DeepSAGE based differential gene expression analysis under cold and freeze stress in seabuckthorn (hippophae rhamnoides L.)

PLoS ONE

Volumn 10, Issue 3, 2015, Pages

  Chaudhary, Saurabh ^a   Sharma, Prakash C ^a  

^a GURU GOBIND SINGH INDRAPRASTHA UNIVERSITY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COLD STRESS; CONTROLLED STUDY; DEEP SERIAL ANALYSIS OF GENE EXPRESSION; DIFFERENTIALLY EXPRESSED GENE; DOWN REGULATION; FREEZE STRESS; GENE EXPRESSION; GENE MAPPING; GENE ONTOLOGY; GENE SEQUENCE; HIPPOPHAE RHAMNOIDES; NONHUMAN; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SERIAL ANALYSIS OF GENE EXPRESSION; TEMPERATURE STRESS; UPREGULATION; COLD SHOCK RESPONSE; EXPRESSED SEQUENCE TAG; FREEZING; GENE EXPRESSION PROFILING; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; HIPPOPHAE; METABOLISM; PHYSIOLOGY; PLANT GENE; PROCEDURES;

HIPPOPHAE; HIPPOPHAE RHAMNOIDES;

COLD-SHOCK RESPONSE; EXPRESSED SEQUENCE TAGS; FREEZING; GENE EXPRESSION PROFILING; GENES, PLANT; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HIPPOPHAE;

EID: 84925863528     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0121982     Document Type: Article

References (51)

1. Rodríguez M, Canales E, Borrás-Hidalgo O. Molecular aspects of abiotic stress in plants. Biotecnol Apl. 2005; 22: 1-10.
2. Chinnusamy V, Zhu J, Zhu JK. Cold stress regulation of gene expression in plants. Trends Plant Sci. 2007; 12: 444-451. PMID: 17855156
3. Chinnusamy V, Zhu J, Zhu JK. Gene regulation during cold acclimation in plants. Physiol Plant. 2006; 126: 52-61.
4. Shinozaki K, Yamaguchi-Shinozaki K. Molecular responses to drought and cold stress. Curr Opin Biotechnol. 1996; 7: 161-167. PMID: 8791336
5. Thomashow MF. Plant cold acclimation: freezing tolerance genes and regulatory mechanisms. Annu Rev Plant Biol. 1999; 50: 571-599.
6. Lu R. Seabuckthorn- A multipurpose plant for fragile mountains. International Centre for Integrated Mountain Development (ICIMOD) occasional paper no. 20. 1992. Kathmandu, Nepal.
7. Gupta R, Deswal R. Low temperature stress modulated secretome analysis and purification of antifreeze protein from Hippophae rhamnoides, a Himalayan wonder plant. J Proteome Res. 2012; 11: 2684-2696. doi: 10.1021/pr200944z PMID: 22486727
8. Bartish IV, Jeppsson N, Nybom H, Swenson U. Phylogeny of Hippophae (Elaeagnaceae) inferred from parsimony analysis of chloroplast DNA and morphology. Syst Bot. 2002; 27: 41-54.
9. Yang Y, Yao Y, Xu G, Li C. Growth and physiological responses to drought and elevated ultraviolet?B in two contrasting populations of Hippophae rhamnoides. Physiol Plant. 2005; 124: 431-440.
10. Trajkovsk V, Jeppsson N. Domestication of sea buckthorn. Bot Lith. 1999; 2: 37-46.
11. Zeb A. Anticarcinogenic potential of lipids from Hippophae; Evidence from the recent literature. Asian Pac J Cancer Prev. 2006; 7: 32-35. PMID: 16629511
12. Teng BS, Lu YH, Wang ZT, Tao XY, Wei DZ. In vitro anti-tumor activity of isorhamnetin isolated from Hippophae rhamnoides L. against BEL-7402 cells. Pharmacol Res. 2006; 54: 186-194. PMID: 16765054
13. Suryakumar G, Gupta A. Medicinal and therapeutic potential of Sea buckthorn (Hippophae rhamnoides L.). J Ethnopharmacol. 2011; 138: 268-278. doi: 10.1016/j.jep.2011.09.024 PMID: 21963559
14. Gupta SM, Ahmed Z, Kumar N. Isolation of cDNA fragment of glycerol-3-phosphate acyltransferase gene from seabuckthorn. Def Sci J. 2009; 59: 147-151.
15. Jain A, Ghangal R, Grover A, Raghuvanshi S, Sharma PC. Development of EST-based new SSR markers in seabuckthorn. Physiol Mol Biol Plants. 2010; 16: 375-378. doi: 10.1007/s12298-010-0037-3 PMID: 23572988
16. Ghangal R, Raghuvanshi S, Sharma PC. Expressed sequence tag based identification and expression analysis of some cold inducible elements in seabuckthorn (Hippophae rhamnoides L.). Plant Physiol Biochem. 2012; 51: 123-128. doi: 10.1016/j.plaphy.2011.10.005 PMID: 22153248
17. Fatima T, Snydrez CL, Schoeder WR, Cram D, Datla R, Wishat D, et al. Fatty acid composition of developing Seabuckthorn (Hippophae rhamnoides L.) berry and transcriptome of the mature seeds. PloS One. 2012; 7: 4, e34099. doi: 10.1371/journal.pone.0034099 PMID: 22558083
18. Ghangal R, Chaudhary S, Jain M, Purty RS, Sharma PC. Optimization of de novo short read assembly of seabuckthorn (Hippophae rhamnoides L.) transcriptome. PloS One. 2013; 8: 8, e72516. doi: 10. 1371/journal.pone.0072516 PMID: 23991119
19. Jain A, Chaudhary S, Sharma PC. Mining of microsatellites using next generation sequencing of seabuckthorn (Hippophae rhamnoides L.) transcriptome. Physiol Mol Biol Plants. 2014; 20: 115-123. doi: 10.1007/s12298-013-0210-6 PMID: 24554845
20. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW. Serial analysis of gene expression. Science. 1995; 270: 484-487. PMID: 7570003
21. Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, Johnson D, et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol. 2000; 18: 630-634. PMID: 10835600
22. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol. 1996; 14: 1675-1680. PMID: 9634850
23. Nielsen KL, Hogh AL, Emmersen J. DeepSAGE-digital transcriptomics with high sensitivity, simple experimental protocol and multiplexing of samples. Nucleic Acids Res. 2006; 34: e133. PMID: 17028099
24. t'Hoen PA, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RH, deMenezes RX, et al. Deep sequencing based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res. 2008; 36: e141. doi: 10.1093/nar/gkn705 PMID: 18927111
25. Ozsolak F, Milos PM. RNA sequencing: advances, challenges and opportunities. Nat Rev Genet. 2011; 12: 87-98. doi: 10.1038/nrg2934 PMID: 21191423
26. Jain M. Next-generation sequencing technologies for gene expression profiling in plants. Brief Funct Genomics. 2011; 11: 63-70. doi: 10.1093/bfgp/elr038 PMID: 22155524
27. Ghangal R, Raghuvanshi S, Sharma PC. Isolation of good quality RNA from a medicinal plant seabuckthorn, rich in secondary metabolites. Plant Physiol Biochem. 2009; 47: 1113-1115. doi: 10.1016/j. plaphy.2009.09.004 PMID: 19804984
28. Conesa S, Götz J, García-Gómez M, Terol J, Talón M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005; 21: 3674-3676. PMID: 16081474
29. Morrissy S, Morin RD, Delaney A, Zeng T, McDonald H, Jones S, et al. Next-generation tag sequencing for cancer gene expression profiling. Genome Res. 2009; 19: 1825-1835. doi: 10.1101/gr.094482.109 PMID: 19541910
30. Audic S, Claverie JM. The significance of digital gene expression profiles. Genome Res. 1997; 7: 986-995. PMID: 9331369
31. Benjamini Y, Yekutieli D. The control of the false discovery rate in multiple testing under dependency. Annu Stat. 2001; 29: 1165-1188.
32. Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci. 1998; 95: 14863-14868. PMID: 9843981
33. Saldanha AJ. Java Treeview-extensible visualization of microarray data. Bioinformatics. 2004; 20: 3246-3248. PMID: 15180930
34. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 2008; 36: D480-D484. PMID: 18077471
35. Tian DQ, Pan XY, Yu YM, Wang WY, Zhang F, Ge YY, et al. De novo characterization of the Anthurium transcriptome and analysis of its digital gene expression under cold stress. BMC Genomics. 2013; 14.1: 827. doi: 10.1186/1471-2164-14-827 PMID: 24267953
36. Fowler S, Thomashow MF. Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway. Plant Cell. 2002; 14: 1675-1690. PMID: 12172015
37. Winfield MO, Lu C, Wilson ID, Coghill JA, Edwards KJ. Plant responses to cold: transcriptome analysis of wheat. Plant Biotechnol J. 2010; 8: 749-771. doi: 10.1111/j.1467-7652.2010.00536.x PMID: 20561247
38. Stiff M, Hurry V. A plant for all season: alterations in photosynthetic carbon metabolism during cold acclimation in Arabidopsis. Curr Opin Plant Biol. 2002; 5: 199-206. PMID: 11960736
39. Svensson JT, Crosatti C, Campoli C, Bassi R, Stanca AM, Close TJ et al. Transcriptome analysis of cold acclimation in barley Albina and Xantha mutants. Plant Physiol. 2006; 141: 257-270. PMID: 16603669
40. Hannah MA, Wiese D, Freund S, Fiehn O, Heyer AG, Hincha DK. Natural genetic variation of freezing tolerance in Arabidopsis. Plant Physiol. 2006; 142: 98-112. PMID: 16844837
41. Nicot N, Hausman JF, Hoffmann L, Evers D. Housekeeping gene selection for real-time RT-PCR normalization in potato during biotic and abiotic stress. J Exp Bot. 2005; 56: 2907-2914. PMID: 16188960
42. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using Real Time Quantitative PCR and the 2-ÄÄCT Method. Methods. 2001; 25: 402-408. PMID: 11846609
43. Alceazar R, Marco F, Cuevas JC, Patron M, Ferrando A, Carrasco P, et al. Involvement of polyamines in plant response to abiotic stress. Biotechnol Lett. 2006; 28: 1867-1876. PMID: 17028780
44. Gong Z, Lee H, Xiong L, Jagendorf A, Stevenson B, Zhu JK. RNA helicase-like protein as an early regulator of transcription factors for plant chilling and freezing tolerance. Proc Natl Acad Sci. 2002; 99: 11507-11512. PMID: 12165572
45. Yamaguchi-Shinozaki K, Shinozaki K. Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stress. Annu Rev Plant Biol. 2006; 57: 781-803. PMID: 16669782
46. Joubes J, Raffaele S, Bourdenx B, Garcia C, Traineau JL, Moreau P, et al. The VLCFA elongase gene family in Arabidopsis thaliana: phylogenetic analysis 3D modeling and expression profiling. Plant Mol Biol. 2008; 67: 547-566. doi: 10.1007/s11103-008-9339-z PMID: 18465198
47. Sakuma Y, Liu Q, Dubouzet JG, Abe H, Shinozaki K, Shinozaki KY. DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration and cold-inducible gene expression. Biochem Biophys Res Comm. 2002; 290: 998-1009. PMID: 11798174
48. Zhu J, Jeong JC, Zhu Y, Sokolchik I, Miyazaki S, Zhu JK, et al. Involvement of Arabidopsis HOS15 in histone deacetylation and cold tolerance. Proc Natl Acad Sci. 2008; 105: 4945-4950. doi: 10.1073/ pnas.0801029105 PMID: 18356294
49. Lee B, Henderson DA, Zhua JK. The Arabidopsis cold-responsive transcriptome and its regulation by ICE1. Plant Cell. 2005; 17: 3155-3175. PMID: 16214899
50. Kim KY, Park SW, Chung YS, Chung CH, Kim JI, Lee JH. Molecular cloning of low?temperature?inducible ribosomal proteins from soybean. J Exp Bot. 2004; 55: 1153-1155. PMID: 15020631
51. Sasaki K, Imai R. Pleiotropic roles of cold shock domain proteins in plants. Front Plant Sci. 2011; 2: 1-6. doi: 10.3389/fpls.2011.00001 PMID: 22639570