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Advances in Transgenic Breeding of Anthurium andraeanum

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Agricultural Biotechnology 2015年第1期4卷 1-5页

作者： Bo YU Genfa ZHU Yingbo SUN Environmental Horticulture Research Institute Guangdong Academy of Agricultural Sciences/Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization

At present, transgenic technologies have become important means of plant breeding, and the application and promotion of transgenic technologies have created huge economic and social benefits. Transgenic plant products have significantly affected human life. Anthurium andraeanum is the second major tropical potted flower and its transgenic breeding has a promising prospect of application. In this paper, acceptors, transformation methods and introduced exogenous genes （ including reporter genes, selectable marker genes and target genes） of Anthurium andraeanum were summarized; in addition, several issues related to transforma- tion of Anthurium andraeanum were analyzed, aiming at providing reference for transgenic breeding of Anthurium andraeanum.

关键词： Anthurium andraeanum Transgene Acceptors Transformation methods Exogenous genes

Enrichment of beneficial cucumber rhizosphere microbes mediated by organic acid secretion

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Horticulture Research 2020年第1期7卷 662-674页

作者： Tao Wen Jun Yuan Xiaoming He Yue Lin Qiwei Huang Qirong Shen Jiangsu provincial key lab for Organic Solid Waste utilization Key Laboratory of Plant ImmunityJiangsu Collaborative Innovation Center for Solid Organic WastesEducational Ministry Engineering Center of Resource-saving FertilizersNanjing Agricultural University210095 NanjingChina Vegetable Research Institute Guangdong Academy of Agricultural SciencesGuangzhou510640 GuangdongChina

Resistant cultivars have played important roles in controlling Fusarium wilt disease,but the roles of rhizosphere interactions among different levels of resistant cultivars are still ***,two phenotypes of cucumber,one resistant and one with increased susceptibility to Fusarium oxysporum ***(Foc),were grown in the soil and hydroponically,and then 16S rRNA gene sequencing and nontargeted metabolomics techniques were used to investigate rhizosphere microflora and root exudate *** high microbial community evenness for the Foc-susceptible cultivar was detected,and the relative abundances of Comamonadaceae and Xanthomonadaceae were higher for the Foc-susceptible cultivar than for the other *** analysis revealed that specific functional traits,such as protein synthesis and secretion,bacterial chemotaxis,and small organic acid metabolism pathways,were significantly upregulated in the rhizobacterial community of the Foc-susceptible cultivar.A machinelearning approach in conjunction with FishTaco plus metabolic pathway analysis revealed that four organic acids(citric acid,pyruvate acid,succinic acid,and fumarate)were released at higher abundance by the Foc-susceptible cultivar compared with the resistant cultivar,which may be responsible for the recruitment of Comamonadaceae,a potential beneficial microbial *** validation demonstrated that Comamonadaceae can be“cultured”by these organic ***,compared with the resistant cultivar,the susceptible cucumber tends to assemble beneficial microbes by secreting more organic acids.

关键词： group susceptibility synthesis

The genomic and bulked segregant analysis of Curcuma alismatifolia revealed its diverse bract pigmentation

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aBIOTECH 2022年第3期3卷 178-196页

作者： Xuezhu Liao Yuanjun Ye Xiaoni Zhang Dan Peng Mengmeng Hou Gaofei Fu Jianjun Tan Jianli Zhao Rihong Jiang Yechun Xu Jinmei Liu Jinliang Yang Wusheng Liu Luke RTembrock Genfa Zhu Zhiqiang Wu Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen518120China guangdong provincial key lab of ornamental plant germplasm innovation and utilization Environmental Horticulture Research InstituteGuangdong Academy of Agricultural SciencesGuangzhou510640China Yunnan key laboratory of plant Reproductive Adaptation and Evolutionary Ecology Yunnan UniversityKunming650504China Guangxi Engineering and Technology Research Center for Woody Spices Guangxi Key Laboratory for Cultivation and Utilization of Special Non-Timber Forest CropsGuangxi Forestry Research InstituteNanning530002China Department of Agronomy and Horticulture University of Nebraska-LincolnLincolnNE68583USA Department of Horticultural Science North Carolina State UniversityRaleighNC27607USA Department of Agricultural Biology Colorado State UniversityFort CollinsCO80523USA Kunpeng Institute of Modern Agriculture at Foshan Foshan528200China

Compared with most flowers where the showy part comprises specialized leaves(petals)directly subtending the reproductive structures,most Zingiberaceae species produce showy“flowers”through modifications of leaves(bracts)subtending the true flowers throughout an *** alismatifolia,belonging to the Zingiberaceae family,a plant species originating from Southeast Asia,has become increasingly popular in the flower market worldwide because of its varied and esthetically pleasing bracts produced in different ***,we present the chromosome-scale genome assembly of ***“Chiang Mai Pink”and explore the underlying mechanisms of bract *** genomic analysis revealed *** contains a residual signal of whole-genome *** genes,including pigment-related genes,exhibit functional and structural differentiation resulting in diverse bract colors among *** *** addition,we identified the key genes that produce different colored bracts in ***,such as F3′5'H,DFR,ANS and several transcription factors for anthocyanin synthesis,as well as chlH and CAO in the chlorophyll synthesis pathway by conducting transcriptomic analysis,bulked segregant analysis using both DNA and RNA data,and population genomic *** work provides data for understanding the mechanism of bract pigmentation and will accelerate breeding in developing novel cultivars with richly colored bracts in *** and related *** is also important to understand the variation in the evolution of the Zingiberaceae family.

关键词： Anthocyanin synthesis Siam tulip Floriculture Zingiberaceae Genome evolution

The best practice for microbiome analysis using R

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Protein & Cell 2023年第10期14卷 713-725页

作者： Tao Wen Guoqing Niu Tong Chen Qirong Shen Jun Yuan Yong-Xin Liu Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China The key laboratory of plant Immunity Jiangsu provincial key lab for Organic Solid Waste utilization Jiangsu Collaborative innovation Center for Solid Organic Waste Resource utilization National Engineering Research Center for Organic-based FertilizersNanjing Agricultural UniversityNanjing 210095China National Resource Center for Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing 100700China

With the gradual maturity of sequencing technology,many microbiome studies have published,driving the emergence and advance of related analysis tools.R language is the widely used platform for microbiome data analysis for powerful ***,tens of thousands of R packages and numerous similar analysis tools have brought major challenges for many researchers to explore microbiome *** to choose suitable,efficient,convenient,and easy-to-learn tools from the numerous R packages has become a problem for many microbiome *** have organized 324 common R packages for microbiome analysis and classified them according to application categories(diversity,difference,biomarker,correlation and network,functional prediction,and others),which could help researchers quickly find relevant R packages for microbiome ***,we systematically sorted the integrated R packages(phyloseq,microbiome,MicrobiomeAnalystR,Animalcules,microeco,and amplicon)for microbiome analysis,and summarized the advantages and limitations,which will help researchers choose the appropriate ***,we thoroughly reviewed the R packages for microbiome analysis,summarized most of the common analysis content in the microbiome,and formed the most suitable pipeline for microbiome *** paper is accompanied by hundreds of examples with 10,000 lines codes in GitHub,which can help beginners to learn,also help analysts compare and test different *** paper systematically sorts the application of R in microbiome,providing an important theoretical basis and practical reference for the development of better microbiome tools in the *** the code is available at GitHub ***/taowenmicro/EasyMicrobiomeR.

关键词： R package microbiome data analysis visualization amplicon metagenome

The Asian lotus (Nelumbo nucifera) pan-plastome: diversity and divergence in a living fossil grown for seed, rhizome, and aesthetics

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ornamental plant Research 2022年第1期2卷 8-17页

作者： Jie Wang Xuezhu Liao Cuihua Gu Kunli Xiang Jie Wang Sen Li Luke R.Tembrock Zhiqiang Wu Wenchuang He College of Landscape and Architecture Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden PlantsKey Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden PlantsZhejiang Agriculture&Forestry UniversityHangzhou 311300China Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China College of Horticulture Shanxi Agricultural UniversityShanxi 030801China Department of Agricultural Biology Colorado State UniversityFort CollinsCO 80523USA

The Asian lotus(Nelumbo nucifera)has a history of cultivation in Asia dating back over 3,000 years where it has been an important food crop producing edible rhizomes and seeds as well as flowers of great aesthetic and cultural ***,we de novo assembled the plastomes of 316 lotus accessions including five North American lotus(***)and 311 Asian lotus(***)to construct a pan-plastome genome map,and investigate the phylogeography and genetic diversity among the only two extant species within this living fossil lineage.A total of 113 unique genes were annotated and plastome sizes varied between 163,457 and 163,672 bp with only minor differences in each of the four major genomic *** most abundant nucleotide differences among plastomes were single nucleotide variants followed by insertions/deletions and block substitutions mainly found in intergenic spacer regions of the large single copy portion of the *** well-supported genetic clusters were resolved using multiple different population structure *** different lotus types(flower,seed,rhizome,or wild)were disproportionally assigned to multiple different genetic *** pattern indicates that the domestication of Asian lotus involved multiple genetic origins and possible matrilineal *** mapping of accessions also revealed that genetic diversity is unevenly distributed with eastern China possessing the highest genetic diversity and regions such as Yunnan,Indonesian,and Thailand possessing unique *** results provide an important maternal history of Nelumbo and necessary groundwork for future studies on intergenomic gene transfer,cytonuclear incompatibility,and conservation genetics.

关键词： flowers divergence insertion

A high-quality genome assembly of Morinda officinalis,a famous native southern herb in the Lingnan region of southern China

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Horticulture Research 2021年第1期8卷 1668-1683页

作者： Jihua Wang Shiqiang Xu Yu Mei Shike Cai Yan Gu Minyang Sun Zhan Liang Yong Xiao Muqing Zhang Shaohai Yang guangdong provincial key laboratory of Crops Genetics&Improvement Crops Research InstituteGuangdong Academy of Agricultural Sciences510640 GuangzhouChina DongFuhang High-tech Agricultural planting and Management Co. Ltd526000 ZhaoqingChina Coconut Research Institute Chinese Academy of Tropical Agricultural Sciences571339 WenchangChina State key lab for Conservation and utilization of Subtropical Agric-Biological Resources Guangxi University530005 NanningChina

Morinda officinalis is a well-known medicinal and edible plant that is widely cultivated in the Lingnan region of southern *** dried roots(called bajitian in traditional Chinese medicine)are broadly used to treat various diseases,such as impotence and ***,we report a high-quality chromosome-scale genome assembly of *** using Nanopore single-molecule sequencing and Hi-C *** assembled genome size was 484.85Mb with a scaffold N50 of 40.97 Mb,and 90.77%of the assembled sequences were anchored on eleven *** genome includes 27,698 protein-coding genes,and most of the assemblies are repetitive *** evolution analysis revealed that *** underwent core eudicotγgenome triplication events but no recent whole-genome duplication(WGD).Likewise,comparative genomic analysis showed no large-scale structural variation after species divergence between *** and Coffea ***,gene family analysis indicated that gene families associated with plant–pathogen interactions and sugar metabolism were significantly expanded in ***,we identified many candidate genes involved in the biosynthesis of major active components such as anthraquinones,iridoids and *** addition,we also found that the DHQS,GGPPS,TPS-Clin,TPS04,sacA,and UGDH gene families—which include the critical genes for active component biosynthesis—were expanded in *** study provides a valuable resource for understanding *** genome evolution and active component *** work will facilitate genetic improvement and molecular breeding of this commercially important plant.

关键词： expanded breeding metabolism

Chromosome-scale assembly of the Dendrobium chrysotoxum genome enhances the understanding of orchid evolution

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Horticulture Research 2021年第1期8卷 2684-2697页

作者： Yongxia Zhang Guo-Qiang Zhang Diyang Zhang Xue-Die Liu Xin-Yu Xu Wei-Hong Sun Xia Yu Xiaoen Zhu Zhi-Wen Wang Xiang Zhao Wen-Ying Zhong Hongfeng Chen Wei-Lun Yin Tengbo Huang Shan-Ce Niu Zhong-Jian Liu guangdong provincial key laboratory for plant Epigenetics College of Life Sciences and OceanographyShenzhen UniversityShenzhen 518071China laboratory for Orchid Conservation and utilization Orchid Conservation and Research CenterThe National Orchid Conservation CenterShenzhen 518114China School of Food Science and Technology Foshan UniversityFoshan 528225China key laboratory of National Forestry and Grassland Administration for Orchid Conservation and utilization at College of Landscape Architecture Fujian Agriculture and Forestry UniversityFuzhou 350002China College of Forestry Fujian Agriculture and Forestry UniversityFuzhou 350002China PubBio-Tech Wuhan 430070China key laboratory of plant Resources Conservation Sustainable utilization South China Botanical GardenChinese Academy of SciencesGuangzhou 510650China College of Biological Sciences and Technology Beijing Forestry UniversityBeijing 100083China College of Horticulture Hebei Agricultural UniversityBaoding 071000China

As one of the largest families of angiosperms,the Orchidaceae family is *** represents the second largest genus of the ***,an assembled high-quality genome of species in this genus is ***,we report a chromosome-scale reference genome of Dendrobium chrysotoxum,an important ornamental and medicinal orchid *** assembled genome size of *** was 1.37 Gb,with a contig N50 value of 1.54 *** the sequences,95.75%were anchored to 19 *** were 30,044 genes predicted in the *** *** whole-genome polyploidization events occurred in *** terms of the second event,whole-genome duplication(WGD)was also found to have occurred in other Orchidaceae members,which diverged mainly via gene loss immediately after the WGD event occurred;the first duplication was found to have occurred in most monocots(tau event).We identified sugar transporter(SWEET)gene family expansion,which might be related to the abundant medicinal compounds and fleshy stems of ***-box genes were identified in ***,as well as members of TPS and Hsp90 gene families,which are associated with resistance,which may contribute to the adaptive evolution of *** also investigated the interplay among carotenoid,ABA,and ethylene biosynthesis in *** to elucidate the regulatory mechanisms of the short flowering period of orchids with yellow *** reference *** genome will provide important insights for further research on medicinal active ingredients and breeding and enhances the understanding of orchid evolution.

关键词： evolution flowers breeding

Evolution of freshwater Diaporthomycetidae(Sordariomycetes)provides evidence for five new orders and six new families

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Fungal Diversity 2021年第2期107卷 71-105页

作者： Kevin D.Hyde Dan-Feng Bao Sinang Hongsanan K.W.Thilini Chethana Jing Yang Nakarin Suwannarach Center of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand Research Centre of Microbial Diversity and Sustainable Ultilization Chiang Mai UniversityChiang Mai 50200Thailand Innovative Institute of plant Health Zhongkai University of Agriculture and EngineeringHaizhu DistrictGuangzhou 510225PR China Department of Entomology and plant Pathology Faculty of AgricultureChiang Mai UniversityChiang Mai 50200Thailand College of Agriculture and Biological Sciences Dali UniversityDali 671003YunnanPR China guangdong provincial key laboratory for plant Epigenetics Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Science and OceanographyShenzhen UniversityShenzhen 518060China School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand Guizhou key laboratory of Agricultural Biotechnology Guizhou Academy of Agricultural SciencesGuiyang 550006GuizhouChina Department of Biology Faculty of ScienceChiang Mai UniversityChiang Mai 50200Thailand

Cancellidium is a remarkable fungal genus which has been collected from wood submerged in freshwater and has unique conidia that are important in dispersal in running *** such a remarkable morphology,one would have expected it to be a distinct family or ***,due to the dearth of molecular evidence in related taxa,this genus has previ-ously been placed in the order Hypocreales,subclass Hypocreomycetidae of *** this study,we made three new collections of this remarkable aquatic genus from streams in China and Thailand,isolated them into culture,extracted DNA and carried out multigene phylogenetic analysis and divergence time estimation which placed the genus in *** is one of the seven subclasses of Sordariomycetes and contains 30 lineages that are only known from *** subclass is therefore of interest when considering the evolution of freshwater *** lineages of Diaporthomycetidae are morphologically unique and taxa cluster with strong support,but have weak support at the base of the *** phylogenetic and MCC trees generated in this study indicate that Aquapteridospora,Barbatosphaeriaceae,Bullimyces,Cancellidium,Ceratolenta,Conlarium,Phialemoniopsis,Pseudostanjehughesia and Rhamphoriaceae are distinct genera/families that evolved in the family/order time *** new orders Barbatosphaeriales(177 MYA),Cancellidiales(137 MYA),Ceratolentales(147 MYA),Conlariales(138 MYA)and Rhamphoriales(133 MYA)and six new families,Aquapteridosporaceae(110 MYA),Cancellidiaceae(137 MYA),Ceratolentaceae(81 MYA),Bullimycetaceae(81 MYA),Phialemoniopsaceae(59 MYA),and Pseudostanjehughesiaceae(111 MYA)are introduced with evidence from phylogenies,divergence estimates and distinct *** these families,Aquapteridosporaceae,Cancellidiaceae,Bullimycetaceae,and Pseudostanjehughesiaceae are only known from freshwater.

关键词： 14 new taxa Evolution Freshwater fungi New family New order

Emerging contaminants:A One Health perspective

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The innovation 2024年第4期5卷 140-170,139页

作者： Fang Wang Leilei Xiang Kelvin Sze-Yin Leung Martin Elsner Ying Zhang Yuming Guo Bo Pan Hongwen Sun Taicheng An Guangguo Ying Bryan WBrooks Deyi Hou Damian EHelbling Jianqiang Sun Hao Qiu Timothy MVogel Wei Zhang Yanzheng Gao Myrna JSimpson Yi Luo Scott XChang Guanyong Su Bryan MWong Tzung-May Fu Dong Zhu Karl JJobst Chengjun Ge Frederic Coulon Jean Damascene Harindintwali Xiankui Zeng Haijun Wang Yuhao Fu Zhong Wei Rainer Lohmann Changer Chen Yang Song Concepcion Sanchez-Cid Yu Wang Ali El-Naggar Yiming Yao Yanran Huang Japhet Cheuk-Fung Law Chenggang Gu Huizhong Shen Yanpeng Gao Chao Qin Hao Li Tong Zhang Natàlia Corcoll Min Liu Daniel SAlessi Hui Li Kristian KBrandt Yolanda Pico Cheng Gu Jianhua Guo Jianqiang Su Philippe Corvini Mao Ye Teresa Rocha-Santos Huan He Yi Yang Meiping Tong Weina Zhang Fidèle Suanon Ferdi Brahushi Zhenyu Wang Syed AHashsham Marko Virta Qingbin Yuan Gaofei Jiang Louis A.Tremblay Qingwei Bu Jichun Wu Willie Peijnenburg Edward Topp Xinde Cao Xin Jiang Minghui Zheng Taolin Zhang Yongming Luo Lizhong Zhu Xiangdong Li DamiàBarceló Jianmin Chen Baoshan Xing Wulf Amelung Zongwei Cai Ravi Naidu Qirong Shen Janusz Pawliszyn Yong-guan Zhu Andreas Schaeffer Matthias C.Rillig Fengchang Wu Gang Yu James M.Tiedje State key laboratory of Soil and Sustainable Agriculture Institute of Soil ScienceChinese Academy of SciencesNanjing 210008China University of Chinese Academy of Sciences Beijing 100049China Department of Chemistry Hong Kong Baptist UniversityHong KongChina HKBU Institute of Research and Continuing Education Shenzhen Virtual University ParkShenzhenChina Technical University of Munich TUM School of Natural SciencesInstitute of Hydrochemistry85748 GarchingGermany School of Resources&Environment Northeast Agricultural UniversityHarbin 150030China Climate Air Quality Research UnitSchool of Public Health and Preventive MedicineMonash UniversityMelbourneVICAustralia Faculty of Environmental Science&Engineering Kunming University of Science&TechnologyKunming 650500China Ministry of Education key laboratory of Pollution Processes and Environmental Criteria College of Environmental Science and EngineeringNankai UniversityTianjin 300350China guangdong key laboratory of Environmental Catalysis and Health Risk Control School of Environmental Science and EngineeringInstitute of Environmental Health and Pollution ControlGuangdong University of TechnologyGuangzhou 510006China Ministry of Education key laboratory of Environmental Theoretical Chemistry South China Normal UniversityGuangzhouGuangdong 510006China Department of Environmental Science Baylor UniversityWacoTXUSA Center for Reservoir and Aquatic Systems Research(CRASR) Baylor UniversityWacoTXUSA School of Environment Tsinghua UniversityBeijing 100084China School of Civil and Environmental Engineering Cornell UniversityIthacaNY 14853USA key laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province Zhejiang University of TechnologyHangzhou 310014China School of Environmental Science and Engineering Shanghai Jiao Tong UniversityShanghai 200240China laboratoire d’Ecologie Microbienne Universite Claude Bernard Lyon 1UMR CNRS 5557UMR INRAE 1418VetAgro Sup69622 VilleurbanneFrance Department of Pla

Environmental pollution is escalating due to rapid global development that often prioritizes human needs over planetary *** global efforts to mitigate legacy pollutants,the continuous introduction of new substances remains a major threat to both people and the *** response,global initiatives are focusing on risk assessment and regulation of emerging contaminants,as demonstrated by the ongoing efforts to establish the UN’s Intergovernmental Science-Policy Panel on Chemicals,Waste,and Pollution *** review identifies the sources and impacts of emerging contaminants on planetary health,emphasizing the importance of adopting a One Health *** for monitoring and addressing these pollutants are discussed,underscoring the need for robust and socially equitable environmental policies at both regional and international *** actions are needed to transition toward sustainable pollution management practices to safeguard our planet for future generations.

关键词： pollution planet contaminants