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| 1 | Genome of Wild Mandarin and Domestication History of Mandarin显示文摘官员(柠檬 reticulata ) 是世界范围的最重要的柠檬庄稼之一。它的驯服被相信发生在华南,它是四几千年的官员耕作的中心之一。我们在 Nanling 区域附近收集了官员的自然野人口并且在附近栽培了 landraces。我们发现柠檬性的酸水平戏剧性地在栽培官员被减少。理解 ? 官员驯服的基因基础,我们 de novo 装配了野官员的一个草稿染色体并且分析了一套 104 个柠檬染色体。我们发现 Mangshan 官员是一种原始类型并且二个独立驯服事件发生了,分别地导致在北方和南方 Nanling 山的二组栽培官员(MD1 和 MD2 ) 。二个瓶颈和有效人口尺寸的二扩大为栽培官员的 MD1 组被识别。然而,在 MD2 组织 ? 在人口尺寸有长、连续的减少。MD1 和 MD2 官员从栽培 pummelo 种类显示出种间的基因渗入的不同模式。我们在官员的驯服期间在选择下面可能在基因在柠檬酸盐内容的规定包含了的 aconitate hydratase (ACO ) 识别了高分叉的一个区域,它是。这研究为现存野官员人口的地理起源提供具体基因证据并且使驯服和官员的进化历史清楚些。 | Lun Wang Fa He Yue Huang Jiaxian He Shuizhi Yang Jiwu Zeng Chongling Deng Xiaolin Jiang Yiwen Fang Shaohua Wen Rangwei Xu Huiwen Yu Xiaoming Yang Guangyan Zhong Chuanwu Chen Xiang Yan Changfu Zhou Hongyan Zhang Zongzhou Xie Robert M. Larkin Xiuxin Deng Qiang Xu | 2018 | Molecular Plant2018，11，8： | 14 |
| 2 | The influence of urban park characteristics on bird diversity in Nanjing, China显示文摘Background:Habitat loss,fragmentation and decrease of habitat quality caused by urbanization have led to a dramatic decline in biodiversity worldwide.For highly urbanized areas,parks have become“islands”or habitat fragments for wildlife.As an important indicator group of urban ecosystem health,the response of birds to urbanization has attracted the global attention of ecologists.Understanding the key factors affecting bird diversity in urbanized environment is crucial to the protection of biodiversity in urban ecosystems.Methods:We used the line-transect method to survey birds in 37 urban parks in Nanjing,China.We also measured a number of park characteristics(area,isolation,shape index,environmental noise,distance to city center,and habitat diversity)that are commonly assumed to influence bird diversity.We then used the information-theoretic multi-model inference approach to determine which park characteristics had significant impacts on bird species richness.Results:We found that park area,habitat diversity and the distance to city center were the best positive predictors of bird species richness in Nanjing urban parks.By contrast,park isolation,park shape and environmental noise had little or no influence on bird diversity.Conclusions:Our study highlights the importance of park area,habitat diversity and the distance to city center in determining bird diversity in Nanjing city parks.Therefore,from a conservation viewpoint,we recommend that large parks with complex and diverse habitats far away from the city center should be retained or constructed to increase bird diversity in urban design and planning. | Xueru Yang Xinwei Tan Chuanwu Chen Yanping Wang | 2020 | Avian Research2020，11，4： | 5 |
| 3 | Drug resistance mutation profiles of the drug-nave and first-line regimen-treated HIV-1-infected population of Suzhou, China显示文摘Little is known about the prevalence of drug-resistant mutations in HIV-1-positive individuals in Suzhou, China. To elucidate the transmitted drug resistance(TDR) and acquired drug resistance mutation(ADR) profiles, we collected blood specimens from 127 drug-naive and 117 first-line drugtreated HIV-1-infected individuals sampled from 2014 to 2016 in Suzhou. We successfully amplified po/fragments from 100 drug-naive and 20 drug-treated samples. We then determined the drugresistant mutations to protease(PR) and reverse-transcriptase(RT) inhibitors according to the Stanford drug resistance database. Overall, 11 and 13 individuals had transmitted(drug-naive group) and acquired(treated group) resistance mutations, respectively. Six transmitted drugresistant mutations were found, including two mutations(L33F and L76V) in the protease region and four(K70N/E and V179D/E) in the RT region. Only L76 V was a major mutation, and K70N/E and V179D/E are known to cause low-level resistance to RT inhibitors. All 13 treated participants who had major drug resistance mutations demonstrated intermediate to high resistance to efavirenz and nevirapine, and six had a treatment duration of less than three months. No major mutations to RT inhibitors were found, implying that the epidemic of transmitted resistance mutations was not significant in this area. Our results suggest that more frequent virus load and drug resistance mutation tests should be conducted for individuals receiving antiretroviral treatment, especially for newly treated patients. Our research provides insights into the occurrence of HIV-1 drug resistance in Suzhou and will help to optimize the treatment strategy for this population. | Tingting Li Feng Qian Ting Yuan Weilu Xu Li Zhu Jinlong Huang Haiyan Wang Yueping Zhu Yinling Wang Xiaohong Li Saihong Gu Zhuqing Tan Hui Chen Xiangrong Luo Wei Zhu Weniuan Lu Ping Xu Ming Li Yuying Chen Yong Gao Rongge Yang Chuanwu Zhu Binlian Sun | 2017 | Virologica Sinica2017，32，4： | 2 |
| 4 | CHH methylation of genes associated with fatty acid and jasmonate biosynthesis contributes to cold tolerance in autotetraploids of Poncirus trifoliata显示文摘Polyploids have elevated stress tolerance,but the underlying mechanisms remain largely elusive.In this study,we showed that naturally occurring tetraploid plants of trifoliate orange(Poncirus trifoliata(L.) Raf.) exhibited enhanced cold tolerance relative to their diploid progenitors.Transcriptome analysis revealed that whole-genome duplication was associated with higher expression levels of a range of well-characterized cold stress-responsive genes.Global DNA methylation profiling demonstrated that the tetraploids underwent more extensive DNA demethylation in comparison with the diploids under cold stress.CHH methylation in the promoters was associated with up-regulation of related genes,whereas CG,CHG,and CHH methylation in the 3’-regions was relevant to gene down-regulation.Of note,genes involved in unsaturated fatty acids(UFAs) and jasmonate(JA)biosynthesis in the tetraploids displayed different CHH methylation in the gene flanking regions and were prominently up-regulated,consistent with greater accumulation of UFAs and JA when exposed to the cold stress.Collectively,our findings explored the difference in cold stress response between diploids and tetraploids at both transcriptional and epigenetic levels,and gained new insight into the molecular mechanisms underlying enhanced cold tolerance of the tetraploid.These results contribute to uncovering a novel regulatory role of DNA methylation in better cold tolerance of polyploids. | Yue Wang Lanlan Zuo Tonglu Wei Yu Zhang Yang Zhang Ruhong Ming Dahro Bachar Wei Xiao Khan Madiha Chuanwu Chen Qijun Fan Chunlong Li Ji-Hong Liu | 2022 | Journal of Integrative Plant Biology2022，64，12： | 2 |
| 5 | Down regulated expression of S_(2)-RNase attenuates self-incompatibility in “Guiyou No.1”pummelo显示文摘Self-incompatibility(SI)substantially restricts the yield and quality of citrus.Therefore,breeding and analyzing selfcompatible germplasm is of great theoretical and practical signi ficance for citrus.Here,we focus on the mechanism of a self-compatibility mutation in‘Guiyou No.1'pummelo(Citrus maxima),which is a spontaneous mutant of‘Shatian’pummelo(Citrus maxima,self-incompatibility).The rate of fruit set and the growth of pollen tubes in the pistil con firmed that a spontaneous mutation in the pistil is responsible for the self-compatibility of‘Guiyou No.1'.Segregation ratios of the S genotype in progeny,expression analysis,and western blotting validated that the reduced levels of S_(2)-RNase mRNA contribute to the loss of SI in‘Guiyou No.1'.Furthermore,we report a phased assembly of the‘Guiyou No.1'pummelo genome and obtained two complete and well-annotated S haplotypes.Coupled with an analysis of SV variations,methylation levels,and gene expression,we identi fied a candidate gene(CgHB40),that may in fluence the regulation of the S/^RNase promoter.Our data provide evidence that a mutation that affects the pistilled to the loss of SI in‘Guiyou No.1'by in fluencing a poorly understood mechanism that affects transcriptional regulation.This work signi ficantly advances our understanding of the genetic basis of the SI system in citrus and provides information on the regulation of S-RNase genes. | ianbing Hu Qiang Xu Chenchen Liu Binghao Liu Chongling Deng Chuanwu Chen Zhuangmin Wei Muhammad Husnain Ahmad Kang Peng Hao Wen Xiangling Chen Peng Chen Robert MLarkin Junli Ye Xiuxin Deng Lijun Chai | 2021 | Horticulture Research2021，8，1： | 2 |
| 6 | Nestedness and underlying processes of bird assemblages in Nanjing urban parks显示文摘Nestedness is an important pattern frequently reported for species assemblages on islands or fragmented systems.However,to date,there are few studies that comprehensively investigated faunal nestedness and underlying processes in urbanized landscapes.In this study,we examined the nestedness of bird assemblages and its underlying causal mechanisms in 37 urban parks in Nanjing,China.We used the line-transect method to survey birds from April 2019 to January 2020.We used the Weighted Nestedness metric based on Overlap and Decreasing Fill(WNODF)to estimate the nestedness of bird assemblages.We applied spearman partial correlation test to examine the relationships between nestedness ranks of sites and park characteristics(area,isolation,anthropogenic noise,number of habitat types,and building index),as well as between nestedness ranks of species and their ecological traits(body size,geographic range size,clutch size,minimum area requirement,dispersal ratio,and habitat specificity).We found that bird assemblages in urban parks were significantly nested.Park area,habitat diversity,building index,habitat specificity,and minimum area requirement of birds were significantly correlated with nestedness.Therefore,the nestedness of bird assemblages was caused by selective extinction,habitat nestedness,and urbanization.However,the nestedness of bird assemblages did not result from passive sampling,selective colonization,or human disturbance.Overall,to maximize the number of species preserved in our system,conservation priority should be given to parks with large area,rich habitat diversity,and less building index.From a species perspective,we should focus on species with large area requirement and high habitat specificity for their effective conservation. | Xinwei Tan Xueru Yang Chuanwu Chen Yanping Wang | 2021 | Current Zoology2021，67，4： | 2 |
| 7 | Correlates of extinction risk in Chinese endemic birds显示文摘Background: China has a relative high degree of endemism of birds due to its large area, diversified topography, and varied climates and habitats. Among the 77 Chinese endemic birds, 29 species are classified as threatened according to the officially released China Biodiversity Red List in 2015. Chinese endemic birds should be the focus of conservation because their local extinction in China means complete global extinction. However, to date, no study has explicitly examined the patterns and processes of extinction and threat in Chinese endemic birds. Methods: We obtained eleven biological traits and four extrinsic factors that are commonly hypothesized to influence extinction risk. After phylogenetic correction, these factors were used separately and in combination to assess their associations with extinction risk. Results: We found that 37.7% of Chinese endemic birds were listed as threatened (Vulnerable, Endangered and Critically Endangered). Small range size, high hunting vulnerability, and high human population density were important predictors of high extinction risk in Chinese endemic birds. Conclusions: Our study is the first to systematically investigate the patterns and processes of extinction risk in Chinese endemic birds. We suggest that endemic species with small range size and living in area with high human densities require conservation priorities. Conservation efforts should also focus on the reduction of human threats, such as human hunting and habitat degradation, for the effective preservation of Chinese endemic birds. | Chuanwu Chen Di Zeng Yuhao Zhao Yiru Wu Junfeng Xu Yanping Wang | 2019 | Avian Research2019，10，2： | 1 |
| 8 | A comprehensive proteomic analysis of elaioplasts from citrus fruits reveals insights into elaioplast biogenesis and function显示文摘Elaioplasts of citrus peel are colorless plastids which accumulate significant amounts of terpenes.However,other functions of elaioplasts have not been fully characterized to date.Here,a LC–MS/MS shotgun technology was applied to identify the proteins from elaioplasts that were highly purified from young fruit peel of kumquat.A total of 655 putative plastid proteins were identified from elaioplasts according to sequence homology in silico and manual curation.Based on functional classification via Mapman,~50%of the identified proteins fall into six categories,including protein metabolism,transport,and lipid metabolism.Of note,elaioplasts contained ATP synthase and ADP,ATP carrier proteins at high abundance,indicating important roles for ATP generation and transport in elaioplast biogenesis.Additionally,a comparison of proteins between citrus chromoplast and elaioplast proteomes suggest a high level of functional conservation.However,some distinctive protein profiles were also observed in both types of plastids notably for isoprene biosynthesis in elaioplasts,and carotenoid metabolism in chromoplasts.In conclusion,this comprehensive proteomic study provides new insights into the major metabolic pathways and unique characteristics of elaioplasts and chromoplasts in citrus fruit. | Man Zhu Jiajia Lin Junli Ye Rui Wang Chao Yang Jinli Gong Yun Liu Chongling Deng Ping Liu Chuanwu Chen Yunjiang Cheng Xiuxin Deng Yunliu Zeng | 2018 | Horticulture Research2018，5，1： | 1 |
| 9 | A new diagnostic system for ultra-sensitive and specific detection and quantification of Candidatus Liberibacter asiaticus, the bacterium associated with citrus Huanglongbing显示文摘 | Hong Lin Chuanwu Chen Harshavardhan Doddapaneni Yongping Duan Edwin L. Civerolo Xianjin Bai Xiaolong Zhao | 2010 | Journal of Microbiological Methods2010，，1： | 1 |
| 10 | NEW INSIGHTS INTO THE PHYLOGENY AND SPECIATION OF KUMQUAT (FORTUNELLA SPP.) BASED ON CHLOROPLAST SNP, NUCLEAR SSR AND WHOLE-GENOME SEQUENCING显示文摘Kumquat(Fortunella spp.)is a fruit and ornamental crop worldwide due to the palatable taste and high ornamental value of its fruit.Although Fortunella is classified into the economically important true citrus fruit tree group together with Citrus and Poncirus,few studies have been focused on its evolutionary scenario.In this study,analysis of five chloroplast loci and 47 nuclear microsatellites(nSSR)loci from 38 kumquat and 10 citrus accessions revealed the independent phylogeny of Fortunella among citrus taxa,and that Fortunella mainly comprises two populations:CUL,cultivated Fortunella spp.(F.margarita,F.crassifolia and F.japonica);and HK,wild Hong Kong kumquat(Fortunella hindsii).Genomic analysis based on whole-genome SNPs indicated that the allele frequency of both pupations deviated from the neutral selection model,suggesting directional selection was a force driving their evolutions.CUL exhibited lower genomic diversity and higher linkage strength than HK,suggesting artificial selection involved in its origin.A high level of genetic differentiation(Fst=0.364)was detected and obviously asynchronous demographic changes were observed between CUL and HK.Based on these results,a new hypothesis for the speciation of Fortunella is proposed. | Chenqiao ZHU Peng CHEN Junli YE Hang LI Yue HUANG Xiaoming YANG Chuanwu CHEN Chenglei ZHANG Yuantao XU Xiaoli WANG Xiang YAN Guangzhou DENG Xiaolin JIANG Nan WANG Hongxing WANG Quan SUN Yun LIU Di FENG Min YU Xietian SONG Zongzhou XIE Yunliu ZENG Lijun CHAI Qiang XU Chongling DENG Yunjiang CHENG Xiuxin DENG | 2022 | Frontiers of Agricultural Science and Engineering2022，9，4： | 0 |
| 11 | Spatiotemporal distribution of seasonal bird assemblages on land-bridge islands: linking dynamic and static views of metacommunities显示文摘Background: Although assessing temporal dynamics of populations is crucial for understanding metacommunities, empirical studies have primarily analyzed only static snapshots of communities. Here, we present a holistic view of how species traits and habitat characteristics relate to metacommunity dynamics and use it to test for differences in the spatiotemporal distribution of seasonal bird assemblages. Methods: We surveyed forest birds in breeding and winter seasons within 36 islands for 9 years. We then grouped birds into four landbird assemblages, selected on the basis of published differences in biology or ecology: winter residents, migratory winter visitors, breeding summer residents, and migratory summer visitors. We estimated dynamic species colonization and extirpation through the 9-year period, and evaluated the associations among island attributes, species attributes and community composition. Results: Overall, winter and summer residents showed strong associations between composition and habitat structure of the islands. In addition, winter and summer residents on large islands had lower extirpation and turnover than winter and summer visitors. Visitor assemblages showed no significant habitat associations, and in winter had high extirpation rates and small body sizes. By contrast, local extirpation of summer visitors was correlated with local species richness, indicating a likely effect of competition on extirpation. Conclusions: Our results demonstrated repeated patterns among species composition, bird traits, habitat/island characteristics and observed metacommunity dynamics. Winter and summer residents best matched species sorting and patch dynamics, respectively, due to differences in resource availability and requirements of overwinter survival versus breeding. Summer visitors were consistent with species sorting and winter visitors were randomly distributed, likely because of interactions with resident competitors. Our results highlight that coexisting seasonal migrant and resident assemblages differ in their spatial dynamics, with consequences for relevant conservation and management strategies. | Chuanwu Chen Marcel Holyoak Yanping Wang Xingfeng Si Ping Ding | 2019 | Avian Research2019，10，3： | 0 |
| 12 | A Rapid Identification Method for Germplasm Materials Resistant to Citrus Huanglongbing Disease显示文摘[Objectives]This study was conducted to develop a rapid identification method for citrus germline materials resistant to Huanglongbing disease and lay a basis for accelerating citrus breeding for resistance to Huanglongbing and increasing the breeding efficiency.[Methods]Thirty-six citrus germplasms suspected to be resistant to citrus Huanglongbing disease were collected.The method of direct high grafting to citrus trees infected with Huanglongbing pathogen was adopted.The resistance of the test materials was identified and evaluated by field symptoms combined with quantitative PCR.It was defined as the top grafting identification method.[Results]The test materials that were grafted in spring started to germinate after one month,and three months late(June 5,2018)typical mottled yellowing on leaves was observed on KH-14 for the first time.After four months(July 5,2018)of top grafting,typical mottled yellowing occurred on 23 materials,and 11 materials showed no such symptom.After six months(September 4,2018)of top grafting,although the growth of KH-18,KH-12,KHY-4,KHY-5 and KHY-6 were normal,yellowing was observed on their leaves.Only KH-21 grew well,and showed no yellow shoots and yellowing leaves.It was identified as the material with resistance to Huanglongbing disease.Quantitative PCR tests on the above six materials showed that KH-21 was negative and other five were positive.Real-time fluorescence quantitative PCR test indicated that the average Huanglongbing bacteria amount in KH-21 was 1870.0 cell/μg DNA,and the average Huanglongbing bacteria amount in the control material was 372285.5 cell/μg DNA,indicating KH-21 was resistant to Huanglongbing bacteria.[Conclusions]The method for infecting bacteria by top grafting takes six months,can detect large amount of seedlings,and is time-saving,efficient,cost-saving and accurate.This method can quickly identify the resistance of citrus varieties to citrus Huanglongbing disease,and can be popularized and used in the identification of citrus Huanglongbing disease resistance. | Yan TANG Xiaoxiao WU Binghai LOU Ping LIU Chuanwu CHEN Ying NIU Gebi ZHANG Jiawen YAN Chongling DENG | 2020 | Agricultural Biotechnology2020，9，6： | 0 |
| 13 | Illuminating the cells:transient transformation of citrus to study gene functions and organelle activities related to fruit quality显示文摘Although multiple microscopic techniques have been applied to horticultural research,few studies of individual organelles in living fruit cells have been reported to date.In this paper,we established an efficient system for the transient transformation of citrus fruits using an Agrobacterium-mediated method.Kumquat(Fortunella crassifolia Swingle)was used;it exhibits higher transformation efficiency than all citrus fruits that have been tested and a prolonged-expression window.Fruits were transformed with fluorescent reporters,and confocal microscopy and live-cell imaging were used to study their localization and dynamics.Moreover,various pH sensors targeting different subcellular compartments were expressed,and the local pH environments in cells from different plant tissues were compared.The results indicated that vacuoles are most likely the main organelles that contribute to the low pH of citrus fruits.In summary,our method is effective for studying various membrane trafficking events,protein localization,and cell physiology in fruit and can provide new insight into fruit biology research. | Jinli Gong Zhen Tian Xiaolu Qu Qiunan Meng Yajie Guan Ping Liu Chuanwu Chen Xiuxin Deng Wenwu Guo Yunjiang Cheng Pengwei Wang | 2021 | Horticulture Research2021，8，1： | 0 |
| 14 | Mechanical properties of rock bolt and analysis for the full-process of sliding failure based on rock mass absolute displacement显示文摘Previous studies rarely involved the mechanical properties of anchorage system under the condition of internal absolute displacement of surrounding rock and the solution of important parameters of anchorage system. In this paper, the absolute displacement law of rock mass under the anchorage system is analyzed by the fiber grating(FBG) multi-point displacement meter and multidirectional displacement conversion formula. Based on the coordinated deformation principle for rock bolt and rock mass, the mechanical analysis model for rock bolt-rock mass system is established, and the influence rules of rock bolt length, rock bolt diameter and rock bolt preload on the internal force distribution of rock bolt is studied based on the stress analysis of full-length rock bolt in a tunnel engineering.The results show that:(1) with the increase of rock bolt length, the anchoring effect gradually enhances, but the improvement degree decreases gradually;(2) with the increase of rock bolt diameter, the anchoring effect is enhanced;at the same time, however, the shear stress of rock bolt is larger, and the possibility of rock bolt sliding also increases;and(3) with the increase of preload, the increase of “anchor length” makes the anti-sliding ability of rock bolt increase correspondingly, and the supporting effect of rock bolt increases gradually. Then the full-process analysis for the mechanical mechanism of rock bolt sliding failure and the iterative calculation method for rock bolt displacement are studied. At last, the numerical simulation for pull-out test is carried out through the finite element analysis to verify the calculation results of mechanical model, and according to the iterative operation, the two important parameters such as the interface shear stiffness K and the interface peak shear strength τPare solved. The analysis show that the numerical simulation results are in good agreement with the mechanical model calculation. This study can provide a theoretical basis for rock bolt support technology and support structure design. | Yanbin Luo Zhou Shi Chuanwu Wang Jianxun Chen Weiwei Liu Yao Li Yunfei Wu | 2022 | Journal of Traffic and Transportation Engineering(English Edition)2022，9，3： | 0 |
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