Erratum to: Mining NGS transcriptomes for miRNAs and dissecting their role in regulating growth, development, and secondary metabolites production in different organs of a medicinal herb, Picrorhiza kurroa [Planta, DOI 10.1007/s00425-015-2255-y];Mining NGS transcriptomes for miRNAs and dissecting their role in regulating growth, development, and secondary metabolites production in different organs of a medicinal herb, Picrorhiza kurroa

Planta

Volumn 241, Issue 5, 2015, Pages 1255-1268

  Vashisht, Ira ^a   Mishra, Prashant ^a   Pal, Tarun ^a   Chanumolu, Sreekrishna ^a   Singh, Tiratha Raj ^a   Chauhan, Rajinder Singh ^a  

^a JAYPEE UNIVERSITY OF INFORMATION TECHNOLOGY   (India)

Author keywords

miRNA; Picrorhiza; Picroside I; Picroside II; Secondary metabolism

Indexed keywords

MICRORNA; TRANSCRIPTOME;

GENE EXPRESSION PROFILING; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; PICRORHIZA KURROA; PLANT GENE; REAL TIME POLYMERASE CHAIN REACTION;

GENE EXPRESSION PROFILING; GENES, PLANT; MICRORNAS; PICRORHIZA; REAL-TIME POLYMERASE CHAIN REACTION; TRANSCRIPTOME;

EID: 84939963083     PISSN: 00320935     EISSN: 14322048     Source Type: Journal    
DOI: 10.1007/s00425-015-2268-6     Document Type: Erratum

References (54)

1. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
2. Bartel B, Bartel DP (2003) MicroRNAs: at the root of plant development? Plant Physiol 132:709–717
3. Cassells AC, Curry RF (2001) Oxidative stress and physiological, epigenetic and genetic variability in plant tissue culture: implications for micropropagators and genetic engineers. Plant Cell Tiss Org 64:145–157
4. Chopra RN, Ghosh S (1934) Some common indigenous remedies. Indian J Med Res 22:263–264
5. Das A, Mondal TK (2010) Computational identification of conserved microRNAs and their targets in tea (Camellia sinensis). Am J Plant Sci 1:77
6. Davuluri GR, van Tuinen A, Fraser PD, Manfredonia A, Newman R, Burgess D, Brummell DA, King SR, Palys J, Uhlig J (2005) Fruit-specific RNAi-mediated suppression of DET1 enhances carotenoid and flavonoid content in tomatoes. Nat Biotechnol 23:890–895
7. Dhawan B (1995) Picroliv—a new hepatoprotective agent from an Indian medicinal plant, Picrorhiza kurroa. Med Chem Res 5:595–605
8. Dudareva N, Pichersky E, Gershenzon J (2004) Biochemistry of plant volatiles. Plant Physiol 135:1893–1902
9. Fu C, Sunkar R, Zhou C, Shen H, Zhang JY, Matts J, Wolf J, Mann DGJ, Stewart CN Jr, Tang Y, Wang ZY (2012) Overexpression of miR156 in switchgrass (Panicum virgatum L.) results in various morphological alterations and leads to improved biomass production. Plant Biotechnol J 10:443–452
10. Gahlan P, Singh HR, Shankar R, Sharma N, Kumari A, Chawla V, Ahuja PS, Kumar S (2012) De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments. BMC Genom 13:126
11. German MA, Luo S, Schroth G, Meyers BC, Green PJ (2009) Construction of parallel analysis of RNA ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome. Nat Protoc 4:356–362
12. Gou J, Felippes F, Liu C, Weigel D, Wang J (2011) Negative regulation of anthocyanin biosynthesis in Arabidopsis by a miR156-targeted SPL transcription factor. Plant Cell 23:1512–1522
13. Gupta N, Sharma SK, Rana JC, Chauhan RS (2011) Expression of flavonoid biosynthesis genes vis-a-vis rutin content variation in different growth stages of Fagopyrum species. J Plant Physiol 168:2117–2123
14. He L, Hannon GJ (2004) MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 5:522–531
15. Jiao Y, Wang Y, Xue D, Wang J, Yan M, Liu G, Dong G, Zeng D, Lu Z, Zhu X, Qian Q, Li J (2010) Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat Genet 42:541–544
16. Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57:19–53
17. Kawoosa T, Singh H, Kumar A, Sharma SK, Devi K, Dutt S (2010) Light and temperature regulated terpene biosynthesis: hepatoprotective monoterpene picroside accumulation in Picrorhiza kurrooa. Funct Integr Genomic 10:393–404
18. Krek A, Grün D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, Rajewsky N (2005) Combinatorial microRNA target predictions. Nat Genet 37(5):495–500
19. Kumar V, Sood H, Sharma M, Chauhan RS (2012) A proposed biosynthetic pathway of picrosides linked through the detection of biochemical intermediates in the endangered medicinal herb Picrorhiza kurroa. Phytochem Anal 24:598–602
20. Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75:843–854
21. Legrand S, Valot N, Nicole F, Moja S, Baudino S, Jullien F, Magnard JL, Caissard JC, Legendre L (2010) One-step identification of conserved miRNAs, their targets, potential transcription factors and effector genes of complete secondary metabolism pathways after 454 pyrosequencing of calyx cDNAs from the Labiate Salvia sclarea L. Gene 450:55–62
22. Li H, Zhao X, Dai H, Wu W, Mao W, Zhang Z (2012) Tissue culture responsive microRNAs in strawberry. Plant Mol Biol Rep 30:1047–1054
23. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433:769–773
24. Mahmoud SS, Croteau RB (2002) Strategies for transgenic manipulation of monoterpene biosynthesis in plants. Trends Plant Sci 7:366–373
25. Mallory AC, Vaucheret H (2006) Functions of microRNAs and related small RNAs in plants. Nat Genet 38:S31–S36
26. Martin A, Adam H, Díaz-Mendoza M, Zurczak M, González-Schain ND, Suárez-López P (2009) Graft-transmissible induction of potato tuberization by the microRNA miR172. Development 136:2873–2881
27. Mehra TS, Chand R, Sharma Y (2007) Reproductive biology of Picrorhiza kurroa—a critically endangered high value temperate medicinal plant. Open Acc J Med Arom Pl 1:40–43
28. Ng DWK, Zhang C, Miller M, Palmer G, Whiteley M, Tholl D, Chen ZJ (2011) cis-and trans-Regulation of miR163 and target genes confers natural variation of secondary metabolites in two Arabidopsis species and their allopolyploids. Plant Cell 23:1729–1740
29. Pandit S, Shitiz K, Sood H, Chauhan RS (2012) Differential biosynthesis and accumulation of picrosides in an endangered medicinal herb Picrorhiza kurroa. J Plant Biochem Biot 22:335–342
30. Pandit S, Shitiz K, Sood H, Naik PK, Chauhan RS (2013) Expression pattern of fifteen genes of non-mevalonate (MEP) and mevalonate (MVA) pathways in different tissues of endangered medicinal herb Picrorhizakurroa with respect to picrosides content. Mol Biol Rep 40:1053–1063
31. Pradervand S, Weber J, Lemoine F, Consales F, Paillusson A, Dupasquier M, Thomas J, Richter H, Kaessmann H, Beaudoing E (2010) Concordance among digital gene expression, microarrays, and qPCR when measuring differential expression of microRNAs. Biotechniques 48:219–222
32. Qiao M, Zhao Z, Song Y, Liu Z, Cao L, Yu Y, Li S, Xiang F (2012) Proper regeneration from in vitro cultured Arabidopsis thaliana requires the microRNA-directed action of an auxin response factor. Plant J 71:14–22
33. Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP (2002) MicroRNAs in plants. Gene Dev 16:1616–1626
34. Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP (2002) Prediction of plant microRNA targets. Cell 110:513–520
35. Robert-Seilaniantz A, MacLean D, Jikumaru Y, Hill L, Yamaguchi S, Kamiya Y, Jones JDG (2011) The microRNA miR393 re-directs secondary metabolite biosynthesis away from camalexin and towards glucosinolates. Plant J 67:218–231
36. Rodriguez RE, Mecchia MA, Debernardi JM, Schommer C, Weigel D, Palatnik JF (2010) Control of cell proliferation in Arabidopsis thaliana by microRNA miR396. Development 137:103–112
37. Samanani N, Park SU, Facchini PJ (2005) Cell type specific localization of transcripts encoding nine consecutive enzymes involved in protoberberine alkaloid biosynthesis. Plant Cell 17:915–926
38. Sato F, Tsuchiya S, Meltzer SJ, Shimizu K (2011) MicroRNAs and epigenetics. FEBS J 278:1598–1609
39. Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D (2005) Specific effects of microRNAs on the plant transcriptome. Dev Cell 8:517–527
40. Shamimuzzaman M, Vodkin L (2012) Identification of soybean seed developmental stage-specific and tissue-specific miRNA targets by degradome sequencing. BMC Genom 13:310
41. Singh TR, Gupta A, Suravajhala P (2013) Challenges in the miRNA research. Int J Bioinformatics Res 9:576–583
42. Smit HF (2000) Picrorhiza scrophulariiflora, from traditional use to immunomodulatory activity. Dissertation, Proefschrift, Universiteit Utrecht, The Netherlands
43. Sood H, Chauhan RS (2010) Biosynthesis and accumulation of a medicinal compound, picroside-I, in cultures of Picrorhiza kurroa Royle ex Benth. Plant Cell Tiss Org 100:113–117
44. Stuppner H, Wagner H (1989) New cucurbitacin glycosides from Picrorhiza kurroa. Planta Med 55:559–563
45. Sud A, Chauhan RS, Tandon C (2013) Identification of imperative enzymes by differential protein expression in Picrorhiza kurroa under metabolite accumulating and non-accumulating conditions. Protein Peptide Lett 20:826–835
46. Voinnet O (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136:669–687
47. Wang CM, Liu P, Sun F, Li L, Liu P, Ye J, Yue GH (2012) Isolation and Identification of miRNAs in Jatropha curcas. Int J Biol Sci 8(3):418–429
48. Wu G, Park MY, Conway SR, Wang J-W, Weigel D, Poethig RS (2009) The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell 138:750–759
49. Xie F, Frazier TP, Zhang B (2010) Identification and characterization of microRNA and their targets in the bioenergy plant switchgrass (Panicum virgatum). Planta 232:417–434
50. Xie K, Shen J, Hou X, Yao J, Li X, Xiao J, Xiong L (2012) Gradual increase of miR156 regulates temporal expression changes of numerous genes during leaf development in rice. Plant Physiol 158:1382–1394
51. Xu W, Cui Q, Li F, Liu A (2013) Transcriptome-wide identification and characterization of microRNAs from castor bean (Ricinus communis L.). PLoS ONE 8:e69995
52. Zhang B, Pan X, Anderson TA (2006) Identification of 188 conserved maize microRNAs and their targets. FEBS Lett 580:3753–3762
53. Zhou M, Lou H (2013) MicroRNA-mediated gene regulation: potential applications for plant genetic engineering. Plant Mol Biol 83:59–75
54. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415