Advances in genomic, transcriptomic, proteomic, and metabolomic approaches to study biotic stress in fruit crops

A novel wheat NAC transcription factor, Ta NAC30, negatively regulates resistance of wheat to stripe rust

(2018) Bing Wang et al.   Journal of Integrative Plant Biology

Combination of LC–MS based metabolomics and antioxidant activity for evaluation of bioactive compounds in Fragaria vesca leaves from Italy

(2018) Gilda D’Urso et al.   JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS

iTRAQ-Based Identification of Proteins Related to Lignin Synthesis in the Pear Pollinated with Pollen from Different Varieties

(2018) Shumei Li et al.   MOLECULES

The red bayberry genome and genetic basis of sex determination

(2018) Hui-Min Jia et al.   PLANT BIOTECHNOLOGY JOURNAL

The miRNAome dynamics during developmental and metabolic reprogramming of tomato root infected with potato cyst nematode

(2018) Marek D. Koter et al.   PLANT SCIENCE

Antioxidant genes of plants and fungal pathogens are distinctly regulated during disease development in different Rhizoctonia solani pathosystems

(2018) Jamil Samsatly et al.   PLoS One

An R2R3-MYB transcription factor, SlMYB28, involved in the regulation of TYLCV infection in tomato

(2018) Tong Li et al.   SCIENTIA HORTICULTURAE

Molecular dissection of distinct symptoms induced by tomato chlorosis virus and tomato yellow leaf curl virus based on comparative transcriptome analysis

(2018) Jang-Kyun Seo et al.   VIROLOGY

A role for small RNA in regulating innate immunity during plant growth

(2018) Yingtian Deng et al.   PLoS Pathogens

Roles of E3 Ubiquitin-Ligases in Nuclear Protein Homeostasis during Plant Stress Responses

(2018) Irene Serrano et al.   Frontiers in Plant Science

The Role of Tomato WRKY Genes in Plant Responses to Combined Abiotic and Biotic Stresses

(2018) Yuling Bai et al.   Frontiers in Plant Science

Integrated transcriptomic and metabolomic analyses of a wax deficient citrus mutant exhibiting jasmonic acid-mediated defense against fungal pathogens

(2018) Yizhong He et al.   Horticulture Research

Ectopic expression of FvWRKY42 , a WRKY transcription factor from the diploid woodland strawberry ( Fragaria vesca ), enhances resistance to powdery mildew, improves osmotic stress resistance, and increases abscisic acid sensitivity in Arabidopsis

(2018) Wei Wei et al.   PLANT SCIENCE

Complementary iTRAQ-based proteomic and RNA sequencing-based transcriptomic analyses reveal a complex network regulating pomegranate (Punica granatum L.) fruit peel colour

(2018) Xiang Luo et al.   Scientific Reports

Identification and characterization of known and novel microRNAs in strawberry fruits induced by Botrytis cinerea

(2018) Yaoxin Liang et al.   Scientific Reports

Role of ethylene and the APETALA 2/ethylene response factor superfamily in rice under various abiotic and biotic stress conditions

(2017) Rambod Abiri et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

WRKY transcription factors in plant responses to stresses

(2017) Jingjing Jiang et al.   Journal of Integrative Plant Biology

The pomegranate (Punica granatum L.) genome and the genomics of punicalagin biosynthesis

(2017) Gaihua Qin et al.   PLANT JOURNAL

PacMYBA, a sweet cherry R2R3-MYB transcription factor, is a positive regulator of salt stress tolerance and pathogen resistance

(2017) Xinjie Shen et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Six NAC transcription factors involved in response to TYLCV infection in resistant and susceptible tomato cultivars

(2017) Ying Huang et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Genome-wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol-rich characteristics

(2017) Yuling Lin et al.   GigaScience

Members of WRKY Group III transcription factors are important in TYLCV defense signaling pathway in tomato (Solanum lycopersicum)

(2016) Ying Huang et al.   BMC GENOMICS

Comparative proteomic analysis provides novel insight into the interaction between resistant vs susceptible tomato cultivars and TYLCV infection

(2016) Ying Huang et al.   BMC PLANT BIOLOGY

AP2/ERF Transcription Factors Involved in Response to Tomato Yellow Leaf Curly Virus in Tomato

(2016) Ying Huang et al.   Plant Genome

Genome-wide analysis of Dof transcription factors reveals functional characteristics during development and response to biotic stresses in pepper

(2016) Won-Hee Kang et al.   Scientific Reports

Single- versus Multiple-Pest Infestation Affects Differently the Biochemistry of Tomato (Solanum lycopersicum ‘Ailsa Craig’)

(2015) Audrey Errard et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

The pineapple genome and the evolution of CAM photosynthesis

(2015) Ray Ming et al.   NATURE GENETICS

PsAP2 an AP2/ERF family transcription factor from Papaver somniferum enhances abiotic and biotic stress tolerance in transgenic tobacco

(2015) Sonal Mishra et al.   PLANT MOLECULAR BIOLOGY

Ethylene responsive factors in the orchestration of stress responses in monocotyledonous plants

(2015) Sanjukta Dey et al.   Frontiers in Plant Science

Comparative metabolomics and transcriptomics of plant response to Tomato yellow leaf curl virus infection in resistant and susceptible tomato cultivars

(2014) Dagan Sade et al.   Metabolomics

The complex jujube genome provides insights into fruit tree biology

(2014) Meng-Jun Liu et al.   Nature Communications

Small RNA Profiling Reveals Phosphorus Deficiency as a Contributing Factor in Symptom Expression for Citrus Huanglongbing Disease

(2013) Hongwei Zhao et al.   Molecular Plant

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution

(2013) Ignazio Verde et al.   NATURE GENETICS

Comparative Transcriptome Profiling of a Resistant vs. Susceptible Tomato (Solanum lycopersicum) Cultivar in Response to Infection by Tomato Yellow Leaf Curl Virus

(2013) Tianzi Chen et al.   PLoS One

Draft genome of the kiwifruit Actinidia chinensis

(2013) Shengxiong Huang et al.   Nature Communications

Roles of NAC transcription factors in the regulation of biotic and abiotic stress responses in plants

(2013) Mohammed Nuruzzaman et al.   Frontiers in Microbiology

High-throughput sequencing of small RNAs and analysis of differentially expressed microRNAs associated with pistil development in Japanese apricot

(2012) Zhihong Gao et al.   BMC GENOMICS

Identification of microRNAs from Amur grape (vitis amurensis Rupr.) by deep sequencing and analysis of microRNA variations with bioinformatics

(2012) Chen Wang et al.   BMC GENOMICS

smRNAome profiling to identify conserved and novel microRNAs in Stevia rebaudiana Bertoni

(2012) Vibha Mandhan et al.   BMC PLANT BIOLOGY

The genome of the pear (Pyrus bretschneideri Rehd.)

(2012) J. Wu et al.   GENOME RESEARCH

Biogenesis, functions and fate of plant microRNAs

(2012) Afsar Raza Naqvi et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Proteomic analysis of grapevine resistance induced by Trichoderma harzianum T39 reveals specific defence pathways activated against downy mildew

(2012) Maria Cristina Palmieri et al.   JOURNAL OF EXPERIMENTAL BOTANY

Proteomic Analysis of Mn-induced Resistance to Powdery Mildew in Grapevine

(2012) Y. A. Yao et al.   JOURNAL OF EXPERIMENTAL BOTANY

Metabolomics reveals simultaneous influences of plant defence system and fungal growth in Botrytis cinerea-infected Vitis vinifera cv. Chardonnay berries

(2012) Young-Shick Hong et al.   JOURNAL OF EXPERIMENTAL BOTANY

Proteomic Analysis of Ripening Tomato Fruit Infected by Botrytis cinerea

(2012) Punit Shah et al.   JOURNAL OF PROTEOME RESEARCH

Metabolomic Analysis of Citrus Infection by ‘Candidatus Liberibacter’ Reveals Insight into Pathogenicity

(2012) Anne M. Slisz et al.   JOURNAL OF PROTEOME RESEARCH

The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

(2012) Angélique D’Hont et al.   NATURE

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Mapping recently identified nucleotide variants in the genome and transcriptome

(2012) Chun-Xiao Song et al.   NATURE BIOTECHNOLOGY

The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions

(2012) Shaogui Guo et al.   NATURE GENETICS

The draft genome of sweet orange (Citrus sinensis)

(2012) Qiang Xu et al.   NATURE GENETICS

Vascular plant one-zinc-finger protein 1/2 transcription factors regulate abiotic and biotic stress responses in Arabidopsis

(2012) Yusuke Nakai et al.   PLANT JOURNAL

The Lateral Organ Boundaries Domain Transcription Factor LBD20 Functions in Fusarium Wilt Susceptibility and Jasmonate Signaling in Arabidopsis

(2012) L. F. Thatcher et al.   PLANT PHYSIOLOGY

A bZIP Protein, VIP1, Is a Regulator of Osmosensory Signaling in Arabidopsis

(2012) D. Tsugama et al.   PLANT PHYSIOLOGY

Identification of Differentially-Expressed Genes Associated with Pistil Abortion in Japanese Apricot by Genome-Wide Transcriptional Analysis

(2012) Ting Shi et al.   PLoS One

Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants

(2011) Basel Khraiwesh et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Trichoderma harzianum T39 induces resistance against downy mildew by priming for defense without costs for grapevine

(2011) Michele Perazzolli et al.   BIOLOGICAL CONTROL

Identification of tissue-specific, abiotic stress-responsive gene expression patterns in wine grape (Vitis vinifera L.) based on curation and mining of large-scale EST data sets

(2011) Richard L Tillett et al.   BMC PLANT BIOLOGY

Cell Wall Modifying Proteins Mediate Plant Acclimatization to Biotic and Abiotic Stresses

(2011) Rashmi Sasidharan et al.   CRITICAL REVIEWS IN PLANT SCIENCES

Genome-wide identification, phylogeny and expression analysis of the lipoxygenase gene family in cucumber

(2011) S.Q. Liu et al.   GENETICS AND MOLECULAR RESEARCH

Floral reversion mechanism in longan (Dimocarpus longan Lour.) revealed by proteomic and anatomic analyses

(2011) Xiangrong You et al.   Journal of Proteomics

Proteomic analysis of the compatible interaction between Vitis vinifera and Plasmopara viticola

(2011) Alberto Milli et al.   Journal of Proteomics

Identification of miRNAs and Their Target Genes Using Deep Sequencing and Degradome Analysis in Trifoliate Orange [Poncirus trifoliate (L.) Raf]

(2011) Jin-Zhi Zhang et al.   MOLECULAR BIOTECHNOLOGY

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

Identification of avocado (Persea americana) root proteins induced by infection with the oomycete Phytophthora cinnamomi using a proteomic approach

(2011) Carlos H. Acosta-Muñiz et al.   PHYSIOLOGIA PLANTARUM

ABA signal transduction at the crossroad of biotic and abiotic stress responses

(2011) SUNG CHUL LEE et al.   PLANT CELL AND ENVIRONMENT

Conservation and divergence in plant microRNAs

(2011) Matthew W. Jones-Rhoades   PLANT MOLECULAR BIOLOGY

MicroRNAs and their diverse functions in plants

(2011) Guiling Sun   PLANT MOLECULAR BIOLOGY

Polyamines, polyamine oxidases and nitric oxide in development, abiotic and biotic stresses

(2011) Rinukshi Wimalasekera et al.   PLANT SCIENCE

High-Throughput Sequencing of RNA Silencing-Associated Small RNAs in Olive (Olea europaea L.)

(2011) Livia Donaire et al.   PLoS One

Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata)

(2010) Changnian Song et al.   BMC GENOMICS

General and species-specific transcriptional responses to downy mildew infection in a susceptible (Vitis vinifera) and a resistant (V. riparia) grapevine species

(2010) Marianna Polesani et al.   BMC GENOMICS

Characterisation of the Vitis vinifera PR10 multigene family

(2010) Sylvain Lebel et al.   BMC PLANT BIOLOGY

Whole genome wide expression profiles of Vitis amurensis grape responding to downy mildew by using Solexa sequencing technology

(2010) Jiao Wu et al.   BMC PLANT BIOLOGY

‘Omics’ analyses of regulatory networks in plant abiotic stress responses

(2010) Kaoru Urano et al.   CURRENT OPINION IN PLANT BIOLOGY

Ecological genetics and genomics of plant defences: evidence and approaches

(2010) Jill T. Anderson et al.   FUNCTIONAL ECOLOGY

Abiotic and Biotic Stresses and Changes in the Lignin Content and Composition in Plants

(2010) Jullyana Cristina Magalhães Silva Moura et al.   Journal of Integrative Plant Biology

Proteomic Analysis of the Plant−Virus Interaction in Cucumber Mosaic Virus (CMV) Resistant Transgenic Tomato

(2010) Mariasole Di Carli et al.   JOURNAL OF PROTEOME RESEARCH

Overexpression of an AP2/ERF-type Transcription Factor CRF5 Confers Pathogen Resistance to Arabidopsis Plants

(2010) Ying Shi Liang   Journal of the Korean Society for Applied Biological Chemistry

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

The genome of Theobroma cacao

(2010) Xavier Argout et al.   NATURE GENETICS

The genome of woodland strawberry (Fragaria vesca)

(2010) Vladimir Shulaev et al.   NATURE GENETICS

The genome of the domesticated apple (Malus × domestica Borkh.)

(2010) Riccardo Velasco et al.   NATURE GENETICS

PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database

(2010) He Zhang et al.   NUCLEIC ACIDS RESEARCH

WRKY transcription factors

(2010) Paul J. Rushton et al.   TRENDS IN PLANT SCIENCE

MYB transcription factors in Arabidopsis

(2010) Christian Dubos et al.   TRENDS IN PLANT SCIENCE

Roles of Plant Small RNAs in Biotic Stress Responses

(2009) Virginia Ruiz-Ferrer et al.   Annual Review of Plant Biology

Metabolomics for Functional Genomics, Systems Biology, and Biotechnology

(2009) Kazuki Saito et al.   Annual Review of Plant Biology

High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera

(2009) Erica Mica et al.   BMC GENOMICS

Mass spectrometry based metabolomics and enzymatic assays for functional genomics

(2009) Richard Baran et al.   CURRENT OPINION IN MICROBIOLOGY

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

Metabolic response of tomato leaves upon different plant–pathogen interactions

(2009) M. Pilar López-Gresa et al.   PHYTOCHEMICAL ANALYSIS

Identification and characterization of 27 conserved microRNAs in citrus

(2009) Changnian Song et al.   PLANTA

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

The role of microRNAs and other endogenous small RNAs in plant stress responses

(2008) L SHUKLA et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Induction of systemic resistance against Plasmopara viticola in grapevine by Trichoderma harzianum T39 and benzothiadiazole

(2008) Michele Perazzolli et al.   BIOLOGICAL CONTROL

Identification of grapevineMLOgene candidates involved in susceptibility to powdery mildew

(2008) Angela Feechan et al.   FUNCTIONAL PLANT BIOLOGY

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

(2008) Ray Ming et al.   NATURE

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Biosynthesis of plant-derived flavor compounds

(2008) Wilfried Schwab et al.   PLANT JOURNAL

Genome-wide identification of NBS resistance genes in Populus trichocarpa

(2008) Annegret Kohler et al.   PLANT MOLECULAR BIOLOGY

Abiotic stress response in plants: When post-transcriptional and post-translational regulations control transcription

(2008) Elisabetta Mazzucotelli et al.   PLANT SCIENCE