Genome-wide annotation of genes and noncoding RNAs of foxtail millet in response to simulated drought stress by deep sequencing

Genome-wide annotation of genes and noncoding RNAs of foxtail millet in response to simulated... Drought is a major abiotic stress that affects plant growth, production, and survival. Plants have evolved sophisticated and highly complex reactions to drought stress, including large-scale transcriptome reconfiguration. Foxtail millet (Setaria italica) is a member of the Poaceae family. Because of its outstanding tolerance to drought stress foxtail millet has the potential to become a new model organism. To enrich our knowledge of the processes that contribute to drought resistance, we have used a deep sequencing approach to generate a genome-wide transcriptome of foxtail millet after exposure to simulated drought stress. A large number of differentially expressed genes were characterized; in particular, we examined the roles of small interfering RNAs (siRNAs) and long noncoding RNAs (lncRNAs) in response to a water-deficit condition. These RNAs have remained largely unexplored in previous studies of stress-induced transcriptomes. We found that the reduced levels of 24-nt siRNA flanking genes were associated, for the most part, with proximal up-regulated genes, indicating a potential effect of 24-nt siRNAs on drought-regulated gene expression. Several lncRNAs that responded to the simulated drought stress were also identified, and we found that one of them shared sequence conservation and colinearity with its counterpart in sorghum (Sorghum bicolor). Our findings provide new insights into drought-induced changes in the foxtail millet transcriptome. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Plant Molecular Biology Springer Journals

Genome-wide annotation of genes and noncoding RNAs of foxtail millet in response to simulated drought stress by deep sequencing

15 pages
Read Article

Loading next page...
 
/lp/springer_journal/genome-wide-annotation-of-genes-and-noncoding-rnas-of-foxtail-millet-nY0G0VWMm0
Publisher
Springer Netherlands
Copyright
Copyright © 2013 by Springer Science+Business Media Dordrecht
Subject
Life Sciences; Plant Sciences; Biochemistry, general; Plant Pathology
ISSN
0167-4412
eISSN
1573-5028
D.O.I.
10.1007/s11103-013-0104-6
Publisher site
See Article on Publisher Site

Abstract

Drought is a major abiotic stress that affects plant growth, production, and survival. Plants have evolved sophisticated and highly complex reactions to drought stress, including large-scale transcriptome reconfiguration. Foxtail millet (Setaria italica) is a member of the Poaceae family. Because of its outstanding tolerance to drought stress foxtail millet has the potential to become a new model organism. To enrich our knowledge of the processes that contribute to drought resistance, we have used a deep sequencing approach to generate a genome-wide transcriptome of foxtail millet after exposure to simulated drought stress. A large number of differentially expressed genes were characterized; in particular, we examined the roles of small interfering RNAs (siRNAs) and long noncoding RNAs (lncRNAs) in response to a water-deficit condition. These RNAs have remained largely unexplored in previous studies of stress-induced transcriptomes. We found that the reduced levels of 24-nt siRNA flanking genes were associated, for the most part, with proximal up-regulated genes, indicating a potential effect of 24-nt siRNAs on drought-regulated gene expression. Several lncRNAs that responded to the simulated drought stress were also identified, and we found that one of them shared sequence conservation and colinearity with its counterpart in sorghum (Sorghum bicolor). Our findings provide new insights into drought-induced changes in the foxtail millet transcriptome.

Journal

Plant Molecular Biology – Springer Journals

Published: Jul 17, 2013

References

  • The true story of the HD-Zip family
    Ariel, FD; Manavella, PA; Dezar, CA; Chan, RL
  • The 5′-region of Arabidopsis thaliana cor15a has cis-acting elements that confer cold-, drought- and ABA-regulated gene expression
    Baker, SS; Wilhelm, KS; Thomashow, MF
  • Repeat associated small RNAs vary among parents and following hybridization in maize
    Barber, WT; Zhang, W; Win, H; Varala, KK; Dorweiler, JE; Hudson, ME; Moose, SP
  • Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses
    Ben Amor, B; Wirth, S; Merchan, F; Laporte, P; d’Aubenton-Carafa, Y; Hirsch, J; Maizel, A; Mallory, A; Lucas, A; Deragon, JM; Vaucheret, H; Thermes, C; Crespi, M
  • Reference genome sequence of the model plant Setaria
    Bennetzen, JL; Schmutz, J; Wang, H; Percifield, R; Hawkins, J; Pontaroli, AC; Estep, M; Feng, L; Vaughn, JN; Grimwood, J; Jenkins, J; Barry, K; Lindquist, E; Hellsten, U; Deshpande, S; Wang, X; Wu, X; Mitros, T; Triplett, J; Yang, X; Ye, CY; Mauro-Herrera, M; Wang, L; Li, P; Sharma, M; Sharma, R; Ronald, PC; Panaud, O; Kellogg, EA; Brutnell, TP; Doust, AN; Tuskan, GA; Rokhsar, D; Devos, KM
    Bookmark
  • Computational Identification and Functional Predictions of Long Noncoding RNA in Zea mays
    Boerner, S; McGinnis, KM
  • Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis
    Borsani, O; Zhu, J; Verslues, PE; Sunkar, R; Zhu, JK
  • Plant productivity and environment
    Boyer, JS
  • Involvement of CDSP 32, a drought-induced thioredoxin, in the response to oxidative stress in potato plants
    Broin, M; Cuine, S; Peltier, G; Rey, P
  • Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast
    Bumgarner, SL; Dowell, RD; Grisafi, P; Gifford, DK; Fink, GR
  • Rfam 11.0: 10 years of RNA families
    Burge, SW; Daub, J; Eberhardt, R; Tate, J; Barquist, L; Nawrocki, EP; Eddy, SR; Gardner, PP; Bateman, A
  • Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    Cabili, MN; Trapnell, C; Goff, L; Koziol, M; Tazon-Vega, B; Regev, A; Rinn, JL
  • Small RNAs, DNA methylation and transposable elements in wheat
    Cantu, D; Vanzetti, LS; Sumner, A; Dubcovsky, M; Matvienko, M; Distelfeld, A; Michelmore, RW; Dubcovsky, J
  • Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat
    Carrieri, C; Cimatti, L; Biagioli, M; Beugnet, A; Zucchelli, S; Fedele, S; Pesce, E; Ferrer, I; Collavin, L; Santoro, C; Forrest, AR; Carninci, P; Biffo, S; Stupka, E; Gustincich, S
    Bookmark
  • Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
    Conesa, A; Gotz, S; Garcia-Gomez, JM; Terol, J; Talon, M; Robles, M
    Bookmark
  • Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution
    Davidson, RM; Gowda, M; Moghe, G; Lin, H; Vaillancourt, B; Shiu, SH; Jiang, N; Robin Buell, C
  • Long non-coding RNAs and chromatin regulation
    Lucia, F; Dean, C
  • Role of hydroxyproline-rich glycoproteins in resistance of pearl millet against downy mildew pathogen Sclerospora graminicola
    Deepak, S; Shailasree, S; Kini, RK; Hause, B; Shetty, SH; Mithofer, A
    Bookmark
  • Hahb-4, a sunflower homeobox-leucine zipper gene, is a developmental regulator and confers drought tolerance to Arabidopsis thaliana plants
    Dezar, CA; Gago, GM; Gonzalez, DH; Chan, RL
  • Advances in foxtail millet biotechnology and its future directions
    Diao, Xianmin
  • The industrial development of China special crops
    Diao, Xianmin
  • A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice
    Ding, J; Lu, Q; Ouyang, Y; Mao, H; Zhang, P; Yao, J; Xu, C; Li, X; Xiao, J; Zhang, Q
  • Widespread dynamic DNA methylation in response to biotic stress
    Dowen, RH; Pelizzola, M; Schmitz, RJ; Lister, R; Dowen, JM; Nery, JR; Dixon, JE; Ecker, JR
  • OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought-, high-salt- and cold-responsive gene expression
    Dubouzet, JG; Sakuma, Y; Ito, Y; Kasuga, M; Dubouzet, EG; Miura, S; Seki, M; Shinozaki, K; Yamaguchi-Shinozaki, K
  • Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid
    Dugas, DV; Monaco, MK; Olsen, A; Klein, RR; Kumari, S; Ware, D; Klein, PE
  • Transcriptome pathways unique to dehydration tolerant relatives of modern wheat
    Ergen, NZ; Thimmapuram, J; Bohnert, HJ; Budak, H
  • The maize abscisic acid-responsive protein Rab17 is located in the nucleus and interacts with nuclear localization signals
    Goday, A; Jensen, AB; Culianez-Macia, FA; Mar Alba, M; Figueras, M; Serratosa, J; Torrent, M; Pages, M
  • The evolution of CONSTANS-like gene families in barley, rice, and Arabidopsis
    Griffiths, S; Dunford, RP; Coupland, G; Laurie, DA
  • Changes in 24-nt siRNA levels in Arabidopsis hybrids suggest an epigenetic contribution to hybrid vigor
    Groszmann, M; Greaves, IK; Albertyn, ZI; Scofield, GN; Peacock, WJ; Dennis, ES
  • The ARF family of transcription factors and their role in plant hormone-responsive transcription
    Guilfoyle, TJ; Ulmasov, T; Hagen, G
  • PlantTFDB: a comprehensive plant transcription factor database
    Guo, AY; Chen, X; Gao, G; Zhang, H; Zhu, QH; Liu, XC; Zhong, YF; Gu, X; He, K; Luo, J
  • Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
    Guttman, M; Amit, I; Garber, M; French, C; Lin, MF; Feldser, D; Huarte, M; Zuk, O; Carey, BW; Cassady, JP; Cabili, MN; Jaenisch, R; Mikkelsen, TS; Jacks, T; Hacohen, N; Bernstein, BE; Kellis, M; Regev, A; Rinn, JL; Lander, ES
  • lincRNAs act in the circuitry controlling pluripotency and differentiation
    Guttman, M; Donaghey, J; Carey, BW; Garber, M; Grenier, JK; Munson, G; Young, G; Lucas, AB; Ach, R; Bruhn, L; Yang, X; Amit, I; Meissner, A; Regev, A; Rinn, JL; Root, DE; Lander, ES
  • The cell wall hydroxyproline-rich glycoprotein RSH is essential for normal embryo development in Arabidopsis
    Hall, Q; Cannon, MC
  • Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA
    Heo, JB; Sung, S
  • Plant cis-acting regulatory DNA elements (PLACE) database: 1999
    Higo, K; Ugawa, Y; Iwamoto, M; Korenaga, T
  • An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress
    Ito, H; Gaubert, H; Bucher, E; Mirouze, M; Vaillant, I; Paszkowski, J
  • Regulation of drought tolerance by gene manipulation of 9-cis-epoxycarotenoid dioxygenase, a key enzyme in abscisic acid biosynthesis in Arabidopsis
    Iuchi, S; Kobayashi, M; Taji, T; Naramoto, M; Seki, M; Kato, T; Tabata, S; Kakubari, Y; Yamaguchi-Shinozaki, K; Shinozaki, K
  • bZIP transcription factors in Arabidopsis
    Jakoby, M; Weisshaar, B; Droge-Laser, W; Vicente-Carbajosa, J; Tiedemann, J; Kroj, T; Parcy, F
  • cDNA-AFLP analysis reveals differential gene expression in response to salt stress in foxtail millet (Setaria italica L.)
    Jayaraman, A; Puranik, S; Rai, NK; Vidapu, S; Sahu, PP; Lata, C; Prasad, M
  • Effects of drought on gene expression in maize reproductive and leaf meristem tissue revealed by RNA-Seq
    Kakumanu, A; Ambavaram, MM; Klumas, CM; Krishnan, A; Batlang, U; Myers, E; Grene, R; Pereira, A
  • Long noncoding RNA: unveiling hidden layer of gene regulatory networks
    Kim, ED; Sung, S
  • ABF2, an ABRE-binding bZIP factor, is an essential component of glucose signaling and its overexpression affects multiple stress tolerance
    Kim, S; Kang, JY; Cho, DI; Park, JH; Kim, SY
  • Widespread transcription at neuronal activity-regulated enhancers
    Kim, TK; Hemberg, M; Gray, JM; Costa, AM; Bear, DM; Wu, J; Harmin, DA; Laptewicz, M; Barbara-Haley, K; Kuersten, S; Markenscoff-Papadimitriou, E; Kuhl, D; Bito, H; Worley, PF; Kreiman, G; Greenberg, ME
  • CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine
    Kong, L; Zhang, Y; Ye, ZQ; Liu, XQ; Zhao, SQ; Wei, L; Gao, G
  • miRBase: integrating microRNA annotation and deep-sequencing data
    Kozomara, A; Griffiths-Jones, S
  • The common function of a novel subfamily of B-Box zinc finger proteins with reference to circadian-associated events in Arabidopsis thaliana
    Kumagai, T; Ito, S; Nakamichi, N; Niwa, Y; Murakami, M; Yamashino, T; Mizuno, T
  • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    Langmead, B; Trapnell, C; Pop, M; Salzberg, SL
  • Comparative transcriptome analysis of differentially expressed genes in foxtail millet (Setaria italica L.) during dehydration stress
    Lata, C; Sahu, PP; Prasad, M
  • Establishing, maintaining and modifying DNA methylation patterns in plants and animals
    Law, JA; Jacobsen, SE
  • Comparative analysis of drought-responsive transcriptome in Indica rice genotypes with contrasting drought tolerance
    Lenka, SK; Katiyar, A; Chinnusamy, V; Bansal, KC
  • Setaria viridis and Setaria italica, model genetic systems for the Panicoid grasses
    Li, P; Brutnell, TP
  • The developmental dynamics of the maize leaf transcriptome
    Li, P; Ponnala, L; Gandotra, N; Wang, L; Si, Y; Tausta, SL; Kebrom, TH; Provart, N; Patel, R; Myers, CR; Reidel, EJ; Turgeon, R; Liu, P; Sun, Q; Nelson, T; Brutnell, TP
  • Role of transposable elements in heterochromatin and epigenetic control
    Lippman, Z; Gendrel, AV; Black, M; Vaughn, MW; Dedhia, N; McCombie, WR; Lavine, K; Mittal, V; May, B; Kasschau, KD; Carrington, JC; Doerge, RW; Colot, V; Martienssen, R
  • Oxidative stress induced heat shock factor phosphorylation and HSF-dependent activation of yeast metallothionein gene transcription
    Liu, XD; Thiele, DJ
  • Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis
    Liu, J; Jung, C; Xu, J; Wang, H; Deng, S; Bernad, L; Arenas-Huertero, C; Chua, NH
  • Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method
    Livak, KJ; Schmittgen, TD
  • Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq
    Lu, T; Lu, G; Fan, D; Zhu, C; Li, W; Zhao, Q; Feng, Q; Zhao, Y; Guo, Y; Huang, X; Han, B
  • Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array
    Matsui, A; Ishida, J; Morosawa, T; Mochizuki, Y; Kaminuma, E; Endo, TA; Okamoto, M; Nambara, E; Nakajima, M; Kawashima, M; Satou, M; Kim, JM; Kobayashi, N; Toyoda, T; Shinozaki, K; Seki, M
  • Long non-coding RNAs: insights into functions
    Mercer, TR; Dinger, ME; Mattick, JS
  • Sequencing technologies—the next generation
    Metzker, ML
  • Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs
    Moran, VA; Perera, RJ; Khalil, AM
  • Genome-wide profiling of stored mRNA in Arabidopsis thaliana seed germination: epigenetic and genetic regulation of transcription in seed
    Nakabayashi, K; Okamoto, M; Koshiba, T; Kamiya, Y; Nambara, E
  • Transcriptional regulatory networks in response to abiotic stresses in Arabidopsis and grasses
    Nakashima, K; Ito, Y; Yamaguchi-Shinozaki, K
  • An expression atlas of rice mRNAs and small RNAs
    Nobuta, K; Venu, RC; Lu, C; Belo, A; Vemaraju, K; Kulkarni, K; Wang, W; Pillay, M; Green, PJ; Wang, GL; Meyers, BC
  • Distinct size distribution of endogeneous siRNAs in maize: evidence from deep sequencing in the mop1-1 mutant
    Nobuta, K; Lu, C; Shrivastava, R; Pillay, M; Paoli, E; Accerbi, M; Arteaga-Vazquez, M; Sidorenko, L; Jeong, DH; Yen, Y; Green, PJ; Chandler, VL; Meyers, BC
  • Long noncoding RNAs with enhancer-like function in human cells
    Orom, UA; Derrien, T; Beringer, M; Gumireddy, K; Gardini, A; Bussotti, G; Lai, F; Zytnicki, M; Notredame, C; Huang, Q; Guigo, R; Shiekhattar, R
  • Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
    Pauli, A; Valen, E; Lin, MF; Garber, M; Vastenhouw, NL; Levin, JZ; Fan, L; Sandelin, A; Rinn, JL; Regev, A; Schier, AF
  • The role of small RNAs in abiotic stress
    Phillips, JR; Dalmay, T; Bartels, D
  • BEDTools: a flexible suite of utilities for comparing genomic features
    Quinlan, AR; Hall, IM
  • ABO3, a WRKY transcription factor, mediates plant responses to abscisic acid and drought tolerance in Arabidopsis
    Ren, X; Chen, Z; Liu, Y; Zhang, H; Zhang, M; Liu, Q; Hong, X; Zhu, JK; Gong, Z
  • Rational siRNA design for RNA interference
    Reynolds, A; Leake, D; Boese, Q; Scaringe, S; Marshall, WS; Khvorova, A
  • Functional importance of conserved domains in the flowering-time gene CONSTANS demonstrated by analysis of mutant alleles and transgenic plants
    Robson, F; Costa, MM; Hepworth, SR; Vizir, I; Pineiro, M; Reeves, PH; Putterill, J; Coupland, G
  • Functional analysis of an Arabidopsis transcription factor, DREB2A, involved in drought-responsive gene expression
    Sakuma, Y; Maruyama, K; Osakabe, Y; Qin, F; Seki, M; Shinozaki, K; Yamaguchi-Shinozaki, K
  • A novel function for a redox-related LEA protein (SAG21/AtLEA5) in root development and biotic stress responses
    Salleh, FM; Evans, K; Goodall, B; Machin, H; Mowla, SB; Mur, LA; Runions, J; Theodoulou, FL; Foyer, CH; Rogers, HJ
  • Quality control and preprocessing of metagenomic datasets
    Schmieder, R; Edwards, R
  • Plant PP2C phosphatases: emerging functions in stress signaling
    Schweighofer, A; Hirt, H; Meskiene, I
  • Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray
    Seki, M; Narusaka, M; Abe, H; Kasuga, M; Yamaguchi-Shinozaki, K; Carninci, P; Hayashizaki, Y; Shinozaki, K
  • Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray
    Seki, M; Narusaka, M; Ishida, J; Nanjo, T; Fujita, M; Oono, Y; Kamiya, A; Nakajima, M; Enju, A; Sakurai, T; Satou, M; Akiyama, K; Taji, T; Yamaguchi-Shinozaki, K; Carninci, P; Kawai, J; Hayashizaki, Y; Shinozaki, K
  • Functional dissection of an abscisic acid (ABA)-inducible gene reveals two independent ABA-responsive complexes each containing a G-box and a novel cis-acting element
    Shen, Q; Ho, TH
  • Molecular responses to dehydration and low temperature: differences and cross-talk between two stress signaling pathways
    Shinozaki, K; Yamaguchi-Shinozaki, K
  • Regulatory network of gene expression in the drought and cold stress responses
    Shinozaki, K; Yamaguchi-Shinozaki, K; Seki, M
  • Transcription factors in plant defense and stress responses
    Singh, K; Foley, RC; Onate-Sanchez, L
  • Small RNAs as big players in plant abiotic stress responses and nutrient deprivation
    Sunkar, R; Chinnusamy, V; Zhu, J; Zhu, JK
  • Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target
    Swiezewski, S; Liu, F; Magusin, A; Dean, C
  • Proline: a multifunctional amino acid
    Szabados, L; Savoure, A
  • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    Trapnell, C; Williams, BA; Pertea, G; Mortazavi, A; Kwan, G; Baren, MJ; Salzberg, SL; Wold, BJ; Pachter, L
  • Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
    Trapnell, C; Roberts, A; Goff, L; Pertea, G; Kim, D; Kelley, DR; Pimentel, H; Salzberg, SL; Rinn, JL; Pachter, L
  • Long noncoding RNA as modular scaffold of histone modification complexes
    Tsai, MC; Manor, O; Wan, Y; Mosammaparast, N; Wang, JK; Lan, F; Shi, Y; Segal, E; Chang, HY
  • Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution
    Ulitsky, I; Shkumatava, A; Jan, CH; Sive, H; Bartel, DP
  • Activation and repression of transcription by auxin-response factors
    Ulmasov, T; Hagen, G; Guilfoyle, TJ
  • Arabidopsis basic leucine zipper transcription factors involved in an abscisic acid-dependent signal transduction pathway under drought and high-salinity conditions
    Uno, Y; Furihata, T; Abe, H; Yoshida, R; Shinozaki, K; Yamaguchi-Shinozaki, K
  • A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize
    Usadel, B; Poree, F; Nagel, A; Lohse, M; Czedik-Eysenberg, A; Stitt, M
  • Senescence- and drought-related changes in peroxidase and superoxide dismutase isoforms in leaves of Ramonda serbica
    Veljovic-Jovanovic, S; Kukavica, B; Stevanovic, B; Navari-Izzo, F
  • RNA-Seq: a revolutionary tool for transcriptomics
    Wang, Z; Gerstein, M; Snyder, M
  • Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing
    Wang, B; Guo, G; Wang, C; Lin, Y; Wang, X; Zhao, M; Guo, Y; He, M; Zhang, Y; Pan, L
  • DEGseq: an R package for identifying differentially expressed genes from RNA-seq data
    Wang, L; Feng, Z; Wang, X; Zhang, X
  • Time of day shapes Arabidopsis drought transcriptomes
    Wilkins, O; Brautigam, K; Campbell, MM
  • Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing
    Xin, M; Wang, Y; Yao, Y; Song, N; Hu, Z; Qin, D; Xie, C; Peng, H; Ni, Z; Sun, Q
  • Organization of cis-acting regulatory elements in osmotic- and cold-stress-responsive promoters
    Yamaguchi-Shinozaki, K; Shinozaki, K
  • An abiotic stress-responsive bZIP transcription factor from wild and cultivated tomatoes regulates stress-related genes
    Yanez, M; Caceres, S; Orellana, S; Bastias, A; Verdugo, I; Ruiz-Lara, S; Casaretto, JA
  • WEGO: a web tool for plotting GO annotations
    Ye, J; Fang, L; Zheng, H; Zhang, Y; Chen, J; Zhang, Z; Wang, J; Li, S; Li, R; Bolund, L
  • Gramene database in 2010: updates and extensions
    Youens-Clark, K; Buckler, E; Casstevens, T; Chen, C; Declerck, G; Derwent, P; Dharmawardhana, P; Jaiswal, P; Kersey, P; Karthikeyan, AS; Lu, J; McCouch, SR; Ren, L; Spooner, W; Stein, JC; Thomason, J; Wei, S; Ware, D
  • Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays
    Zeller, G; Henz, SR; Widmer, CK; Sachsenberg, T; Ratsch, G; Weigel, D; Laubinger, S
  • PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database
    Zhang, H; Jin, J; Tang, L; Zhao, Y; Gu, X; Gao, G; Luo, J
  • Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential
    Zhang, G; Liu, X; Quan, Z; Cheng, S; Xu, X; Pan, S; Xie, M; Zeng, P; Yue, Z; Wang, W; Tao, Y; Bian, C; Han, C; Xia, Q; Peng, X; Cao, R; Yang, X; Zhan, D; Hu, J; Zhang, Y; Li, H; Li, N; Wang, J; Wang, C; Wang, R; Guo, T; Cai, Y; Liu, C; Xiang, H; Shi, Q; Huang, P; Chen, Q; Li, Y; Zhao, Z
  • Genome-wide transcriptome analysis of two maize inbred lines under drought stress
    Zheng, J; Fu, J; Gou, M; Huai, J; Liu, Y; Jian, M; Huang, Q; Guo, X; Dong, Z; Wang, H; Wang, G
  • Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle
    Zhou, J; Wang, X; Jiao, Y; Qin, Y; Liu, X; He, K; Chen, C; Ma, L; Wang, J; Xiong, L; Zhang, Q; Fan, L; Deng, XW

You’re reading a free preview. Subscribe to read the entire article.

Try 2 weeks free now

DeepDyve is your
personal research library

It’s your single place to instantly
discover and read the research
that matters to you.

Enjoy affordable access to
over 18 million articles from more than
15,000 peer-reviewed journals.

All for just $49/month

Explore the DeepDyve Library

or browse the journals available

Search

Query the DeepDyve database, plus search all of PubMed and Google Scholar seamlessly

Organize

Save any article or search result from DeepDyve, PubMed, and Google Scholar... all in one place.

Access

Get unlimited, online access to over 18 million full-text articles from more than 15,000 scientific journals.

Your journals are on DeepDyve

Read from thousands of the leading scholarly journals from SpringerNature, Elsevier, Wiley-Blackwell, Oxford University Press and more.

All the latest content is available, no embargo periods.

See the journals in your area

DeepDyve

Freelancer

DeepDyve

Pro

Price

FREE

$49/month
$360/year

Save searches from
Google Scholar,
PubMed

Create lists to
organize your research

Export lists, citations

Read DeepDyve articles

Abstract access only

Unlimited access to over
18 million full-text articles

Print

20 pages / month

PDF Discount

20% off

Sign up
for free
Start 14 day
Free Trial