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Analysis of Transcriptome and Alternative Splicing Landscape in Pineapple

  • Ching Man Wai
  • Brian Powell
  • Ray Ming
  • Xiang Jia MinEmail author
Chapter
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 22)

Abstract

Gene expression profiling and alternative splicing (AS) landscapes were analyzed in pineapple. Among 27,024 protein-coding genes, based on the transcripts to gene models mapping data, a total of 17,308 predicted genes are supported by expressed transcripts. Between leaf and root tissue, 795 genes were upregulated in leaf tissue relative to root tissue, and 1391 genes were upregulated in root tissue relative to leaf tissue. Between young fruit tissue and ripening fruit tissue, 931 genes were upregulated, and 189 genes were downregulated in ripening fruit tissue relative to young fruit tissue. Genes involved in crassulacean acid metabolism (CAM) pathway and in ethylene biosynthesis and responses were identified and further analyzed in details. A total of 10,348 AS events involving 13,449 unique transcripts which were generated from a total of 5146 genes were identified. The identification of differentially expressed genes, assembled transcripts, along with the identified AS isoforms and events, provides a solid foundation for further examination of the gene functions in pineapple metabolism, growth, development, and fruit ripening. The data are available at Plant Alternative Splicing Database (http://proteomics.ysu.edu/altsplice/).

Keywords

Alternative splicing Expressed sequence tags Gene expression mRNA Transcriptome Pineapple 

Abbreviations

AS

Alternative splicing

CAM

Crassulacean acid metabolism

ESTs

Expressed sequence tags

FPKM

Fragments per kilobase of exon model per million mapped reads

PUT

Pineapple unique transcript

Notes

Acknowledgments

The work was supported by the University of Illinois at Urbana-Champaign to RM and the Youngstown State University Research Professorship award to XJM.

References

  1. Bartholomew DP (2013) History and perspectives on the role of ethylene in pineapple flowering. In: XII International Symposium on Plant Bioregulators in Fruit Production. Acta Hortic 1042:269–284Google Scholar
  2. Bartholomew DP, Kadzimin SB (1997) Pineapple. In: Alvin PT, Kozeowski TT (eds) Ecophysiology of tropical crops. Academic Press, New York, NY, pp 113–156Google Scholar
  3. Bartholomew DP, Malézieux EP (1994) Pineapple. In: Schaffer B, Andersen PC (eds) Handbook of environmental physiology of fruit crops, vol 2. CRC Press, Boca Raton, pp 243–291Google Scholar
  4. Bartholomew DP, Paull RE, Rohrbach KG (2002) The pineapple: botany, production, and uses. CABI, WallingfordGoogle Scholar
  5. Barz M, Delivand MK (2011) Agricultural residues as promising biofuels for biomass power generation in Thailand. J Sustain Energy Environ Spec Issue 2011:21–27Google Scholar
  6. Brown JW, Simpson CG, Marquez Y, Gadd GM, Barta A, Kalyna M (2015) Lost in translation: pitfalls in deciphering plant alternative splicing transcripts. Plant Cell 27(8):2083–2087CrossRefGoogle Scholar
  7. Di Scala F, Dupuis L, Gaiddon C, De Tapia M, Jokic N, Gonzalez de Aguilar JL, Raul JS, Ludes B, Loeffler JP (2005) Tissue specificity and regulation of the N-terminal diversity of reticulon 3. Biochem J 385(Pt 1):125–134PubMedGoogle Scholar
  8. Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9:868–877CrossRefGoogle Scholar
  9. Li J, Li X, Guo L et al (2006) A subgroup of MYB transcription factor genes undergoes highly conserved alternative splicing in Arabidopsis and rice. J Exp Bot 57:1263–1273CrossRefGoogle Scholar
  10. Lind MI, Ekengren S, Melefors Ö, Söderhäll K (1998) Drosophila ferritin mRNA: alternative RNA splicing regulates the presence of the iron-responsive element. FEBS Lett 436:476–482CrossRefGoogle Scholar
  11. Lum G, Meinken J, Orr J, Frazier S, Min XJ (2014) PlantSecKB: the plant secretome and subcellular proteome knowledgebase. Comput Mol Biol 4:1–17Google Scholar
  12. Marquez Y, Brown JW, Simpson C, Barta A, Kalyna M (2012) Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Res 22:1184–1195CrossRefGoogle Scholar
  13. Marzola DL, Bartholomew DP (1979) Photosynthetic pathway and biomass energy production. Science 205(4406):555–559CrossRefGoogle Scholar
  14. Min XJ (2013) ASFinder: a tool for genome-wide identification of alternatively spliced transcripts from EST-derived sequences. Int J Bioinf Res App 9:221–226CrossRefGoogle Scholar
  15. Min X, Bartholomew DP (1993) Effects of growth regulators on ethylene production and floral initiation of pineapple. Acta Hortic 334:101–112CrossRefGoogle Scholar
  16. Min X, Bartholomew DP (1996) Effect of plant growth regulators on ethylene production, 1-aminocyclopropane-1-carboxylic acid oxidase activity, and initiation of inflorescence development of pineapple. J Plant Growth Regul 15:121–128CrossRefGoogle Scholar
  17. Min XJ, Butler G, Storms R, Tsang A (2005a) OrfPredictor: predicting protein-coding regions in EST-derived sequences. Nucleic Acids Res 33:W677–W680CrossRefGoogle Scholar
  18. Min XJ, Butler G, Storms R, Tsang A (2005b) TargetIdentifier: a web server for identifying full-length cDNAs from EST sequences. Nucleic Acids Res 33:W669–W672CrossRefGoogle Scholar
  19. Min XJ, Powell B, Braessler J, Meinken J, Yu F, Sablok G (2015) Genome-wide cataloging and analysis of alternatively spliced genes in cereal crops. BMC Genomics 16:721CrossRefGoogle Scholar
  20. Ming R, VanBuren R, Wai CM et al (2015) The pineapple genome and the evolution of CAM photosynthesis. Nat Genet 47(12):1435–1442.  https://doi.org/10.1038/ng.3435CrossRefPubMedPubMedCentralGoogle Scholar
  21. Morello L, Breviario D (2008) Plant spliceosomal introns: not only cut and paste. Curr Genomics 9:227–238CrossRefGoogle Scholar
  22. Moyle R, Fairbairn DJ, Ripi J, Crowe M, Botella JR (2005) Developing pineapple fruit has a small transcriptome dominated by metallothionein. J Exp Bot 56:101–112CrossRefGoogle Scholar
  23. Nievola CC, Kraus JE, Freschi L, Souza BM, Mercier H (2005) Temperature determines the occurrence of CAM or C3 photosynthesis in pineapple plantlets grown in vitro. In Vitro Cell Dev Biol Plant 41:832–837CrossRefGoogle Scholar
  24. Nziengui H, Bouhidel K, Pillon D, Der C, Marty F, Schoefs B (2007) Reticulon-like proteins in Arabidopsis thaliana: structural organization and ER localization. FEBS Lett 581:3356–3362CrossRefGoogle Scholar
  25. Ong WD, Voo LYC, Kumar VS (2012) De novo assembly, characterization and functional annotation of pineapple fruit transcriptome through massively parallel sequencing. PLoS One 7:e46937CrossRefGoogle Scholar
  26. Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40:1413–1415CrossRefGoogle Scholar
  27. Reddy AS, Marquez Y, Kalyna M, Barta A (2013) Complexity of the alternative splicing landscape in plants. Plant Cell 25:3657–3683CrossRefGoogle Scholar
  28. Redwan RM, Saidin A, Kumar SV (2016) The draft genome of MD-2 pineapple using hybrid error correction of long reads. DNA Res 23(5):427–439.  https://doi.org/10.1093/dnares/dsw026CrossRefPubMedCentralGoogle Scholar
  29. Sablok G, Gupta PK, Baek JM, Vazquez F, Min XJ (2011) Genome-wide survey of alternative splicing in the grass Brachypodium distachyon: an emerging model biosystem for plant functional genomics. Biotechnol Lett 33:629–636CrossRefGoogle Scholar
  30. Sablok G, Harikrishna JA, Min XJ (2013) Next generation sequencing for better understanding alternative splicing: way ahead for model and non-model plants. Transcriptomics 1:e103Google Scholar
  31. Shikata H, Hanada K, Ushijima T, Nakashima M, Suzuki Y, Matsushita T (2014) Phytochrome controls alternative splicing to mediate light responses in Arabidopsis. Proc Natl Acad Sci U S A 111:18781–18786CrossRefGoogle Scholar
  32. Staiger D, Brown JW (2013) Alternative splicing at the intersection of biological timing, development, and stress responses. Plant Cell 25:3640–3656CrossRefGoogle Scholar
  33. Surles T, Foley M, Turn S, Staackmann M (2009) A scenario for accelerated use of renewable resources for transportation fuels in Hawaii. University of Hawaii, Hawaii Natural Energy Institute, School of Ocean and Earth Science and Technology, Hawaii, pp 1–38Google Scholar
  34. Taussig SJ, Batkin S (1988) Bromelain, the enzyme complex of pineapple (Ananas comosus) and its clinical application: an update. J Ethnopharmacol 22:191–203CrossRefGoogle Scholar
  35. Trusov Y, Botella JR (2006) Silencing of the ACC synthase gene ACACS2 causes delayed flowering in pineapple [Ananas comosus (L.) Merr.]. J Exp Bot 57:3953–3960CrossRefGoogle Scholar
  36. VanBuren R, Walters B, Ming R, Min XJ (2013) Analysis of expressed sequence tags and alternative splicing genes in sacred lotus (Nelumbo nucifera Gaertn.). Plant Omics J 6:311–317Google Scholar
  37. Wai CM, Powell B, Ming R, Min XJ (2016a) Analysis of alternative splicing landscape in pineapple (Ananas comosus). Trop Plant Biol 9(3):150–160.  https://doi.org/10.1007/s12042-016-9168-1CrossRefGoogle Scholar
  38. Wai CM, Powell B, Ming R, Min XJ (2016b) Genome-wide identification and analysis of genes encoding proteolytic enzymes in pineapple. Trop Plant Biol 9(3):161–175.  https://doi.org/10.1007/s12042-016-9172-5CrossRefGoogle Scholar
  39. Walters B, Lum G, Sablok G, Min XJ (2013) Genome-wide landscape of alternative splicing events in Brachypodium distachyon. DNA Res 20:163–171CrossRefGoogle Scholar
  40. Wang B, Brendel V (2006) Genome wide comparative analysis of alternative splicing in plants. Proc Natl Acad Sci U S A 103:7175–7180CrossRefGoogle Scholar
  41. Wang RH, Hsu YM, Bartholomew DP, Maruthasalam S, Lin CH (2007) Delaying natural flowering in pineapple through foliar application of aviglycine, an inhibitor of ethylene biosynthesis. HortSci 42:1188–1191Google Scholar
  42. Yang SF, Hoffman NE (1984) Ethylene biosynthesis and its regulation in higher plants. Ann Rev Plant Physiol 35:155–189CrossRefGoogle Scholar
  43. Yang YS, Strittmatter SM (2007) The reticulons: a family of proteins with diverse functions. Genome Biol 8:234CrossRefGoogle Scholar
  44. Yu H, Tian C, Yu Y, Jiao Y (2016) Transcriptome survey of the contribution of alternative splicing to proteome diversity in arabidopsis thaliana. Mol Plant 9:749–952CrossRefGoogle Scholar
  45. Zancani M, Peresson C, Biroccio A, Federici G, Urbani A, Murgia I et al (2004) Evidence for the presence of ferritin in plant mitochondria. Eur J Biochem 271:3657–3664CrossRefGoogle Scholar
  46. Zhang J, Liu J, Ming R (2014) Genomic analyses of the CAM plant pineapple. J Exp Bot 65:3395–3404CrossRefGoogle Scholar
  47. Zhao C, Beers E (2013) Alternative splicing of Myb-related genes MYR1 and MYR2 may modulate activities through changes in dimerization, localization, or protein folding. Plant Signal Behav 11:e27325CrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  • Ching Man Wai
    • 1
  • Brian Powell
    • 2
  • Ray Ming
    • 1
  • Xiang Jia Min
    • 3
  1. 1.Department of Plant BiologyUniversity of Illinois at Urbana-ChampaignUrbanaUSA
  2. 2.Department of Computer Science and Information SystemsYoungstown State UniversityYoungstownUSA
  3. 3.Center for Applied Chemical Biology, Department of Biological SciencesYoungstown State UniversityYoungstownUSA

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