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| 1 | Genetic Architecture of Natural Variation in Rice Chlorophyll Content Revealed by a Genome-Wide Association Study显示文摘 | Quanxiu. Wang Weibo Xie Hongkun Xing Ju Yan Xiangzhou Meng Xinglei Li Xiangkui Fu Jiuyue Xu Xingming Lian Sibin Yu Yongzhong Xing Gongwei Wang | 2015 | Molecular Plant2015，8，6： | 20 |
| 2 | N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression,Plant Development, and Stress Responses显示文摘N6-Methyladenine (6mA)DNA methylation has recently been implicated as a potential new epigenetic marker in eukaryotes,including the dioot modelArabidopsis thaliana.However,the conservation and divergence of 6mA distribution patterns and functions in plants remain elusive.Here we report high-quality 6mA methylomes at single-nucleotide resolution in rice based on substantially improved genome sequences of two rice cultivars,Nipponbare (Nip;Japonica)and 93-11 (Indica).Analysis of 6mA genomic distribution and its association with transcription suggest that 6mA distribution and function is rather conserved between rice and Arabidopsis.We found that 6mA levels are positively correlated with the expression of key stressrelated genes,which may be responsible for the difference in stress tolerance between Nip and 93-11. Moreover,we showed that mutations in DDM1 cause defects in plant growth and decreased 6mA level. Our results reveal that 6mA is a conserved DNA modification that is positively associated with gene expression and contributes to key agronomic traits in plants. | Qian Zhang Zhe Liang Xuean Cui Changmian Ji Yun Li Pingxian Zhang Jingrong Liu Adeel Riaz Pu Yao Min Liu Yunpeng Wang Tiegang Lu Hao Yu Donglei Yang Hongkun Zheng Xiaofeng Gu | 2018 | Molecular Plant2018，11，12： | 18 |
| 3 | A Chromosome-Scale Genome Assembly of Paper Mulberry(Bmussonetia papyrifera)Provides New Insights into Its Forage and Papermaking Usage显示文摘Paper mulberry(Broussonetia papyrifera)is a well-known woody tree historically used for Cai Lun papermaking,one of the four great inventions of ancient China.More recently,Paper mulberry has also been used as forage to address the shortage of feedstuff because of its digestible crude fiber and high protein contents.In this study,we obtained a chromosome-scale genome assembly for Paper mulberry using integrated approaches,including Illumina and PacBio sequencing platform as well as Hi-C,optical,and genetic maps.The assembled Paper mulberry genome consists of 386.83 Mb,which is close to the estimated size,and 99.25%(383.93 Mb)of the assembly was assigned to 13 pseudochromosomes.Comparative genomic analysis revealed the expansion and contraction in the flavonoid and lignin biosynthetic gene families,respectively,accounting for the enhanced flavonoid and decreased lignin biosynthesis in Paper mulberry.Moreover,the increased ratio of syringyl-lignin to guaiacyl-lignin in Paper mulberry underscores its suitability for use in medicine,forage,papermaking,and barkcloth making.We also identified the rootassociated microbiota of Paper mulberry and found that Pseudomonas and Rhizobia were enriched in its roots and may provide the source of nitrogen for its stems and leaves via symbiotic nitrogen fixation.Collectively,these results suggest that Paper mulberry might have undergone adaptive evolution and recruited nitrogen-fixing microbes to promote growth by enhancing flavonoid production and altering lignin monomer composition.Our study provides significant insights into genetic basis of the usefulness of Paper mulberry in papermaking and barkcloth making,and as forage.These insights will facilitate further domestication and selection as well as industrial utilization of Paper mulberry worldwide. | Xianjun Peng Hui Liu Peilin Chen Feng Tang Yanmin Hu Fenfen Wang Zhi Pi Meiling Zhao Naizhi Chen Hui Chen Xiaokang Zhang Xueqing Yan Min Liu Xiaojun Fu Guofeng Zhao Pu Yao Lili Wang He Dai Xuming Li Wei Xiong Wencai Xu Hongkun Zheng Haiyan Yu Shihua Shen | 2019 | Molecular Plant2019，12，5： | 18 |
| 4 | Whole-Genome Resequencing of a Worldwide Collection of Rapeseed Accessions Reveals the Genetic Basis of Ecotype Divergence显示文摘Rapeseed (Brassica napus),an important oilseed crop,has adapted to diverse climate zones and latitudes by forming three main ecotype groups,namely winter,semiwinter,and spring types. However,genetic variations underlying the divergence of these ecotypes are largely unknown. Here,we report the global pattern of genetic polymorphisms in rapeseed determined by resequencing a worldwide collection of 991 germplasm accessions.A total of 5.56 and 5.53 million singlenucleotide polymorphisms (SNPs)as Well as 1.86 and 1.92 million InDels were identified by mapping reads to the reference genomes of 'Darmor-bzh'and 'Tapidor,'respectively.We generated a map of allelic drift paths that shows splits and mixtures of the main populations,and revealed an asymmetric evolution of the two subgenomes of B.napus by calculating the genetic diversity and linkage disequilibrium parameters.Selective-sweep analysis revealed genetic changes in genes orthologous to those regulating various aspects of plant development and response to stresses.A genome-wide association study identified SNPs in the promoter regions of FLOWERING LOCUS T and FLOWERING LOCUS C orthologs that corresponded to the different rapeseed ecotype groups. Our study provides important insights into the genomic footprints of rapeseed evolution and flowering-time divergence among three ecotype groups,and will facilitate screening of molecular markers for accelerating rapeseed breeding. | Dezhi Wu Zhe Liang Tao Yan Ying Xu Lijie Xuan Juan Tang Gang Zhou Ulrike Lohwasser Shuijin Hua Haoyi Wang Xiaoyang Chen Qian Wang Le Zhu Antony Maodzeka Nazim Hussain Zhilan Li Xuming Li Imran Haider Shamsi Ghulam Jilani Linde Wu Hongkun Zheng Guoping Zhang Boulos Chalhoub Lisha Shen Hao Yu Lixi Jiang | 2019 | Molecular Plant2019，12，1： | 10 |
| 5 | Comparison of microwave assisted extraction with hot reflux extraction in acquirement and degradation of anthocyanin from powdered blueberry显示文摘Acquirement and degradation kinetics of anthocyanin from powdered blueberry were studied to analyze the degradation reason and improve the yield of anthocyanin under microwave assisted extraction(MAE)conditions.Hot reflux extraction(HRE)method was employed as a reference with MAE to discriminate the influences of the microwave irradiation under the same extraction temperature at 30℃-70℃.Ethanol was selected as extraction solvent.Microwave volumetric heating improves the diffusion and solubility of anthocyanin within powdered blueberry particles in the pre-heating period.The kinetic coefficients,in terms of delivery kinetic and diffusion kinetic,are lower in MAE than that in HRE.Four anthocyanins including delphinidin,cyanidin,malvidin and pelaronidin were detected in the anthocyanin extracts from blueberry.Delphinidin,cyaniding,and pelargonidin contents significantly decrease,but malvidin was unchanged in MAE.Anthocyanin yield increases with elevating extraction temperatures,but anthocyanin degradation occurred at 41.2℃.The acquirement amount of anthocyanin is lower than its degradation amount when microwave extraction temperature is higher than 53.6℃.The self-aggregation of anthocyanin molecules and degradation results in the reduction of anthocyanin yield extracted from blueberry powder.In MAE,microwave volumetric heating results in the rapidly elevated temperature in pre-heating stage and generation of internal pressure to improve the acquirement of anthocyanin and the non-thermal effect from microwave field may weak the effect of temperature to decline the degradation of anthocyanin to monomer.The non-thermal microwave irradiation has pronounced effects compared to the effects of temperature on the structure changes of anthocyanin molecules at extraction temperature below 50℃.In HRE,convection mode of heat transfer in extraction system form the non-uniform distribution of temperature in the extraction vials to decrease the acquirement yield of anthocyanin from the blueberry powder.The research results provide valuable data to optimize extraction temperature for high extraction yield and bioactivity of anthocyanin in microwave extraction process. | Sun Yu Xue Hongkun Liu Chenghai Liu Chai Su Xiaolin Zheng Xianzhe | 2016 | International Journal of Agricultural and Biological Engineering2016，9，6： | 7 |
| 6 | A Genomic Variation Map Provides Insights into the Genetic Basis of Spring Chinese Cabbage (Brassica rapa ssp.pekinensis)Selection显示文摘Chinese cabbage is the most consumed leafy crop in East Asian countries.However,premature bolting induced by continuous low temperatures severely decreases the yield and quality of the Chinese cabbage, and therefore restricts its planting season and geographic distribution.In the past 40years,spring Chinese cabbage with strong winterness has been selected to meet the market demand.Here,we report a genome variation map of Chinese cabbage generated from the resequencing data of 194 geographically diverse accessions of three ecotypes.In-depth analyses of the selection sweeps and genome-wide patterns revealed that spring Chinese cabbage was selected from a specific population of autumn Chinese cabbage around the area of Shandong peninsula in northern China.We identified 23 genomic loci that underwent intensive selection,and further demonstrated by gene expression and haplotype analyses that the incorporation of elite alleles of VERNALISATION INSENTIVE 3.1(BrVIN3.1)and FLOWER LOCUS C 1(BrFLC1)is a determinant genetic source of variation during selection.Moreover,we showed that the quantitative response of BrVIN3.1 to cold due to the sequence variations in the cis elements of the BrVlN3.1 promoter significantly contributes to bolting-time variation in Chinese cabbage.Collectively, our study provides valuable insights into the genetic basis of spring Chinese cabbage selection and will facilitate the breeding of bolting-resistant Varieties by molecular-marker-assisted selection,transgenic or gene editingapproaches. | Tongbing Su Weihong Wang Peirong Li Bin Zhang Pan Li Xiaoyun Xin Honghe Sun Yangjun Yu Deshuang Zhang Xiuyun Zhao Changlong Wen Gang Zhou Yuntong Wang Hongkun Zheng Shuancang Yu Fenglan Zhang | 2018 | Molecular Plant2018，11，11： | 6 |
| 7 | Structure and composition of the surface of urethane/acrylic composite latex films显示文摘 | Limin Wu Hongkun Yu Jian Yan | 2001 | Polymer International2001，50，12： | 1 |
| 8 | Fenton Pre-Oxidation Followed by Microbial Degradation for Removing Crude Oil from Contaminated Soil显示文摘Through the Fenton pre-oxidation followed by microbial degradation,this study gave full play to its advantages while avoiding its shortcomings for the remediation of crude oil contaminated soil.The Fenton reagent coupled with different volumes of H2O2 was applied to the oil contaminated soil and then the microbial agents were introduced to biodegrade the residual oil for 15 days.The correlation between the characteristics of residual oil in soil,the changes in soil physical-chemical property after the Fenton pre-oxidation,and the biodegradation were analyzed in this paper.The results show that the above factors are strongly correlated with the subsequent biodegradation rate,and the order of correlation is as follows:the ratio of TOC to NH4+-N(R^2=0.9513)>the ratio of light oil components to the heavy oil components(R^2=0.9095)>the proportion of hydrocarbons with carbon chain number of less than C23(R^2=0.8259)>the crude oil content(R^2=0.7603)>the soil pH(R^2=0.7492)>the number of microorganisms(R^2=0.6506).During the biodegradation and pre-oxidation reactions of heavy oil components,an appropriate C:N ratio turns out to be the most critical factor in this study. | Gao Chunyang Zhang Yu Han Zhantao Song Quanwei Chen Changzhao Chen Hongkun Zheng Jin | 2019 | China Petroleum Processing & Petrochemical Technology2019，21，3： | 1 |
| 9 | Analysis of gener- al network coding conditions and design of a free-ride-oriented routing metric显示文摘 | Guo Bin Li Hongkun 2aaou Chi Cheng Yu | 2011 | 1EEE Transactions on Vehicular Technolo- gy2011，60，4： | 1 |
| 10 | Structure and composition of the surface of urethane/acrylic composite latex films显示文摘 | Limin Wu Hongkun Yu | 2001 | Polymer International2001，50，： | 1 |
| 11 | Analysis of general network coding conditions and design of a free-ride oriented routing metric 显示文摘 | Bin Guo Hongkun Li Chi Zhou Yu Cheng | 2011 | Vehicular Techno- logy IEEE Transactions on2011，60，4： | 1 |
| 12 | Structure and composition of the surface of urethane/acrylic composite latex films 显示文摘 | Wu Limin Yu Hongkun Yan Jian | 2001 | Polymer International2001，50，： | 1 |
| 13 | A theoretical framework h~r optimal cooperative networking in multi radio multi channel wireless networks 显示文摘 | Yu Cheng Hongkun Li Peng-Jun Wan | 2012 | Wireless Communications2012，，4： | 1 |
| 14 | Routing metrics for minimizing end-to-end delay in multiradio multichan- nel wireless networks显示文摘 | Li Hongkun Cheng Yu Zou Chi | 2013 | IEEE Transactions on Parallel and Distributed Systems2013，24，11： | 1 |
| 15 | Evolution of Asian drying since 30 Ma revealed by clay minerals record in the West Pacific and its tectonic-climatic forcing显示文摘As the second largest dust source on the globe,the tectonic and climatic evolution of continental Asia has an important impact on regional and global climate change.The West Pacific is the main sediment sink for eolian dust transported eastward from the Asian interior.Clay minerals,as the major fine-grained weathering products of continental rocks,can be readily transported by wind or currents over long distances and thus have been widely used in the reconstruction of paleoclimate and weathering history.However,the overall evolutionary tendency and response mechanism of clay mineral records over large spatial and long timescales across Asia remain unclear.Here,two continuous and high-resolution clay mineral records since 30 Ma were reconstructed from sediments at Deep Sea Drilling Program(DSDP)Sites 292 and 296 in the Philippine Sea.Clay minerals and Sr-Nd isotope compositions were used to constrain provenance and reconstruct the drying history of the dust source region since the Oligocene.The results show that the clay-sized detrital sediments in the Philippine Sea are a mixture of Asian eolian dust and volcanic materials from the West Pacific arcs.Based on the clay mineral compositions and eolian flux,we reveal that the Asian interior has been continuously drying since the late Oligocene and that stepwise enhanced aridification occurred at approximately 20,14,7,and 3 Ma.Compared with other regions of the world,the relative contents of illite and chlorite increased more dramatically in Asia during the late Cenozoic,and the inconsistency became more obvious at approximately 20 Ma.Since 3 Ma,illite and chlorite have increased consistently across the globe.Combined with the Asian tectonic and climatic history,we suggest that the increase in illite and chlorite from Asia between 20 and 3 Ma was mainly in response to the uplift of the Himalayan-Tibetan Plateau,whereas after 3 Ma,it was primarily controlled by global cooling driven by the expansion of the Arctic ice sheet. | Yi TANG Shiming WAN Debo ZHAO Zhaojie YU Zhaokai XU Jin ZHANG Zehua SONG Mengjun LI Hualong JIN Wenjun JIAO Hongkun DONG Anchun LI | 2023 | Science China Earth Sciences2023，66，6： | 0 |
| 16 | Evolutionary Transients in the Rice Transcriptome显示文摘In the canonical version of evolution by gene duplication, one copy is kept unaltered while the other is free to evolve. This process of evolutionary experimentation can persist for millions of years. Since it is so short lived in comparison to the lifetime of the core genes that make up the majority of most genomes, a substantial fraction of the genome and the transcriptome may-in principle-be attributable to what we will refer to as 'evolutionary transients', referring here to both the process and the genes that have gone or are undergoing this process. Using the rice gene set as a test case, we argue that this phenomenon goes a long way towards explaining why there are so many more rice genes than Arabidopsis genes, and why most excess rice genes show low similarity to eudicots. | Jun Wang Jianguo Zhang Ruiqiang Li Hongkun Zheng Jun Li Yong Zhang Heng Li Peixiang Ni Songgang Li Shengting Li Jingqiang Wang Dongyuan Liu Jason McDermott Ram Samudrala Siqi Liu Jian Wang Huanming Yang Jun Yu Gane Ka-Shu Wong | 2010 | Genomics, Proteomics & Bioinformatics2010，8，4： | 0 |
| 17 | Expert consensus on difficulty assessment of endodontic therapy显示文摘Endodontic diseases are a kind of chronic infectious oral disease. Common endodontic treatment concepts are based on the removal of inflamed or necrotic pulp tissue and the replacement by gutta-percha. However, it is very essential for endodontic treatment to debride the root canal system and prevent the root canal system from bacterial reinfection after root canal therapy(RCT). Recent research, encompassing bacterial etiology and advanced imaging techniques, contributes to our understanding of the root canal system’s anatomy intricacies and the technique sensitivity of RCT. Success in RCT hinges on factors like patients, infection severity, root canal anatomy, and treatment techniques. Therefore, improving disease management is a key issue to combat endodontic diseases and cure periapical lesions. The clinical difficulty assessment system of RCT is established based on patient conditions, tooth conditions, root canal configuration, and root canal needing retreatment, and emphasizes pre-treatment risk assessment for optimal outcomes. The findings suggest that the presence of risk factors may correlate with the challenge of achieving the high standard required for RCT. These insights contribute not only to improve education but also aid practitioners in treatment planning and referral decision-making within the field of endodontics. | Dingming Huang Xiaoyan Wang Jingping Liang Junqi Ling Zhuan Bian Qing Yu Benxiang Hou Xinmei Chen Jiyao Li Ling Ye Lei Cheng Xin Xu Tao Hu Hongkun Wu Bin Guo Qin Su Zhi Chen Lihong Qiu Wenxia Chen Xi Wei Zhengwei Huang Jinhua Yu Zhengmei Lin Qi Zhang Deqin Yang Jin Zhao Shuang Pan Jian Yang Jiayuan Wu Yihuai Pan Xiaoli Xie Shuli Deng Xiaojing Huang Lan Zhang Lin Yue Xuedong Zhou | 2024 | International Journal of Oral Science2024，16，1： | 0 |
| 18 | Surgical intervention combined with weight-bearing walking training promotes recovery in patients with chronic spinal cord injury:a randomized controlled study显示文摘For patients with chronic spinal cord injury,the co nventional treatment is rehabilitation and treatment of spinal cord injury complications such as urinary tract infection,pressure sores,osteoporosis,and deep vein thrombosis.Surgery is rarely perfo rmed on spinal co rd injury in the chronic phase,and few treatments have been proven effective in chronic spinal cord injury patients.Development of effective therapies fo r chronic spinal co rd injury patients is needed.We conducted a randomized controlled clinical trial in patients with chronic complete thoracic spinal co rd injury to compare intensive rehabilitation(weight-bearing walking training)alone with surgical intervention plus intensive rehabilitation.This clinical trial was registered at ClinicalTrials.gov(NCT02663310).The goal of surgical intervention was spinal cord detethering,restoration of cerebrospinal fluid flow,and elimination of residual spinal cord compression.We found that surgical intervention plus weight-bearing walking training was associated with a higher incidence of American Spinal Injury Association Impairment Scale improvement,reduced spasticity,and more rapid bowel and bladder functional recovery than weight-bearing walking training alone.Overall,the surgical procedures and intensive rehabilitation were safe.American Spinal Injury Association Impairment Scale improvement was more common in T7-T11 injuries than in T2-T6 injuries.Surgery combined with rehabilitation appears to have a role in treatment of chronic spinal cord injury patients. | Hui Zhu James D.Guest Sarah Dunlop Jia-Xin Xie Sujuan Gao Zhuojing Luo Joe E.Springer Wutian Wu Wise Young Wai Sang Poon Song Liu Hongkun Gao Tao Yu Dianchun Wang Libing Zhou Shengping Wu Lei Zhong Fang Niu Xiaomei Wang Yansheng Liu Kwok-Fai So Xiao-Ming Xu | 2024 | Neural Regeneration Research2024，19，12： | 0 |
| 19 | Detecting positive darwinian selection in brain-expressed genes during human evolution显示文摘To understand the genetic basis that underlies the phenotypic divergence between human and non- human primates, we screened a total of 7176 protein-coding genes expressed in the human brain and compared them with the chimpanzee orthologs to identify genes that show evidence of rapid evolution in the human lineage. Our results showed that the nonsynonymous/synonymous substitution (Ka/Ks) ratio for genes expressed in the brain of human and chimpanzee is 0.3854, suggesting that the brain-expressed genes are under functional constraint. The X-linked human brain-expressed genes evolved more rapidly than autosomal ones. We further dissected the molecular evolutionary patterns of 34 candidate genes by sequencing representative primate species to identify lineage-specific adaptive evolution. Fifteen out of the 34 candidate genes showed evidence of positive Darwinian selection in human and/or chimpanzee lineages. These genes are predicted to play diverse functional roles in em- bryonic development, spermatogenesis and male fertility, signal transduction, sensory nociception, and neural function. This study together with others demonstrated the usefulness and power of phy- logenetic comparison of multiple closely related species in detecting lineage-specific adaptive evolu- tion, and the identification of the positively selected brain-expressed genes may add new knowledge to the understanding of molecular mechanism of human origin. | QI XueBin YANG Su ZHENG HongKun WANG YinQiu LIAO ChengHong LIU Ying CHEN XiaoHua SHI Hong YU xiaoJing Alice A. LIN Luca L. CAVALLI-SFORZA WANG Jun SU Bing | 2007 | Chinese Science Bulletin2007，52，3： | 0 |
| 20 | Comparative Genomics Reveals Evolutionary Drivers of Sessile Life and Left-right Shell Asymmetry in Bivalves显示文摘Bivalves are species-rich mollusks with prominent protective roles in coastal ecosystems.Across these ancient lineages,colony-founding larvae anchor themselves either by byssus production or by cemented attachment.The latter mode of sessile life is strongly molded by left-right shell asymmetry during larval development of Ostreoida oysters such as Crassostrea hongkongensis.Here,we sequenced the genome of C.hongkongensis in high resolution and compared it to reference bivalve genomes to unveil genomic determinants driving cemented attachment and shell asymmetry.Importantly,loss of the homeobox gene Antennapedia(Antp)and broad expansion of lineagespecific extracellular gene families are implicated in a shift from byssal to cemented attachment in bivalves.Comparative transcriptomic analysis shows a conspicuous divergence between leftright asymmetrical C.hongkongensis and symmetrical Pinctada fucata in their expression profiles.Especially,a couple of orthologous transcription factor genes and lineage-specific shell-related gene families including that encoding tyrosinases are elevated,and may cooperatively govern asymmetrical shell formation in Ostreoida oysters. | Yang Zhang Fan Mao Shu Xiao Haiyan Yu Zhiming Xiang Fei Xu Jun Li Lili Wang Yuanyan Xiong Mengqiu Chen Yongbo Bao Yuewen Deng Quan Huo Lvping Zhang Wenguang Liu Xuming Li Haitao Ma Yuehuan Zhang Xiyu Mu Min Liu Hongkun Zheng Nai-Kei Wong Ziniu Yu | 2022 | Genomics, Proteomics & Bioinformatics2022，20，6： | 0 |
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