Association between influenza vaccination and one-year all-cause and cardiovascular mortality risk: A self-controlled case series and matched case-control study.

Debates surrounding the efficacy of influenza vaccination for survival benefits persist, and there is a lack of data regarding its duration of protection. A self-controlled case series (SCCS) and a 1:4 matched case-control study were conducted using the National Health Interview Survey (NHIS) and public-use mortality data from 2005 to 2018 in the United States. The SCCS study identified participants who received influenza vaccination within 12 months before the survey and subsequently died within 1 year of postvaccination. The matched case-control study paired participants who died during the influenza season at the time of survey with four survivors. Among 1167 participants in the SCCS study, there was a 46% reduction in all-cause mortality and a 43% reduction in cardiovascular mortality within 29-196 days of postvaccination. The greatest protection was observed during days 29-56 (all-cause mortality: RI: 0.19; 95% CI: 0.12-0.29; cardiovascular mortality: RI: 0.28; 95% CI: 0.14-0.56). Among 626 cases and 2504 controls included in the matched case-control study, influenza vaccination was associated with a reduction in all-cause mortality (OR: 0.74, 95% CI: 0.60-0.92) and cardiovascular mortality (OR: 0.64, 95% CI: 0.44-0.93) during the influenza season. This study highlights the importance of influenza vaccination in reducing the risks of all-cause and cardiovascular mortality, with effects lasting for approximately 6 months.

Understanding Electrochemical Performance Enhancement with Quaternary NCMA Cathode Materials.

Ni-rich cathode materials show promise for use in lithium-ion batteries. However, a significant obstacle to their widespread adoption is the structural damage caused by microcracks. This research paper presents the synthesis of Ni-rich cathode materials, including LiNi0.8Co0.1Mn0.1O2 (referred to as NCM) and Li(Ni0.8Co0.1Mn0.1)0.98Al0.02O2 (referred to as NCMA), achieved through the high-temperature solid-phase method. Electrochemical (EC) testing results reveal the impressive EC performance of NCMA. NCMA exhibited a discharge capacity of 141.6 mAh g-1 and maintained a cycle retention rate of up to 74.92% after 300 cycles at a 1 C rate. In contrast, the NCM had a discharge capacity of 109.7 mAh g-1 and a cycle retention rate of 61.22%. Atomic force microscopy showed that the Derjaguin-Muller-Toporov (DMT) modulus value of NCMA exceeded that of NCM, signifying a greater mechanical strength of NCMA. Density functional theory calculations demonstrated that the addition of aluminum during the delithiation process led to the mitigation of anisotropic lattice changes and the stabilization of the NCMA structure. This improvement was attributed to the relatively stronger Al-O bonds compared to the Ni(Co, Mn)-O bonds, which reduced the formation of microcracks by enhancing NCMA's mechanical strength.

Improving the Cycle Stability of LiNiO2 through Al3+ Doping and LiAlO2 Coating.

In this study, we addressed the poor cycling and rate performance of LiNiO2, a material with ultrahigh nickel content considered a strong contender for high-energy-density lithium-ion battery cathodes. We introduced nano-Al2O3 during the lithiation process to achieve dual modified material through bulk phase element doping and in situ LiAlO2 coating. Comparison revealed notable improvements in the modified materials. In particular, LiNi0.99Al0.01O2 maintained a capacity retention rate of 73.1% after 300 cycles in a long-cycle test at 0.5C current density, outperforming the undoped material. In rate performance tests, the doped samples consistently exhibited higher discharge-specific capacities than that of the undoped counterpart. Notably, at a high current density of 5C, LiNi0.99Al0.01O2 exhibited a discharge-specific capacity of 101.75 mAh g-1. The results indicate that an appropriate amount of Al doping can effectively stabilize the layered structure of the cathode material and delay the irreversible phase transition from H2 to H3. Further, Al doping facilitates the formation of a LiAlO2 coating on the surface of the particles. This coating acts as a fast-ion conductor, enhancing the transport of lithium ions and reducing the erosion of the active material by the electrolyte.

Ball-Milling-Assisted N/O Codoping for Enhanced Sodium Storage Performance of Coconut-Shell-Derived Hard Carbon Anodes in Sodium-Ion Batteries.

Sodium-ion batteries (SIBs) are regarded as cost-effective alternatives or competitors to lithium-ion batteries for large-scale electric energy storage applications. However, their development has been hindered by the high cost of hard carbon (HC) anodes and poor electrochemical performance. To enhance the sodium storage capacity and rate performance of HC, this study accelerated the electrochemical performance of coconut-shell-derived HC anodes for SIBs through N/O codoping using ball milling and pyrolysis. Experimental results demonstrate that the simultaneous introduction of N and O generates a synergistic effect, increasing the surface oxygen-containing functional groups, defects, and interlayer spacing of coconut-shell-derived HC through the codoping of light elements. The excellent strategy has increased the slope capacity and platform capacity of HC, and the synergistic modification of N/O has increased its reversible specific capacity from 272 to 343 mA h g-1 (30 mA g-1), with a retention rate of approximately 92.1% after 100 cycles. In addition, it also exhibits an excellent rate performance, reaching 178 mA h g-1 at 1500 mA g-1. In summary, this study presents an effective strategy for modifying biomass-derived HC.

Enhanced Cathode Performance: The Heterostructure Construction of LiCoO2@Co3O4@Li6.4La3Zr1.4Ta0.6O12.

In this study, the heterostructure cathode material LiCoO2@Co3O4@Li6.4La3Zr1.4Ta0.6O12 was prepared by coating Li6.4La3Zr1.4Ta0.6O12 on the surface of LiCoO2 through a one-step solid-phase synthesis. The morphology, structure, electrical state, and elemental contents of both pristine and modified materials were assessed through a range of characterization techniques. Theoretical calculations revealed that the LCO@LLZTO material possessed a reduced diffusion barrier compared to LiCoO2, thereby facilitating the movement of Li ions. Electrochemical tests indicated that the capacity retention rate of the modified cathode composites stood at 70.43% following 300 cycles at a 2C rate. This high rate occurred because the Li6.4La3Zr1.4Ta0.6O12 film on the surface enhanced the migration of Li+, and the spinel phase of Co3O4 had better interfacial stability to alleviate the generation of microcracks by inhibiting the phase change from the layered phase to the rock-salt phase, which considerably improved the electrochemical properties.

One-Year Temporal Changes in Long COVID Prevalence and Characteristics: A Systematic Review and Meta-Analysis.

OBJECTIVES: This study aimed to explore the 1-year temporal change in prevalence, variety, and potential risk factors of long COVID symptoms and to further predict the prognostic trends of long COVID. METHODS: We searched electronic databases for related studies published from January 2020 to February 2022 and conducted 1-group meta-analysis and locally weighted regression to explore the monthly temporal change in the prevalence of each long COVID symptom in 1-year follow-up period. RESULTS: A total of 137 studies were included in meta-analysis, including 134 093 participants. The temporal change of any long COVID symptom showed a steep decrease initially (from 92% at acute phase to 55% at 1-month follow-up), followed by stabilization at approximately 50% during 1-year follow-up. Six months or more after the acute phase, the odds ratio of population characteristic-related factors increased, such as female (from 1.62 to 1.82), whereas the odds ratio value of acute phase-related factors (severe or critical cases and hospitalization) decreased. As for specific symptoms, approximately two-thirds of the symptoms did not significantly reduce during the 1-year follow-up, and the neuropsychiatric symptoms showed a higher long-term prevalence (approximately 25%) and longer persistence than physical symptoms. CONCLUSIONS: The temporal changes in the prevalence and characteristics speculate that long COVID may persist longer than expected. In particular, we should pay more attention to neuropsychiatric symptoms and other symptoms for which there is no significant downward trend in prevalence. The influence of acute phase-related factors for long COVID gradually decreases over time, whereas the influence of population characteristic-related factors gradually increases.

Goal-directed fluid therapy using stroke volume variation on length of stay and postoperative gastrointestinal function after major abdominal surgery-a randomized controlled trial.

BACKGROUND AND OBJECTIVE: The effectiveness of goal-directed fluid therapy (GDFT) in promoting postoperative recovery remains unclear, the aim of this study was to evaluate the effect of GDFT on length of hospital stay and postoperative recovery of GI function in patients undergoing major abdominal oncologic surgery. METHODS: In this randomized, double- blinded, controlled trial, adult patients scheduled for elective major abdominal surgery with general anesthesia, were randomly divided into the GDFT protocol (group G) or conventional fluid therapy group (group C). Patients in group C underwent conventional fluid therapy based on mean arterial pressure (MAP) and central venous pressure (CVP) whereas those in group G received GDFT protocol associated with the SVV less than 12% and the cardiac index (CI) was controlled at a minimum of 2.5 L/min/m2. The primary outcomes were the length of hospital stay and postoperative GI function. RESULTS: One hundred patients completed the study protocol. The length of hospital stay was significantly shorter in group G compared with group C [9.0 ± 5.8 days versus 12.0 ± 4.6 days, P = 0.001]. Postoperative gastrointestinal dysfunction (POGD) occurred in two of 50 patients (4%) in group G and 16 of 50 patients (32%) in the control group (P < 0.001). GDFT significantly also shorten time to first flatus by 11 h (P = 0.009) and time to first tolerate oral diet by 2 days (P < 0.001). CONCLUSIONS: Guided by SVV and CI, the application of GDFT has the potential to expedite postoperative recovery of GI function and reduce hospitalization duration after major abdominal surgery. TRIAL REGISTRATION: This study was registered on www. CLINICALTRIALS: gov on 07/05/2019 with registration number: NCT03940144.

Influenza Epidemic Trend Surveillance and Prediction Based on Search Engine Data: Deep Learning Model Study.

BACKGROUND: Influenza outbreaks pose a significant threat to global public health. Traditional surveillance systems and simple algorithms often struggle to predict influenza outbreaks in an accurate and timely manner. Big data and modern technology have offered new modalities for disease surveillance and prediction. Influenza-like illness can serve as a valuable surveillance tool for emerging respiratory infectious diseases like influenza and COVID-19, especially when reported case data may not fully reflect the actual epidemic curve. OBJECTIVE: This study aimed to develop a predictive model for influenza outbreaks by combining Baidu search query data with traditional virological surveillance data. The goal was to improve early detection and preparedness for influenza outbreaks in both northern and southern China, providing evidence for supplementing modern intelligence epidemic surveillance methods. METHODS: We collected virological data from the National Influenza Surveillance Network and Baidu search query data from January 2011 to July 2018, totaling 3,691,865 and 1,563,361 respective samples. Relevant search terms related to influenza were identified and analyzed for their correlation with influenza-positive rates using Pearson correlation analysis. A distributed lag nonlinear model was used to assess the lag correlation of the search terms with influenza activity. Subsequently, a predictive model based on the gated recurrent unit and multiple attention mechanisms was developed to forecast the influenza-positive trend. RESULTS: This study revealed a high correlation between specific Baidu search terms and influenza-positive rates in both northern and southern China, except for 1 term. The search terms were categorized into 4 groups: essential facts on influenza, influenza symptoms, influenza treatment and medicine, and influenza prevention, all of which showed correlation with the influenza-positive rate. The influenza prevention and influenza symptom groups had a lag correlation of 1.4-3.2 and 5.0-8.0 days, respectively. The Baidu search terms could help predict the influenza-positive rate 14-22 days in advance in southern China but interfered with influenza surveillance in northern China. CONCLUSIONS: Complementing traditional disease surveillance systems with information from web-based data sources can aid in detecting warning signs of influenza outbreaks earlier. However, supplementation of modern surveillance with search engine information should be approached cautiously. This approach provides valuable insights for digital epidemiology and has the potential for broader application in respiratory infectious disease surveillance. Further research should explore the optimization and customization of search terms for different regions and languages to improve the accuracy of influenza prediction models.

Detection of the effect of microvibrational stimulation on human discarded immature oocytes by single-cell transcriptome sequencing technology.

OBJECTIVE: This study aimed to investigate the changes in oocytes at the transcriptome level after applying continuous microvibrational mechanical stimulation to human immature oocytes during in vitro maturation. METHODS: The discarded germinal-vesicle stage (GV) oocytes with no fertilization value after oocytes retrieval in assisted reproduction cycles were collected. Part of them was stimulated with vibration (n = 6) at 10 Hz for 24 h after obtaining informed consent; the other was cultured in static condition (n = 6). Single-cell transcriptome sequencing was used to detect the differences in oocyte transcriptome compared with the static culture group. RESULTS: The applied 10-Hz continuous microvibrational stimulation altered the expression of 352 genes compared with the static culture. Gene Ontology (GO) analysis suggested that the altered genes were mainly enriched with 31 biological processes. The mechanical stimulation upregulated 155 of these genes and downregulated 197 genes. Among them, the genes related to mechanical signaling, such as protein localization to intercellular adhesion (DSP and DLG-5) and cytoskeleton (DSP, FGD6, DNAJC7, KRT16, KLHL1, HSPB1, MAP2K6), were detected. DLG-5, which was related to protein localization to intercellular adhesion, was selected for immunofluorescence experiments based on the transcriptome sequencing results. The protein expression of DLG-5 in the microvibration-stimulated oocytes was higher than that in the static culture oocytes. CONCLUSIONS: Mechanical stimulation affects the transcriptome during oocyte maturation, causing the express changes in intercellular adhesion and cytoskeleton-related genes. We speculate that the mechanical signal may be transmitted to the cell through DLG-5 protein and cytoskeleton-related protein to regulate cellular activities.

Population Genomic Analyses Suggest a Hybrid Origin, Cryptic Sexuality, and Decay of Genes Regulating Seed Development for the Putatively Strictly Asexual Kingdonia uniflora (Circaeasteraceae, Ranunculales).

Asexual lineages are perceived to be short-lived on evolutionary timescales. Hence, reports for exceptional cases of putative 'ancient asexuals' usually raise questions about the persistence of such species. So far, there have been few studies to solve the mystery in plants. The monotypic Kingdonia dating to the early Eocene, contains only K. uniflora that has no known definitive evidence for sexual reproduction nor records for having congeneric sexual species, raising the possibility that the species has persisted under strict asexuality for a long period of time. Here, we analyze whole genome polymorphism and divergence in K. uniflora. Our results show that K. uniflora is characterized by high allelic heterozygosity and elevated πN/πS ratio, in line with theoretical expectations under asexual evolution. Allele frequency spectrum analysis reveals the origin of asexuality in K. uniflora occurred prior to lineage differentiation of the species. Although divergence within K. uniflora individuals exceeds that between populations, the topologies of the two haplotype trees, however, fail to match each other, indicating long-term asexuality is unlikely to account for the high allele divergence and K. uniflora may have a recent hybrid origin. Phi-test shows a statistical probability of recombination for the conflicting phylogenetic signals revealed by the split network, suggesting K. uniflora engages in undetected sexual reproduction. Detection of elevated genetic differentiation and premature stop codons (in some populations) in genes regulating seed development indicates mutational degradation of sexuality-specific genes in K. uniflora. This study unfolds the origin and persistence mechanism of a plant lineage that has been known to reproduce asexually and presents the genomic consequences of lack of sexuality.

Genomic convergence underlying high-altitude adaptation in alpine plants.

Evolutionary convergence is one of the most striking examples of adaptation driven by natural selection. However, genomic evidence for convergent adaptation to extreme environments remains scarce. Here, we assembled reference genomes of two alpine plants, Saussurea obvallata (Asteraceae) and Rheum alexandrae (Polygonaceae), with 37,938 and 61,463 annotated protein-coding genes. By integrating an additional five alpine genomes, we elucidated genomic convergence underlying high-altitude adaptation in alpine plants. Our results detected convergent contractions of disease-resistance genes in alpine genomes, which might be an energy-saving strategy for surviving in hostile environments with only a few pathogens present. We identified signatures of positive selection on a set of genes involved in reproduction and respiration (e.g., MMD1, NBS1, and HPR), and revealed signatures of molecular convergence on genes involved in self-incompatibility, cell wall modification, DNA repair and stress resistance, which may underlie adaptation to extreme cold, high ultraviolet radiation and hypoxia environments. Incorporating transcriptomic data, we further demonstrated that genes associated with cuticular wax and flavonoid biosynthetic pathways exhibit higher expression levels in leafy bracts, shedding light on the genetic mechanisms of the adaptive "greenhouse" morphology. Our integrative data provide novel insights into convergent evolution at a high-taxonomic level, aiding in a deep understanding of genetic adaptation to complex environments.

Exploring meteorological impacts based on Köppen-Geiger climate classification after reviewing China's response to COVID-19.

More than 30 months into the novel coronavirus 2019 (COVID-19) pandemic, efforts to bring this prevalence under control have achieved tentative achievements in China. However, the continuing increase in confirmed cases worldwide and the novel variants imply a severe risk of imported viruses. High-intensity non-pharmaceutical interventions (NPIs) are the mainly used measures of China's early response to COVID-19, which enabled effective control in the first wave of the epidemic. However, their efficiency is relatively low across China at the current stage. Therefore, this study focuses on whether measurable meteorological variables be found through global data to learn more about COVID-19 and explore flexible controls. This study first examines the control measures, such as NPIs and vaccination, on COVID-19 transmission across 189 countries, especially in China. Subsequently, we estimate the association between meteorological factors and time-varying reproduction numbers based on the global data by meta-population epidemic model, eliminating the aforementioned anthropogenic factors. According to this study, we find that the basic reproduction number of COVID-19 transmission varied wildly among Köppen-Geiger climate classifications, which is of great significance for the flexible adjustment of China's control protocols. We obtain that in southeast China, Köppen-Geiger climate sub-classifications, Cwb, Cfa, and Cfb, are more likely to spread COVID-19. In August, the RSIM of Cwb climate subclassification is about three times that of Dwc in April, which implies that the intensity of control efforts in different sub-regions may differ three times under the same imported risk. However, BSk and BWk, the most widely distributed in northwest China, have smaller basic reproduction numbers than Cfa, distributed in southeast coastal areas. It indicates that northwest China's control intensity could be appropriately weaker than southeast China under the same prevention objectives.

OFDM Network Optimization Using a QPSK Based on a Wind-Driven Genetic Algorithm.

Quadrature phase shift keying (QPSK) is a digital modulation technique that transmits data at a constant frequency whilst varying the phases of the carrier signal. QPSK is one of the fundamental modulation schemes for orthogonal frequency division multiplexing systems (OFDM). It is a stable modulation technique with good spectral efficiency. However, during transmission, the carrier signal can undergo numerous phase changes. This creates phase ambiguity problems at the receiver end. This results in inter-symbol interference (ISI) and a high bit error rate (BER). In this paper, the wind-driven optimization was incorporated into the genetic algorithm (GA) as its population selection function. This hybrid algorithm was used to determine the phase assignments for the QPSK. The developed QPSK was implemented on an OFDM network and the message signal was recovered at more than 92% accuracy in a noisy Rayleigh fading channel and 100% accuracy in a noiseless channel. The enhancements greatly mitigated phase ambiguity and bit errors.

Macroevolutionary pattern of Saussurea (Asteraceae) provides insights into the drivers of radiating diversification.

Evolutionary radiations have intrigued biologists for more than a century, yet our understanding of the drivers of radiating diversification is still limited. We investigate the roles of environmental and species-intrinsic factors in driving the rapid radiation of Saussurea (Asteraceae) by deploying a number of palaeoenvironment-, diversity- and trait-dependent models, as well as ecological distribution data. We show that three main clades of Saussurea began to diversify in the Miocene almost simultaneously, with increasing diversification rates (DRs) negatively dependent on palaeotemperature but not dependent on species diversity. Our trait-dependent models detect some adaptive morphological innovations associated with DR shifts, while indicating additional unobserved traits are also likely driving diversification. Accounting for ecological niche data, we further reveal that accelerations in DRs are correlated with niche breadth and the size of species' range. Our results point out a macroevolutionary scenario where both adaptive morphological evolution and ecological opportunities provided by palaeoenvironmental fluctuations triggered an exceptionally radiating diversification. Our study highlights the importance of integrating phylogenomic, morphological, ecological and model-based approaches to illustrate evolutionary dynamics of lineages in biodiversity hotspots.

Plastome phylogenomic study of Gentianeae (Gentianaceae): widespread gene tree discordance and its association with evolutionary rate heterogeneity of plastid genes.

BACKGROUND: Plastome-scale data have been prevalent in reconstructing the plant Tree of Life. However, phylogenomic studies currently based on plastomes rely primarily on maximum likelihood inference of concatenated alignments of plastid genes, and thus phylogenetic discordance produced by individual plastid genes has generally been ignored. Moreover, structural and functional characteristics of plastomes indicate that plastid genes may not evolve as a single locus and are experiencing different evolutionary forces, yet the genetic characteristics of plastid genes within a lineage remain poorly studied. RESULTS: We sequenced and annotated 10 plastome sequences of Gentianeae. Phylogenomic analyses yielded robust relationships among genera within Gentianeae. We detected great variation of gene tree topologies and revealed that more than half of the genes, including one (atpB) of the three widely used plastid markers (rbcL, atpB and matK) in phylogenetic inference of Gentianeae, are likely contributing to phylogenetic ambiguity of Gentianeae. Estimation of nucleotide substitution rates showed extensive rate heterogeneity among different plastid genes and among different functional groups of genes. Comparative analysis suggested that the ribosomal protein (RPL and RPS) genes and the RNA polymerase (RPO) genes have higher substitution rates and genetic variations among plastid genes in Gentianeae. Our study revealed that just one (matK) of the three (matK, ndhB and rbcL) widely used markers show high phylogenetic informativeness (PI) value. Due to the high PI and lowest gene-tree discordance, rpoC2 is advocated as a promising plastid DNA barcode for taxonomic studies of Gentianeae. Furthermore, our analyses revealed a positive correlation of evolutionary rates with genetic variation of plastid genes, but a negative correlation with gene-tree discordance under purifying selection. CONCLUSIONS: Overall, our results demonstrate the heterogeneity of nucleotide substitution rates and genetic characteristics among plastid genes providing new insights into plastome evolution, while highlighting the necessity of considering gene-tree discordance into phylogenomic studies based on plastome-scale data.

Genomic insights into adaptation to heterogeneous environments for the ancient relictual Circaeaster agrestis (Circaeasteraceae, Ranunculales).

Investigating the interaction between environmental heterogeneity and local adaptation is critical for understanding the evolutionary history of a species, providing the premise for studying the response of organisms to rapid climate change. However, for most species how exactly the spatial heterogeneity promotes population divergence and how genomic variations contribute to adaptive evolution remain poorly understood. We examine the contributions of geographical and environmental variables to population divergence of the relictual, alpine herb Circaeaster agrestis, as well as the genetic basis of local adaptation using RAD-seq and plastome data. We detected significant genetic structure with an extraordinary disequilibrium of genetic diversity among regions, and signals of isolation-by-distance along with isolation-by-resistance. The populations were estimated to begin diverging in the late Miocene, along with a possible ancestral distribution of the Hengduan Mountains and adjacent regions. Both environmental gradient and redundancy analyses revealed significant association between genetic variation and temperature variables. Genome-environment association analyses identified 16 putatively adaptive loci related mainly to biotic and abiotic stress resistance. Our genome-wide data provide new insights into the important role of environmental heterogeneity in shaping genetic structure, and access the footprints of local adaptation in an ancient relictual species, informing future conservation efforts.

Investigation into the underlying regulatory mechanisms shaping inflorescence architecture in Chenopodium quinoa.

BACKGROUND: Inflorescence architecture is denoted by the spatial arrangement of various lateral branches and florets formed on them, which is shaped by a complex of regulators. Unveiling of the regulatory mechanisms underlying inflorescence architecture is pivotal for improving crop yield potential. Quinoa (Chenopodium quinoa Willd), a pseudo cereal originated from Andean region of South America, has been widely recognized as a functional super food due to its excellent nutritional elements. Increasing worldwide consumption of this crop urgently calls for its yield improvement. However, dissection of the regulatory networks underlying quinoa inflorescence patterning is lacking. RESULTS: In this study, we performed RNA-seq analysis on quinoa inflorescence samples collected from six developmental stages, yielding a total of 138.8 GB data. We screened 21,610 differentially expressed genes (DEGs) among all the stages through comparative analysis. Weighted Gene Co-Expression Network Analysis (WGCNA) was performed to categorize the DEGs into ten different modules. Subsequently, we placed emphasis on investigating the modules associated with none branched and branched inflorescence samples. We manually refined the coexpression networks with stringent edge weight cutoffs, and generated core networks using transcription factors and key inflorescence architecture related genes as seed nodes. The core networks were visualized and analyzed by Cytoscape to obtain hub genes in each network. Our finding indicates that the specific occurrence of B3, TALE, WOX, LSH, LFY, GRAS, bHLH, EIL, DOF, G2-like and YABBY family members in early reproductive stage modules, and of TFL, ERF, bZIP, HD-ZIP, C2H2, LBD, NAC, C3H, Nin-like and FAR1 family members in late reproductive stage modules, as well as the several different MADS subfamily members identified in both stages may account for shaping quinoa inflorescence architecture. CONCLUSION: In this study we carried out comparative transcriptome analysis of six different stages quinoa inflorescences, and using WGCNA we obtained the most highly potential central hubs for shaping inflorescence. The data obtained from this study will enhance our understanding of the gene network regulating quinoa inflorescence architecture, as well will supply with valuable genetic resources for high-yield elite breeding in the future.

Plastome phylogenomics of Saussurea (Asteraceae: Cardueae).

BACKGROUND: Saussurea DC. is one of the largest and most morphologically heterogeneous genera in Asteraceae. The relationships within Saussurea have been poorly resolved, probably due an early, rapid radiation. To examine plastome evolution and resolve backbone relationships within Saussurea, we sequenced the complete plastomes of 17 species representing all four subgenera. RESULTS: All Saussurea plastomes shared the gene content and structure of most Asteraceae plastomes. Molecular evolutionary analysis showed most of the plastid protein-coding genes have been under purifying selection. Phylogenomic analyses of 20 Saussurea plastomes that alternatively included nucleotide or amino acid sequences of all protein-coding genes, vs. the nucleotide sequence of the entire plastome, supported the monophyly of Saussurea and identified three clades within it. Three of the four traditional subgenera were recovered as paraphyletic. Seven plastome regions were identified as containing the highest nucleotide variability. CONCLUSIONS: Our analyses reveal both the structural conservatism and power of the plastome for resolving relationships in congeneric taxa. It is very likely that differences in topology among data sets is due primarily to differences in numbers of parsimony-informative characters. Our study demonstrates that the current taxonomy of Saussurea is likely based at least partly on convergent morphological character states. Greater taxon sampling will be necessary to explore character evolution and biogeography in the genus. Our results here provide helpful insight into which loci will provide the most phylogenetic signal in Saussurea and Cardueae.

Plastome phylogenomics of the early-diverging eudicot family Berberidaceae.

The relationships among the genera of the early-diverging eudicot family Berberidaceae have long been controversial. To resolve these relationships and to better understand plastome evolution within the family, we sequenced the complete plastome sequences of ten Berberidaceae genera, combined these with six existing plastomes for the family, and conducted a series of phylogenomic analyses on the resulting data set. Five of the newly sequenced plastomes were found to possess the typical angiosperm plastome complement of 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. The infA gene was found to be pseudogenized in Bongardia, Diphylleia, Dysosma and Vancouveria; rps7 was found to be severely truncated in Diphylleia, Dysosma and Podophyllum; clpP was found to be highly divergent in Vancouveria; and a ∼19 kb inversion was detected in Bongardia. Maximum likelihood phylogenetic analyses of a 79-gene, 24-taxon data set including nearly all genera of Berberidaceae recovered four chromosome groups (x = 6, 7, 8, 10), resolved the x = 8 group as the sister to the x = 10 group, and supported the monophyly of the clade comprising x = 7, 8, 10. The generic relationships within each group were all resolved with high support. Based on gene presence within the Inverted Repeat (IR), a total of seven plastome IR types were identified within Berberidaceae. Biogeographical analysis indicated the origin and diversification of Berberidaceae has likely been strongly influenced by the distribution of its favored habitat: temperate forests.

Complete plastome sequencing of both living species of Circaeasteraceae (Ranunculales) reveals unusual rearrangements and the loss of the ndh gene family.

BACKGROUND: Among the 13 families of early-diverging eudicots, only Circaeasteraceae (Ranunculales), which consists of the two monotypic genera Circaeaster and Kingdonia, lacks a published complete plastome sequence. In addition, the phylogenetic position of Circaeasteraceae as sister to Lardizabalaceae has only been weakly or moderately supported in previous studies using smaller data sets. Moreover, previous plastome studies have documented a number of novel structural rearrangements among early-divergent eudicots. Hence it is important to sequence plastomes from Circaeasteraceae to better understand plastome evolution in early-diverging eudicots and to further investigate the phylogenetic position of Circaeasteraceae. RESULTS: Using an Illumina HiSeq 2000, complete plastomes were sequenced from both living members of Circaeasteraceae: Circaeaster agrestis and Kingdonia uniflora . Plastome structure and gene content were compared between these two plastomes, and with those of other early-diverging eudicot plastomes. Phylogenetic analysis of a 79-gene, 99-taxon data set including exemplars of all families of early-diverging eudicots was conducted to resolve the phylogenetic position of Circaeasteraceae. Both plastomes possess the typical quadripartite structure of land plant plastomes. However, a large ~49 kb inversion and a small ~3.5 kb inversion were found in the large single-copy regions of both plastomes, while Circaeaster possesses a number of other rearrangements, particularly in the Inverted Repeat. In addition, infA was found to be a pseudogene and accD was found to be absent within Circaeaster, whereas all ndh genes, except for ndhE and ndhJ, were found to be either pseudogenized (ΨndhA, ΨndhB, ΨndhD, ΨndhH and ΨndhK) or absent (ndhC, ndhF, ndhI and ndhG) in Kingdonia. Circaeasteraceae was strongly supported as sister to Lardizabalaceae in phylogenetic analyses. CONCLUSION: The first plastome sequencing of Circaeasteraceae resulted in the discovery of several unusual rearrangements and the loss of ndh genes, and confirms the sister relationship between Circaeasteraceae and Lardizabalaceae. This research provides new insight to characterize plastome structural evolution in early-diverging eudicots and to better understand relationships within Ranunculales .