Skip to main content
SpringerLink
Log in

Development of ESTs and data mining of pineapple EST-SSRs

  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

Abstract:

Improving the quality of the non-climacteric fruit, pineapple, is possible with information on the expression of genes that occur during the process of fruit ripening. This can be made known though the generation of partial mRNA transcript sequences known as expressed sequence tags (ESTs). ESTs are useful not only for gene discovery but also function as a resource for the identification of molecular markers, such as simple sequence repeats (SSRs). This paper reports on firstly, the construction of a normalized library of the mature green pineapple fruit and secondly, the mining of EST-SSRs markers using the newly obtained pineapple ESTs as well as publically available pineapple ESTs deposited in GenBank. Sequencing of the clones from the EST library resulted in 282 good sequences. Assembly of sequences generated 168 unique transcripts (UTs) consisting of 34 contigs and 134 singletons with an average length of ≈500 bp. Annotation of the UTs categorized the known proteins transcripts into the three ontologies as: molecular function (34.88%), biological process (38.43%), and cellular component (26.69%). Approximately 7% (416) of the pineapple ESTs contained SSRs with an abundance of trinucleotide SSRs (48.3%) being identified. This was followed by dinucleotide and tetranucleotide SSRs with frequency of 46 and 57%, respectively. From these EST-containing SSRs, 355 (85.3%) matched to known proteins while 133 contained flanking regions for primer design. Both the ESTs were sequenced and the mined EST-SSRs will be useful in the understanding of non-climacteric ripening and the screening of biomarkers linked to fruit quality traits.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    PubMed  CAS  Google Scholar 

  2. Andersen JR, Lübberstedt T (2003) Functional markers in plants. Trends Plant Sci 8:554–560

    Article  PubMed  CAS  Google Scholar 

  3. Bombarely A, Merchante C, Csukasi F, Cruz-Rus E, Caballero JL, Medina-Escobar N, Blanco-Portales R, Botella MA, Munoz-Blanco J, Sánchez-Sevilla JF, Valpuesta V (2010) Generation and anlysis of ESTs from strawberry (Fragaria xananassa) fruits and evaluation of their utility in genetic and molecular studies. BMC Genomics 11:503–520

    Article  PubMed  Google Scholar 

  4. Borstnik B, Pumpemik D (2002) Tandem repeats in protein coding regions of primate genes. Genome Res 12:909–915

    Article  PubMed  CAS  Google Scholar 

  5. Burland TG (1999) DNASTAR’s lasergene sequence analysis software. Meth Mol Biol 132:71–91

    Google Scholar 

  6. Cho YB, Jeon HJ, Hong CB (2003) Cloning and functional annotation rare mRNA species from drought-stressed hot pepper (Capsicum annuum). J Plant Biol 46:83–89

    Article  CAS  Google Scholar 

  7. Conesa A, Gotz S, Garcia-Gornez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis of functional genomics research. Bioinformatics 21:3674–3676

    Article  PubMed  CAS  Google Scholar 

  8. Cordeiro GM, Casu R, McIntyre CL, Manners JM, Henry RJ (2001) Microsatellite markers from sugarcane ESTs cross transferable to erianthus and sorghum. Plant Sci 160:1115–1123

    Article  PubMed  CAS  Google Scholar 

  9. Gao L, Tang J, Li H, Jia J (2003) Analysis of microsatellites in major crops assessed by computational and experimental approaches. Mol Breed 12:245–261

    Article  CAS  Google Scholar 

  10. Giovannoni J (2001) Molecular biology of fruit maturation and ripening. Annu Rev Plant Physiol 52:725–749

    Article  CAS  Google Scholar 

  11. Giovannoni JJ (2004) Genetic regulation of fruit development and ripening. Plant Cell 16:S170–S180

    Article  PubMed  CAS  Google Scholar 

  12. Jiang D, Zhong GY, Hong QB (2006) Analysis of microsatellites in citrus unigenes. Act Genet Sin 33:345–353

    Article  CAS  Google Scholar 

  13. Kantety RV, La Rota M, Matthews DE, Sorrells ME (2002) Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol 48:501–510

    Article  PubMed  CAS  Google Scholar 

  14. Kisiel A, Podknowinski J (2005) Expressed sequence tags and their application for plant research. Acta Physiol Plant 27:157–161

    Article  CAS  Google Scholar 

  15. Kumar SV, Tan SG, Quah SC, Yusoff K (2002) Isolation and characterization of seven microsatellite loci in mungbean, Vigna radiata. Mol Ecol Notes 2:293–295

    Article  CAS  Google Scholar 

  16. Lagercrantz U, Ellegren H, Andersson L (1993) The abundance of various polymorphic microsatellites motifs differs between plants and vertebrates. Nucleic Acids Res 21:1111–1115

    Article  PubMed  CAS  Google Scholar 

  17. La Rota M, Kantety RV, Yu J-K, Sorrells ME (2005) Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat and barley. BMC Genomics 6:1–12

    Article  Google Scholar 

  18. Li JH, Tang CH, Song CY, Chen MJ, Feng ZY, Pan YJ (2006) A simple and effective method for total RNA extraction from Lentinula edodes. Biotech Lett 28:1193–1197

    Article  CAS  Google Scholar 

  19. Minoru K, Susumu G (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30

    Article  Google Scholar 

  20. Morgante M, Olivieri AM (1993) PCR-amplified microsatellites as markers in plant genetics. Plant J 3:175–182

    Article  PubMed  CAS  Google Scholar 

  21. Moyle RL, Fairbairn DJ, Ripi J, Crowre M, Botella JR (2005) Developing pineapple fruit has a small transcriptome dominated by metallothionein. J Exp Bot 56:101–112

    PubMed  CAS  Google Scholar 

  22. Pan YW, Chou HH, You EM, Yu HT (2004) Isolation and characterization of 23 polymorphic microsatellite markers for diversity and stock analysis in tiger shrimp (Panaeus monodon). Mol Ecol Notes 4:345–347

    Article  CAS  Google Scholar 

  23. Qureshi SN, Saha S, Kantety RV, Jenkins JN (2004) EST-SSR: a new class of genetic markers in cotton. J Cotton Sci 8:112–123

    CAS  Google Scholar 

  24. Rozen R, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols. Methods in molecular biology. Humana Press, Totowa, pp 365–386

  25. Scott KD, Eggler P, Seaton G, Rossetto M, Ablett EM, Lee LS, Henry RJ (2000) Analysis of SSRs derieved from grape ESTs. Theor Appl Genet 100:723–726

    Article  CAS  Google Scholar 

  26. Serapion J, Kucuktas H, Feng J, Liu Z (2004) Bioinformatic mining of type I microsatellites from expressed sequence tags of channel catfish (Ictalurus punctatus). Marine Biotech 6:364–377

    Article  CAS  Google Scholar 

  27. Simko I (2009) Development of EST-SSR markers for the study of population structure in lettuce (Lactuca sativa L.). J Heridity 100:256–262

    Article  CAS  Google Scholar 

  28. Soares VLF, Rodrigues SM, de Oliveira TM, de Queiroz TO, Lima LS, Hora-Júnior BT, Gramacho KP, Micheli F, Cascardo CM, Otoni WC, Gesteira AS, Costa MGC (2011) Unraveling new genes associated with seed development and metabolism in Bixa orellana L. by expressed sequence tag (EST) analysis. Mol Bio Rep 38:1329–1340

    Article  CAS  Google Scholar 

  29. Tassanakajon A, Klinbunga S, Paunglarp N, Rimphanitchayakit V, Udomkit A, Jitrapakdee S, Sritunyalucksana K, Phongdara A, Pongsomboon S, Supungul P, Tang S, Kuphanumart K, Pichyangkura R, Lursinsap C (2006) Panaeus monodon gene discovery project: the generation of an EST collection and establishment of a database. Gene 384:104–112

    Article  PubMed  CAS  Google Scholar 

  30. Terrier N, Ageorges A, Abbal P, Romieu C (2001) Generation of ESTs from grape berry at various development stages. J Plant Physiol 158:1575–1583

    Article  CAS  Google Scholar 

  31. Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley. Theor Appl Genet 100:411–422

    Google Scholar 

  32. Varshney RK, Sigmund R, Börner A, Korzun V, Stein N, Sorrels ME, Langridge P, Graner A (2005) Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice. Plant Sci 168:195–202

    Article  CAS  Google Scholar 

  33. Varshney RV, Thiel T, Stein N, Langridge P, Graner A (2002) In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell Mol Biol Lett 7:537–546

    PubMed  CAS  Google Scholar 

  34. Zhang L, Yuan D, Yu S, Li Z, Cao Y, Miao Z, Qian H, Tang K (2004) Preference of simple sequence repeats in coding and non-coding regions of Arabiodopsis thaliana. Bioinformatics 20:1081–1086

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgment

The authors would like to thank the Ministry of Science, Technology and Innovation, Malaysia for the research grant SCF0007-BIO-2006.

Author information

Authors and Affiliations

  1. Biotechnology Research Institute, University Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia

    W. D. Ong, C. L. Y. Voo & S. V. Kumar

Authors
  1. W. D. Ong
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. C. L. Y. Voo
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. S. V. Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to S. V. Kumar.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 54 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Ong, W.D., Voo, C.L.Y. & Kumar, S.V. Development of ESTs and data mining of pineapple EST-SSRs. Mol Biol Rep 39, 5889–5896 (2012). https://doi.org/10.1007/s11033-011-1400-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-011-1400-3

Keywords

Search

Navigation