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Transcriptome profiling of the coffee (C. arabica L.) seedlings under salt stress condition

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This research was conducted to study the gene expression of coffee (Coffea arabica L.) seedlings under salt stress condition. A solution of five percent (2.3 dS m-1) deep sea water was used for the salt treatment, and it was thereby compared to normal irrigation water (0.2 dS m-1) used for the control treatment. The mRNA was extracted from the leaves of the coffee seedlings for a comprehensive analysis. In this study, a total of 19,581 genes were identified and aligned to the reference sequences available in the coffee genome database. The gene ontology analysis was performed to estimate the number of genes associated with the identified biological processes, cellular components and molecular functions. Among the 19,581 genes, 7369 (37.64%) were associated with biological processes, 5909 (30.18%) with cellular components, and 5325 (27.19%) with molecular functions. The remaining 978 (4.99%) genes were therefore grouped as unclassified. A differential gene expression analysis was performed using the DESeq2 package to identify the genes that were differentially expressed between the treatments based on fold changes and p-values. Namely, a total of 611 differentially expressed genes were identified (treatment/control) in that case. Among these, 336 genes were up-regulated while 275 of the genes were downregulated. Of the differentially expressed genes, 60 genes showed statistically significant (p < 0.05) expression, 44 of which were up-regulated and 16 which were down-regulated. We also identified 11 differentially expressed transcription factor genes, 6 of which were up-regulated and rest 5 genes were down-regulated. The data generated from this study will help in the continued interest and understanding of the responses of coffee seedlings genes associated with salinity stress, in particular. This study will also provide important resources for further functional genomics studies.

Abstract

This research was conducted to study the gene expression of coffee (Coffea arabica L.) seedlings under salt stress condition. A solution of five percent (2.3 dS m-1) deep sea water was used for the salt treatment, and it was thereby compared to normal irrigation water (0.2 dS m-1) used for the control treatment. The mRNA was extracted from the leaves of the coffee seedlings for a comprehensive analysis. In this study, a total of 19,581 genes were identified and aligned to the reference sequences available in the coffee genome database. The gene ontology analysis was performed to estimate the number of genes associated with the identified biological processes, cellular components and molecular functions. Among the 19,581 genes, 7369 (37.64%) were associated with biological processes, 5909 (30.18%) with cellular components, and 5325 (27.19%) with molecular functions. The remaining 978 (4.99%) genes were therefore grouped as unclassified. A differential gene expression analysis was performed using the DESeq2 package to identify the genes that were differentially expressed between the treatments based on fold changes and p-values. Namely, a total of 611 differentially expressed genes were identified (treatment/control) in that case. Among these, 336 genes were up-regulated while 275 of the genes were downregulated. Of the differentially expressed genes, 60 genes showed statistically significant (p < 0.05) expression, 44 of which were up-regulated and 16 which were down-regulated. We also identified 11 differentially expressed transcription factor genes, 6 of which were up-regulated and rest 5 genes were down-regulated. The data generated from this study will help in the continued interest and understanding of the responses of coffee seedlings genes associated with salinity stress, in particular. This study will also provide important resources for further functional genomics studies.

참고문헌 (51)

  1. Ali GS, "Differential expression of genes encoding calmodulin-binding proteins in response to bacterial pathogens and inducers of defense responses", Plant Mol Biol, 51, pp.803~815 (2003)[DOI]
  2. Anders S, "Differential expression analysis for sequence count data", Genome Biol, 11, pp.106~ (2010)[DOI]
  3. Annadurai RS, "Next generation sequencing and de novo transcriptome analysis of Costus pictus D. Don, a non-model plant with potent anti-diabetic properties", BMC Genomics, 13, pp.663~ (2012)
  4. Banzai T, "Identification and characterization of mRNA transcripts differentially expressed in response to high salinity by means of differential display in the mangrove, Bruguiera gymnorrhiza", Plant Sci, 162, pp.499~505 (2002)[DOI]
  5. Bartels D, "Drought and salt tolerance in plants", Crit Rev Plant Sci, 24, pp.23~58 (2005)[DOI]
  6. Belozersky MA, "Aspartic proteinase from wheat seeds: isolation, properties and action on gliadin", Planta, 177, pp.321~326 (1989)[DOI]
  7. Bray EA, "Responses to abiotic stresses", Biochem Mol Biol Plants, pp.1158~1249 (2000)
  8. Camargo MBP, "The impact of climatic variability and climate change on arabica coffee crop in Brazil", Bragantia, 69, pp.239~247 (2010)[DOI]
  9. Chen J, "A triallelic system of S5 is a major regulator of the reproductive barrier and compatibility of indica-japonica hybrids in rice", Proc Natl Acad of Sci USA, 105, pp.11436~11441 (2008)[DOI]
  10. Chinnusamy V, "ICE1: a regulator of cold-induced transcriptome and freezing tolerance in Arabidopsis", Genes Dev, 17, pp.1043~1054 (2003)[DOI]
  11. Cho SK, "Arabidopsis PUB22 and PUB23 are homologous U-Box E3 ubiquitin ligases that play combinatory roles in response to drought stress", Plant Cell, 20, pp.1899~1914 (2008)[DOI]
  12. Davis AP, "The impact of climate change on indigenous arabica coffee (Coffea arabica L.): predicting future trends and identifying priorities", PLoS One, 7, pp.e47981~ (2012)[DOI]
  13. Dubos C, "MYB transcription factors in Arabidopsis", Trends Plant Sci, 15, pp.573~581 (2010)
  14. Dunaevsky YE, "Wheat seed carboxypeptidase and joint action on gliadin of proteases from dry and germinating seeds", J Exp Bot, 40, pp.1323~1329 (1989)[DOI]
  15. Fernandez‐Garcia N, "Role of phi cells and the endodermis under salt stress in Brassica oleracea", New Phytol, 181, pp.347~360 (2009)
  16. Gao Y, "Expression of a conifer COBRA-like gene ClCOBL1 from Chinese fir (Cunninghamia lanceolata) alters the leaf architecture in tobacco", Plant Physiol Biochem, 70, pp.483~491 (2013)[DOI]
  17. Ge X, "An Arabidopsis aspartic protease functions as an anti‐cell‐death component in reproduction and embryogenesis", EMBO Rep, 6, pp.282~288 (2005)
  18. Huang HH, "De novo characterization of the Chinese fir (Cunninghamia lanceolata) transcriptome and analysis of candidate genes involved in cellulose and lignin biosynthesis", BMC Genomics, 13, pp.648~ (2012)[DOI]
  19. "Coffee Statistics International Coffee Organization. Trade Statistics of Total Production of Exporting Countries"[URL]
  20. Jain M, "Transcript profiling reveals diverse roles of auxin‐responsive genes during reproductive development and abiotic stress in rice", FEBS J, 276, pp.3148~3162 (2009)[DOI]
  21. Joseph B, "Development of salt stress-tolerant plants by gene manipulation of antioxidant enzymes", Asian J Agric Res, 5, pp.17~27 (2011)
  22. Kato Y, "The DNA-binding protease, CND41, and the degradation of ribulose-1, 5-bisphosphate carboxylase", oxygenase in senescent leaves of tobacco, 2004, pp.220, 97~104
  23. Kiribuchi K, "RERJ1, a jasmonic acid-responsive gene from rice, encodes a basic helix-loop-helix protein", Biochem Biophys Res Commun, 325, pp.857~863 (2004)[DOI]
  24. Leivar P, "The Arabidopsis phytochrome-interacting factor PIF7, together with PIF3 and PIF4, regulates responses to prolonged red light by modulating phyB levels", Plant Cell, 20, pp.337~352 (2008)[DOI]
  25. Liu GT, "Transcriptomic analysis of grape (Vitis vinifera L.) leaves during and after recovery from heat stress", BMC Plant Biol, 12, pp.174~ (2012)[DOI]
  26. Livaja M, "BSTA: a targeted approach combines bulked segregant analysis with next-generation sequencing and de novo transcriptome assembly for SNP discovery in sunflower", BMC Genomics, 14, pp.628~ (2013)[DOI]
  27. Lu X, "The differential transcription network between embryo and endosperm in the early developing maize seed", Plant Physiol, 162, pp.440~455 (2013)[DOI]
  28. Mao K, "Genome wide identification and characterization of apple bHLH transcription factors and expression analysis in response to drought and salt stress", Front Plant Sci, 8 (2017)
  29. Mizuno H, "Global transcriptome analysis reveals distinct expression among duplicated genes during sorghum-Bipolaris sorghicola interaction", BMC Plant Biol, 12, pp.121~ (2012)[DOI]
  30. Mortazavi A, "Mapping and quantifying mammalian transcriptomes by RNA-Seq", Nature Methods, 5, pp.621~628 (2008)[DOI]
  31. Munns R, "Approaches to increasing the salt tolerance of wheat and other cereals", J Exp Bot, 57, pp.1025~1043 (2006)[DOI]
  32. Munns R, "Comparative physiology of salt and water stress", Plant Cell Enviro, 25, pp.239~250 (2002)[DOI]
  33. Murakami S, "Protease activity of CND41, a chloroplast nucleoid DNA‐binding protein, isolated from cultured tobacco cells", FEBS Letters, 468, pp.15~18 (2000)[DOI]
  34. Mutlu A, "Plant aspartic proteinases: enzymes on the way to a function", Physiol Plant, 105, pp.569~576 (1999)
  35. Nakashima K, "Transcriptional regulatory networks in response to abiotic stresses in Arabidopsis and grasses", Plant Physiol, 149, pp.88~95 (2009)[DOI]
  36. Nakashima K, "NAC transcription factors in plant abiotic stress responses", Biochim Biophys Acta, 1819, pp.97~103 (2012)[DOI]
  37. Neves GYS, "Root growth inhibition and lignification induced by salt stress in soybean", J Agron Crop Sci, 196, pp.467~473 (2010)[DOI]
  38. Parida AK, "Salt tolerance mechanisms in mangroves: a review", Trees, 24, pp.199~217 (2010)[DOI]
  39. Park HC, "Pathogen-and NaCl-induced expression of the SCaM-4 promoter is mediated in part by a GT-1 box that interacts with a GT-1-like transcription factor", Plant Physiol, 135, pp.2150~2161 (2004)[DOI]
  40. Rahaie M, "A MYB gene from wheat (Triticum aestivum L.) is up-regulated during salt and drought stresses and differentially regulated between salt-tolerant and sensitive genotypes", Plant Cell Rep, 29, pp.835~844 (2010)[DOI]
  41. Roig‐Villanova I, "Interaction of shade avoidance and auxin responses: a role for two novel atypical bHLH proteins", EMBO J, 26, pp.4756~4767 (2007)[DOI]
  42. Sharma M, "Role of Plant U-BOX (PUB) Protein in Stress and Development", Plant Stress, 7, pp.1~9 (2013)
  43. Shrivastava P, "Soil salinity: a serious environmental issue and plant growth promoting bacteria as one of the tools for its alleviation", Saudi J Biol Sci, 22, pp.123~131 (2015)[DOI]
  44. Singh KB, "Transcription factors in plant defense and stress responses", Curr Opin Plant Biol, 5, pp.430~436 (2002)[DOI]
  45. Wan D, "Calmodulin-binding protein CBP60g is a positive regulator of both disease resistance and drought tolerance in Arabidopsis", Plant Cell Rep, 31, pp.1269~1281 (2012)[DOI]
  46. Wang H, "Temporal progression of gene expression responses to salt shock in maize roots", Plant Mol Biol, 52, pp.873~891 (2003)[DOI]
  47. Wang Z, "Comprehensive analysis of trihelix genes and their expression under biotic and abiotic stresses in Populus trichocarpa", Sci Rep, 6 (2016)
  48. Xia Y, "An extracellular aspartic protease functions in Arabidopsis disease resistance signaling", EMBO J, 23, pp.980~988 (2004)[DOI]
  49. Yao D, "Transcriptome analysis reveals salt-stress-regulated biological processes and key pathways in roots of cotton (Gossypium hirsutum L.)", Genomics, 98, pp.47~55 (2011)
  50. Yao X, "Overexpression of the aspartic protease ASPG1 gene confers drought avoidance in Arabidopsis", J Exp Bot, 63, pp.2579~2593 (2012)[DOI]
  51. Zhang L, "Molecular characterization of 60 isolated wheat MYB genes and analysis of their expression during abiotic stress", J Exp Bot, 63, pp.203~214 (2011)

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