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11 08, 2022;12 (1): 18988.

Reliable reference genes and abiotic stress marker genes in Klebsormidium nitens.

Pauline Chatelain, Cécile Blanchard, Jeremy Astier, Agnès Klinguer, David Wendehenne, Sylvain Jeandroz, Claire Rosnoblet
Author Information
  1. Pauline Chatelain: Agroécologie, CNRS, INRAE, Institut Agro, Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France.
  2. Cécile Blanchard: Agroécologie, CNRS, INRAE, Institut Agro, Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France.
  3. Jeremy Astier: Agroécologie, CNRS, INRAE, Institut Agro, Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France.
  4. Agnès Klinguer: Agroécologie, CNRS, INRAE, Institut Agro, Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France.
  5. David Wendehenne: Agroécologie, CNRS, INRAE, Institut Agro, Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France.
  6. Sylvain Jeandroz: Agroécologie, CNRS, INRAE, Institut Agro, Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France.
  7. Claire Rosnoblet: Agroécologie, CNRS, INRAE, Institut Agro, Université de Bourgogne, Université Bourgogne Franche-Comté, Dijon, France. claire.rosnoblet@u-bourgogne.fr.
PMID: 36348043 DOI: 10.1038/s41598-022-23783-9

Abstract

Microalgae have recently emerged as a key research topic, especially as biological models. Among them, the green alga Klebsormidium nitens, thanks to its particular adaptation to environmental stresses, represents an interesting photosynthetic eukaryote for studying the transition stages leading to the colonization of terrestrial life. The tolerance to different stresses is manifested by changes in gene expression, which can be monitored by quantifying the amounts of transcripts by RT-qPCR. The identification of optimal reference genes for experiment normalization was therefore necessary. In this study, using four statistical algorithms followed by the RankAggreg package, we determined the best reference gene pairs suitable for normalizing RT-qPCR data in K. nitens in response to three abiotic stresses: high salinity, PEG-induced dehydration and heat shock. Based on these reference genes, we were able to identify marker genes in response to the three abiotic stresses in K. nitens.

References

  1. Science. 2010 Aug 13;329(5993):796-9 [PMID: 20705853]
  2. Microb Cell Fact. 2018 Mar 5;17(1):36 [PMID: 29506528]
  3. Mol Plant Pathol. 2021 Nov;22(11):1427-1435 [PMID: 34390122]
  4. Front Plant Sci. 2021 Dec 22;12:797451 [PMID: 35003186]
  5. BMC Bioinformatics. 2009 Feb 19;10:62 [PMID: 19228411]
  6. Sci Rep. 2021 Apr 7;11(1):7573 [PMID: 33828187]
  7. Environ Toxicol Chem. 2008 Aug;27(8):1668-75 [PMID: 18384239]
  8. PLoS One. 2014 Oct 23;9(10):e110630 [PMID: 25340847]
  9. Mar Drugs. 2019 May 24;17(5): [PMID: 31137657]
  10. Proc Natl Acad Sci U S A. 2021 Jun 22;118(25): [PMID: 34161289]
  11. J Cell Biol. 1980 Feb;84(2):327-39 [PMID: 7189756]
  12. Cell Stress Chaperones. 2018 Mar;23(2):253-267 [PMID: 28889352]
  13. Cancer Res. 2004 Aug 1;64(15):5245-50 [PMID: 15289330]
  14. Clin Chem. 2009 Apr;55(4):611-22 [PMID: 19246619]
  15. Plants (Basel). 2020 Oct 26;9(11): [PMID: 33114570]
  16. BMC Bioinformatics. 2017 Dec 1;18(1):534 [PMID: 29191175]
  17. Genome Biol. 2002 Jun 18;3(7):RESEARCH0034 [PMID: 12184808]
  18. Ecotoxicology. 2015 May;24(4):863-72 [PMID: 25724346]
  19. BMC Genomics. 2017 Nov 16;18(1):885 [PMID: 29145809]
  20. J Phycol. 1967 Dec;3(4):182-98 [PMID: 27065028]
  21. Ecotoxicol Environ Saf. 2016 Nov;133:501-8 [PMID: 27552343]
  22. Anal Biochem. 2009 Apr 15;387(2):238-42 [PMID: 19454243]
  23. Front Plant Sci. 2017 Mar 17;8:349 [PMID: 28367152]
  24. Plant Cell Rep. 2012 Jul;31(7):1245-54 [PMID: 22451089]
  25. Genet Mol Res. 2015 Mar 27;14(1):2384-98 [PMID: 25867385]
  26. J Phycol. 2021 Aug;57(4):1151-1166 [PMID: 33529378]
  27. Planta. 2009 Mar;229(4):861-71 [PMID: 19125289]
  28. Protoplasma. 2021 Nov;258(6):1335-1346 [PMID: 34304308]
  29. Nat Genet. 2022 May;54(5):705-714 [PMID: 35513725]
  30. Curr Biol. 2020 Mar 23;30(6):962-971.e3 [PMID: 32142692]
  31. Comput Biol Chem. 2015 Feb;54:18-32 [PMID: 25531538]
  32. Plant Mol Biol. 2018 Feb;96(3):265-278 [PMID: 29270890]
  33. J Exp Bot. 2017 May 17;68(11):3017-3031 [PMID: 28830103]
  34. Nat Commun. 2014 May 28;5:3978 [PMID: 24865297]
  35. Genes Immun. 2005 Jun;6(4):279-84 [PMID: 15815687]
  36. Biotechnol Lett. 2004 Mar;26(6):509-15 [PMID: 15127793]
  37. Curr Biol. 2020 Dec 21;30(24):4815-4825.e4 [PMID: 33035480]
  38. Front Plant Sci. 2020 Jun 11;11:782 [PMID: 32595674]
  39. Front Plant Sci. 2016 Apr 25;7:536 [PMID: 27200013]
  40. Plant Signal Behav. 2011 Feb;6(2):232-6 [PMID: 21427533]
  41. Gene. 2013 Nov 1;530(1):44-50 [PMID: 23933278]
  42. Front Plant Sci. 2022 May 06;13:855243 [PMID: 35599877]
  43. Plant Cell Environ. 2008 Jun;31(6):872-85 [PMID: 18315534]
  44. Planta. 1985 Jun;164(3):308-20 [PMID: 24249600]
  45. Plant Physiol. 2017 Jul;174(3):1621-1632 [PMID: 28533212]
  46. J Phycol. 2014 Feb;50(1):131-9 [PMID: 26988014]
  47. BMC Res Notes. 2008 Oct 20;1:93 [PMID: 18937828]
  48. Sci Rep. 2020 Jul 23;10(1):12275 [PMID: 32704005]
  49. Plant Cell Rep. 2012 May;31(5):827-38 [PMID: 22193338]
  50. BMC Mol Biol. 2006 Oct 06;7:33 [PMID: 17026756]
  51. Plant Physiol. 2005 Sep;139(1):5-17 [PMID: 16166256]
  52. Sci Rep. 2020 Apr 30;10(1):7374 [PMID: 32355237]
  53. Physiol Plant. 2010 Jun 1;139(2):170-80 [PMID: 20088904]
  54. Plant Pathol J. 2019 Feb;35(1):11-18 [PMID: 30828275]
  55. Plant Sci. 2018 Jul;272:157-163 [PMID: 29807587]
  56. Curr Genet. 2012 Feb;58(1):13-20 [PMID: 22205301]
  57. Plant Methods. 2017 Oct 16;13:85 [PMID: 29075311]
  58. Neurosci Lett. 2003 Mar 13;339(1):62-6 [PMID: 12618301]

Grants

  1. ALGAE-NOS ANR-18-CE20-0022-02/Agence Nationale de la Recherche
  2. NOISELESS-RA18041.AEC.IS/ISITE-BFC

MeSH Term

Gene Expression Regulation, Plant
Stress, Physiological
Streptophyta
Genes, Plant
Salinity
Real-Time Polymerase Chain Reaction
Reference Standards
Gene Expression Profiling
Journal Article Research Support, Non-U.S. Gov't

Word Cloud

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