Abstract
De novo assembly of reads produced by next-generation sequencing (NGS) technologies offers a rapid approach to obtain expressed gene sequences for non-model organisms. Senna (Cassia angustifolia Vahl.) is a drought-tolerant annual undershrub of Caesalpiniaceae, a subfamily of Fabaceae. There are insufficient transcriptomic and genomic data in public databases for understanding the molecular mechanism underlying the drought tolerance of senna. Therefore, the main purpose of this study was to know the transcriptome profile of senna, with special reference to drought stress. RNA from two different stages of leaf development was extracted and sequenced separately using the Illumina technology. A total of 200 million reads were generated, and a de novo assembly of processed reads in the pooled transcriptome using Trinity yielded 43,413 transcripts which were further annotated using NCBI BLAST with “green plant database (txid 33090),” Swiss Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG), and Gene Ontology (GO). Out of the total transcripts, 42,280 (95.0 %) were annotated by BLASTX against the green plant database of NCBI. Senna transcriptome showed the highest similarity to Glycine max (41 %), followed by Phaseolus vulgaris (16 %), Cicer arietinum (15 %), and Medicago trancatula (5 %). The highest number of GO terms were enriched for the molecular functions category; of these “catalytic activity” (GO: 0003824) (25.10 %) and “binding activity” (GO: 0005488) (20.10 %) were most abundantly represented. We used InterProscan to see protein similarity at domain level; a total of 33,256 transcripts were annotated against the Pfam domains. The transcripts were assigned with various KEGG pathways. Coding DNA sequences (CDS) encoding various drought stress-regulated pathways such as signaling factors, protein-modifying/degrading enzymes, biosynthesis of phytohormone, phytohormone signaling, osmotically active compounds, free radical scavengers, chlorophyll metabolism, leaf cuticular wax, polyamines, and protective proteins were identified through BLASTX search. The lucine-rich repeat kinase family was the most abundantly found group of protein kinases. Orphan, bHLH, and bZIP family TFs were the most abundantly found in senna. Six genes encoding MYC2 transcription factor, 9-cis-epoxycarotenoid dioxygenase (NCED), l -ascorbate peroxidase (APX), aminocyclopropane carboxylate oxidase (ACO), abscisic acid 8′-hydroxylase (ABA), and WRKY transcription factor were confirmed through reverse transcriptase-PCR (RT-PCR) and Sanger sequencing for the first time in senna. The potential drought stress-related transcripts identified in this study provide a good start for further investigation into the drought adaptation in senna. Additionally, our transcriptome sequences are the valuable resource for accelerated genomics-assisted genetic improvement programs and facilitate manipulation of biochemical pathways for developing drought-tolerant genotypes of crop plants.
Similar content being viewed by others
References
Abe H, Yamaguchi-Shinozaki K, Urao T, Iwasaki T, Hosokawa D, Shinozaki K (1997) Role of Arabidopsis MYC and MYB homologs in drought- and abscisic acid-regulated gene expression. Plant Cell 9(10):1859–1868
Abulafatih HA (1987) Medicinal plants of Southern Arabia. Econ Bot 41:354–360
Agarwal S, Pandey V (2004) Antioxidant enzyme responses to NaCl stress in Cassia angustifolia. Biol Plantarum 48(4):555–560
Akpinar BA, Avsar B, Lucas SJ, Budak H (2012) Plant abiotic stress signalling. Plant Signal Behav 7(11):1450–1455
Akpinar BA, Lucas SJ, Budak H (2013) Genomics approaches for crop improvement against abiotic stress. Sci World J 15:361921
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410
Argueso CT, Hansen M, Kieber JJ (2007) Regulation of ethylene biosynthesis. J Plant Growth Regul 26(2):92–105
Arraes FB, Beneventi MA, Lisei de Sa ME, Paixao JF, Albuquerque EV, Marin SR, Purgatto E, Nepomuceno AL, Grossi-de-Sa MF (2015) Implications of ethylene biosynthesis and signaling in soybean drought stress tolerance. BMC Plant Biol 15:213
Ayoub AT (1977) Some primary features of salt tolerance in senna (Cassia angastifolia). J Exp Bot 28:484–492
Bartels D, Sunkar R (2005) Drought and salt tolerance in plants. Cr Rev Plant Sci 24(1):23–58
Beale SI (2005) Green genes gleaned. Trends Plant Sci 10(7):309–312
Bleecker AB, Kende H (2000) Ethylene: a gaseous signal molecule in plants. Annu Rev Cell Dev Biol 16:1–18
Blum A (1988) Plant breeding for stress environments. CRC Press, Inc., Boca Raton
Boatwright JL, Pajerowska-Mukhtar K (2013) Salicylic acid: an old hormone up to new tricks. Mol Plant Pathol 14(6):623–634
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics 30:2114–2120
Boston RS, Viitanen PV, Vierling E (1996) Molecular chaperones and protein folding in plants. In: Filipowicz W, Hohn T (eds) Post-transcriptional control of gene expression in plants. Springer, Dordrecht, pp 191–222
Bowman MJ, Park W, Bauer PJ, Udall JA, Page JT, Raney J, Scheffler BE, Jones DC, Campbell BT (2013) RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress. PLoS One 8(12):e82634
Budak H, Kantar M, Kurtoglu KY (2013) Drought tolerance in modern and wild wheat. Sci World J 15:548246
Ciftci-Yilmaz S, Mittler R (2008) The zinc finger network of plants. Cell Mol Life Sci 65(7–8):1150–1160
Cutler AJ, Krochko JE (1999) Formation and breakdown of ABA. Trends Plant Sci 4(12):472–478
Cutler SR, Rodriguez PL, Finkelstein RR, Abrams SR (2010) Abscisic acid: emergence of a core signaling network. Annu Rev Plant Biol 61:651–679
D’Autréaux B, Toledano MB (2007) ROS as signalling molecules: mechanisms that generate specificity in ROS homeostasis. Nat Rev Mol Cell Biol 8(10):813–824
Daviere JM, Achard P (2013) Gibberellin signaling in plants. Development 140(6):1147–1151
Devoto A, Ellis C, Magusin A, Chang HS, Chilcott C, Zhu T, Turner JG (2005) Expression profiling reveals COI1 to be a key regulator of genes involved in wound- and methyl jasmonate-induced secondary metabolism, defence, and hormone interactions. Plant Mol Biol 58(4):497–513
do Amaral MN, Arge LW, Benitez LC, Danielowski R, Silveira SF, Farias DD, de Oliveira AC, da Maia LC, Braga EJ (2016) Comparative transcriptomics of rice plants under cold, iron, and salt stresses. Funct Integr Genom 16(5):567–579
Do PT, Degenkolbe T, Erban A, Heyer AG, Kopka J, Köhl KI, Hincha DK, Zuther E (2013) Dissecting rice polyamine metabolism under controlled long-term drought stress. PLoS One 8(4):e60325
Dong Y, Fan G, Deng M, Xu E, Zhao Z (2014) Genome-wide expression profiling of the transcriptomes of four Paulownia tomentosa accessions in response to drought. Genomics 104(4):295–305
Du H, Wang N, Cui F, Li X, Xiao J, Xiong L (2010) Characterization of the beta-carotene hydroxylase gene DSM2 conferring drought and oxidative stress resistance by increasing xanthophylls and abscisic acid synthesis in rice. Plant Physiol 154(3):1304–1318
Ergen NZ, Budak H (2009) Sequencing over 13 000 expressed sequence tags from six subtractive cDNA libraries of wild and modern wheats following slow drought stress. Plant Cell Environ 32(3):220–236
Ergen NZ, Thimmapuram, Bohnert J, Hans J, Budak H (2009) Transcriptome pathways unique to dehydration tolerant relatives of modern wheat. Funct Integr Genomics 9(3):377–396
Fang Y, You J, Xie K, Xie W, Xiong L (2008) Systematic sequence analysis and identification of tissue-specific or stress-responsive genes of NAC transcription factor family in rice. Mol Genet Genomics 280(6):547–563
Folkard C (1995) Encyclopedia of herbs and their uses. Herb Society of America, Dorling Kindersley Publishing Inc., New York
Gao T, Wu Y, Zhang Y, Liu L, Ning Y, Wang D, Tong H, Chen S, Chu C, Xie Q (2011) OsSDIR1 overexpression greatly improves drought tolerance in transgenic rice. Plant Mol Biol 76(1–2):145–156
Gao JP, Wang D, Cao LY, Sun HF (2015) Transcriptome sequencing of Codonopsis pilosula and identification of candidate genes involved in polysaccharide biosynthesis. PLoS One 10(2):e0117342
Ghazanfar SA, Al-Sabahi AA (1993) Medicinal plants of northern and central Oman (Arabia). Econ Bot 41:89–98
Gill SS, Tuteja N (2010) Polyamines and abiotic stress tolerance in plants. Plant Signal Behav 5(1):26–33
Gill SS, Anjum NA, Hasanuzzaman M, Gill R, Trivedi DK, Ahmad I, Pereira E, Tuteja N (2013) Glutathione and glutathione reductase: a boon in disguise for plant abiotic stress defense operations. Plant Physiol Biochem 70:204–212
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full length transcriptome assembly from RNA-seq data without a reference genome. Nat Biotechnol 29:644–652
Hammouda FM, Ismail SI, Abdel-Azim NS, Shams KA (2005) A guide to medicinal plants in North Africa. In: Batanouny KH (eds) IUCN Centre for Mediterranean Cooperation, Malaga, Andalusia, Spain, pp 217–218
Hirayama T, Shinozaki K (2010) Research on plant abiotic stress responses in the postgenome era: past, present and future. Plant J 61(6):1041–1052
Hiz MC, Canher B, Niron H, Turet M (2014) Transcriptome analysis of salt tolerant common bean (Phaseolus vulgaris L.) under saline conditions. PLoS One 9(3):e92598
Hooker TS, Millar AA, Kunst L (2002) Significance of the expression of the CER6 condensing enzyme for cuticular wax production in Arabidopsis. Plant Physiol 129(4):1568–1580
Hortensteiner S (2006) Chlorophyll degradation during senescence. Annu Rev Plant Biol 57:55–77
Hu H, Xiong L (2014) Genetic engineering and breeding of drought-resistant crops. Annu Rev Plant Biol 65:715–741
Hu T, Sun X, Zhang X, Nevo E, Fu J (2014) An RNA sequencing transcriptome analysis of the high-temperature stressed tall fescue reveals novel insights into plant thermotolerance. BMC Genomics 15:1147
Jiang SY, Bhalla R, Ramamoorthy R, Luan HF, Venkatesh PN, Cai M, Ramachandran S (2012) Over-expression of OSRIP18 increases drought and salt tolerance in transgenic rice plants. Transgenic Res 21(4):785–795
Jin JP, Zhang H, Kong L, Gao G, Luo JC (2014) PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucleic Acids Res 42(D1):1182–1187
Kantar M, Lucas SJ, Budak H (2011) Drought stress: molecular genetics and genomics approaches. Adv Bot Res 57:445–493
Kawano T, Furuichi T, Muso S (2004) Controlled free salicylic acid levels and corresponding signaling mechanisms in plants. Plant Biotechnol 21:319–335
Khalid H, Abdalla WE, Abdelgadir H, Opatz T, Effert T (2012) Gems from traditional north-African medicine: medicinal and aromatic plants from Sudan. Nat Prod Bioprospect 2(3):92–103
Khammari I, Galavi M, Ghanbari A, Solouki M, Poorchaman MRA (2012) The effect of drought stress and nitrogen levels on antioxidant enzymes, proline and yield of Indian Senna (Cassia angustifolia L.). J Med Plants Res 6(11):2125–2130
Khan NA, Nazar R, Iqbal N, Anjum NA (2012) Phytohormones and abiotic stress tolerance in plants. Springer, Berlin
Kim J, Jung JH, Lee SB, Go YS, Kim HJ, Cahoon R, Markham JE, Cahoon EB, Suh MC (2013) Arabidopsis 3-ketoacyl-coenzyme a synthase9 is involved in the synthesis of tetracosanoic acids as precursors of cuticular waxes, suberins, sphingolipids, and phospholipids. Plant Physiol 162(2):567–580
Kohli A, Sreenivasulu N, Lakshmanan P, Kuman PP (2013) The phytohormone crosstalk paradigm takes center stage in understanding how plants respond to abiotic stresses. Plant Cell Rep 32(7):945–957
Krugman T, Chagué V, Peleg Z, Balzergue S, Just J, Korol AB, Nevo E, Saranga Y, Chalhoub B, Fahima T (2010) Multilevel regulation and signalling processes associated with adaptation to terminal drought in wild emmer wheat. Funct Integr Genomics 10(2):167–186
Kumari S, Joshi R, Singh K, Roy S, Tripathi AK, Singh P, Singla-Pareek SL, Pareek A (2015) Expression of a cyclophilin OsCyp2-P isolated from a salt-tolerant landrace of rice in tobacco alleviates stress via ion homeostasis and limiting ROS accumulation. Funct Integr Genomics 15(4):395–412
Kusaba M, Tanaka A, Tanaka R (2013) Stay-green plants: what do they tell us about the molecular mechanism of leaf senescence. Photosynth Res 117(1–3):221–234
Kushiro T, Okamoto M, Nakabayashi K, Yamagishi K, Kitamura S, Asami T, Hirai N, Koshiba T, Kamiya Y, Nambara E (2004) The Arabidopsis cytochrome P450 CYP707A encodes ABA 8′-hydroxylases: key enzymes in ABA catabolism. EMBO J 23(7):1647–1656
Kuzuoglu-Ozturk D, Cebeci Yalcinkaya O, Akpinar BA, Mitou G, Korkmaz G, Gozuacik D, Budak H (2012) Autophagy-related gene, TdAtg8, in wild emmer wheat plays a role in drought and osmotic stress response. Planta 236(4):1081–1092
Lemli J (1986) The chemistry of senna. Fitoterapia 57:33–40
Leng X, Mu Q, Wang X, Li X, Zhu X, Shangguan L, Fang J (2015) Transporters, chaperones, and P-type ATPases controlling grapevine copper homeostasis. Funct Integr Genomics 15(6):673–684
Levitt J (1980) Responses of plants to environmental stress: chilling, freezing and high temperature stresses, vol 1, 2nd edn. Academic, New York
Li WX, Oono Y, Zhu J, He XJ, Wu JM, Iida K, Lu XY, Cui X, Jin H, Zhu JK (2008) The Arabidopsis NFYA5 transcription factor is regulated transcriptionally and post-transcriptionally to promote drought resistance. Plant Cell 20(8):2238–2251
Li MY, Tan HW, Wang F, Jiang Q, Xu ZS, Tian C, Xiong AS (2014) De novo transcriptome sequence assembly and identification of AP2/ERF transcription factor related to abiotic stress in parsley (Petroselinum crispum). PLoS One 9(9):e108977
Li PS, Yu TF, He GH, Chen M, Zhou YB, Chai SC, Xu ZS, Ma YZ (2014) Genome-wide analysis of the Hsf family in soybean and functional identification of GmHsf-34 involvement in drought and heat stresses. BMC Genom 15:1009
Lim GH, Zhang X, Chung MS, Lee DJ, Woo YM, Cheong HS, Kim CS (2010) A putative novel transcription factor, AtSKIP, is involved in abscisic acid signalling and confers salt and osmotic tolerance in Arabidopsis. New Phytol 185(1):103–113
Liu Q, Kasuga M, Sakuma Y, Abe H, Miura S, Yamaguchi-Shinozaki K, Shinozaki K (1998) Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought- and low-temperature-responsive gene expression, respectively, in Arabidopsis. Plant Cell 10(8):1391–1406
Liu Z, Song T, Zhu Q, Wang W, Zhou J, Liao H (2014) De novo assembly and analysis of Cassia obtusifolia seed transcriptome to identify genes involved in the biosynthesis of active metabolites. Biosci Biotechnol Biochem 78(5):791–799
Liu H, Che Z, Zeng X, Zhou X, Sitoe HM, Wang H, Yu D (2016) Genome-wide analysis of calcium-dependent protein kinases and their expression patterns in response to herbivore and wounding stresses in soybean. Funct Integr Genom 16(5):481–493
Long L, Gao W, Xu L, Liu M, Luo X, He X, Yang X, Zhang X, Zhu L (2014) GbMPK3, a mitogen-activated protein kinase from cotton, enhances drought and oxidative stress tolerance in tobacco. Plant Cell Tiss Organ Cult 116:153–162
Lucas S, Dogan E, Budak H (2011a) TMPIT1 from wild emmer wheat: first characterisation of a stress-inducible integral membrane protein. Gene 483(1):22–28
Lucas S, Durmaz E, Akpınar BA, Budak H (2011b) The drought response displayed by a DRE-binding protein from Tritium dicoccoides. Plant Physiol Biochem 49(3):346–351
Manavalan LP, Chen X, Clarke J, Salmeron J, Nguyen HT (2012) RNAi-mediated disruption of squalene synthase improves drought tolerance and yield in rice. J Exp Bot 63(1):163–175
Min XJ, Butler G, Storms R, Tsang A (2005) OrfPredictor: predicting protein-coding regions in EST-derived sequences. Nucleic Acids Res. Web Server Issue W677–W680. (http://bioinformatics.ysu.edu/tools/OrfPredictor.html)
Mockaitis K, Estelle M (2008) Auxin receptors and plant development: a new signaling paradigm. Annu Rev Cell Dev Biol 24:55–80
Moriya Y, Itoh M, Okuda S, Yoshizawa A, Kanehisa M (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35:W182–W185
Munné-Bosch S, Queval G, Foyer CH (2013) The impact of global change factors on redox signaling underpinning stress tolerance. Plant Physiol 161(1):5–19
Mustafa NR, Kim HK, Choi YH, Erkelens C, Lefeber AW, Spijksma G, van der Heijden R, Verpoorte R (2009) Biosynthesis of salicylic acid in fungus elicited Catharanthus roseus cells. Phytochemistry 70(4):532–539
Nakashima K, Takasaki H, Mizoi J, Shinozaki K, Yamaguchi-Shinozaki K (2012) NAC transcription factors in plant abiotic stress responses. Biochim Biophys Acta 1819(2):97–103
Ning Y, Jantasuriyarat C, Zhao Q, Zhang H, Chen S, Liu J, Liu L, Tang S, Park CH, Wang X, Liu X, Dai L, Xie Q, Wang GL (2011) The SINA E3 ligase OsDIS1 negatively regulates drought response in rice. Plant Physiol 157(1):242–255
Pandey N, Ranjan A, Pant P, Tripathi RK, Ateek F, Pandey HP, Patre UV, Sawant SV (2013) CAMTA 1 regulates drought responses in Arabidopsis thaliana. BMC Genomics 14:216
Park GG, Park JJ, Yoon J, Yu SN, An G (2010) A RING finger E3 ligase gene, Oryza sativa delayed seed germination 1 (OsDSG1), controls seed germination and stress responses in rice. Plant Mol Biol 74(4–5):467–478
Peleg Z, Blumwald E (2011) Hormone balance and abiotic stress tolerance in crop plants. Curr Opin Plant Biol 14(3):290–295
Qureshi MI, Abdin MZ, Qadir S, Iqbal M (2007) Lead-induced oxidative stress and metabolic alterations in Cassia angustifolia Vahl. Biol Plantarum 51(1):121–128
Rama Reddy NR, Ragimasalawada M, Sabbavarapu MM, Nadoor S, Patil JV (2014) Detection and validation of stay-green QTL in post-rainy sorghum involving widely adapted cultivar, M35-1 and a popular stay-green genotype B35. BMC Genom 18(15):909
Rama Reddy NR, Mehta RH, Soni PH, Makasana J, Gajbhiye NA, Ponnuchamy M, Kumar J (2015) Next generation sequencing and transcriptome analysis predicts biosynthetic pathway of sennosides from senna (Cassia angustifolia Vahl.), a non-model plant with potent laxative properties. PLoS One 10(6):e0129422
Ramchandra Reddy A, Chaitanya KV, Vivekanandan M (2004) Drought induced responses of photosynthesis and antioxidant metabolism in higher plants. J Plant Physiol 161(11):1189–1202
Raney JA, Reynolds DJ, Elzinga DB, Page J, Udall JA, Jellen EN, Bonfacio A, Fairbanks DJ, Maughan PJ (2014) Transcriptome analysis of drought induced stress in Chenopodium quinoa. Am J Plant Sci 5(3):338–357
Ratnayaka HH, Kincaid D (2005) Gas exchange and leaf ultrastructure of tinnevelly senna, cassia angustifolia, under drought and nitrogen stress. Crop Sci 45(3):840–847
Ren X, Chen Z, Liu Y, Zhang H, Zhang M, Liu Q, Hong X, Zhu J, Gong Z (2010) ABO3, a WRKY transcription factor, mediates plant responses to abscisic acid and drought tolerance in Arabidopsis. Plant J 63(3):417–429
Richards DE, King KE, Ait-Ali T, Harberd NP (2001) How gibberellin regulates plant growth and development: a molecular genetic analysis of gibberellins signaling. Annu Rev Plant Physiol Plant Mol Biol 52:67–88
Rocheta M, Becker JD, Coito JL, Carvalho L, Amâncio S (2014) Heat and water stress induce unique transcriptional signatures of heat-shock proteins and transcription factors in grapevine. Funct Integr Genomics 14(1):135–148
Rodriguez MC, Petersen M, Mundy J (2010) Mitogen-activated protein kinase signaling in plants. Annu Rev Plant Biol 61:621–649
Roje S (2006) S-adenosyl-L-methionine: beyond the universal methyl group donor. Phytochemistry 67(15):1686–1698
Ryu MY, Cho SK, Kim WT (2010) The Arabidopsis C3H2C3-type RING E3 ubiquitin ligase AtAIRP1 is a positive regulator of an abscisic acid-dependent response to drought stress. Plant Physiol 154(4):1983–1997
Saito S, Hirai N, Matsumoto C, Ohigashi H, Ohta D, Sakata K, Mizutani M (2004) Arabidopsis CYP707As encode (+)-abscisic acid 8′-hydroxylase, a key enzyme in the oxidative catabolism of abscisic acid. Plant Physiol 134(4):1439–1449
Santner A, Calderon-Villalobos LI, Estelle M (2009) Plant hormones are versatile chemical regulators of plant growth. Nat Chem Biol 5(5):301–307
Schroeder JI, Allen GJ, Hugouvieux V, Kwak JM, Waner D (2001) Guard cell signal transduction. Annu Rev Plant Physiol Plant Mol Biol 52:627–658
Seki M, Umezawa T, Urano K, Shinozaki K (2007) Regulatory metabolic networks in drought stress responses. Curr Opin Plant Biol 10(3):296–302
Shakeel SN, Wang X, Binder BM, Schaller GE (2013) Mechanisms of signal transduction by ethylene: overlapping and non-overlapping signalling roles in a receptor family. AoB Plants 5:plt010
Shang J, Song P, Ma B, Qi X, Zeng Q, Xiang Z, He N (2014) Identification of the mulberry genes involved in ethylene biosynthesis and signaling pathways and the expression of MaERF-B2-1 and MaERF-B2-2 in the response to flooding stress. Funct Integr Genomics 14(4):767–777
Shanker AK, Maheswari M, Yadav SK, Desai S, Bhanu D, Attal NB, Venkateswarlu B (2014) Drought stress responses in crops. Funct Integr Genomics 14(1):11–22
Sharma S, Villamor JG, Verslues PE (2011) Essential role of tissue-specific proline synthesis and catabolism in growth and redox balance at low water potential. Plant Physiol 157(1):292–304
Shi H, Wang X, Ye T, Chen F, Deng J, Yang P, Zhang Y, Chan Z (2014) The cysteine2/histidine2-type transcription factor ZINC FINGER OF ARABIDOPSIS THALIANA6 modulates biotic and abiotic stress responses by activating salicylic acid-related genes and C-REPEAT-BINDING FACTOR Genes in Arabidopsis. Plant Physiol 165(3):1367–1379
Singh R, Kumar R, Mahato AK, Paliwal R, Singh AK, Kumar S, Marla SS, Kumar A, Singh NK (2016) De novo transcriptome sequencing facilitates genomic resource generation in Tinospora cordifolia. Funct Integr Genomics 16(5):581–591
Song A, Zhu X, Chen F, Gao H, Jiang J, Chen S (2014) A chrysanthemum heat shock protein confers tolerance to abiotic stress. Int J Mol Sci 15(3):5063–5078
Song L, Jiang L, Chen Y, Shu Y, Bai Y, Guo C (2016) Deep-sequencing transcriptome analysis of field-grown Medicago sativa L. crown buds acclimated to freezing stress. Funct Integr Genom 16(5):495–511
Sreedhar RV, Kumari P, Rupwate SD, Rajasekharan R, Srinivasan M (2015) Exploring triacylglycerol biosynthetic pathway in developing seeds of Chia (Salvia hispanica L.): a transcriptomic approach. PLoS One 10(4):e0123580
Su LT, Li JW, Liu DQ, Zhai Y, Zhang HJ, Li XW, Zhang QL, Wang Y, Wang QY (2014) A novel MYB transcription factor, GmMYBJ1, from soybean confers drought and cold tolerance in Arabidopsis thaliana. Gene 538(1):46–55
Sun R, Wang K, Guo T, Jones DC, Cobb J, Zhang B, Wang Q (2015a) Genome-wide identification of auxin response factor (ARF) genes and its tissue-specific prominent expression in Gossypium raimondii. Funct Integr Genomics 15(4):481–493
Sun W, Chen H, Wang J, Sun HW, Yang SK, Sang YL, Lu XB, Xu XH (2015b) Expression analysis of genes encoding mitogen-activated protein kinases in maize provides a keylink between abiotic stress signaling and plant reproduction. Funct Integr Genomics 15(1):107–120
Sun X, Xie Z, Zhang C, Mu Q, Wu W, Wang B, Fang J (2016) A characterization of grapevine of GRAS domain transcription factor gene family. Funct Integr Genomics 16(4):347–363
Swamy PM, Smith BN (1999) Role of abscisic acid in plant stress tolerance. Curr Sci 76:1220–1227
Thomas H, Ougham H (2014) The stay-green trait. J Exp Bot 65(14):3889–3900
Thumma BR, Sharma N, Southerton SG (2012) Transcriptome sequencing of Eucalyptus camaldulensis seedlings subjected to water stress reveals functional single nucleotide polymorphisms and genes under selection. BMC Genomics 13:364
Tran LS, Nakashima K, Sakuma Y, Osakabe Y, Qin F, Simpson SD, Maruyama K, Fujita Y, Shinozaki K, Yamaguchi-Shinozaki K (2007) Co-expression of the stress-inducible zinc finger homeodomain ZFHD1 and NAC transcription factors enhances expression of the ERD1 gene in Arabidopsis. Plant J 49(1):46–63
Turner JG, Ellis C, Devoto A (2002) The jasmonate signal pathway. Plant Cell 14(Suppl):S153–S164
Umezawa T, Fujita M, Fujita Y, Yamaguchi-Shinozaki K, Shinozaki K (2006) Engineering drought tolerance in plants: discovering and tailoring genes to unlock the future. Curr Opin Biotechnol 17(2):113–122
Van Eck L, Davidson RM, Wu S, Zhao BY, Botha AM, Leach JE, Lapitan NL (2014) The transcriptional network of WRKY53 in cereals links oxidative responses to biotic and abiotic stress inputs. Funct Integr Genomics 14(2):351–362
Venkatesh J, Park SW (2014) Role of L-ascorbate in alleviating abiotic stresses in crop plants. Botan Stud 55:38
Wang S, Bai Y, Shen C, Wu Y, Zhang S, Jiang D, Guilfoyle TJ, Chen M, Qi Y (2010) Auxin-related gene families in abiotic stress response in Sorghum bicolor. Funct Integr Genomics 10(4):533–546
Wang Z, Jia C, Li J, Huang S, Xu B, Jin Z (2015) Activation of salicylic acid metabolism and signal transduction can enhance resistance to Fusarium wilt in banana (Musa acuminata L. AAA group, cv. Cavendish). Funct Integr Genomics 15(1):47–62
Wang YN, Tang L, Hou Y, Wang P, Yang H, Wei CL (2016) Differential transcriptome analysis of leaves of tea plant (Camellia sinensis) provides comprehensive insights into the defense responses to Ectropis oblique attack using RNA-Seq. Funct Integr Genomics 16(4):383–398
Wei S, Hu W, Deng X, Zhang Y, Liu X, Zhao X, Luo Q, Jin Z, Li Y, Zhou S, Sun T, Wang L, Yang G, He G (2014) A rice calcium-dependent protein kinase OsCPK9 positively regulates drought stress tolerance and spikelet fertility. BMC Plant Biol 14:133
Wu G, Zhang L, Yin Y, Wu J, Yu L, Zhou Y, Li M (2015) Sequencing, de novo assembly and comparative analysis of Raphanus sativus transcriptome. Front Plant Sci 6:198
Wu ZJ, Li XH, Liu ZW, Li H, Wang YX, Zhuang J (2016) Transcriptome-based discovery of AP2/ERF transcription factors related to temperature stress in tea plant (Camellia sinensis). Funct Integr Genomics 15(6):741–752
Xiong H, Li J, Liu P, Duan J, Zhao Y, Guo X, Li Y, Zhang H, Ali J, Li Z (2014) Overexpression of OsMYB48-1, a novel MYB-related transcription factor, enhances drought and salinity tolerance in rice. PLoS One 9(3):e92913
Xu Y, Gao S, Yang Y, Huang M, Cheng L, Wei Q, Fei Z, Gao J, Hong B (2013) Transcriptome sequencing and whole genome expression profiling of chrysanthemum under dehydration stress. BMC Genomics 14:662
Xu A, Zhang W, Wen CK (2014a) Enhancing ctr1-10 ethylene response2 is a novel allele involved in constitutive triple-response 1-mediated ethylene receptor signaling in Arabidopsis. BMC Plant Biol 14:48
Xu DB, Gao SQ, Ma YZ, Xu ZS, Zhao CP, Tang YM, Xy L, Li LC, Chen YF, Chen M (2014b) ABI-like transcription factor gene TaABL1 from wheat improves multiple abiotic stress tolerances in transgenic plants. Funct Integr Genomics 14(4):717–730
Yamaguchi-Shinozaki K, Shinozaki K (2006) Transcriptional regulatory networks in cellular response and tolerance to dehydration and cold stresses. Annu Rev Plant Biol 57:781–803
Yang W, Kong Z, Omo-Ikerodah E, Xu W, Li Q, Xue Y (2008) Calcineurin B-like interacting protein kinase OsCIPK23 functions in pollination and drought stress responses in rice (Oryza sativa L.). J Genet Genomics 35(9):531–543, S1-2
Zhang J, Mao Z, Chong K (2013) A global profiling of uncapped mRNAs under cold stress reveals specific decay patterns and endonucleolytic cleavages in Brachypodium distachyon. Genome Biol 14(8):R92
Zhang F, Yao J, Ke J, Zhang L, Lam VQ, Xin XF, Zhou XE, Chen J, Brunzelle J, Griffin PR, Zhou M, Xu HE, Melcher K, He SY (2015a) Structural basis of JAZ repression of MYC transcription factors in jasmonate signalling. Nature 525(7568):269–273
Zhang L, Hu W, Wang Y, Feng R, Zhang Y, Liu J, Jia C, Miao H, Zhang J, Xu B, Jin Z (2015b) The MaASR gene as a crucial component in multiple drought stress response pathways in Arabidopsis. Funct Integr Genomics 15(2):247–260
Zhang X, Allan AC, Li C, Wang Y, Yao Q (2015c) De novo assembly and characterization of the transcriptome of the Chinese medicinal herb, Gentiana rigescens. Int J Mol Sci 16(5):11550–11573
Zhao J, Gao Y, Zhang Z, Chen T, Guo W, Zhang T (2013) A receptor-like kinase gene (GbRLK) from Gossypium barbadense enhances salinity and drought-stress tolerance in Arabidopsis. BMC Plant Biol 13:110
Zhong L, Chen D, Min D, Li W, Xu Z, Zhou Y, Li L, Chen M, Ma Y (2015) AtTGA4, a bZIP transcription factor, confers drought resistance by enhancing nitrate transport and assimilation in Arabidopsis thaliana. Biochem Biophys Res Commun 457(3):433–439
Zhou Y, Gao F, Liu R, Feng J, Li H (2012) De novo sequencing and analysis of root transcriptome using 454 pyrosequencing to discover putative genes associated with drought tolerance in Ammopiptanthus mongolicus. BMC Genomics 13:266
Zhou X, Li L, Xiang J, Gao G, Xu F, Liu A, Zhang X, Peng Y, Chen X, Wan X (2015) OsGL1-3 is involved in cuticular wax biosynthesis and tolerance to water deficit in rice. PLoS One 10(1):e116676
Zhu H, Dardick CD, Beers EP, Callanhan AM, Xia R, Yuan R (2011) Transcriptomics of shading-induced and NAA-induced abscission in apple (Malus domestica) reveals a shared pathway involving reduced photosynthesis, alterations in carbohydrate transport and signaling and hormone crosstalk. BMC Plant Biol 11:138
Acknowledgments
The authors gratefully acknowledge the Department of Science and Technology (DST), Government of India (GOI), for supporting this work under the Fast Track Scheme for Young Scientist under grant number SB/FT/LS-329/2012 and the project entitled “Transcriptome analysis of senna (Cassia angustifolia Vahl.) to identify potential genes involved in the biosynthesis of sennosides” and the Director, ICAR-Directorate of Medicinal and Aromatic Plants Research, Boriavi, Anand, Gujarat, India, and Indian Council of Agricultural research (ICAR), New Delhi, India for the facilities to undertake the study.
Authors’ contributions
Conceived and designed the experiments: NRRR. Performed the experiments: NRRR RHM. Analyzed the data: NRRR MP JK. Contributed reagents/materials/analysis tools: NRRR MP JK. Wrote the paper: RHM NRRR MP JK
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflicts of interest.
Availability of supporting data
The datasets supporting the results of this article are available at the National Center for Biotechnology Information (NCBI) BioProject database (Short Read Archive) under accession number PRJNA273534 and the Transcriptome Shotgun Assembly (TSA) at DDBJ/EMBL/GenBank under the accession GEEB00000000. The version described in this paper is the first version, GEEB01000000.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Figure S1
Transcript size (bp) distribution (DOC 61 kb)
Figure S2
Size distribution of CDS (DOC 67 kb)
Figure S3
Sequence alignment to show conformity between transcriptome assembly (trans) and Sanger sequencing (seq) of the in vitro amplified PCR product of drought stress regulated genes in senna (DOCX 30 kb)
Table S1
KEGG categories of CDS in the transcriptome of leaf of C. angustifolia (PDF 3957 kb)
Rights and permissions
About this article
Cite this article
Mehta, R.H., Ponnuchamy, M., Kumar, J. et al. Exploring drought stress-regulated genes in senna (Cassia angustifolia Vahl.): a transcriptomic approach. Funct Integr Genomics 17, 1–25 (2017). https://doi.org/10.1007/s10142-016-0523-y
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10142-016-0523-y