, vascular structure segmentation in IVUS images has the challenge of structure-dependent distractions. Structure-dependent distractions are categorized into two cases, structural intrinsic distractions and inter-structural distractions. Traditional machine learning methods often rely solely on low-level features, overlooking high-level features. This way limits the generalization of these methods. The existing semantic segmentation methods integrate low-level and high-level features to enhance generalization performance. But these methods also introduce additional interference, which is harmful to solving structural intrinsic distractions. Distraction cue methods attempt to address structural intrinsic distractions by removing interference from the features through a unique decoder. However, they tend to overlook the problem of inter-structural distractions. In this paper, we propose distraction-aware hierarchical learning (DHL) for vascular structure segmentation in IVUS images. Inspired by distraction cue methods for removing interference in a decoder, the DHL is designed as a hierarchical decoder that gradually removes structure-dependent distractions. The DHL includes global perception process, distraction perception process and structural perception process. The global perception process and distraction perception process remove structural intrinsic distractions then the structural perception process removes inter-structural distractions. In the global perception process, the DHL searches for the coarse structural region of the vascular structures on the slice of IVUS sequence. In the distraction perception process, the DHL progressively refines the coarse structural region of the vascular structures to remove structural distractions. In the structural perception process, the DHL detects regions of inter-structural distractions in fused structure features then separates them. Extensive experiments on 361 subjects show that the DHL is effective (e.g., the average Dice is greater than 0.95), and superior to ten state-of-the-art IVUS vascular structure segmentation methods.

Characteristics of MDR E. coli strains isolated from Pet Dogs with clinic diarrhea: A pool of antibiotic resistance genes and virulence-associated genes.

The increasing number of multi-drug resistant (MDR) bacteria in companion animals poses a threat to both pet treatment and public health. To investigate the characteristics of MDR Escherichia coli (E. coli) from dogs, we detected the antimicrobial resistance (AMR) of 135 E. coli isolates from diarrheal pet dogs by disc diffusion method (K-B method), and screened antibiotic resistance genes (ARGs), virulence-associated genes (VAGs), and population structure (phylogenetic groups and MLST) by polymerase chain reaction (PCR) for 74 MDR strains, then further analyzed the association between AMRs and ARGs or VAGs. Our results showed that 135 isolates exhibited high resistance to AMP (71.11%, 96/135), TET (62.22%, 84/135), and SXT (59.26%, 80/135). Additionally, 54.81% (74/135) of the isolates were identified as MDR E. coli. In 74 MDR strains, a total of 12 ARGs in 6 categories and 14 VAGs in 4 categories were observed, of which tetA (95.95%, 71/74) and fimC (100%, 74/74) were the most prevalent. Further analysis of associations between ARGs and AMRs or VAGs in MDR strains revealed 23 significant positive associated pairs were observed between ARGs and AMRs, while only 5 associated pairs were observed between ARGs and VAGs (3 positive associated pairs and 2 negative associated pairs). Results of population structure analysis showed that B2 and D groups were the prevalent phylogroups (90.54%, 67/74), and 74 MDR strains belonged to 42 STs (6 clonal complexes and 23 singletons), of which ST10 was the dominant lineage. Our findings indicated that MDR E. coli from pet dogs carry a high diversity of ARGs and VAGs, and were mostly belong to B2/D groups and ST10. Measures should be taken to prevent the transmission of MDR E. coli between companion animals and humans, as the fecal shedding of MDR E. coli from pet dogs may pose a threat to humans.

Characterization of antibiotic resistance genes and mobile genetic elements in Escherichia coli isolated from captive black bears.

The objective of this study was to analyze the antimicrobial resistance (AMR) characteristics produced by antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and gene cassettes in Escherichia coli isolated from the feces of captive black bears. Antimicrobial susceptibility testing was performed by using the disk diffusion method, and both MGEs and integron gene cassettes were detected by polymerase chain reaction. Our results showed that 43.7% (62/142) of the isolates were multidrug resistant strains and 97.9% (139/142) of the isolates were resistant to at least one antibiotic. The highest AMR phenotype was observed for tetracycline (79.6%, 113/142), followed by ampicillin (50.0%, 71/142), trimethoprim-sulfamethoxazole (43.7%, 62/142) and cefotaxime (35.9%, 51/142). However, all isolates were susceptible to tobramycin. tetA had the highest occurrence in 6 ARGs in 142 E. coli isolates (76.8%, 109/142). Ten mobile genetic elements were observed and IS26 was dominant (88.0%, 125/142). ISECP1 was positively associated with five ß-lactam antibiotics. ISCR3/14, IS1133 and intI3 were not detected. Seventy-five E. coli isolates (65 intI1-positive isolates, 2 intI2-positive isolates and 8 intI1 + intI2-positive isolates) carried integrons. Five gene cassettes (dfrA1, aadA2, dfrA17-aadA5, aadA2-dfrA12 and dfrA1-aadA1) were identified in the intI1-positive isolates and 2 gene cassettes (dfrA1-catB2-sat2-aadA1 and dfrA1-catB2-sat1-aadA1) were observed in the intI2-positive isolates. Monitoring of ARGs, MGEs and gene cassettes is important to understand the prevalence of AMR, which may help to introduce measures to prevent and control of AMR in E. coli for captive black bears.

Modulating root system architecture: cross-talk between auxin and phytohormones.

Root architecture is an important agronomic trait that plays an essential role in water uptake, soil compactions, nutrient recycling, plant-microbe interactions, and hormone-mediated signaling pathways. Recently, significant advancements have been made in understanding how the complex interactions of phytohormones regulate the dynamic organization of root architecture in crops. Moreover, phytohormones, particularly auxin, act as internal regulators of root development in soil, starting from the early organogenesis to the formation of root hair (RH) through diverse signaling mechanisms. However, a considerable gap remains in understanding the hormonal cross-talk during various developmental stages of roots. This review examines the dynamic aspects of phytohormone signaling, cross-talk mechanisms, and the activation of transcription factors (TFs) throughout various developmental stages of the root life cycle. Understanding these developmental processes, together with hormonal signaling and molecular engineering in crops, can improve our knowledge of root development under various environmental conditions.

Cellular nucleus image-based smarter microscope system for single cell analysis.

Cell imaging technology is undoubtedly a powerful tool for studying single-cell heterogeneity due to its non-invasive and visual advantages. It covers microscope hardware, software, and image analysis techniques, which are hindered by low throughput owing to abundant hands-on time and expertise. Herein, a cellular nucleus image-based smarter microscope system for single-cell analysis is reported to achieve high-throughput analysis and high-content detection of cells. By combining the hardware of an automatic fluorescence microscope and multi-object recognition/acquisition software, we have achieved more advanced process automation with the assistance of Robotic Process Automation (RPA), which realizes a high-throughput collection of single-cell images. Automated acquisition of single-cell images has benefits beyond ease and throughout and can lead to uniform standard and higher quality images. We further constructed a single-cell image database-based convolutional neural network (Efficient Convolutional Neural Network, E-CNN) exceeding 20618 single-cell nucleus images. Computational analysis of large and complex data sets enhances the content and efficiency of single-cell analysis with the assistance of Artificial Intelligence (AI), which breaks through the super-resolution microscope's hardware limitation, such as specialized light sources with specific wavelengths, advanced optical components, and high-performance graphics cards. Our system can identify single-cell nucleus images that cannot be artificially distinguished with an accuracy of 95.3%. Overall, we build an ordinary microscope into a high-throughput analysis and high-content smarter microscope system, making it a candidate tool for Imaging cytology.

QTL Mapping of Zeaxanthin Content in Sweet Corn Using Recombinant Inbred Line Population across Different Environments.

Zeaxanthin is a naturally occurring xanthophyll carotenoid obtained from diet sources. Particularly, sweet corn is a major source of dietary zeaxanthin. To investigate the genetic basis of zeaxanthin content regulation in sweet corn, a recombinant inbred line (RIL) population comprising 191 families was constructed using two inbred lines (K44 and F22) with contrasting zeaxanthin content in the grain. The zeaxanthin content in the dry grains of this population grown at different locations was determined using high performance liquid chromatography (HPLC). Subsequently, 175 polymorphic simple sequence repeat (SSR) markers were used to construct a linkage map with a total length of 4322.37 cM and with an average distance of 24.4 cM. A total of eight QTLs located on chromosomes 4, 5, 7, 9, and 10 were detected. The QTLs located in umc1632-umc1401 on chromosome 7 were detected in different environments and explained 11.28-20.25% of the phenotypic variation, implying it is the main QTL controlling zeaxanthin content in the dry grains of sweet corn. Collectively, the present study provides a genetic map and theoretical guidance for the cultivation of sweet corn varieties with a high zeaxanthin content.

Integrated proteomics and phosphoproteomics analyses of esophageal cancer cells with different invasive abilities.

AIMS: Esophageal squamous cell carcinoma (ESCC) is one of the aggressive and lethal malignancies with an extremely poor prognosis. It is necessary to explore the molecular mechanisms of ESCC invasion. MAIN METHODS: We utilized high-throughput mass spectrometry to analyze the proteomes and phosphorylation profiles of two ESCC cell lines with differing invasion capacities (HK vs TE10). Differentially expressed proteins and phosphorites were identified, followed by comprehensive bioinformatics analyses encompassing function and pathway enrichment, protein-protein interaction (PPI) network analysis, hub gene identification, co-expression analysis, kinase-substrate prediction, and drug-target network analysis. CCK-8 assay, transwell examination, wound-healing assay, and western blot was used to validate the effects of fostamatinib on ESCC cells proliferation, invasion, migration, and LYN expression. KEY FINDINGS: The Q4 cluster of differentially phosphorylated proteins was primarily associated with functions and pathways relevant to tumor metastasis. Phosphorylated hub proteins including ARHGAP35, CTNNA1, and SHC1 were identified through the analysis of PPI network, and their respective regulated kinases were predicted. Among the predicted kinases, LYN was validated to be associated with lymph node metastasis (N0 vs. N1-3) and prognosis in ESCC patients at mRNA levels using TGGA data and protein levels in ESCC tissues (p < 0.05). Validation experiments confirmed the inhibitory effects of fostamatinib on ESCC cells proliferation, migration, invasion, and LYN expression. SIGNIFICANCE: Our multi-omics analysis offers deeper perspectives on ESCC invasiveness and unveils new phosphorylated hub proteins with their regulatory kinase. This study also suggests that fostamatinib may be a potential agent for treating ESCC.

Cerebral delivery of redox-responsive lenalidomide prodrug plus methotrexate for primary central nerve system lymphoma combination therapy.

Primary central nervous system lymphoma (PCNSL) is an extremely malignant CNS tumor with high incidence and mortality rates. Its chemotherapy in the clinic has been restricted owing to unsatisfactory drug distribution in the cerebral tissues. In this study, a redox-responsive prodrug of disulfide-lenalidomide-methoxy polyethylene glycol (LND-DSDA-mPEG) was successfully developed for the cerebral delivery of lenalidomide (LND), and methotrexate (MTX) via subcutaneous (s.c.) administration at the neck for combined anti-angiogenesis and chemotherapy on PCNSL. Both the subcutaneous xenograft tumor model and orthotopic intracranial tumor model demonstrated that the co-delivery of LND and MTX nanoparticles (MTX@LND NPs) may significantly inhibit the growth of lymphoma and effectively prevent liver metastasis by downregulating CD31 and VEGF expression. Moreover, an orthotopic intracranial tumor model further verified that through s.c. administration at the neck, redox-responsive MTX@LND NPs could bypass the blood-brain barrier (BBB), efficiently distribute into brain tissues, and effectively inhibit lymphoma growth in the brain, as detected by magnetic resonance imaging (MRI). Taken together, this biodegradable, biocompatible, and redox-responsive nano-prodrug with highly effective targeted delivery of LND and MTX in the brain through the lymphatic vasculature may provide a facile and feasible treatment strategy for PCNSL in the clinic.

Redox-responsive self-assembled polymeric nanoprodrug for delivery of gemcitabine in B-cell lymphoma therapy.

Gemcitabine, as a standard and classic strategy for B-cell lymphoma in the clinic, is limited by its poor pharmacodynamics. Although stimuli-responsive polymeric nanodelivery systems have been widely investigated in the past decade, issues such as complicated procedures, low loading capacity, and uncontrollable release kinetics still hinder their clinical translation. In view of the above considerations, we attempt to construct hyperbranched polyprodrug micelles with considerable drug loading via simple procedures and make use of the particularity of the tumor microenvironment to ensure that the micelles are "inactivated" in normal tissues and "activated" in the tumor microenvironment. Hence, in this work, a redox-responsive polymeric gemcitabine-prodrug (GEM-S-S-PEG) was one-pot synthesized via facile esterification and acylation. The self-assembled subsize (< 100 nm) GEM-S-S-PEG (GSP NPs) with considerable loading capacity (≈ 24.6%) exhibited on-demand and accurate control of gemcitabine release under a simulated tumor microenvironment and thus significantly induced the apoptosis of B-cell lymphoma in vitro. Moreover, in the A20 tumor xenograft murine model, GSP NPs efficiently decreased the expansion of tumor tissues with minimal systemic toxicity. In summary, these redox-responsive and self-assembling GSP NPs with a facile one-pot synthesis procedure may hold great potency in clinical translation for enhanced chemotherapy of B-cell lymphoma. STATEMENT OF SIGNIFICANCE: A redox-responsive polymeric gemcitabine-prodrug (GEM-S-S-PEG) was one-pot synthesized via facile esterification and acylation. The self-assembled subsize (< 100 nm) GEM-S-S-PEG (GSP NPs) exhibited significant tumor therapeutic effects in vitro and in vivo. The polyprodrug GEM-S-S-PEG prepared in this study shows the great potential of redox-responsive nanodrugs for antitumor activity, which provides a reference value for the optimization of the design of functional polyprodrugs.

Nanomedicine as a promising strategy for the theranostics of infectious diseases.

Infectious diseases caused by bacteria, viruses, and fungi and their global spread pose a great threat to human health. The 2019 World Health Organization report predicted that infection-related mortality will be similar to cancer mortality by 2050. Particularly, the global cumulative numbers of the recent outbreak of coronavirus disease (COVID-19) have reached 110.7 million cases and over 2.4 million deaths as of February 23, 2021. Moreover, the crisis of these infectious diseases exposes the many problems of traditional diagnosis, treatment, and prevention, such as time-consuming and unselective detection methods, the emergence of drug-resistant bacteria, serious side effects, and poor drug delivery. There is an urgent need for rapid and sensitive diagnosis as well as high efficacy and low toxicity treatments. The emergence of nanomedicine has provided a promising strategy to greatly enhance detection methods and drug treatment efficacy. Owing to their unique optical, magnetic, and electrical properties, nanoparticles (NPs) have great potential for the fast and selective detection of bacteria, viruses, and fungi. NPs exhibit remarkable antibacterial activity by releasing reactive oxygen species and metal ions, exerting photothermal effects, and causing destruction of the cell membrane. Nano-based delivery systems can further improve drug permeability, reduce the side effects of drugs, and prolong systemic circulation time and drug half-life. Moreover, effective drugs against COVID-19 are still lacking. Recently, nanomedicine has shown great potential to accelerate the development of safe and novel anti-COVID-19 drugs. This article reviews the fundamental mechanisms and the latest developments in the treatment and diagnosis of bacteria, viruses, and fungi and discusses the challenges and perspectives in the application of nanomedicine.

The Number of Patients with Acute Myocardial Infarction Decreased and Door-to-Balloon Time Delayed in COVID-19.

BACKGROUND: At present, COVID-19 is sweeping the world, and all countries are actively responding. During the COVID-19 epidemic, the treatment of patients with acute myocardial infarction (AMI) may be affected. METHODS: We reviewed data of patients with AMI from January 23 to April 23, 2020 (2020), and January 23 to April 23, 2019 (2019), who were admitted to two hospitals from Southern China. We collected clinical characteristics, comorbidities, treatment, prognosis, and key time segments to analyze. RESULTS: The total number of patients that had been diagnosed with AMI in the two hospitals was 218 in 2020 and 260 in 2019. The number of AMI patients that were admitted to hospitals per day decreased in 2020. The percentage of patients with AMI who refused hospitalization in 2020 was significantly higher than that in 2019 (5.0% vs 1.5%, p=0.028). There is no statistical difference in symptoms of the first medical contact (S2FMC) time between 2020 and 2019 (p=0.552). Door-to-balloon (D2B) time of ST-elevation myocardial infarction (STEMI) patients who were treated with a primary percutaneous coronary intervention (pPCI) in 2020 was 79 (63.75-105.25) mins, while D2B time in 2019 was 57.5 (41.5-76.5) mins, which was statistically different from the two groups. CONCLUSIONS: COVID-19 had an impact on the number of AMI patients who were admitted to hospitals and the time of treatment. During the COVID-19 epidemic, the number of AMI patients that were admitted to hospitals per day was decreased, while the percentage of AMI patients that refused therapy in these two hospitals increased, and the D2B time of STEMI patients was also delayed.

Occupational identity, job satisfaction and their effects on turnover intention among Chinese Paediatricians: a cross-sectional study.

BACKGROUND: This study contributes to research on the paediatrician shortage by examining occupational identity, job satisfaction and their effects on turnover intention among paediatricians in China. METHODS: A multi-stage stratified random sampling method was employed to conduct a questionnaire survey. Of the 4906 survey recipients, valid data were collected from 4198 of the respondents (85.6%). The participants were from seven geographic regions of China (south, central, north, east, northwest, southwest, and northeast). Paediatricians who volunteered and provided written informed consent participated. All variables including basic socio-demographics and work-related characteristics, occupational identity, job satisfaction and turnover intention were based on available literature, and measured on a 5- point Likert scale. Statistical methods such as exploratory factor analysis (EFA), descriptive analysis, common method bias, one-way ANOVA test, Pearson correlation analysis and mediation analysis were used. RESULTS: Significant differences were observed among the respondents in terms of turnover intention based on age, education level, marital status, region, the type and grade of practice setting, professional title, years in practise, workload, rest days, and monthly income. Occupational identity and job satisfaction were both negatively related to turnover intention, and occupational identity was positively correlated with job satisfaction (r1 = - 0.601, p < 0.01; r2 = - 0.605, p < 0.01). The results also showed that job satisfaction played a mediating role in the association between occupational identity and turnover intention among Chinese paediatricians. CONCLUSIONS: Work conditions, workload and salary are crucial factors of turnover intention among paediatricians in China. Therefore, we suggest that healthcare managers should increase investment in paediatrics, implement salary reforms and dedicate more attention to female and young paediatricians, thus reducing turnover intention among Chinese paediatricians.

Recent applications and strategies in nanotechnology for lung diseases.

Lung diseases, including COVID-19 and lung cancers, is a huge threat to human health. However, for the treatment and diagnosis of various lung diseases, such as pneumonia, asthma, cancer, and pulmonary tuberculosis, are becoming increasingly challenging. Currently, several types of treatments and/or diagnostic methods are used to treat lung diseases; however, the occurrence of adverse reactions to chemotherapy, drug-resistant bacteria, side effects that can be significantly toxic, and poor drug delivery necessitates the development of more promising treatments. Nanotechnology, as an emerging technology, has been extensively studied in medicine. Several studies have shown that nano-delivery systems can significantly enhance the targeting of drug delivery. When compared to traditional delivery methods, several nanoparticle delivery strategies are used to improve the detection methods and drug treatment efficacy. Transporting nanoparticles to the lungs, loading appropriate therapeutic drugs, and the incorporation of intelligent functions to overcome various lung barriers have broad prospects as they can aid in locating target tissues and can enhance the therapeutic effect while minimizing systemic side effects. In addition, as a new and highly contagious respiratory infection disease, COVID-19 is spreading worldwide. However, there is no specific drug for COVID-19. Clinical trials are being conducted in several countries to develop antiviral drugs or vaccines. In recent years, nanotechnology has provided a feasible platform for improving the diagnosis and treatment of diseases, nanotechnology-based strategies may have broad prospects in the diagnosis and treatment of COVID-19. This article reviews the latest developments in nanotechnology drug delivery strategies in the lungs in recent years and studies the clinical application value of nanomedicine in the drug delivery strategy pertaining to the lung.

Advancements in nanotechnology for the diagnosis and treatment of multiple myeloma.

Multiple myeloma (MM), known as a tumor of plasma cells, is not only refractory but also has a high relapse rate, and is the second-most common hematologic tumor after lymphoma. It is often accompanied by multiple osteolytic damage, hypercalcemia, anemia, and renal insufficiency. In terms of diagnosis, conventional detection methods have many limitations, such as it is invasive and time-consuming and has low accuracy. Measures to change these limitations are urgently needed. At the therapeutic level, although the survival of MM continues to prolong with the advent of new drugs, MM remains incurable and has a high recurrence rate. With the development of nanotechnology, nanomedicine has become a powerful way to improve the current diagnosis and treatment of MM. In this review, the research progress and breakthroughs of nanomedicine in MM will be presented. Meanwhile, both superiorities and challenges of nanomedicine were discussed. As a new idea for the diagnosis and treatments of MM, nanomedicine will play a very important role in the research field of MM.

The YAP/SERCA2a signaling pathway protects cardiomyocytes against reperfusion-induced apoptosis.

Mitochondria and the endoplasmic reticulum (ER) are known to promote cardiac ischemia/reperfusion (I/R) injury. Overexpression of yes-associated protein (YAP) and/or sarcoplasmic reticulum calcium ATPase 2a (SERCA2a) has been shown to protect cardiomyocytes against I/R-induced injury. Here, we show that activation of the YAP/SERCA2a pathway attenuated mitochondrial damage and ER stress (ERS) to maintain cardiomyocyte viability in the setting of I/R injury. Our results demonstrate that I/R treatment reduced the transcription and expression of YAP and SERCA2a, along with a decline in cardiomyocyte viability. The overexpression of YAP promoted SERCA2a transcription, whereas SERCA2a upregulation did not affect the YAP transcription, suggesting that YAP functions upstream of SERCA2a. Activation of the YAP/SERCA2a pathway suppressed mitochondrial damage by sustaining the mitochondrial redox balance and restoring mitochondrial bioenergetics. Additionally, its activation repressed ERS, reduced calcium overload, and eventually blocked caspase activation. The knockdown of SERCA2a suppressed the protective effects of YAP overexpression on mitochondrial damage and ERS. Overall, our findings reveal that the YAP/SERCA2a pathway attenuates the mitochondrial damage and ERS in response to cardiac I/R injury by regulating the mitochondria-ER communication.

[Genetic diversity and genetic structure evaluation of cultivated Chinese wolfberry (Lycium barbarum) based on microsatellite population genetics].

A total of 178 Chinese wolfberry individuals from 17 populations were detected by 7 pairs of SSR primers to evaluate genetic diversity and structure, using software GenALEx 6.5,NTSYS,STRUCTURE, the effects of cultivation on genetic diversity and structure were clarified aiming to find the strategies for genetic management and sustainable use. The results showed that the genetic diversity of cultivated Chinese wolfberry was low. The average number of alleles N_A, expected heterozygosity H_E, observed heterozygosity H_O, and Shannon's information index H' was 3.9, 0.443 7, 0.556 6, 0.788 1, respectively. STRUCTURE, UPGMA clustering and PCA test indicated that Chinese wolfberry varieties were severely intermixed but no differentiation among varieties. Mantel test showed no significant correlation between genetic distance and geographic distance. AMOVA analysis showed that genetic variation mainly occurred among individuals within the population(84.58%, P<0.001), and there was almost no genetic differentiation between varieties(3.63%, P<0.001) and between populations(11.79%, P<0.001). The cultivation has caused a significant decline in the genetic diversity of Chinese wolfberry, which may cause inbreeding decline. New germplasm resources should be sought from the wild to improve the existing cultivars. On the other hand, there are obvious homogenization and germplasm intermixing between cultivated varieties and populations. Meanwhile, Chinese wolfberry cultivars should be purified and prevented from flowing into the wild population, in case of causing pollution of the wild germplasm.

Complete chloroplast genome sequences of Dioscorea: Characterization, genomic resources, and phylogenetic analyses.

Dioscorea L., the largest genus of the family Dioscoreaceae with over 600 species, is not only an important food but also a medicinal plant. The identification and classification of Dioscorea L. is a rather difficult task. In this study, we sequenced five Dioscorea chloroplast genomes, and analyzed with four other chloroplast genomes of Dioscorea species from GenBank. The Dioscorea chloroplast genomes displayed the typical quadripartite structure of angiosperms, which consisted of a pair of inverted repeats separated by a large single-copy region, and a small single-copy region. The location and distribution of repeat sequences and microsatellites were determined, and the rapidly evolving chloroplast genome regions (trnK-trnQ, trnS-trnG, trnC-petN, trnE-trnT, petG-trnW-trnP, ndhF, trnL-rpl32, and ycf1) were detected. Phylogenetic relationships of Dioscorea inferred from chloroplast genomes obtained high support even in shortest internodes. Thus, chloroplast genome sequences provide potential molecular markers and genomic resources for phylogeny and species identification.

Development of Chloroplast Genomic Resources in Chinese Yam (Dioscorea polystachya).

Chinese yam has been used both as a food and in traditional herbal medicine. Developing more effective genetic markers in this species is necessary to assess its genetic diversity and perform cultivar identification. In this study, new chloroplast genomic resources were developed using whole chloroplast genomes from six genotypes originating from different geographical locations. The Dioscorea polystachya chloroplast genome is a circular molecule consisting of two single-copy regions separated by a pair of inverted repeats. Comparative analyses of six D. polystachya chloroplast genomes revealed 141 single nucleotide polymorphisms (SNPs). Seventy simple sequence repeats (SSRs) were found in the six genotypes, including 24 polymorphic SSRs. Forty-three common indels and five small inversions were detected. Phylogenetic analysis based on the complete chloroplast genome provided the best resolution among the genotypes. Our evaluation of chloroplast genome resources among these genotypes led us to consider the complete chloroplast genome sequence of D. polystachya as a source of reliable and valuable molecular markers for revealing biogeographical structure and the extent of genetic variation in wild populations and for identifying different cultivars.

The Chloroplast Genome Sequence of Scutellaria baicalensis Provides Insight into Intraspecific and Interspecific Chloroplast Genome Diversity in Scutellaria.

Scutellaria baicalensis Georgi (Lamiaceae) is the source of the well-known traditional Chinese medicine "HuangQin" (Radix Scutellariae). Natural sources of S. baicalensis are rapidly declining due to high market demand and overexploitation. Moreover, the commercial products of Radix Scutellariae have often been found to contain adulterants in recent years, which may give rise to issues regarding drug efficacy and safety. In this study, we developed valuable chloroplast molecular resources by comparing intraspecific and interspecific chloroplast genome. The S. baicalensis chloroplast genome is a circular molecule consisting of two single-copy regions separated by a pair of inverted repeats. Comparative analyses of three Scutellaria chloroplast genomes revealed six variable regions (trnH-psbA, trnK-rps16, petN-psbM, trnT-trnL, petA-psbJ, and ycf1) that could be used as DNA barcodes. There were 25 single nucleotide polymorphisms(SNPs) and 29 indels between the two S. baicalensis genotypes. All of the indels occurred within non-coding regions. Phylogenetic analysis suggested that Scutellarioideae is a sister taxon to Lamioideae. These resources could be used to explore the variation present in Scutellaria populations and for further evolutionary, phylogenetic, barcoding and genetic engineering studies, in addition to effective exploration and conservation of S. baicalensis.