26 results on '"Xie, Dengfeng"'
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2. Molecular evolution and phylogenetic relationships of Ligusticum (Apiaceae) inferred from the whole plastome sequences
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Ren, Ting, Xie, Dengfeng, Peng, Chang, Gui, Lingjian, Price, Megan, Zhou, Songdong, and He, Xingjin
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- 2022
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3. Effects of Undergraduates' Academic Self-Efficacy on Their Academic Help-Seeking Behaviors: The Mediating Effect of Professional Commitment and the Moderating Effect of Gender
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Xie, Dengfeng and Xie, Zhangming
- Abstract
When learners perceive they cannot master what they are trying to learn, they should seek assistance from others who can help them; however, an increasing number of undergraduates are unable to seek help effectively (Kun, Jyh, & Chin, 2013). Self-efficacy has a significant influence on whether individuals are able to deal with a difficult situation. For example, learners with high self-efficacy know whom to ask for help to attain better academic performance (Meera & Dustin, 2013). Professional commitment, which refers to one's attitude towards one's profession (Lian, Yang, & Wu, 2005), is an important determinant of whether or not students actively learn. It acts as a positive emotion and attitude that has a significant correlation with academic self-efficacy (Meera & Dustin, 2013). Gender also has a significant influence on academic self-efficacy and help-seeking (Drago, Rheinheimer, & Detweiler, 2018). The theory of gender roles proposes that female social behavior is based on interpersonal relationships, and thus, it is plausible to assume that the association between academic self-efficacy and help-seeking may be stronger among women than men (Addis & Mahalik, 2003); however, there is a gap in the research literature about the moderating role of gender on their association. As a result, the authors expected gender to play a moderating role in the association between academic self-efficacy and academic help-seeking. Five hundred fifty-nine university students in China responded to the survey used in this study. The participants completed a battery of scales, including an 8-item Academic Self-efficacy Survey. As predicted, executive help-seeking and avoidance of help-seeking were negatively correlated with academic self-efficacy and professional commitment, whereas instrumental help-seeking was positively correlated with both of these variables; however, gender was not significantly correlated with any of the other variables, so it was not implicated in the links among them.
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- 2019
4. Generation and delivery of “Yamanaka factor” recombinant proteins mediated with magnetic iron oxide nanoparticles (MIONPs)
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Xiao, Xiong, Zhang, Dapeng, Wang, Mingyu, Ling, Wenhui, Xiong, Chunxia, Xie, Dengfeng, Chu, Xinyue, Li, Yunxin, Huang, Yun, Li, Tong, Li, Yuemin, and Qiu, Xiaoyan
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- 2020
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5. Seismic Performance Experiment Involving One-Story, Two-Bay Self-control Energy Dissipation UPPC Frames under Low Cyclic Loads
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Qian, Cheng, Li, Yanhe, Xie, Dengfeng, Li, Ning, and Wen, Xiaoying
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- 2019
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6. Synthesis, surface modification, and applications of magnetic iron oxide nanoparticles
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Ling, Wenhui, Wang, Mingyu, Xiong, Chunxia, Xie, Dengfeng, Chen, Qiyu, Chu, Xinyue, Qiu, Xiaoyan, Li, Yuemin, and Xiao, Xiong
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- 2019
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7. Delivery of plasmid DNA encoding Oct 4 with polyethylenimine-modified superparamagnetic iron oxide nanoparticles in HEK-293T cells
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Xiao, Xiong, Li, Nan, Wang, Mingyu, Xiong, Chunxia, Xie, Dengfeng, Chu, Xinyue, Li, Yunxin, Huang, Yun, Ling, Wenhui, Li, Yuemin, and Qiu, Xiaoyan
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- 2020
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8. Emotion experience and regulation in undergraduates following social rejection: A daily diary study.
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Xie, Dengfeng, Lu, Jiamei, and Xie, Zhangming
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EMOTION regulation , *DIARY (Literary form) , *EMOTIONAL experience , *SOCIAL acceptance , *REJECTION (Psychology) , *UNDERGRADUATES - Abstract
We used a 30-day daily diary assessment method to examine the within-person associations between social rejection, emotional experiences, and emotion regulation strategies in a sample of 34 college students. Taking emotional experience as the dependent variable, we explored and analyzed cumulative and hysteresis effects using a random regression coefficient model. The results showed that situations of social rejection tended to induce negative emotional experiences, for which college students mostly adopted attention transfer strategies. In contrast, positive emotional experience increased in situations of social acceptance, and college students mostly adopted cognitive reappraisal strategies in this setting. Further, cognitive reappraisal strategies had time accumulation and overlapping effects on individual positive emotional experiences, and attention transfer strategies had a lag effect on individual emotional experiences. These findings advance understanding of the negative affect–emotion regulation association among individuals exposed to social rejection. [ABSTRACT FROM AUTHOR]
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- 2023
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9. Effects of undergraduates' conscientiousness on their cyber aggression: The roles of online moral anger and gender.
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Xie, Dengfeng and Xie, Zhangming
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AGGRESSION (Psychology) , *CONSCIENTIOUSNESS , *ANGER , *GENDER , *UNDERGRADUATES - Abstract
Although, in theory, the conscientiousness of college students should reduce their aggressive behavior, the basic process underlying this relationship remains unknown. This study investigated the relationship between the conscientiousness of college students and their cyber aggression, the mediating effect of online moral anger, and the moderating effect of gender. Participants were 92 college students, who completed a survey questionnaire about their conscientiousness, cyber aggression, and online moral anger. The results showed that conscientiousness negatively predicted the cyber aggression of college students. Further, online moral anger partially mediated the link between conscientiousness and cyber aggression, and the mediating effect of conscientiousness on cyber aggression was moderated by gender, with the effect only observed in male students. The results indicate that the conscientiousness of college students can reduce cyber aggression, and male college students can reduce cyber aggression through appropriately displaying enhanced moral anger. [ABSTRACT FROM AUTHOR]
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- 2023
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10. Plastid Phylogenomic Analyses Reveal the Taxonomic Position of Peucedanum franchetii.
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Song, Boni, Liu, Changkun, Xie, Dengfeng, Xiao, Yulin, Tian, Rongming, Li, Zixuan, Zhou, Songdong, and He, Xingjin
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RNA editing ,MICROSATELLITE repeats ,MEDICINAL plants - Abstract
Peucedanum franchetii is a famous folk medicinal plant in China. However, the taxonomy of the P. franchetii has not been sufficiently resolved. Due to similar morphological features between P. franchetii and Ligusticopsis members, the World Flora Online (WFO) Plant List suggested that this species transformed into the genus Ligusticopsis and merged with Ligusticopsis likiangensis. However, both species are obviously diverse in leaf shape, bracts, and bracteoles. To check the taxonomic position of P. franchetii, we newly sequenced and assembled the plastome of P. franchetii and compared it with nine other plastomes of the genus Ligusticopsis. Ten plastomes were highly conserved and similar in gene order, codon bias, RNA editing sites, IR borders, and SSRs. Nevertheless, 10 mutation hotspot regions (infA, rps8, matK, ndhF, rps15, psbA-trnH, rps2-rpoC2, psbA-trnK, ycf2-trnL, and ccsA-ndhD) were still detected. In addition, both phylogenetic analyses based on plastome data and ITS sequences robustly supported that P. franchetii was not clustered with members of Peucedanum but nested in Ligusticopsis. P. franchetii was sister to L. likiangensis in the ITS topology but clustered with L. capillacea in the plastome tree. These findings implied that P. franchetii should be transferred to genus Ligusticopsis and not merged with L. likiangensis, but as an independent species, which was further verified by morphological evidences. Therefore, transferring P. franchetii under the genus Ligusticopsis as an independent species was reasonable, and a new combination was presented. [ABSTRACT FROM AUTHOR]
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- 2023
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11. Comparative Analysis of the Complete Chloroplast Genomes in Allium Section Bromatorrhiza Species (Amaryllidaceae): Phylogenetic Relationship and Adaptive Evolution.
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Chen, Junpei, Xie, Dengfeng, He, Xingjin, Yang, Yi, and Li, Xufeng
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CHLOROPLAST DNA , *ALLIUM , *AMARYLLIDACEAE , *SPECIES , *HYPERVARIABLE regions , *RNA editing - Abstract
With the development of molecular sequencing approaches, many taxonomic and phylogenetic problems of the genus Allium L. have been solved; however, the phylogenetic relationships of some subgenera or sections, such as section Bromatorrhiza, remain unresolved, which has greatly impeded our full understanding of the species relationships among the major clades of Allium. In this study, the complete chloroplast (cp) genomes of nine species in the Allium sect. Bromatorrhiza were determined using the Illumina paired-end sequencing, the NOVOPlasty de novo assembly strategy, and the PGA annotation method. The results showed that the cp genome exhibited high conservation and revealed a typical circular tetrad structure. Among the sect. Bromatorrhiza species, the gene content, SSRs, codon usage, and RNA editing site were similar. The genome structure and IR regions' fluctuation were investigated while genes, CDSs, and non-coding regions were extracted for phylogeny reconstruction. Evolutionary rates (Ka/Ks values) were calculated, and positive selection analysis was further performed using the branch-site model. Five hypervariable regions were identified as candidate molecular markers for species authentication. A clear relationship among the sect. Bromatorrhiza species were detected based on concatenated genes and CDSs, respectively, which suggested that sect. Bromatorrhiza is monophyly. In addition, there were three genes with higher Ka/Ks values (rps2, ycf1, and ycf2), and four genes (rpoC2, atpF, atpI, and rpl14) were further revealed to own positive selected sites. These results provide new insights into the plastome component, phylogeny, and evolution of Allium species. [ABSTRACT FROM AUTHOR]
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- 2022
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12. Simulation and Analysis of Bistatic Radar Scattering From Oil-Covered Sea Surface.
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Meng, Tingyu, Chen, Kun-Shan, Yang, Xiaofeng, Nunziata, Ferdinando, Xie, Dengfeng, and Buono, Andrea
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BISTATIC radar ,MARINE pollution ,OIL spills ,WIND speed ,SURFACE scattering ,INTEGRAL equations - Abstract
In this study, the bistatic radar scattering coefficients related to an oil-covered sea surface are predicted by modeling both the oil damping effect on surface roughness–through the advanced integral equation method–and the oil modification on the dielectric properties of the scattering surface. The bistatic scattering is analyzed in the whole upper scattering space under different radar frequencies, incidence angles, wind speeds, and oil thicknesses. Numerical predictions show that the scattering energy of an oil-covered sea surface is generally higher in the forward scattering zone than that in the backward one. In addition, the oil damping effect is the main mechanism ruling the scattering behavior in the backward region. The information related to the bistatic scattering geometry is also explored to retrieve oil thickness, representing one of the key parameters for radar-based marine oil pollution observation. A new index is proposed to quantify the sensitivity of bistatic scattering coefficients to oil thickness in different cases: single-polarization features, dual co-polarization features, namely, the polarization ratio (PR) and the normalized polarization difference index (NPDI), and dual-angular scattering features. Numerical results show that the bistatic scattering coefficients result in an enhanced sensitivity to oil thickness with respect to the monostatic case. The single HH-polarized scattering coefficients show better oil thickness sensitivity in the backward region, while the VV-polarized ones are more sensitive to oil thickness in the forward region. The combination of dual-polarized scattering coefficients significantly improves the oil thickness sensitivity compared to single-polarization radar observations, especially in the forward region. PR outperforms NPDI, even though the latter can suppress the effect of wind speed. The combination of dual-angular observations can significantly increase its sensitivity of oil thickness in the backward region but at the expense of reduced sensitivity in the forward region. [ABSTRACT FROM AUTHOR]
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- 2022
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13. Advances in Isolation and Culture of Chicken Embryonic Stem Cells In Vitro.
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Xiong, Chunxia, Wang, Mingyu, Ling, Wenhui, Xie, Dengfeng, Chu, Xinyue, Li, Yunxin, Huang, Yun, Li, Tong, Otieno, Edward, Qiu, Xiaoyan, and Xiao, Xiong
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EMBRYONIC stem cells ,LEUKEMIA inhibitory factor ,BONE morphogenetic proteins ,CHICKENS ,GERMPLASM ,TRANSFORMING growth factors-beta - Abstract
Chicken embryonic stem cells (cESCs) isolated from the egg at the stage X hold great promise for cell therapy, tissue engineering, pharmaceutical, and biotechnological applications. They are considered to be pluripotent cells with the capacity to self-renewal and differentiate into specialized cells. However, long-term maintenance of cESCs cannot be realized now, which impedes the establishment of cESC line and limits their applications. Therefore, the separation locations, isolation methods, and culture conditions especially the supplements and action mechanisms of cytokines, including leukemia inhibitory factor, fibroblast growth factor, transforming growth factor beta, bone morphogenic protein, and activin for cESCs in vitro, have been reviewed here. These defined strategies will contribute to identify the key mechanism on the self-renewal of cESCs, facilitate to optimize system that supports the derivation and longtime maintenance of cESCs, establish the cESC line, and develop the biobank of genetic resources in chicken. [ABSTRACT FROM AUTHOR]
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- 2020
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14. Effect of Bispectrum on Radar Backscattering From Non-Gaussian Sea Surface.
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Xie, Dengfeng, Chen, Kun-Shan, and Yang, Xiaofeng
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The upwind–downwind asymmetry in normalized radar backscattering cross section (NRBCS) from ocean surface is well known; one acceptable and convincing reasoning is explained by the fact that the surface height distribution deviates from Gaussian one, which causes a nonzero skewness function, and consequently affects the radar cross section in up and down wind directions. Specific forms of skewness function, in between Gaussian and exponential, have been proposed in previous studies to account for the upwind/downwind asymmetry in radar backscatter. Attempt is made, through numerical simulation, in this article to examine the impact of these two types of skewness functions on NRBCS. The simulated NBRCSs, with and without skewness contributions, are compared with measured data in upwind and downwind directions at L-, C-, and Ku-bands for different wind speeds. The results indicate that the Gaussian-type skewness function works better to account for the upwind/downwind asymmetry of NBRCS by choosing an appropriate root mean square (RMS) height appearing in skewness function and as the wind speed or radar frequency increases, the RMS height increases but regardless of wind direction and radar incidence angle. [ABSTRACT FROM AUTHOR]
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- 2019
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15. Effects of Wind Wave Spectra on Radar Backscatter From Sea Surface at Different Microwave Bands: A Numerical Study.
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Xie, Dengfeng, Chen, Kun-Shan, and Yang, Xiaofeng
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RADAR cross sections , *WIND waves , *RADAR , *MICROWAVE remote sensing , *WIND speed , *ELECTROMAGNETIC wave scattering - Abstract
Wind wave spectrum describes the quasi-periodic nature of the ocean surface oscillations and plays an indispensable role in the study of microwave electromagnetic scattering from sea surface. A reliable spectrum model suitable for radar cross section (RCS) predictions at different radar frequencies is desired. This paper evaluated the performances of five common spectrum models (i.e., Fung spectrum, Durden–Vesecky spectrum, Apel spectrum, Elfouhaily spectrum, and the newest version of Hwang spectrum, H18) on the normalized radar backscattering cross section (NRBCS) simulations based on advanced integral equation model (AIEM) at L-, C-, X-, and Ku-bands versus incidence angle, wind direction, and wind speed by comparing with the model and measured data for validation. These results indicate no single wave spectrum of them is satisfying for all the four radar frequencies, e.g., Apel and H18 spectra are better for L- and C-bands, Apel spectrum for X-band, and Elfouhaily and H18 spectra for Ku-band. Given this, three average composite spectrum models are constructed using different spectral models (i.e., all five spectra, Apel + Elfouhaily + H18, and Apel + H18) to simulate NRBCSs, similar to that of the individual spectrum model. It is concluded that the combination of Apel and H18 spectra overall performs best among the individual one and other composited spectra in like-polarized NRBCSs versus incidence angles, wind directions, and wind speeds, for wind speed greater than 30 m/s where the combination of the five spectra work well at Ku-band. [ABSTRACT FROM AUTHOR]
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- 2019
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16. Potential Strategies for Cardiac Diseases: Lineage Reprogramming of Somatic Cells into Induced Cardiomyocytes.
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Wang, Mingyu, Ling, Wenhui, Xiong, Chunxia, Xie, Dengfeng, Chu, Xinyue, Li, Yunxin, Qiu, Xiaoyan, Li, Yuemin, and Xiao, Xiong
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PLURIPOTENT stem cells ,SOMATIC cells ,INDUCED pluripotent stem cells ,HEART diseases ,SMALL molecules - Abstract
Lineage reprogramming has become a potential strategy for therapy of cardiac diseases. Somatic cells can be directly converted into the induced cardiomyocytes (iCMs) without passing through an induced pluripotent stem cell stage; this strategy has some advantages such as directional differentiation and preferable security. However, there are still many challenges which need to be further studied, such as identification of safer induced factors, exploration of molecular mechanisms, improvement of the mature level of iCMs and so on. Therefore, the structures of key factors, including transcription factors, microRNAs (miRNAs), epigenetic regulators and small molecules and their functions in the cardiac development and lineage reprogramming, molecular mechanisms underlying lineage conversion, strategies for generating matured iCMs, and major challenges were reviewed to lay the foundation for further applications of iCMs. [ABSTRACT FROM AUTHOR]
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- 2019
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17. A Phytogeographic Divide Along the 500 mm Isohyet in the Qinghai-Tibet Plateau: Insights From the Phylogeographic Evidence of Chinese Allium s (Amaryllidaceae).
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Li, MinJie, Xie, DengFeng, Xie, Chuan, Deng, YiQi, Zhong, Yan, Yu, Yan, and He, XingJin
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ALLIUM ,AMARYLLIDACEAE ,PHYTOGEOGRAPHY ,ECOLOGICAL niche ,CHLOROPLAST DNA ,PLANT genetics ,VICARIANCE - Abstract
The Qinghai-Tibet Plateau (QTP) has been biogeographically divided into the eastern monsoonal and the western continental climatic zones along the 500 mm isohyet. However, this biogeographic hypothesis has been rarely tested using a phylogeographic approach. The members of the genus Allium subgenus Cyathophora coincidentally distribute across this biogeographical divide. Intriguingly, Allium fasciculatum of subgenus Amerallium co-occurs in the distribution range of subgenus Cyathophora. To illuminate the role of this biogeographic divide on the genetic divergence, we genotyped 466 individuals of 52 populations of subgenus Cyathophora and 110 individuals of 19 populations of A. fasciculatum using three chloroplast DNA fragments, whole nrITS and nine nuclear microsatellite loci, supplemented with the present environmental space and paleo-distribution modeling. Our phylogeographical evidence recovered the concordant east–west genetic breaks both for subgenus Cyathophora and A. fasciculatum along the 500 mm isohyet. The divergence time estimations and environmental niche differentiations suggested this east–west genetic breaks could have been triggered by the climatic-induced vicariance during the early Pleistocene. Noticeably, this split within subgenus Cyathophora could have been deepened by the morphological vicariance from the eastern umbel to the western spicate, while that within A. fasciculatum could have been obscured due to the pollen flows from the east to west caused by the postglacial expansion. The genetic structures and ecological niche modelings (ENMs) recovered the distinct responses to the Quaternary climatic oscillations for species constricted to different climatic zones, further highlighting the profound effect of the climatic differences and tectonic uplifts on the genetic diversification. Overall, our findings offer strong evidence for the existence of a biogeographic divide between the eastern monsoonal and the west continental climatic zones of the QTP nearly along the 500 mm isohyet. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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18. The complete chloroplast genome of Notholition macrophyllum.
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Li, Juan, Liu, Haiying, Xie, Dengfeng, Zhou, Songdong, and He, Xingjin
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CHLOROPLASTS ,PLANT genomes ,LILIACEAE ,TRANSFER RNA ,PLANT genetics - Abstract
Notholirion macrophyllum (D. Don) Boiss. (Liliaceae) is a floriferous species naturally distributed in Asia. The complete chloroplast genome sequence of N. macrophyllum was generated by de novo assembly using whole genome next generation sequencing data. The complete chloroplast genome of N. macrophyllum was 152143 bp in total sequence length and divided into four distinct regions: small single copy region (17913 bp), large single copy region (82222 bp) and a pair of inverted repeat regions (26004 bp). The genome annotation displayed a total of 135 genes, including 82 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis with 7 Liliaceae species revealed that N. macrophyllum was the basal species of tribe Lilieae and was close to Cardiocrinum giganteum. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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19. The Frequency Selective Effect of Radar Backscattering from Multiscale Sea Surface.
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Xie, Dengfeng, Chen, Kun-Shan, and Zeng, Jiangyuan
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BACKSCATTERING , *OCEAN temperature , *WAVENUMBER , *STANDARD deviations - Abstract
The sea surface essentially contains multiscale roughness with capillary waves of many sizes riding on large-scale waves that are also of many sizes. It is instructive to exploit the effect of radar frequency and observation geometry on the effective roughness scales responsible for radar backscattering so that the scattering mechanism and the scattering source can be better understood and quantitated. Based on common sea spectra and a theoretical scattering model, an attempt is made to attain the above objective. Model predictions, with selective roughness scales, are compared with wide validation data, including L-band radar observations, and predictions from C-band and Ku-band empirical models: geophysical model function (CMOD7) and NASA scatterometer (NSCAT-4) for C- and Ku-bands at different incident angles. Numerical results indicate that effective roughness scales for radar backscattering vary with radar frequency and incidence angle and are related to a portion of sea spectral components; the low limit of which is linearly proportional to the Bragg wavenumber determined by frequency and incidence angle, and the scale factor of the linear relationship is about 0.05. In addition, the root mean square (RMS) height and the correlation length of the effective roughness (i.e., scattering source) derived from the effective roughness decrease gradually as incident angle increases. In particular, the correlation length also linearly depends on the effective wavelength with a coefficient of 3.2. Moreover, these two coefficients are both independent of wind speed, radar frequency, and incident angle. These findings also reveal the essential properties of the spectral components contributing to radar backscattering and its variation with radar frequency and incident angle. [ABSTRACT FROM AUTHOR]
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- 2019
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20. On the Very High-Resolution Radar Image Statistics of the Exponentially Correlated Rough Surface: Experimental and Numerical Studies.
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Jin, Ming, Chen, Kun-Shan, and Xie, Dengfeng
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REMOTE-sensing images ,ROUGH surfaces ,THREE-dimensional printing ,RAYLEIGH model ,REMOTE sensing - Abstract
The aim of this study is to investigate, by means of experimental measurements and full-wave simulations, the dominant factors for the very high-resolution (VHR) radar image speckles from exponentially correlated rough surfaces. A Ka-band radar system was used to collect the return signal from such a surface sample fabricated by 3D printing and that signal was further processed into images at different resolution scales, where the image samples were obtained by horizontally turning around the surface sample. To cross-validate the results and to further discuss the VHR speckle properties, full wave simulations by full 3D Finite Difference Time Domain (FDTD) method were conducted with 1600 realizations for the speckle analysis. At the considered very high resolution, speckle statistics show divergence from the fully developed Rayleigh distribution. The factors that impact on the high-resolution speckle properties from exponentially correlated rough surface, are analyzed in views of the equivalent number of scatterers theory and scattering scales, respectively. From the data results and extended discussions, it is evident that both of the above factors matter for VHR speckle of backscattering, from the exponentially correlated rough surface as a good representative for the ground surface. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
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21. Analysis of complete chloroplast genomes of Curcuma and the contribution to phylogeny and adaptive evolution.
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Gui, Lingjian, Jiang, Shaofeng, Xie, Dengfeng, Yu, Liying, Huang, Yuan, Zhang, Zhanjiang, and Liu, Yingying
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CHLOROPLAST DNA , *CURCUMA , *MICROSATELLITE repeats , *MOLECULAR phylogeny , *NUCLEAR DNA , *BIOLOGICAL evolution - Abstract
• 4 chloroplast genomes of Curcuma were newly sequenced and assembled. • Multiple SSRs and highly variable regions were identified. • Curcuma has gene introgression with related taxa. • Chloroplast genes of Curcuma may had undergone positive selection pressure in evolution. Curcuma is an important member of Zingiberaceae. Many species of this genus are widely used in traditional medicine and have important cultural value in East Asia. Among them, C. longa is considered to be the main source of curcumin and has a very wide range of uses. The rapid development of molecular phylogeny has deepened our understanding of taxonomy and evolution of Curcuma. However, little is known about the chloroplast genome phylogeny and the genetic bases of adaptative evolution. In this work, we sequenced the complete chloroplast genome of 4 Curcuma species. Curcuma chloroplast genomes showed highly conserved structures and the length ranged from 159,423 bp to 152,723 bp. A total of 133 genes were observed. Multiple repeats and simple sequence repeats (SSRs) were detected. By comparing with related species, 7 highly variable regions were identified as potential specific DNA barcodes for species identification. Phylogenetic analysis of complete plastome sequences and specific data sets revealed discordance with expected genus boundary. Chloroplast phylogenetic relationships were better predicted by geography than by morphological and nuclear DNA, indicating a substantial existence of introgression. 9 genes were proved to have high posteriori probability in positive selection analysis, and 4 of them (psbA , psbD , PetA and rbcL) closely related to photosynthesis, implying that chloroplast genes may had undergone positive selection pressure in evolution. These results are of great significance for us to understand the genetic basis, phylogeny and adaptive evolution of Curcuma chloroplast. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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22. Plastid Phylogenomic Analyses Reveal the Taxonomic Position of Peucedanum franchetii .
- Author
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Song B, Liu C, Xie D, Xiao Y, Tian R, Li Z, Zhou S, and He X
- Abstract
Peucedanum franchetii is a famous folk medicinal plant in China. However, the taxonomy of the P. franchetii has not been sufficiently resolved. Due to similar morphological features between P. franchetii and Ligusticopsis members, the World Flora Online (WFO) Plant List suggested that this species transformed into the genus Ligusticopsis and merged with Ligusticopsis likiangensis . However, both species are obviously diverse in leaf shape, bracts, and bracteoles. To check the taxonomic position of P. franchetii , we newly sequenced and assembled the plastome of P. franchetii and compared it with nine other plastomes of the genus Ligusticopsis . Ten plastomes were highly conserved and similar in gene order, codon bias, RNA editing sites, IR borders, and SSRs. Nevertheless, 10 mutation hotspot regions ( infA , rps8 , matK , ndhF , rps15 , psbA-trnH , rps2-rpoC2 , psbA-trnK , ycf2-trnL , and ccsA-ndhD ) were still detected. In addition, both phylogenetic analyses based on plastome data and ITS sequences robustly supported that P. franchetii was not clustered with members of Peucedanum but nested in Ligusticopsis. P. franchetii was sister to L . likiangensis in the ITS topology but clustered with L. capillacea in the plastome tree. These findings implied that P. franchetii should be transferred to genus Ligusticopsis and not merged with L . likiangensis , but as an independent species, which was further verified by morphological evidences. Therefore, transferring P. franchetii under the genus Ligusticopsis as an independent species was reasonable, and a new combination was presented.
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- 2022
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23. Comparative analysis of complete plastid genomes from Lilium lankongense Franchet and its closely related species and screening of Lilium -specific primers.
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Su D, Xie F, Liu H, Xie D, Li J, He X, Guo X, and Zhou S
- Abstract
Lilium lankongense Franchet is a lily species found on the Qinghai-Tibet Plateau. It is pink with deep red spots, has a high ornamental value, and is used in hybrid breeding of horticultural lily varieties. We have insufficient knowledge of the genetic resources of L. lankongense and its phylogenetic relationships with related species. Recent molecular phylogenetic studies have shown a very close phylogenetic relationship between L. lankongense and the five species L. duchartrei , L. stewartianum , L. matangense , L. lophophorum, and L. nanum . However, molecular markers still lack sufficient signals for population-level research of the genus Lilium . We sequenced and compared the complete plastid sequences of L. lankongense and its five related species. The genomes ranged from 152,307 bp to 152,611 bp. There was a slight inconsistency detected in inverted repeat and single copy boundaries and there were 53 to 63 simple sequence repeats in the six species. Two of the 12 highly variable regions ( t rnC- petN and rpl32 - trnL ) were verified in 11 individuals and are promising for population-level studies. We used the complete sequence of 33 plastid genomes, the protein-coding region sequence, and the nuclear ITS sequence to reconstruct the phylogenetic tree of Lilium species. Our results showed that the plastid gene tree and nuclear gene tree were not completely congruent, which may be caused by hybridization, insufficient information contained in the nuclear ITS, or the small number of samples. The results of phylogenetic analysis based on plastid genomes indicated that the six Lilium species were closely related. Our study provides a preliminarily rebuilt backbone phylogeny that is significant for future molecular and morphological studies of Lilium ., Competing Interests: The authors declare there are no competing interests., (©2021 Su et al.)
- Published
- 2021
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24. Sequencing and analyses on chloroplast genomes of Tetrataenium candicans and two allies give new insights on structural variants, DNA barcoding and phylogeny in Apiaceae subfamily Apioideae.
- Author
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Kang L, Xie D, Xiao Q, Peng C, Yu Y, and He X
- Abstract
Background: Tetrataenium candicans is a traditional Chinese folk herbal medicine used in the treatment of asthma and rheumatic arthritis. Alongside several Tordyliinae species with fleshy roots, it is also regarded as a substitute for a Chinese material medicine called 'Danggui'. However, a lack of sufficient sampling and genomic information has impeded species identification and the protection of wild resources., Methods: The complete chloroplast genomes of T. candicans from two populations, Tetrataenium yunnanense and Semenovia transilliensis , were assembled from two pipelines using data generated from next generation sequencing (NGS). Pseudogenes, inverted repeats (IRs) and hyper-variable regions were located by Geneious 11.1.5. Repeat motifs were searched using MISA and REPuter. DNA polymorphism and segment screening were processed by DNAsp5, and PCR product was sequenced with Sanger's sequencing method. Phylogeny was inferred by MEGA 7.0 and PhyML 3.0., Results: The complete chloroplast genomes of T. candicans from two populations, T. yunnanense and S. transilliensis , were 142,261 bp, 141,985 bp, 142,714 bp and 142,145 bp in length, respectively, indicating conservative genome structures and gene categories. We observed duplications of trnH and psbA caused by exceptional contractions and expansions of the IR regions when comparing the four chloroplast genomes with previously published data. Analyses on DNA polymorphism located 29 candidate cp DNA barcodes for the authentication of 'Danggui' counterfeits. Meanwhile, 34 hyper-variable markers were also located by the five Tordyliinae chloroplast genomes, and 11 of them were screened for population genetics of T. candicans based on plastome information from two individuals. The screening results indicated that populations of T.candicans may have expanded. Phylogeny inference on Apiaceae species by CDS sequences showed most lineages were well clustered, but the five Tordyliinae species failed to recover as a monophyletic group, and the phylogenetic relationship between tribe Coriandreae, tribe Selineae, subtribe Tordyliinae and Sinodielsia clade remains unclear., Discussion: The four chloroplast genomes offer valuable information for further research on species identification, cp genome structure, population demography and phylogeny in Apiaceae subfamily Apioideae., Competing Interests: The authors declare there are no competing interests., (©2019 Kang et al.)
- Published
- 2019
- Full Text
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25. An Improved STARFM with Help of an Unmixing-Based Method to Generate High Spatial and Temporal Resolution Remote Sensing Data in Complex Heterogeneous Regions.
- Author
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Xie D, Zhang J, Zhu X, Pan Y, Liu H, Yuan Z, and Yun Y
- Abstract
Remote sensing technology plays an important role in monitoring rapid changes of the Earth's surface. However, sensors that can simultaneously provide satellite images with both high temporal and spatial resolution haven't been designed yet. This paper proposes an improved spatial and temporal adaptive reflectance fusion model (STARFM) with the help of an Unmixing-based method (USTARFM) to generate the high spatial and temporal data needed for the study of heterogeneous areas. The results showed that the USTARFM had higher accuracy than STARFM methods in two aspects of analysis: individual bands and of heterogeneity analysis. Taking the predicted NIR band as an example, the correlation coefficients (r) for the USTARFM, STARFM and unmixing methods were 0.96, 0.95, 0.90, respectively (p-value < 0.001); Root Mean Square Error (RMSE) values were 0.0245, 0.0300, 0.0401, respectively; and ERGAS values were 0.5416, 0.6507, 0.8737, respectively. The USTARM showed consistently higher performance than STARM when the degree of heterogeneity ranged from 2 to 10, highlighting that the use of this method provides the capacity to solve the data fusion problems faced when using STARFM. Additionally, the USTARFM method could help researchers achieve better performance than STARFM at a smaller window size from its heterogeneous land surface quantitative representation.
- Published
- 2016
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26. Efficient Rutin and Quercetin Biosynthesis through Flavonoids-Related Gene Expression in Fagopyrum tataricum Gaertn. Hairy Root Cultures with UV-B Irradiation.
- Author
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Huang X, Yao J, Zhao Y, Xie D, Jiang X, and Xu Z
- Abstract
Transformed hairy roots had been efficiently induced from the seedlings of Fagopyrum tataricum Gaertn. due to the infection of Agrobacterium rhizogenes. Hairy roots were able to display active elongation with high root branching in 1/2 MS medium without growth regulators. The stable introduction of rolB and aux1 genes of A. rhizogenes WT strain 15834 into F. tataricum plants was confirmed by PCR analysis. Besides, the absence of virD gene confirmed hairy root was bacteria-free. After six different media and different sources of concentration were tested, the culturing of TB7 hairy root line in 1/2 MS liquid medium supplemented with 30 g l(-1) sucrose for 20 days resulted in a maximal biomass accumulation (13.5 g l(-1) fresh weight, 1.78 g l(-1) dry weight) and rutin content (0.85 mg g(-1)). The suspension culture of hairy roots led to a 45-fold biomass increase and a 4.11-fold rutin content increase in comparison with the suspension culture of non-transformed roots. The transformation frequency was enhanced through preculturing for 2 days followed by infection for 20 min. The UV-B stress treatment of hairy roots resulted in a striking increase of rutin and quercetin production. Furthermore, the hairy root lines of TB3, TB7, and TB28 were chosen to study the specific effects of UV-B on flavonoid accumulation and flavonoid biosynthetic gene expression by qRT-PCR. This study has demonstrated that the UV-B radiation was an effective elicitor that dramatically changed in the transcript abundance of ftpAL, FtCHI, FtCHS, FtF3H, and FtFLS-1 in F. tataricum hairy roots.
- Published
- 2016
- Full Text
- View/download PDF
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