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Comparative transcriptomics reveals hidden issues in the plant response to arthropod herbivores

Journal of Integrative Plant Biology 2021年第2期63卷 312-326页

作者： M.Estrella Santamaria Alejandro Garcia Ana Amaiz Irene Rosa-Diaz Gara Romero-Hernandez Isabel Diaz Manuel Martinez Centro de biotecnologia y Genomica de Plantas Instituto Nacional de Investigacion y Tecnologia Agraria y AlimentariaUniversidad Politecnica de MadridMadridSpain Departamento de Biotecnologia-Biologia Vegetal Escuela Tecnica Superior de Ingenierfa AgronomicaAlimentaria y de BiosistemasUniversidad Politecnica de MadridMadridSpain

Plants experience different abiotic/biotic stresses,which trigger their molecular machinery to cope with them. Besides general mechanisms prompted by many stresses, specific mechanisms have been introduced to optimize the response to individual threats. However, these key mechanisms are difficult to identify. Here, we introduce an in-depth species-specific transcriptomic analysis and conduct an extensive meta-analysis of the responses to related species to gain more knowledge about plant responses. The spider mite Tetranychus urticae was used as the individual species, several arthropod herbivores as the related species for meta-analysis, and Arabidopsis thaliana plants as the common host. The analysis of the transcriptomic data showed typical common responses to herbivory, such as jasmonate signaling or glucosinolate biosynthesis. Also, a specific set of genes likely involved in the particularities of the Arabidopsis-spider mite interaction was discovered. The new findings have determined a prominent role in this interaction of the jasmonateinduced pathways leading to the biosynthesis of anthocyanins and tocopherols. Therefore, tandem individual/general transcriptomic profiling has been revealed as an effective method to identify novel relevant processes and specificities in the plant response to environmental stresses.

关键词： Arabidopsis thaliana arthropod herbivore comparative transcriptomics plant defense Tetranychus urticae

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OsDMI3,a Ca^(2+)/calmodulin kinase,integrates and amplifies H_(2)O_(2) and Ca^(2+) signaling in ABA-mediated responses

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Molecular Plant 2023年第6期16卷 968-970页

作者： Miguel-Angel Torres Diego Jose Berlanga Centro de biotecnologia y Genomica de Plantas Universidad Politecnica de Madrid(UPM)-Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria(INIA/CSIC)Campus de Montegancedo UPM28223 Pozuelo de AlarconMadridSpain Departamento de Biotecnologia-Biologia Vegetal Escuela Técnica Superior de Ingenieria AgronomicaAlimentaria y de BiosistemasUPM28040 MadridSpain

Abscisic acid(ABA)is an important hormone that regulates both plant development and stress responses(Chen et al.,2020).In the absence of ABA,group A PROTEIN PHOSPHATASE 2Cs(PP2Cs)interact with and inhibit SUCROSE-NON-FERMENTING 1-RELATED KINASES 2(SnRK2s).When ABA is present,ABA receptor PYRABACTIN RESISTANCE 1 and PYRABACTIN RESISTANCE 1-LIKE PROTEINS bind to and inhibit PP2Cs,allowing phosphorylation and activation of SnRK2s that,in turn,phosphorylate downstream targets,such as transcription factors,ion channels,and transporters(Figure 1).

关键词： SnRK2 Figure

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In vitro germination and shoot proliferation of the threatened species Cinchona officinalis L(Rubiaceae).

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Journal of Forestry Research 2016年第6期27卷 1229-1236页

作者： Rosa Armijos-Gonzalez Cesar Perez-Ruiz departamento de Ciencias Naturales Universidad Tecnica Particular de LojaCP 1101 608 LojaEcuador departamento de biotecnologia y biologia vegetal E.T.S.Ingenieros AgronomosUniversidad Politecnica de MadridCP 728040 MadridSpain

Cinchona officinalis （Rubiaceae） is an endemic species of the Loja Valley in southern Ecuador with medicinal uses. Because of over-exploitation in the nine- teenth century and more recent disturbances to its ecosystem, C. officinalis populations are threatened. Currently, natural regeneration of the populations is low, despite its high plant regeneration and seed formation capacity. In the present study, an efficient protocol for germination, shoot proliferation and plantlets regeneration was developed for this species. Phenolic content and germination rate of C. officinalis seeds were compared with a control species, C. pubescens. Nodal segments from seedlings of C. officinalis were cultured on Gamborg medium supplemented with different combinations of plant growth regulators. Because the phenol content is high in C. officinalis, the phenolic should be removed with hydrogen peroxide or water washes to stimulate germination. Shoots and callus developed from nodal segments within 45 days using most of the tested combinations of plant growth regulators. The best rates of shoot proliferation, callus formation and adventitious buds were obtained in medium supplemented with 5.0 mg L^-1 6-benzyl-aminopurine and 3.0 mg L^-1 indole- 3-butyfic acid.

关键词： Callus Cinchona officinalis Germination Phenols Rubiaceae Shoot

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Reconstruction of lateral root formation through single-cell RNA sequencing reveals order of tissue in itiation

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Molecular Plant 2021年第8期14卷 1362-1378页

作者： Laura Serrano-Ron Pablo Perez-Garcia Alvaro Sanchez-Corrionero Inmaculada Gude Javier Cabrera Pui-Leng Ip Kenneth D.Birnbaum Miguel A.Moreno-Risueno Centro de biotecnologia y Genomica de Plantas Universidad Politecnica de Madrid(UPM)-lnstituto Naci on al de Investigacion y Tec no logia Agraria y Alimentaria(INIA)Pozuelo de Alarcon28223 MadridSpain Departamento de Biotecnologia-Biologia Vegetal Escuela Tecnica Superior de Ingenieria AgronomicaAlimentaria y de BiosistemasUniversidad Politecnica de Madrid(UPM)28040 MadridSpain Center for Genomics and Systems Biology Department of BiologyNew York UniversityNew YorkNYUSA

Postembryonic organogenesis is critical for plant development.Underground,lateral roots(LRs)form the bulk of mature root systems,yet the ontogeny of the LR primordium(LRP)is not clear.In this study,we performed the single-cell RNA sequencing through the first four stages of LR formation in Arabidopsis.Our analysis led to a model in which a single group of precursor cells,with a cell identity different from their pericycle origins,rapidly reprograms and splits into a mixed ground tissue/stem cell niche fate and a vascular precursor fate.The ground tissue and stem cell niche fates soon separate and a subset of more specialized vascular cells form sucrose transporting phloem cells that appear to connect to the primary root.We did not detect cells resembling epidermis or root cap,suggesting that outer tissues may form later,preceding LR emergence.At this stage,some remaining initial precursor cells form the primordium flanks,while the rest create a reservoir of pluripotent cells that are able to replace the LR if damaged.Laser ablation of the central and lateral LRP regions showed that remaining cells restart the sequence of tissue initiation to form a LR.Collectively,our study reveals an ontological hierarchy for LR formation with an early and sequential split of main root tissues and stem cells.

关键词： organogenesis patterning stem cells single-cell RNA-seq cell fate regeneration

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Spatiotemporal oxygen dynamics in young leaves reveal cyclic hypoxia in plants

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Molecular Plant 2024年第3期17卷 377-394页

作者： Paolo M.Triozzi Luca Brunello Giacomo Novi Gianmarco Ferri Francesco Cardarelli Elena Loreti Mariano Perales Pierdomenico Perata PlantLab Center of Plant SciencesSant'Anna School of Advanced Studies56010 PisaItaly Centro de biotecnologia y Genomica de Plantas Universidad Politecnica de Madrid(UPM)-Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria(INIA-CSIC)Campus de Montegancedo UPMPozuelo de Alarcon28223 MadridSpain Fondazione Pisana per la Scienza 56017 PisaItaly Laboratorio NEST Scuola Normale SuperioreIstituto Nanoscienze-CNRPiazza S.Silvestro1256127 PisaItaly institute of Agricultural Biology and Biotechnology National Research Council56124 PisaItaly Departamento de Biotecnologia-Biologia Vegetal Escuela Tecnica Superior de Ingenieria AgronomicaAlimentaria y de BiosistemasUniversidad Politecnica de Madrid(UPM)28040 Madrid.Spain

Oxygen is essential for plant growth and development.Hypoxia occurs in plants due to limited oxygen avail-abilityfollowing adverse environmental conditions as well inhypoxic niches in otherwisenormoxic environ-ments.However,the existence and functional integration of spatiotemporal oxygen dynamics with plant development remains unknown.In animal systems dynamic fluctuations in oxygen availability are known as cyclic hypoxia.In this study,we demonstrate that cyclic fluctuations in internal oxygen levels occur in young emerging leaves of Arabidopsis plants.Cyclic hypoxia in plants is based on a mechanism requiring the ETHYLENE RESPONSE FACTORS type VII(ERFVII)that are central components of the oxygen-sensing machinery in plants.The ERFVll-dependent mechanism allows precise adjustment of leaf growth in response to carbon status and oxygen availability within plant cells.This study thus establishes a functional connection between internal spatiotemporal oxygen dynamics and developmental processes of plants.

关键词： Arabidopsis hypoxia cyclic hypoxia leaf development oxygen-sensing mechanism ERFVII

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Engineering Improved Photosynthesis in the Era of Synthetic Biology

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Plant Communications 2020年第2期1卷 1-17页

作者： Willian Batista-Silva Paula da Fonseca-Pereira Auxiliadora Oliveira Martins Agustin Zsogon Adriano Nunes-Nesi Wagner L.Araujo departamento de biologia vegetal Universidade Federal de Vic¸osaVic¸osaMinas Gerais 36570-900Brazil

Much attention has been given to the enhancement of photosynthesis as a strategy for the optimization of crop productivity.As traditional plant breeding is most likely reaching a plateau,there is a timely need to accelerate improvements in photosynthetic efficiency by means of novel tools and biotechnological solutions.The emerging field of synthetic biology offers the potential for building completely novel pathways in predictable directions and,thus,addresses the global requirements for higher yields expected to occur in the 21st century.Here,we discuss recent advances and current challenges of engineering improved photosynthesis in the era of synthetic biology toward optimized utilization of solar energy and carbon sources to optimize the production of food,fiber,and fuel.

关键词： photosynthesis synthetic biology genetic engineering yield improvement targeted manipulation

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The FAIR Data Point:Interfaces and Tooling

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Data Intelligence 2023年第1期5卷 184-201页

作者： Oussama Mohammed Benhamed Kees Burger Rajaram Kaliyaperumal Luiz Olavo Bonino da Silva Santos Marek Suchánek Jan Slifka Mark D.Wilkinsoni Departamento de Biotecnologia-Biologia Vegetal Escuela Tecnica Superior de Ingenieria AgronomicaAlimentaria y de BiosistemasCentro de Biotecnologia y Genomica de Plantas UPM-INIAUniversidad Politecnica de Madrid(UPM)-Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria(INIA)MadridES 28223Spain Leiden University Medical Center Leiden2333 ZCthe Netherlands University of Twente Enschede7513 GBthe Netherlands Czech Technical University in Prague PragueCZ 15000Czech Republic

While the FAIR Principles do not specify a technical solution for'FAIRness',it was clear from the outset of the FAIR initiative that it would be useful to have commodity software and tooling that would simplify the creation of FAIR-compliant resources.The FAIR Data Point is a metadata repository that follows the DCAT(2)schema,and utilizes the Linked Data Platform to manage the hierarchical metadata layers as LDP Containers.There has been a recent flurry of development activity around the FAIR Data Point that has significantly improved its power and ease-of-use.Here we describe five specific tools—an installer,a loader,two Webbased interfaces,and an indexer-aimed at maximizing the uptake and utility of the FAIR Data Point.

关键词： FAIR Data Linked data Semantic Web Metadata User interfaces Tooling Semantic query

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The quest for selective Cs^(+) transport in plants

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Molecular Plant 2021年第4期14卷 552-554页

作者： Manuel Nieves-Cordones Francisco Rubio departamento de Nutricion vegetal Centro de Edafologia y Biologia Aplicada del Segura-CSICCampus de Espinardo30100 MurciaSpain

Nuclear accidents have led to the release to the environment of radioactive isotopes,mainly radioactive cesium(Cs^(+)),contaminating large areas of soil for very long periods of time(Burger and Lichtscheidl,2018).These contaminated soils contain^(134)Cs^(+)and^(137)Cs^(+)radioisotopes that are readily accumulated into plants and that,through the food chain,are transferred to animals and humans,causing important health problems(Burger and Lichtscheidl,2018).

关键词： readily release transport

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Chemical Composition and Allelopathic Activity of the Essential Oil from Callistemon viminalis(Myrtaceae)Blossoms on Lettuce(Lactuca sativa L.)Seedlings

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American Journal of Plant Sciences 2014年第24期5卷 3551-3557页

作者： Christiane Maria de Oliveira Maria das Gracas Cardoso Ana Cristina da Silva Figueiredo Maria Laene Moreira de Carvalho Cintia Alvarenga Santos Fraga de Miranda Luiz Roberto Marques Albuquerque David Lee Nelson Marcos de Souza Gomes Lucilene Fernandes Silva Juliana de Andrade Santiago Maria Luisa Teixeira Rafaela Magalhaes Brandao department of Chemistry Federal University of LavrasLavrasBrazil Centro de biotecnologia vegetal/IBB Departamento de Biologia VegetalFaculdade de Ciencias de LisboaUniversidade de LisboaLisbonPortugal department of Agriculture Federal University of LavrasLavrasBrazil Federal University of Valleys Jequitinhonha and Mucuri DiamantinaBrazil

The extraction of essential oils was performed by using the technique of hydrodistillation modified Clevenger apparatus, identification and quantification of the constituents was achieved by Gas Chromatography coupled to Mass Spectrometry, and Gas Chromatography equipped with a flame ionization detector. Assessment of allelopathic activity was evaluated with the use of the method that assesses the direct contact of essential oils on germination and vigor of lettuce seeds. The major constituents that characterize the essential oil from the flowers of Callistemon viminalis were 1, 8-cineole, α-pinene and limonene at concentrations of 66.9%, 16.0% and 10.0%, respectively. The essential oil presented allelopathic activity at intensities that varied proportionately to the concentration of the essential oil, with a reduction in the percentage of germination and the germination speed index (GSI) of lettuce seeds and in the dry mass and length of shoots and roots of lettuce seedlings.

关键词： Biological Activity Myrtaceae Allelopathy

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Isolation and characterization of nine microsatellite loci from Aphelinus mali （Hymenoptera： Aphelinidae）, a parasitoid of Eriosoma lanigerum （Hemiptera： Aphididae）

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Insect Science 2010年第6期17卷 549-552页

作者： Bias Lavandero Marcos Dominguez Instituto de biologia vegetal y biotecnologia Universidad de Talca Casilla 747 Talca Chile

Nine novel microsatellite markers are presented for Aphelinus mali, a parasitoid of the woolly apple aphid Eriosoma lanigerum. Loci were characterized for 28 individuals from a single orchard in central Chile. Seven loci were polymorphic within A. mali （3-6 alleles per locus; observed heterozygosity ranging from 0.04 to 0.57） and are therefore useful for population genetic studies within this species.

关键词： Aphelinus mali Chalcidoidea Chile microsatellite population genetics

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