Transcriptomics and co-expression networks reveal tissue-specific responses and regulatory hubs under mild and severe drought in papaya (Carica papaya L.)

Plants respond to drought stress through the ABA dependent and independent pathways, which in turn modulate transcriptional regulatory hubs. Here, we employed Illumina RNA-Seq to analyze a total of 18 cDNA libraries from leaves, sap, and roots of papaya plants under drought stress. Reference and de novo transcriptomic analyses identified 8,549 and 6,089 drought-responsive genes and unigenes, respectively. Core sets of 6 and 34 genes were simultaneously up- or down-regulated, respectively, in all stressed samples. Moreover, GO enrichment analysis revealed that under moderate drought stress, processes related to cell cycle and DNA repair were up-regulated in leaves and sap; while responses to abiotic stress, hormone signaling, sucrose metabolism, and suberin biosynthesis were up-regulated in roots. Under severe drought stress, biological processes related to abiotic stress, hormone signaling, and oxidation-reduction were up-regulated in all tissues. Moreover, similar biological processes were commonly down-regulated in all stressed samples. Furthermore, co-expression network analysis revealed three and eight transcriptionally regulated modules in leaves and roots, respectively. Seventeen stress-related TFs were identified, potentially serving as main regulatory hubs in leaves and roots. Our findings provide insight into the molecular responses of papaya plant to drought, which could contribute to the improvement of this important tropical crop.

[1]  N. Friedman,et al.  Trinity : reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2016 .

[2]  J. P. Fabi,et al.  Transcript profiling of papaya fruit reveals differentially expressed genes associated with fruit ripening , 2010 .

[3]  Diogo M. Camacho,et al.  Wisdom of crowds for robust gene network inference , 2012, Nature Methods.

[4]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[5]  S. Horvath,et al.  Conservation and evolution of gene coexpression networks in human and chimpanzee brains , 2006, Proceedings of the National Academy of Sciences.

[6]  Dhriti Singh,et al.  Transcriptional regulation of drought response: a tortuous network of transcriptional factors , 2015, Front. Plant Sci..

[7]  Pornpimol Charoentong,et al.  ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks , 2009, Bioinform..

[8]  D. Xue,et al.  Molecular and Evolutionary Mechanisms of Cuticular Wax for Plant Drought Tolerance , 2017, Front. Plant Sci..

[9]  P. Geurts,et al.  Inferring Regulatory Networks from Expression Data Using Tree-Based Methods , 2010, PloS one.

[10]  Min Chen,et al.  Comparing Statistical Methods for Constructing Large Scale Gene Networks , 2012, PloS one.

[11]  Qingyi Yu,et al.  Transcriptome analysis of the male-to-hermaphrodite sex reversal induced by low temperature in papaya , 2016, Tree Genetics & Genomes.

[12]  Sergey Shabala,et al.  Root-to-shoot signalling: integration of diverse molecules, pathways and functions. , 2016, Functional plant biology : FPB.

[13]  Jianhua Zhu,et al.  High throughput sequencing reveals novel and abiotic stress-regulated microRNAs in the inflorescences of rice , 2012, BMC Plant Biology.

[14]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[15]  David A. Christopher,et al.  Differentially expressed and new non-protein-coding genes from a Carica papaya root transcriptome survey , 2008 .

[16]  R. Ming,et al.  Transcriptome Profiling Revealed Stress-Induced and Disease Resistance Genes Up-Regulated in PRSV Resistant Transgenic Papaya , 2016, Front. Plant Sci..

[17]  H. Shao,et al.  Recent Advances in Utilizing Transcription Factors to Improve Plant Abiotic Stress Tolerance by Transgenic Technology , 2016, Front. Plant Sci..

[18]  Dirk Walther,et al.  Endogenous Arabidopsis messenger RNAs transported to distant tissues , 2015, Nature Plants.

[19]  L. Comas,et al.  Root traits contributing to plant productivity under drought , 2013, Front. Plant Sci..

[20]  M. Talón,et al.  Responses of Papaya Seedlings (Carica papaya L.) to Water Stress and Re-Hydration: Growth, Photosynthesis and Mineral Nutrient Imbalance , 2006, Plant and Soil.

[21]  O. Rowland,et al.  Suberin: biosynthesis, regulation, and polymer assembly of a protective extracellular barrier , 2014, Plant Cell Reports.

[22]  K. Yamaguchi-Shinozaki,et al.  Omics Approaches Toward Defining the Comprehensive Abscisic Acid Signaling Network in Plants. , 2015, Plant & cell physiology.

[23]  Silas P. Rodrigues,et al.  Transcriptome analysis provides insights into the delayed sticky disease symptoms in Carica papaya , 2018, Plant Cell Reports.

[24]  Colin N. Dewey,et al.  De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis , 2013, Nature Protocols.

[25]  David M. Goodstein,et al.  Phytozome: a comparative platform for green plant genomics , 2011, Nucleic Acids Res..

[26]  Allan Kuchinsky,et al.  GLay: community structure analysis of biological networks , 2010, Bioinform..

[27]  F. Kragler,et al.  Long distance RNA movement. , 2018, The New phytologist.

[28]  Stephen M. Mount,et al.  The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus) , 2008, Nature.

[29]  Kazuo Nakashima,et al.  Regulons involved in osmotic stress‐responsive and cold stress‐responsive gene expression in plants , 2006 .

[30]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[31]  E. Schijlen,et al.  A footprint of desiccation tolerance in the genome of Xerophyta viscosa , 2017, Nature Plants.

[32]  M. Robles,et al.  University of Birmingham High throughput functional annotation and data mining with the Blast2GO suite , 2022 .

[33]  Gigliola Sica,et al.  Local Overexpression of V1a-Vasopressin Receptor Enhances Regeneration in Tumor Necrosis Factor-Induced Muscle Atrophy , 2014, BioMed research international.

[34]  Elise A. R. Serin,et al.  Learning from Co-expression Networks: Possibilities and Challenges , 2016, Front. Plant Sci..

[35]  J. Flexas,et al.  Photosynthesis under drought and salt stress: regulation mechanisms from whole plant to cell. , 2009, Annals of botany.

[36]  Chad L. Myers,et al.  Unraveling gene function in agricultural species using gene co-expression networks. , 2017, Biochimica et biophysica acta. Gene regulatory mechanisms.

[37]  E. Baldoni,et al.  Plant MYB Transcription Factors: Their Role in Drought Response Mechanisms , 2015, International journal of molecular sciences.

[38]  K. Rajput,et al.  Secondary growth and occurrence of laticifers in the root of papaya (Carica papaya L.) , 2013 .

[39]  K. Shinozaki,et al.  The transcriptional regulatory network in the drought response and its crosstalk in abiotic stress responses including drought, cold, and heat , 2014, Front. Plant Sci..

[40]  Lizhen Shi,et al.  Construction and Optimization of a Large Gene Coexpression Network in Maize Using RNA-Seq Data1[OPEN] , 2017, Plant Physiology.

[41]  Dena Leshkowitz,et al.  Characterization of phloem-sap transcription profile in melon plants , 2007 .

[42]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[43]  Lukas Schreiber,et al.  Suberin--a biopolyester forming apoplastic plant interfaces. , 2007, Current opinion in plant biology.

[44]  L. Rodríguez-Zapata,et al.  RAP2.4a Is Transported through the Phloem to Regulate Cold and Heat Tolerance in Papaya Tree (Carica papaya cv. Maradol): Implications for Protection Against Abiotic Stress , 2016, PloS one.

[45]  J. Kehr,et al.  Long distance transport and movement of RNA through the phloem. , 2007, Journal of experimental botany.

[46]  R. K. Sharma,et al.  Next Generation Sequencing Technologies: The Doorway to the Unexplored Genomics of Non-Model Plants , 2015, Front. Plant Sci..

[47]  Hadley Wickham,et al.  ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .

[48]  Roland Eils,et al.  Complex heatmaps reveal patterns and correlations in multidimensional genomic data , 2016, Bioinform..

[49]  A. Gómez-Cadenas,et al.  Hormonal changes in papaya seedlings subjected to progressive water stress and re-watering , 2007, Plant Growth Regulation.

[50]  H. Goh,et al.  Genome-wide transcriptome profiling of Carica papaya L. embryogenic callus , 2017, Physiology and Molecular Biology of Plants.

[51]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[52]  Yuji Ikegaya,et al.  Genetically Encoded Green Fluorescent Ca2+ Indicators with Improved Detectability for Neuronal Ca2+ Signals , 2012, PloS one.

[53]  K. Yamaguchi-Shinozaki,et al.  ABA-dependent and ABA-independent signaling in response to osmotic stress in plants. , 2014, Current opinion in plant biology.

[54]  Yves Van de Peer,et al.  PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics , 2017, Nucleic Acids Res..

[55]  S. Wolf,et al.  Don't kill the messenger: Long-distance trafficking of mRNA molecules. , 2013, Plant science : an international journal of experimental plant biology.

[56]  Young Sam Seo,et al.  Arabidopsis Small Rubber Particle Protein Homolog SRPs Play Dual Roles as Positive Factors for Tissue Growth and Development and in Drought Stress Responses1[OPEN] , 2016, Plant Physiology.

[57]  D. Schachtman,et al.  Chemical root to shoot signaling under drought. , 2008, Trends in plant science.

[58]  N. Tuteja,et al.  Genotoxic stress in plants: shedding light on DNA damage, repair and DNA repair helicases. , 2009, Mutation research.

[59]  J. Aerts,et al.  SCENIC: Single-cell regulatory network inference and clustering , 2017, Nature Methods.

[60]  Bin Yan,et al.  PlaMoM: a comprehensive database compiles plant mobile macromolecules , 2016, Nucleic Acids Res..

[61]  Pedro M. Valero-Mora,et al.  ggplot2: Elegant Graphics for Data Analysis , 2010 .

[62]  Brad T. Sherman,et al.  Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists , 2008, Nucleic acids research.

[63]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[64]  Yan Guo,et al.  Advanced Heat Map and Clustering Analysis Using Heatmap3 , 2014, BioMed research international.

[65]  A. Gómez-Cadenas,et al.  Influence of Exogenous Glycine Betaine and Abscisic Acid on Papaya in Responses to Water-deficit Stress , 2011, Journal of Plant Growth Regulation.

[66]  Leo Breiman,et al.  Statistical Modeling: The Two Cultures (with comments and a rejoinder by the author) , 2001 .

[67]  Paul Theodor Pyl,et al.  HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[68]  Z. Fei,et al.  Catalyzing plant science research with RNA-seq , 2013, Front. Plant Sci..

[69]  H. Matsumura,et al.  Digital Transcriptome Analysis of Putative Sex-Determination Genes in Papaya (Carica papaya) , 2012, PloS one.

[70]  Young Sam Seo,et al.  Constitutive expression of CaSRP1, a hot pepper small rubber particle protein homolog, resulted in fast growth and improved drought tolerance in transgenic Arabidopsis plants , 2010, Planta.

[71]  K. Shinozaki,et al.  'Omics' analyses of regulatory networks in plant abiotic stress responses. , 2010, Current opinion in plant biology.

[72]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[73]  R. Wintjens,et al.  Revisiting the enzymes stored in the laticifers of Carica papaya in the context of their possible participation in the plant defence mechanism , 2001, Cellular and Molecular Life Sciences CMLS.

[74]  A C C Gibbs,et al.  Data Analysis , 2009, Encyclopedia of Database Systems.

[75]  N. Friedman,et al.  Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.

[76]  Ling Jiang,et al.  Identification and expression of the WRKY transcription factors of Carica papaya in response to abiotic and biotic stresses , 2014, Molecular Biology Reports.

[77]  F. Gillet,et al.  Cell Wall Metabolism in Response to Abiotic Stress , 2015, Plants.

[78]  T. Shepherd,et al.  The effects of stress on plant cuticular waxes. , 2006, The New phytologist.