Elaboration of Transcriptome During the Induction of Somatic Embryogenesis

  • Elsa Góngora-CastilloEmail author
  • Geovanny I. Nic-Can
  • Rosa M. Galaz-Ávalos
  • Víctor M. Loyola-Vargas
Part of the Methods in Molecular Biology book series (MIMB, volume 1815)


Somatic embryogenesis (SE) is one of the most studied developmental processes due to its applications, such as plant micropropagation, transformation, and germplasm conservation. The use of massive techniques of sequencing, as well as the use of subtractive hybridization and macroarrays, has led to the identification of hundreds of genes involved in the SE process. These have been important developments to study the molecular aspects of the progress of SE. With the advent of the new massive techniques for sequencing RNA, it has been possible to see a more complete picture of whole processes. In this chapter we present a technique to handle the elaboration of the transcriptome from the extraction of RNA until the assembly of the complete transcriptome.

Key words

Bioinformatics Coffea canephora Somatic embryogenesis Transcriptome 



The work from VMLV laboratory was supported by a grant received from the National Council for Science and Technology (CONACyT, 1515).


  1. 1.
    Anis M, Ahmad N (2016) Plant tissue culture: a journey from research to commercialization. In: Anis M, Ahmad N (eds) Plant tissue culture: propagation, conservation and crop improvement. Springer, Singapore, pp 3–13. CrossRefGoogle Scholar
  2. 2.
    Martinez-Montero ME, Gonzalez-Arnao MT, Engelmann F (2012) Cryopreservation of tropical plant germplasm with vegetative propagation – review of sugarcane (Saccharum spp.) and pineapple (Ananas comusus (L.) Merrill) cases. In: Katkov II (ed) Current frontiers in cryobiology. InTech, Rijeka, Croatia, pp 359–396. CrossRefGoogle Scholar
  3. 3.
    Ahmad MM, Ali A, Siddiqui S et al (2017) Methods in transgenic technology. In: Abdin MZ, Kiran U, Kamaluddin M et al (eds) Plant biotechnology: principles and applications. Springer, Singapore, pp 93–115. CrossRefGoogle Scholar
  4. 4.
    Loyola-Vargas VM, Vázquez-Flota FA (2006) An introduction to plant cell culture: back to the future. In: Loyola-Vargas VM, Vázquez-Flota FA (eds) Plant cell culture protocols. Humana Press, Totowa, NJ, pp 1–8Google Scholar
  5. 5.
    Loyola-Vargas VM, Ochoa-Alejo N (2012) An introduction to plant cell culture: the future ahead. In: Loyola-Vargas VM, Ochoa-Alejo N (eds) Plant cell culture protocols, methods in molecular biology, vol 877. Humana Press, Heidelberg, pp 1–8. CrossRefGoogle Scholar
  6. 6.
    Loyola-Vargas VM, Ochoa-Alejo N (2016) Somatic embryogenesis. An overview. In: Loyola-Vargas VM, Ochoa-Alejo N (eds) Somatic embryogenesis. Fundamental aspects and applications. Springer, Switzerland, pp 1–10. CrossRefGoogle Scholar
  7. 7.
    Loyola-Vargas VM, Ochoa-Alejo N (2016) Somatic embryogenesis. Fundamental aspects and applications. Springer, Switzerland. CrossRefGoogle Scholar
  8. 8.
    Loyola-Vargas VM (2016) The history of somatic embryogenesis. In: Loyola-Vargas VM, Ochoa-Alejo N (eds) Somatic embryogenesis. Fundamental aspects and applications. Springer, Switzerland, pp 11–22. CrossRefGoogle Scholar
  9. 9.
    Etienne H, Bertrand B, Georget F et al (2013) Development of coffee somatic and zygotic embryos to plants differs in the morphological, histochemical and hydration aspects. Tree Physiol 33:640–653. CrossRefPubMedGoogle Scholar
  10. 10.
    Jin F, Hu L, Yuan D et al (2014) Comparative transcriptome analysis between somatic embryos (SEs) and zygotic embryos in cotton: evidence for stress response functions in SE development. Plant Biotechnol J 12:161–173. CrossRefPubMedGoogle Scholar
  11. 11.
    Giroux RW, Pauls KP (1997) Characterization of somatic embryogenesis-related cDNAs from alfalfa (Medicago sativa L). Plant Mol Biol 33:393–404. CrossRefPubMedGoogle Scholar
  12. 12.
    Lin HC, Morcillo F, Dussert S et al (2009) Transcriptome analysis during somatic embryogenesis of the tropical monocot Elaeis guineensis: evidence for conserved gene functions in early development. Plant Mol Biol 70:173–192. CrossRefPubMedGoogle Scholar
  13. 13.
    Zeng F, Zhang X, Zhu L et al (2006) Isolation and characterization of genes associated to cotton somatic embryogenesis by suppression subtractive hybridization and macroarray. Plant Mol Biol 60:167–183. CrossRefPubMedGoogle Scholar
  14. 14.
    Yang X, Zhang X, Yuan D et al (2012) Transcript profiling reveals complex auxin signalling pathway and transcription regulation involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton. BMC Plant Biol 12:11010. CrossRefGoogle Scholar
  15. 15.
    Xu Z, Zhang C, Zhang X et al (2013) Transcriptome profiling reveals auxin and cytokinin regulating somatic embryogenesis in different sister lines of cotton cultivar CCRI24. J Int Plant Biol 55:631–642. CrossRefGoogle Scholar
  16. 16.
    Elbl P, Lira BS, Andrade SCS et al (2015) Comparative transcriptome analysis of early somatic embryo formation and seed development in Brazilian pine, Araucaria angustifolia (Bertol.) Kuntze. Plant Cell Tiss Org 120:903–915. CrossRefGoogle Scholar
  17. 17.
    Lai Z, Lin Y (2013) Analysis of the global transcriptome of longan (Dimocarpus longan Lour.) embryogenic callus using Illumina paired-end sequencing. BMC Genomics 14:56110. CrossRefGoogle Scholar
  18. 18.
    Salvo SAGD, Hirsch CN, Buell CR et al (2014) Whole transcriptome profiling of maize during early somatic embryogenesis reveals altered expression of stress factors and embryogenesis-related genes. PLoS One 9:e11140710. CrossRefGoogle Scholar
  19. 19.
    Zhang Y, Zhang S, Han S et al (2012) Transcriptome profiling and in silico analysis of somatic embryos in Japanese larch (Larix leptolepis). Plant Cell Rep 31:1637–1657. CrossRefPubMedGoogle Scholar
  20. 20.
    Rajesh MK, Fayas TP, Naganeeswaran S et al (2015) De novo assembly and characterization of global transcriptome of coconut palm (Cocos nucifera L.) embryogenic calli using Illumina paired-end sequencing. Protoplasma 253:913–928. CrossRefPubMedGoogle Scholar
  21. 21.
    Shi X, Zhang C, Liu Q et al (2016) De novo comparative transcriptome analysis provides new insights into sucrose induced somatic embryogenesis in camphor tree (Cinnamomum camphora L.). BMC Genomics 17:2610. CrossRefGoogle Scholar
  22. 22.
    Michael TP, Jackson S (2013) The first 50 plant genomes. Plant Genome 6:10. CrossRefGoogle Scholar
  23. 23.
    Veeckman E, Ruttink T, Vandepoele K (2016) Are we there yet? Reliably estimating the completeness of plant genome sequences. Plant Cell 28:1759–1768. CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15:473–497. CrossRefGoogle Scholar
  25. 25.
    Quiroz-Figueroa FR, Monforte-González M, Galaz-Ávalos RM et al (2006) Direct somatic embryogenesis in Coffea canephora. In: Loyola-Vargas VM, Vázquez-Flota FA (eds) Plant cell culture protocols. Humana Press, Totowa, NJ, pp 111–117. CrossRefGoogle Scholar
  26. 26.
    Sims D, Sudbery I, Ilott NE et al (2014) Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet 15:121–132. CrossRefPubMedGoogle Scholar
  27. 27.
    Goodwin S, McPherson JD, McCombie WR (2016) Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 17:333–351. CrossRefPubMedGoogle Scholar
  28. 28.
    Grabherr MG, Haas BJ, Yassour M et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652. CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Schulz MH, Zerbino DR, Vingron M et al (2012) Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28:1086–1092. CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Andrews S, A FastQC (2015) A quality control tool for high throughput sequence data. 2010. Google Scholar.
  31. 31.
    Ewing B, Hillier L, Wendl MC et al (1998) Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res 8:175–185. CrossRefPubMedGoogle Scholar
  32. 32.
    Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet journal 17:10–12. CrossRefGoogle Scholar
  33. 33.
    Compeau PEC, Pevzner PA, Tesler G (2011) How to apply de Bruijn graphs to genome assembly. Nat Biotechnol 29:987–991. CrossRefPubMedPubMedCentralGoogle Scholar
  34. 34.
    Martin JA, Wang Z (2011) Next-generation transcriptome assembly. Nat Rev Genet 12:671–682. CrossRefPubMedGoogle Scholar
  35. 35.
    Garber M, Grabherr MG, Guttman M et al (2011) Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Meth 8:469–477. CrossRefGoogle Scholar
  36. 36.
    Haas BJ, Papanicolaou A, Yassour M et al (2013) De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with trinity. Nat Prot 8:1494–1512. CrossRefGoogle Scholar
  37. 37.
    NCBI RC (2016) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 44:D7–D19. CrossRefGoogle Scholar
  38. 38.
    Kanehisa M, Goto S (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30. CrossRefPubMedPubMedCentralGoogle Scholar
  39. 39.
    Wu CH, Apweiler R, Bairoch A et al (2006) The universal protein resource (UniProt): an expanding universe of protein information. Nucleic Acids Res 34:D187–D191. CrossRefPubMedGoogle Scholar
  40. 40.
    Góngora-Castillo E, Fedewa G, Yeo Y et al (2012) Genomic approaches for interrogating the biochemistry of medicinal plant species. In: David AH (ed) Methods in enzymology, Natural product biosynthesis by microorganisms and plants, Part C, vol 517. Academic Press, Boston, pp 139–159. CrossRefGoogle Scholar
  41. 41.
    Góngora-Castillo E, Buell CR (2013) Bioinformatics challenges in de novo transcriptome assembly using short read sequences in the absence of a reference genome sequence. Nat Prod Rep 30:490–500. CrossRefPubMedGoogle Scholar
  42. 42.
    Li B, Fillmore N, Bai Y et al (2014) Evaluation of de novo transcriptome assemblies from RNA-Seq data. Genome Biol 15:553. CrossRefPubMedPubMedCentralGoogle Scholar
  43. 43.
    Honaas LA, Wafula EK, Wickett NJ et al (2016) Selecting superior de novo transcriptome assemblies: lessons learned by leveraging the best plant genome. PLoS One 11:e0146062. CrossRefPubMedPubMedCentralGoogle Scholar
  44. 44.
    Smith-Unna R, Boursnell C, Patro R et al (2016) TransRate: reference-free quality assessment of de novo transcriptome assemblies. Genome Res 26:1134–1144. CrossRefPubMedPubMedCentralGoogle Scholar
  45. 45.
    Langmead B, Salzberg SL (2012) Fast gapped-read alignment with bowtie 2. Nat Meth 9:357–359. CrossRefGoogle Scholar
  46. 46.
    Li H, Handsaker B, Wysoker A et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079. CrossRefPubMedPubMedCentralGoogle Scholar
  47. 47.
    Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215:403–410. CrossRefPubMedGoogle Scholar
  48. 48.
    UniProt Consortium (2008) The universal protein resource (UniProt). Nucleic Acids Res 36:D190–D195. CrossRefGoogle Scholar
  49. 49.
    Suzek BE, Huang H, McGarvey P et al (2007) UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23:1282–1288. CrossRefPubMedGoogle Scholar
  50. 50.
    Fuentes-Cerda CFJ, Monforte-González M, Méndez-Zeel M et al (2001) Modification of the embryogenic response of Coffea arabica by nitrogen source. Biotechnol Lett 23:1341–1343. CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Elsa Góngora-Castillo
    • 1
    Email author
  • Geovanny I. Nic-Can
    • 2
  • Rosa M. Galaz-Ávalos
    • 3
  • Víctor M. Loyola-Vargas
    • 3
  1. 1.CONACYT Research Fellow-Unidad de BiotecnologíaCentro de Investigación Científica de YucatánMéridaMexico
  2. 2.CONACYT Research Fellow-Campus de Ciencias Exactas e IngenieríaUniversidad Autónoma de YucatánMéridaMexico
  3. 3.Unidad de Bioquímica y Biología Molecular de PlantasCentro de Investigación Científica de YucatánMéridaMexico

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