Integrated analyses of metabolomics and transcriptomics reveal the potential regulatory roles of long non-coding RNAs in gingerol biosynthesis

[1]  M. Kanehisa,et al.  KEGG for taxonomy-based analysis of pathways and genomes , 2022, Nucleic Acids Res..

[2]  Yan Liu,et al.  A lncRNA fine-tunes salicylic acid biosynthesis to balance plant immunity and growth. , 2022, Cell host & microbe.

[3]  Yongxing Zhu,et al.  Identification of Reference Genes for Reverse Transcription-Quantitative PCR Analysis of Ginger Under Abiotic Stress and for Postharvest Biology Studies , 2022, Frontiers in Plant Science.

[4]  Lianxia Zhou,et al.  The R2R3-MYB transcription factor VcMYB4a inhibits lignin biosynthesis in blueberry (Vaccinium corymbosum) , 2022, Tree Genetics & Genomes.

[5]  K. Cao,et al.  Identification of key gene networks controlling anthocyanin biosynthesis in peach flower. , 2021, Plant science : an international journal of experimental plant biology.

[6]  Jia Liu,et al.  Analysis of long non-coding RNAs and mRNAs in harvested kiwifruit in response to the yeast antagonist, Wickerhamomyces anomalus , 2021, Computational and structural biotechnology journal.

[7]  Fang Wang,et al.  Metabolomics and Transcriptomics Provide Insights into Anthocyanin Biosynthesis in the Developing Grains of Purple Wheat (Triticum aestivum L.). , 2021, Journal of agricultural and food chemistry.

[8]  Qi Wu,et al.  Comparative metabolomics study of Tartary (Fagopyrum tataricum (L.) Gaertn) and common (Fagopyrum esculentum Moench) buckwheat seeds. , 2021, Food chemistry.

[9]  Jiajia Chen,et al.  LncRNA TCONS_00021861 is functionally associated with drought tolerance in rice (Oryza sativa L.) via competing endogenous RNA regulation , 2021, BMC plant biology.

[10]  Q. Xia,et al.  Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway , 2021, Horticulture Research.

[11]  Ting Wu,et al.  The Long Noncoding RNA MdLNC499 Bridges MdWRKY1 and MdERF109 Function to Regulate Early-Stage Light-Induced Anthocyanin Accumulation in Apple Fruit. , 2021, The Plant cell.

[12]  Kai-li Wang,et al.  MicroRNAs play important roles in regulating rapid growth of the Phyllostachys edulis culm internode. , 2021, The New phytologist.

[13]  F. Ariel,et al.  The lncRNA APOLO interacts with the transcription factor WRKY42 to trigger root hair cell expansion in response to cold. , 2021, Molecular plant.

[14]  Dayong Li,et al.  Identification of long noncoding RNAs involved in resistance to downy mildew in Chinese cabbage , 2021, Horticulture Research.

[15]  Hao Lin,et al.  Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage , 2021, Horticulture Research.

[16]  T. Sharma,et al.  Identification and functional prediction of long non-coding RNAs of rice (Oryza sativa L.) at reproductive stage under salinity stress , 2021, Molecular Biology Reports.

[17]  J. Vencovský,et al.  Plasma Hsp90 levels in patients with systemic sclerosis and relation to lung and skin involvement: a cross-sectional and longitudinal study , 2021, Scientific Reports.

[18]  Meng Xu,et al.  Research Progress on Plant Long Non-Coding RNA , 2020, Plants.

[19]  Ning Tang,et al.  Analysis of transcriptome and phytohormone profiles reveal novel insight into ginger (Zingiber officinale Rose) in response to postharvest dehydration stress , 2020 .

[20]  Yumei Dong,et al.  Comparative transcriptome analysis uncovers regulatory roles of long non-coding RNAs involved in resistance to powdery mildew in melon , 2020, BMC Genomics.

[21]  Shuting Zhang,et al.  Transcriptome and Phytochemical Analyses Provide New Insights Into Long Non-Coding RNAs Modulating Characteristic Secondary Metabolites of Oolong Tea (Camellia sinensis) in Solar-Withering , 2019, Frontiers in Plant Science.

[22]  Yusong Jiang,et al.  Metabolomic analysis of bioactive compounds in mature rhizomes and daughter rhizomes in ginger (Zingiber officinale) , 2019 .

[23]  A. J. Afzal,et al.  Classification and experimental identification of plant long non-coding RNAs. , 2019, Genomics.

[24]  Zhenhua Dang,et al.  Genome-wide identification and characterization of long non-coding RNAs involved in fruit ripening and the climacteric in Cucumis melo , 2019, BMC Plant Biology.

[25]  Steven L Salzberg,et al.  Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype , 2019, Nature Biotechnology.

[26]  S. Iqbal,et al.  Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume , 2019, BMC Plant Biology.

[27]  X. Tao,et al.  Transcriptome Analysis Provides Insights into Gingerol Biosynthesis in Ginger (Zingiber officinale) , 2018, The plant genome.

[28]  T. Mohapatra,et al.  Genome-wide identification and characterization of lncRNAs and miRNAs in cluster bean (Cyamopsis tetragonoloba). , 2018, Gene.

[29]  Caiyun He,et al.  Transcriptomic and functional analyses unveil the role of long non-coding RNAs in anthocyanin biosynthesis during sea buckthorn fruit ripening , 2018, DNA research : an international journal for rapid publication of reports on genes and genomes.

[30]  Yiqing Liu,et al.  Transcriptome analysis reveals the genetic basis underlying the biosynthesis of volatile oil, gingerols, and diarylheptanoids in ginger (Zingiber officinale Rosc.) , 2017, Botanical Studies.

[31]  Dawei Li,et al.  Whole transcriptome sequencing of Pseudomonas syringae pv. actinidiae-infected kiwifruit plants reveals species-specific interaction between long non-coding RNA and coding genes , 2017, Scientific Reports.

[32]  Ge Gao,et al.  CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features , 2017, Nucleic Acids Res..

[33]  Zhanjiang Liu,et al.  Analysis of Long Non‐coding RNAs , 2017 .

[34]  G. Pazour,et al.  Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness , 2017, Scientific Reports.

[35]  D. Gargano,et al.  Footprint of the eastern euroasian past in Italian populations of Cryptotaenia thomasii (Ten.) DC , 2017, Botanical Studies.

[36]  A. Viljoen,et al.  Gingerols and shogaols: Important nutraceutical principles from ginger. , 2015, Phytochemistry.

[37]  S. Salzberg,et al.  StringTie enables improved reconstruction of a transcriptome from RNA-seq reads , 2015, Nature Biotechnology.

[38]  Caroline Dean,et al.  Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization , 2014, Proceedings of the National Academy of Sciences.

[39]  Qingli Guo,et al.  Identification of Maize Long Non-Coding RNAs Responsive to Drought Stress , 2014, PloS one.

[40]  V. Lattanzio,et al.  Plant phenolics: recent advances on their biosynthesis, genetics, and ecophysiology. , 2013, Plant physiology and biochemistry : PPB.

[41]  Cole Trapnell,et al.  Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. , 2011, Genes & development.

[42]  Sibum Sung,et al.  Vernalization-Mediated Epigenetic Silencing by a Long Intronic Noncoding RNA , 2011, Science.

[43]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[44]  Yoshikazu Tanaka,et al.  Biosynthesis of plant pigments: anthocyanins, betalains and carotenoids. , 2008, The Plant journal : for cell and molecular biology.

[45]  Eun Young Seo,et al.  [6]-Gingerol inhibits metastasis of MDA-MB-231 human breast cancer cells. , 2008, The Journal of nutritional biochemistry.

[46]  OUP accepted manuscript , 2022, Plant Physiology.

[47]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..