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Genomic insights into the origin, adaptive evolution, and herbicide resistance of Leptochloa chinensis, a devastating tetraploid weedy grass in rice fields

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Molecular Plant 2022年第6期15卷 1045-1058页

作者： Lifeng Wang Xuepeng Sun Yajun Peng Ke Chen Shan Wu Yanan Guo Jingyuan Zhang Haona Yang Tao Jin Lamei Wu Xiaomao Zhou Bin Liang Zhenghong Zhao Ducai Liu zhangjun fei Lianyang Bai State Key Laboratory of Hybrid Rice Hunan Academy of Agricultural SciencesChangsha 410125China Hunan Weed Science Key Laboratory Hunan Academy of Agricultural SciencesChangsha 410125China Boyce Thompson Institute Cornell UniversityIthacaNY 14853USA College of Horticulture Science Zhejiang A&F UniversityHangzhou 311300China Qingdao Kingagroot Compounds Co.Ltd Qingdao 266000China USDA-ARS Robert W.Holley Center for Agriculture and HealthIthacaNY 14853USA

Chinese sprangletop (Leptochloa chinensis), belonging to the grass subfamily Chloridoideae, is one of the most notorious weeds in rice ecosystems. Here, we report a chromosome-scale reference genome assembly and a genomic variation map of the tetraploid L. chinensis. The L. chinensis genome is derived from two diploid progenitors that diverged ∼10.9 million years ago, and its two subgenomes display neither fractionation bias nor overall gene expression dominance. Comparative genomic analyses reveal substantial genome rearrangements in L. chinensis after its divergence from the common ancestor of Chloridoideae and, together with transcriptome profiling, demonstrate the important contribution of tetraploidization to the gene sources for the herbicide resistance of L. chinensis. Population genomic analyses of 89 accessions from China reveal that L. chinensis accessions collected from southern/southwestern provinces have substantially higher nucleotide diversity than those from the middle and lower reaches of the Yangtze River, suggesting that L. chinensis spread in China from the southern/southwestern provinces to the middle and lower reaches of the Yangtze River. During this spread, L. chinensis developed significantly increased herbicide resistance, accompanied by the selection of numerous genes involved in herbicide resistance. Taken together, our study generated valuable genomic resources for future fundamental research and agricultural management of L. chinensis, and provides significant new insights into the herbicide resistance as well as the origin and adaptive evolution of L. chinensis.

关键词： Leptochloa weed sgenome polyploidization genome evolution genetic diversity adaptive selection herbicide resistance

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Plant Genome Editing Database (PGED): A Call for Submission of Information about Genome-Edited Plant Mutants

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Molecular Plant 2019年第2期12卷 127-129页

作者： Yi Zheng Ning Zhang Gregory B. Martin zhangjun fei Boyce Thompson Institute for Plant Research Ithaca NY 14853 USA Plant Pathology and Plant-Microbe Biology Section School of Integrative 2Plant Pathology and Plant-Microbe Biology Section School of Integrative Plant Science Cornell University Ithaca NY 14853 USA USDA-ARS Robert W. Holley Center for Agriculture and Health Ithaca NY 14853 USA These authors contributed equally to this article

Recent advances in genome editing technologies, particularly CRISPR/Cas, enable the alteration of DNA sequences to produce deletions, insertions, and substitutions in genes (Jaganathan et al., 2018), as well as large ... 详细信息

关键词： Plant Genome Editing Database (PGED) Genome-Edited Plant Mutants

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Plant lncRNAs are enriched in and move systemically through the phloem in response to phosphate deficiency

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Journal of Integrative Plant Biology 2019年第4期61卷 492-508页

作者： Zhaoliang Zhang Yi Zheng Byung-Kook Ham Shupei Zhang zhangjun fei William J.Lucas State Key Laboratory of Tea Biology and Utilization Anhui Agricultural University Boyce Thompson Institute for Plant Research Cornell University Global Institute for Food Security Department of Biology University of Saskatchewan Department of Plant Biology College of Biological Sciences University of California

In response to phosphate(Pi) deficiency, it has been shown that micro-RNAs(miRNAs) and mRNAs are transported through the phloem for delivery to sink tissues. Growing evidence also indicates that long noncoding RNAs(lncRNAs) are critical regulators of Pi homeostasis in plants. However, whether lncRNAs are present in and move through the phloem, in response to Pi deficiency, remains to be established. Here, using cucumber as a model plant, we show that lncRNAs are enriched in the phloem translocation stream and respond,systemically, to an imposed Pi-stress. A well-known lncRNA, IPS1, the target mimic(TM) of miRNA399,accumulates to a high level in the phloem, but is not responsive to early Pi deficiency. An additional 24 miRNA TMs were also detected in the phloem translocation stream; among them miRNA171 TMs and miR166 TMs were induced in response to an imposed Pi stress.Grafting studies identified 22 lncRNAs which move systemically into developing leaves and root tips. A CU-rich PTB motif was further identified in these mobile lncRNAs. Our findings revealed that lncRNAs respond to Pi deficiency, non-cell-autonomously, and may act as systemic signaling agents to coordinate early Pi deficiency signaling, at the whole-plant level.

关键词： Plant lncRNAs enriched phloem phosphate deficiency

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An R2R3-type myeloblastosis transcription factor MYB103 is involved in phosphorus remobilization

食物生产加工与营养(英文)

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食物生产加工与营养(英文) 2020年第1期2卷 241-248页

作者： Fangwei Yu Shenyun Wang Wei Zhang Hong Wang Li Yu zhangjun fei Jianbin Li Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement Institute of Vegetable CropsJiangsu Academy of Agricultural SciencesNanjing 210014China Boyce Thompson Institute Cornell UniversityIthacaNY 14853USA

The members of myeloblastosis transcription factor(MYB TF)family are involved in the regulation of biotic and abiotic stresses in plants.However,the role of MYB TF in phosphorus remobilization remains largely unexplored.In the present study,we show that an R2R3 type MYB transcription factor,MYB103,is involved in phosphorus(P)remobilization.MYB103 was remarkably induced by P deficiency in cabbage(Brassica oleracea var.capitata L.).As cabbage lacks the proper mutant for elucidating the mechanism of MYB103 in P deficiency,another member of the crucifer family,Arabidopsis thaliana was chosen for further study.The transcript of its homologue AtMYB103 was also elevated in response to P deficiency in A.thaliana,while disruption of AtMYB103(myb103)exhibited increased sensitivity to P deficiency,accompanied with decreased tissue biomass and soluble P concentration.Furthermore,AtMYB103 was involved in the P reutilization from cell wall,as less P was released from the cell wall in myb103 than in wildtype,coinciding with the reduction of ethylene production.Taken together,our results uncover an important role of MYB103 in the P remobilization,presumably through ethylene signaling.

关键词： Brassica oleracea var.capitata L. Arabidopsis thaliana Cell wall Ethylene Phosphorus MYB103

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Tecia solanivora infestation increases tuber starch accumulation in Pastusa Suprema potatoes

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Journal of Integrative Plant Biology 2018年第11期60卷 1083-1096页

作者： Pavan Kumar Etzel Garrido Kun Zhao Yi Zheng Saleh Alseekh Erandi Vargas-Ortiz Alisdair R.Fernie zhangjun fei Katja Poveda Georg Jander Boyce Thompson Institute for Plant Research 533 Tower RoadIthacaNY 14853USA Department of Entomology Cornell UniversityIthacaNY 14853USA Max Planck Institute of Molecular Plant Physiology Wissenschaftspark GolmAm Muhlenberg 114476 PotsdamGermany department of entomology and nematology university of floridaGainesvilleFL 32611USA unidad de microbiologia basica y aplicada facultad de ciencias naturalesuniversidad autonoma de queretaroAv.de las Ciencias SINJuriquillaquerdtaroMdxico department of molecular biology institute for scientific and technological research of san luis potosiMexico

In response to infestation with larvae of the Guatemalan tuber moth （Tecia solanivora）, some Solanum tuberosum （potato） varieties exhibit an overcompensa- tion response, whereby the total dry mass of uninfested tubers is increased. Here, we describe early responses, within the first few days, of T. solanivora feeding, in the Colombian potato variety Pastusa Suprema. Non- targeted metabolite profiling showed significant second- ary metabolism changes in T. solanivora-infested tubers, but not in uninfested systemic tubers. In contrast, changes in primary metabolism were greater in unin- fested systemic tubers than in the infested tubers, with a notable 80% decline in systemic tuber sucrose levels within 1 d of T. solanivora infestation. This suggested either decreased sucrose transport from the leaves or increased sink strength, i.e., more rapid sucrose to starch conversion in the tubers. Increased sucrose synthesis was indicated by higher rubisco activase and lower starch synthase gene expression in the leaves of infested plants. Elevated sink strength was demonstrated by 45% more total starch deposition in systemic tubers of T. solanivord- infested plants compared to uninfested control plants. Thus, rather than investing in increased defense of uninfested tubers, Pastusa Suprema promotes deposition of photoassimilates in the form of starch as a response to T. solanivora infestation.

关键词： Tecia solanivora infestation increases tuber starch accumulation in Pastusa Suprema potatoes Figure

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Kiwifruit Genome Database(KGD):a comprehensive resource for kiwifruit genomics

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Horticulture Research 2020年第1期7卷 1076-1083页

作者： Junyang Yue Jiacheng Liu Wei Tang Ya Qing Wu Xiaofeng Tang Wei Li Ying Yang Lihuan Wang Shengxiong Huang Congbing Fang Kun Zhao zhangjun fei Yongsheng Liu Yi Zheng School of Horticulture Anhui Agricultural UniversityHefei 230036China School of Food and Biological Engineering Hefei University of TechnologyHefei 230009China Boyce Thompson Institute Cornell UniversityIthacaNY 14853USA USDA-Agricultural Research Service Robert W.Holley Center for Agriculture and HealthIthacaNY 14853USA Ministry of Education Key Laboratory for Bio-resource and Eco-environment College of Life ScienceState Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengdu 610064China Beijing Advanced Innovation Center for Tree Breeding by Molecular Design Beijing University of AgricultureBeijing 102206China Plant Science and Technology College Beijing University of AgricultureBeijing 102206China

Kiwifruit(Actinidia spp.)plants produce economically important fruits containing abundant,balanced phytonutrients with extraordinarily high vitamin C contents.Since the release of the first kiwifruit reference genome sequence in 2013,large volumes of genome and transcriptome data have been rapidly accumulated for a handful of kiwifruit species.To efficiently store,analyze,integrate,and disseminate these large-scale datasets to the research community,we constructed the Kiwifruit Genome Database(KGD;http://***/).The database currently contains all publicly available genome and gene sequences,gene annotations,biochemical pathways,transcriptome profiles derived from public RNA-Seq datasets,and comparative genomic analysis results such as syntenic blocks and homologous gene pairs between different kiwifruit genome assemblies.A set of user-friendly query interfaces,analysis tools and visualization modules have been implemented in KGD to facilitate translational and applied research in kiwifruit,which include JBrowse,a popular genome browser,and the NCBI BLAST sequence search tool.Other notable tools developed within KGD include a genome synteny viewer and tools for differential gene expression analysis as well as gene ontology(GO)term and pathway enrichment analysis.

关键词： comprehensive fruit

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Differential gene regulatory pathways and co-expression networks associated with fire blight infection in apple(Malus×domestica)

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Horticulture Research 2019年第1期6卷 1116-1128页

作者： Katchen Julliany Pereira Silva Jugpreet Singh Ryland Bednarek zhangjun fei Awais Khan Plant Pathology and Plant-Microbe Biology Section Cornell UniversityGenevaNY 14456USA Boyce Thompson Institute Cornell UniversityIthacaNY 14853USA

Apple cultivars with durable resistance are needed for sustainable management of fire blight,the most destructive bacterial disease of apples.Although studies have identified genetic resistance to fire blight in both wild species and cultivated apples,more research is needed to understand the molecular mechanisms underlying host–pathogen interaction and differential genotypic responses to fire blight infection.We have analyzed phenotypic and transcriptional responses of‘Empire’and‘Gala’apple cultivars to fire blight by infecting them with a highly aggressive E.amylovora strain.Disease progress,based on the percentage of visual shoot necrosis,started showing significant(p<0.001)differences between‘Empire’and‘Gala’4 days after infection(dai).‘Empire’seems to slow down bacterial progress more rapidly after this point.We further compared transcriptome profiles of‘Empire’and‘Gala’at three different time points after fire blight infection.More genes showed differential expression in‘Gala’at earlier stages,but the number of differentially expressed genes increased in‘Empire’at 3 dai.Functional classes related to defense,cell cycle,response to stress,and biotic stress were identified and a few co-expression gene networks showed particular enrichment for plant defense and abiotic stress response genes.Several of these genes also co-localized in previously identified quantitative trait locus regions for fire blight resistance on linkage groups 7 and 12,and can serve as functional candidates for future research.These results highlight different molecular mechanisms for pathogen perception and control in two apple cultivars and will contribute toward better understanding of E.amylovora-Malus pathosystem.

关键词： blight cultivar networks

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A key‘foxy’aroma gene is regulated by homologyinduced promoter indels in the iconic juice grape‘Concord’

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Horticulture Research 2020年第1期7卷 2028-2039页

作者： Yingzhen Yang JoséCuenca Nian Wang Zhenchang Liang Honghe Sun Benjamin Gutierrez Xiaojun Xi Jie Arro YiWang Peige Fan Jason Londo Peter Cousins Shaohua Li zhangjun fei Gan-Yuan Zhong US Department of Agriculture-Agricultural Research Service Grape Genetics Research UnitGenevaNYUSA Beijing Key Laboratory of Grape Sciences and Enology Laboratory of Plant ResourcesInstitute of BotanyChinese Academy of SciencesBeijingChina Boyce Thompson Institute for Plant Research Cornell UniversityIthacaNYUSA US Department of Agriculture-Agricultural Research Service Plant Genetic Resources UnitGenevaNYUSA Forestry and Pomology Research Institute Shanghai Academy of Agricultural SciencesShanghaiChina University of Chinese Academy of Sciences BeijingChina E.&J.Gallo Winery ModestoCAUSA US Department of Agriculture–Agricultural Research Service Robert W.Holley Center for Agriculture and HealthIthacaNYUSA Present address:Centro de Citricultura y Producción Vegetal.Instituto Valenciano de Investigaciones Agrarias MoncadaValenciaSpain Present address:College of Horticulture and Forestry Huazhong Agricultural UniversityWuhanHubeiChina

‘Concord’,the most well-known juice grape with a parentage of the North American grape species Vitis labrusca L.,possesses a special‘foxy’aroma predominantly resulted from the accumulation of methyl anthranilate(MA)in berries.This aroma,however,is often perceived as an undesirable attribute by wine consumers and rarely noticeable in the common table and wine grape species V.vinifera.Here we discovered homology-induced promoter indels as a major genetic mechanism for species-specific regulation of a key‘foxy’aroma gene,anthraniloyl-CoA:methanol acyltransferase(AMAT),that is responsible for MA biosynthesis.We found the absence of a 426-bp and/or a 42-bp sequence in AMAT promoters highly associated with high levels of AMAT expression and MA accumulation in‘Concord’and other V.labrusca-derived grapes.These promoter variants,all with direct and inverted repeats,were further confirmed in more than 1,300 Vitis germplasm.Moreover,functional impact of these indels was validated in transgenic Arabidopsis.Superimposed on the promoter regulation,large structural changes including exonic insertion of a retrotransposon were present at the AMAT locus in some V.vinifera grapes.Elucidation of the AMAT genetic regulation advances our understanding of the‘foxy’aroma trait and makes it genetically trackable and amenable in grapevine breeding.

关键词： insertion aroma grape

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The genome and transcriptome analysis of snake gourd provide insights into its evolution and fruit development and ripening

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Horticulture Research 2020年第1期7卷 204-218页

作者： Lili Ma Qing Wang Jianlou Mu Anzhen Fu Changlong Wen Xiaoyan Zhao Lipu Gao Jian Li Kai Shi Yunxiang Wang Xuewen Zhang Xuechuan Zhang zhangjun fei Donald Grierson Jinhua Zuo Key Laboratory of Vegetable Postharvest Processing Ministry of AgricultureBeijing Key Laboratory of Fruits and Vegetable Storage and ProcessingKey Laboratory of Biology and Genetic Improvement of Horticultural Crops(North China)of Ministry of AgricultureKey Laboratory of Urban Agriculture(North)of Ministry of AgricultureThe Collaborative Innovation Center of Cucurbit CropsBeijing Vegetable Research CenterBeijing Academy of Agriculture and Forestry SciencesBeijing 100097China College of Food Science and Technology Hebei Agricultural UniversityBaoding 071001China Beijing Advanced Innovation Center for Food Nutrition and Human Health Beijing Technology and Business UniversityBeijing 100048China Department of Horticulture Zhejiang UniversityHangzhou 310058China Biomarker Technologies Corporation Beijing 101300China Boyce Thompson Institute for Plant Research Cornell UniversityIthacaNY 14853USA U.S.Department of Agriculture-Agricultural Research Service Robert W.Holley Center for Agriculture and HealthIthacaNY 14853USA School of Biosciences University of NottinghamSutton Bonington CampusLoughboroughLeicestershire LE125RDUK

Snake gourd(Trichosanthes anguina L.),which belongs to the Cucurbitaceae family,is a popular ornamental and food crop species with medicinal value and is grown in many parts of the world.Although progress has been made in its genetic improvement,the organization,composition,and evolution of the snake gourd genome remain largely unknown.Here,we report a high-quality genome assembly for snake gourd,comprising 202 contigs,with a total size of 919.8 Mb and an N50 size of 20.1 Mb.These findings indicate that snake gourd has one of the largest genomes of Cucurbitaceae species sequenced to date.The snake gourd genome assembly harbors 22,874 protein-coding genes and 80.0%of the genome consists of repetitive sequences.Phylogenetic analysis reveals that snake gourd is closely related to sponge gourd but diverged from their common ancestor~33–47 million years ago.The genome sequence reported here serves as a valuable resource for snake gourd genetic research and comparative genomic studies in Cucurbitaceae and other plant species.In addition,fruit transcriptome analysis reveals the candidate genes related to quality traits during snake gourd fruit development and provides a basis for future research on snake gourd fruit development and ripening at the transcript level.

关键词： Snake evolution snake

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Genetic characterization of melon accessions in the U.S. National Plant Germplasm System and construction of a melon core collection

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Molecular Horticulture 2021年第1期1卷 72-84页

作者： Xin Wang Kaori Ando Shan Wu Umesh K.Reddy Prabin Tamang Kan Bao Sue A.Hammar Rebecca Grumet James D.McCreight zhangjun fei Boyce Thompson Institute Cornell UniversityIthacaNY 14853USA U.S.Department of Agriculture-Agricultural Research Service Crop Improvement and Protection Research UnitSalinasCA 93905USA Nunhems USA IncAcampoCA 95220USA Gus R.Douglass Institute and Department of Biology West Virginia State UniversityInstituteWV 25112USA U.S.Department of Agriculture-Agricultural Research Service Natural Products Utilization Research UnitThad Cochran Research CenterP.O.Box 1848OxfordMS 38677USA Department of Horticulture Michigan State UniversityEast LansingMI 48824USA U.S.Department of Agriculture-Agricultural Research Service Robert W.Holley Center for Agriculture and HealthIthacaNY 14853USA.

Melon(C.melo L.)is an economically important vegetable crop cultivated worldwide.The melon collection in the U.S.National Plant Germplasm System(NPGS)is a valuable resource to conserve natural genetic diversity and provide novel traits for melon breeding.Here we use the genotyping-by-sequencing(GBS)technology to characterize 2083 melon accessions in the NPGS collected from major melon production areas as well as regions where primitive melons exist.Population structure and genetic diversity analyses suggested that C.melo ssp.melo was firstly introduced from the centers of origin,Indian and Pakistan,to Central and West Asia,and then brought to Europe and Americas.C.melo ssp.melo from East Asia was likely derived from C.melo ssp.agrestis in India and Pakistan and displayed a distinct genetic background compared to the rest of ssp.melo accessions from other geographic regions.We developed a core collection of 383 accessions capturing more than 98%of genetic variation in the germplasm,providing a publicly accessible collection for future research and genomics-assisted breeding of melon.Thirty-five morphological characters investigated in the core collection indicated high variability of these characters across accessions in the collection.Genome-wide association studies using the core collection panel identified potentially associated genome regions related to fruit quality and other horticultural traits.This study provides insights into melon origin and domestication,and the constructed core collection and identified genome loci potentially associated with important traits provide valuable resources for future melon research and breeding.

关键词： Melon C.melo Germplasm Genetic characterization Core collection Genome-wide association study

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