mRNA-Seq Reveals a Comprehensive Transcriptome Profile of Rice under Phosphate Stress

Plants have developed several morphological and physiological strategies to adapt to phosphate stress. We analyzed the inducible transcripts associated with phosphate starvation and over-abundant phosphate supply to characterize the transcriptome in rice seedlings using the mRNA-Seq strategy. Fifty-three million reads obtained from 16 libraries under various phosphate stress and recovery treatments were uniquely mapped to the rice genome. Transcripts identified specifically tagged to 40,574 (root) and 39,748 (shoot) Rice Annotation Project (RAP) transcripts. Additionally, we detected uniquely 10,388 transcripts with no match to any RAP transcript. These transcripts that showed specific response to Pi stress include those without ORFs that may act as non-protein coding transcripts. With an accompanying browser of the transcriptome under Pi stress, a deeper understanding of the structural and functional features of both annotated and unannotated Pi stress-responsive transcripts can provide useful information in improving Pi acquisition and utilization in rice and other cereal crops.

[1]  C. Vance,et al.  Overexpression of malate dehydrogenase in transgenic alfalfa enhances organic acid synthesis and confers tolerance to aluminum. , 2001, Plant physiology.

[2]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[3]  Aaron P. Smith,et al.  Histone H2A.Z Regulates the Expression of Several Classes of Phosphate Starvation Response Genes But Not as a Transcriptional Activator1[OA] , 2009, Plant Physiology.

[4]  A. Gojon,et al.  Root uptake regulation: a central process for NPS homeostasis in plants. , 2009, Current opinion in plant biology.

[5]  M. Gerstein,et al.  RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.

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

[7]  Ping Wu,et al.  OsPTF1, a Novel Transcription Factor Involved in Tolerance to Phosphate Starvation in Rice1[w] , 2005, Plant Physiology.

[8]  Xuehui Huang,et al.  Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq. , 2010, Genome research.

[9]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[10]  Chuang Wang,et al.  Involvement of OsSPX1 in phosphate homeostasis in rice. , 2009, The Plant journal : for cell and molecular biology.

[11]  J. Cock,et al.  Laboratory manual for physiological studies of rice , 1971 .

[12]  Javier Paz-Ares,et al.  A Central Regulatory System Largely Controls Transcriptional Activation and Repression Responses to Phosphate Starvation in Arabidopsis , 2010, PLoS genetics.

[13]  P. May,et al.  Identification of Nutrient-Responsive Arabidopsis and Rapeseed MicroRNAs by Comprehensive Real-Time Polymerase Chain Reaction Profiling and Small RNA Sequencing1[C][W][OA] , 2009, Plant Physiology.

[14]  Dan S. Prestridge,et al.  SIGNAL SCAN: a computer program that scans DNA sequences for eukaryotic transcriptional elements , 1991, Comput. Appl. Biosci..

[15]  Jian-Kang Zhu,et al.  A miRNA Involved in Phosphate-Starvation Response in Arabidopsis , 2005, Current Biology.

[16]  D. T. Britto,et al.  Cellular mechanisms of potassium transport in plants. , 2008, Physiologia plantarum.

[17]  B. N. Devaiah,et al.  WRKY75 Transcription Factor Is a Modulator of Phosphate Acquisition and Root Development in Arabidopsis1[C][W][OA] , 2007, Plant Physiology.

[18]  A. Ismail,et al.  Is root growth under phosphorus deficiency affected by source or sink limitations? , 2005, Journal of experimental botany.

[19]  Xianghua Li,et al.  The expression profile of genes in rice roots under low phosphorus stress , 2009, Science in China Series C: Life Sciences.

[20]  Lex E. Flagel,et al.  RNase T2 genes from rice and the evolution of secretory ribonucleases in plants , 2010, Molecular Genetics and Genomics.

[21]  M. Todesco,et al.  Target mimicry provides a new mechanism for regulation of microRNA activity , 2007, Nature Genetics.

[22]  Wen-Hsiung Li,et al.  Uncovering Small RNA-Mediated Responses to Phosphate Deficiency in Arabidopsis by Deep Sequencing1[W][OA] , 2009, Plant Physiology.

[23]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[24]  K. Miura,et al.  The Arabidopsis SUMO E3 ligase SIZ1 controls phosphate deficiency responses. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[25]  H. Kanamori,et al.  Massive parallel sequencing of mRNA in identification of unannotated salinity stress-inducible transcripts in rice (Oryza sativa L.) , 2010, BMC Genomics.

[26]  Wei-Hua Wu,et al.  The WRKY6 Transcription Factor Modulates PHOSPHATE1 Expression in Response to Low Pi Stress in Arabidopsis[W][OA] , 2009, The Plant Cell Online.

[27]  E. Delhaize,et al.  Effects of altered citrate synthase and isocitrate dehydrogenase expression on internal citrate concentrations and citrate efflux from tobacco (Nicotiana tabacum L.) roots , 2004, Plant and Soil.

[28]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[29]  M. Stitt,et al.  PHO2, MicroRNA399, and PHR1 Define a Phosphate-Signaling Pathway in Plants1[W][OA] , 2006, Plant Physiology.

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

[31]  U. Paszkowski,et al.  Rice phosphate transporters include an evolutionarily divergent gene specifically activated in arbuscular mycorrhizal symbiosis , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[32]  B. Usadel,et al.  Genome-wide reprogramming of metabolism and regulatory networks of Arabidopsis in response to phosphorus. , 2007, Plant, cell & environment.

[33]  Y. Qi,et al.  Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids[W] , 2010, Plant Cell.

[34]  N. Chua,et al.  Arabidopsis NAC1 transduces auxin signal downstream of TIR1 to promote lateral root development. , 2000, Genes & development.

[35]  W. Karłowski,et al.  Complex regulation of two target genes encoding SPX-MFS proteins by rice miR827 in response to phosphate starvation. , 2010, Plant & cell physiology.

[36]  C. Vance,et al.  Phosphorus acquisition and use: critical adaptations by plants for securing a nonrenewable resource. , 2003, The New phytologist.

[37]  Laurence Lejay,et al.  Oxidative Pentose Phosphate Pathway-Dependent Sugar Sensing as a Mechanism for Regulation of Root Ion Transporters by Photosynthesis1[W] , 2008, Plant Physiology.

[38]  V. Rubio,et al.  A conserved MYB transcription factor involved in phosphate starvation signaling both in vascular plants and in unicellular algae. , 2001, Genes & development.

[39]  J. Hammond,et al.  Sucrose Transport in the Phloem: Integrating Root Responses to Phosphorus Starvation Sensing and Signalling P Availability , 2022 .

[40]  Bertrand Muller,et al.  A Role for Auxin Redistribution in the Responses of the Root System Architecture to Phosphate Starvation in Arabidopsis1 , 2005, Plant Physiology.