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Data Comparison and Software Design for Easy Selection and Application of CRISPR-based Genome Editing Systems in Plants

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Genomics, Proteomics & Bioinformatics 2021年第6期19卷 937-948页

作者： Yi Wang Fatma lecourieux Rui Zhang Zhanwu Dai david lecourieux Shaohua Li Zhenchang Liang Beijing Key Laboratory of Grape Science and Enology and CAS Key Laboratory of Plant ResourcesInstitute of Botanythe Innovative Academy of Seed DesignChinese Academy of SciencesBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China Ecophysiology and Functional Genomics of Vine Bordeaux Sciences AgroINRAEUniversity of BordeauxInstitute of Vine and Wine Sciences Bordeaux-AquitaineVillenave d’Ornon 33140France College of Plant Protection Shandong Agricultural UniversityTaian 271018China Sino-Africa Joint Research Center Chinese Academy of SciencesWuhan 430074China

CRISPR-based genome editing systems have been successfully and effectively used in many ***,only a few studies have reported the comparison between CRISPR/Cas9 and CRISPR/Cpf1 systems in the whole-genome *** many web-based toolkits are available,there is still a shortage of comprehensive,user-friendly,and plant-specific CRISPR databases and desktop *** this study,we identified and analyzed the similarities and differences between CRISPR/Cas9 and CRISPR/Cpf1 systems by considering the abundance of proto-spacer adjacent motif(PAM)sites,the effects of GC content,optimal proto-spacer length,potential universality within the plant kingdom,PAM-rich region(PARR)inhibiting ratio,and the effects of G-quadruplex(G-Q)*** this information,we built a comprehensive CRISPR database(including 138 plant genome data sources,***/pc/***),which provides search tools for the identification of CRISPR editing sites in both CRISPR/Cas9 and CRISPR/Cpf1 *** also developed a desktop software on the basis of the Perl/Tk tool,which facilitates and improves the detection and analysis of CRISPR editing sites at the whole-genome level on Linux and/or Windows ***,this study provides helpful data and software for easy selection and application of CRISPR-based genome editing systems in plants.

关键词： CRISPR/Cas PAM-rich region G-Q Software Database

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Proteomic and metabolomic profiling underlines the stage- and time-dependent effects of high temperature on grape berry metabolism

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Journal of Integrative Plant Biology 2020年第8期62卷 1132-1158页

作者： david lecourieux Christian Kappel Stéphane Claverol Philippe Pieri Regina Feil John E.Lunn Marc Bonneu Lijun Wang Eric Gomès Serge Delrot Fatma lecourieux UMR1287 EGFV INRAEBordeaux Sciences AgroBordeaux UniversityISVV33140 Villenave d'OrnonFrance Institut of Biochemistry and Biology Potsdam UniversityD-14476 PotsdamGermany Proteome Platform Bordeaux Functional Genomic CenterBordeaux University33076 BordeauxFrance Max Planck Institute of Molecular Plant Physiology 14476 PotsdamGolmGermany Institute of Botany the Chinese Academy of SciencesBeijing 100093China UMR1287 EGFV CNRSINRAEBordeaux Sciences AgroBordeaux UniversityISVV33140 Villenave d'OrnonFrance

Climate change scenarios predict an increase in mean air temperatures and in the frequency,intensity,and length of extreme temperature events in many wine-growing regions *** elevated temperature has detrimental effects on berry growth and composition,it threatens the economic and environmental sustainability of wine *** Cabernet Sauvignon fruit-bearing cuttings,we investigated the effects of high temperature(HT)on grapevine berries through a label-free shotgun proteomic analysis coupled to a complementary metabolomic *** the 2,279 proteins identified,592 differentially abundant proteins were found in berries exposed to *** gene ontology categories“stress,”“protein,”“secondary metabolism,”and“cell wall”were predominantly altered under *** temperatures strongly impaired carbohydrate and energy metabolism,and the effects depended on the stage of development and duration of *** amounts correlated poorly with protein expression levels in HT berries,highlighting the value of proteomic studies in the context of heat ***,this work reveals that HT alters key proteins driving berry development and ***,we provide a list of differentially abundant proteins that can be considered as potential markers for developing or selecting grape varieties that are better adapted to warmer climates or extreme heat waves.

关键词： metabolism extreme high

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Proteomic analysis of early-stage incompatible and compatible interactions between grapevine and ***

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Horticulture Research 2021年第1期8卷 1560-1580页

作者： Guo-Tian Liu Bian-Bian Wang david lecourieux Mei-Jie Li Ming-Bo Liu Rui-Qi Liu Bo-Xing Shang Xiao Yin Li-Jun Wang Fatma lecourieux Yan Xu State Key Laboratory of Crop Stress Biology for Arid Areas College of HorticultureNorthwest A&F UniversityYanglingChina Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China Ministry of AgricultureNorthwest A&F UniversityYanglingChina UMR1287 EGFV CNRSUniversitéde BordeauxINRAEBordeaux Sciences AgroISVVVillenave d’OrnonFrance Institute of Botany The Chinese Academy of SciencesBeijingChina

Wild grapevines can show strong resistance to the downy mildew pathogen ***,but the associated mechanisms are poorly described,especially at early stages of ***,we performed comparative proteomic analyses of grapevine leaves from the resistant genotype ***“LiuBa-8”(LB)and susceptible ***“Pinot Noir”(PN)12h after inoculation with *** employing the iTRAQ technique,a total of 444 and 349 differentially expressed proteins(DEPs)were identified in LB and PN,*** majority of these DEPs were related to photosynthesis,respiration,cell wall modification,protein metabolism,stress,and redox *** with PN,LB showed fewer downregulated proteins associated with photosynthesis and more upregulated proteins associated with *** least a subset of PR proteins(PR10.2 and PR10.3)was upregulated upon inoculation in both genotypes,whereas HSP(HSP70.2 and HSP90.6)and cell wall-related XTH and BXL1 proteins were specifically upregulated in LB and PN,*** the incompatible interaction,ROS signaling was evident by the accumulation of H_(2)O_(2),and multiple APX and GST proteins were *** DEPs may play crucial roles in the grapevine response to downy *** results provide new insights into molecular events associated with downy mildew resistance in grapevine,which may be exploited to develop novel protection strategies against this disease.

关键词： metabolism homeostasis analysis

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New insights into the heat responses of grape leaves via combined phosphoproteomic and acetylproteomic analyses

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Horticulture Research 2019年第1期6卷 489-503页

作者： Guo-Tian Liu Jian-Fu Jiang Xin-Na Liu Jin-Zhu Jiang Lei Sun Wei Duan Rui-Min Li Yi Wang david lecourieux Chong-Huai Liu Shao-Hua Li Li-Jun Wang Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources Institute of Botanythe Chinese Academy of SciencesBeijing 100093China Zhengzhou Fruit Research Institute Chinese Academy of Agricultural SciencesZhengzhou 450009China College of Horticulture Northwest A&F UniversityYangling 712100China Universite´de Bordeaux ISVVEcophysiologie et Ge´nomique Fonctionnelle de la VigneUMR 1287F-33140 Villenave d’OrnonFrance INRA ISVVEcophysiologie et Ge´nomique Fonctionnelle de la VigneUMR 1287F-33140 Villenave d’OrnonFrance University of Chinese Academy of Sciences Beijing 100093China

Heat stress is a serious and widespread threat to the quality and yield of many crop species,including grape(Vitis vinifera L.),which is cultivated ***,we conducted phosphoproteomic and acetylproteomic analyses of leaves of grape plants cultivated under four distinct temperature *** phosphorylation or acetylation of a total of 1011 phosphoproteins with 1828 phosphosites and 96 acetyl proteins with 148 acetyl sites changed when plants were grown at 35℃,40℃,and 45℃in comparison with the proteome profiles of plants grown at 25℃.The greatest number of changes was observed at the relatively high *** classification and enrichment analysis indicated that phosphorylation,rather than acetylation,of serine/arginine-rich splicing factors was involved in the response to high *** finding is congruent with previous observations by which alternative splicing events occurred more frequently in grapevine under high *** in acetylation patterns were more common than changes in phosphorylation patterns in photosynthesis-related proteins at high temperatures,while heat-shock proteins were associated more with modifications involving phosphorylation than with those involving *** proteins were identified with changes associated with both phosphorylation and acetylation,which is consistent with crosstalk between these posttranslational modification types.

关键词： temperature cultivated Vitis

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