Molecular Biology Reports

, Volume 45, Issue 4, pp 453–468 | Cite as

Mining and comparative survey of EST–SSR markers among members of Euphorbiaceae family

  • Surojit Sen
  • Budheswar Dehury
  • Jagajjit Sahu
  • Sunayana Rathi
  • Raj Narain Singh Yadav
Original Article


Euphorbiaceae represents flowering plants family of tropical and sub-tropical region rich in secondary metabolites of economic importance. To understand and assess the genetic makeup among the members, this study was undertaken to characterize and compare SSR markers from publicly available ESTs and GSSs of nine selected species of the family. Mining of SSRs was performed by MISA, primer designing by Primer3, while functional annotation, gene ontology (GO) and enrichment analysis were performed by Blast2GO. A total 12,878 number of SSRs were detected from 101,701 number of EST sequences. SSR density ranged from 1 SSR/3.22 kb to 1 SSR/15.65 kb. A total of 1873 primer pairs were designed for the annotated SSR-Contigs. About 77.07% SSR–ESTs could be assigned a significant match to the protein database. 3037 unique SSR–FDM were assigned and IPR003657 (WRKY Domain) was found to be the most dominant FDM among the members. 1810 unique GO terms obtained were further subjected to enrichment analysis to obtain 513 statistically significant GO terms mapped to the SSR containing ESTs. Most frequent enriched GO terms were, GO:0003824 for molecular function, GO:0006350 for biological process and GO:0005886 for cellular component, justifying the richness of defensive secondary metabolites and phytomedicine within the family. The results from this study provides tangible insight to genetic make-up and distribution of SSRs. Functional annotation corresponded many genes of unknown functions which may be considered as novel genes or genes responsible for stress specific secondary metabolites. Further studies are required to understand stress specific genes accountable for leveraging the synthesis of secondary metabolites.


ESTs SSRs Euphorbiaceae Secondary metabolites Functional annotation Gene ontology Enrichment analysis 


Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interests.

Supplementary material

11033_2018_4181_MOESM1_ESM.doc (2.7 mb)
Supplementary material 1 (DOC 2728 KB)


  1. 1.
    Oldfield S (1997) Cactus and succulent plants—status survey and conservation action plan. IUCN, CambridgeGoogle Scholar
  2. 2.
    Palatnick W, Tenenbein M (2000) Hepatotoxicity from castor bean ingestion in a child. J Toxicol Clin Toxicol 38:67–69CrossRefPubMedGoogle Scholar
  3. 3.
    Van Damme PLJ (2001) Euphorbia tirucalli for high biomass production. In: Schlissel A, Pasternak D (eds) Combating desertification with plants, 1st edn. Kluwer, New York, pp 169–187CrossRefGoogle Scholar
  4. 4.
    Kapoor LD (1989) Handbook of ayurvedic medicinal plants: herbal reference library. CRC Press, Boca RatonGoogle Scholar
  5. 5.
    Cataluna P, Rates SMK (1999) The traditional use of the latex from Euphorbia tirucalli Linnaeus (Euphorbiaceae) in the treatment of cancer in South Brazil. In: Martino V et al (eds) Proceedings of WOCMAP-2 pharmacognosy, pharmacology, phytomedicines, toxicology. Acta Horticulture ISHS, Belgium, pp 289–295Google Scholar
  6. 6.
    Duke JA (1983) Handbook of energy crops. Purdue University centre for new crops and plant products. http://www.hort.purdue.educ. Accessed on 1 Mar 2009
  7. 7.
    de Oliveira JS, Leite PM, de Souza LB, Mello VM, Silva EC, Rubim JC, Meneghetti SMP, Suarez PAZ (2009) Characteristics and composition of Jatropha gossypiifolia and Jatropha curcas L. oils and application for biodiesel production. Biomass Bioenergy 33:449–453CrossRefGoogle Scholar
  8. 8.
    Adeniyi OD, Kovo AS, Abdulkareem AS, Chukwudozie C (2007) Ethanol fuel production from cassava as a substitute for gasoline. J Dispers Sci Technol 28:501–504CrossRefGoogle Scholar
  9. 9.
    Benavides A, Benjumea P, Pashova V (2007) Castor oil biodiesel as an alternative fuel for diesel engines. Dyna 74:141–150Google Scholar
  10. 10.
    Iquebal MA, Jaiswal S, Angadi UB, Sablok G, Arora V, Kumar S, Rai A, Kumar D (2015) SBMDb: first whole genome microsatellite DNA marker database of sugarbeet for bioenergy and industrial applications. Database. PubMedPubMedCentralGoogle Scholar
  11. 11.
    Kota R, Varshney RK, Thiel T, Dehmer KJ, Graner A (2001) Generation and comparison of EST-derived SSRs and SNPs in barley (Hordeum vulgare L.). Hereditas 135:145–151CrossRefPubMedGoogle Scholar
  12. 12.
    Milbourne D, Russell J, Waugh R (1998) Comparison of molecular marker assays in inbreeding (barley) and outbreeding (potato) species. In: Karp A et al (eds) Molecular tools for screening biodiversity: plants and animals. Chapman and Hall, London, pp 371–381CrossRefGoogle Scholar
  13. 13.
    Cordeiro GM, Casu R, Mclntyre CL, Manners JM, Henry RJ (2001) Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to erianthus and sorghum. Plant Sci 160:1115–1123CrossRefPubMedGoogle Scholar
  14. 14.
    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 48:501–510CrossRefPubMedGoogle Scholar
  15. 15.
    Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422CrossRefPubMedGoogle Scholar
  16. 16.
    Feng SP, Li WG, Huang HS, Wang JY, Wu YT (2009) Development, characterization and cross-species/genera transferability of EST-SSR markers for rubber tree (Hevea brasiliensis). Mol Breed 23:85–97CrossRefGoogle Scholar
  17. 17.
    Parkinson J, Blaxter M (2004) Expressed sequence tags: analysis and annotation. In: Melville SE (ed) Methods in molecular biology parasite genomics protocols. Humana Press, Totowa, pp 93–126CrossRefGoogle Scholar
  18. 18.
    Yan Q, Zhang Y, Li H, Wei C, Niu L, Guan S, Li S, Du L (2008) Identification of microsatellites in cattle unigenes. J Genet Genom 35:261–266CrossRefGoogle Scholar
  19. 19.
    Ashkani S, Rafii MY, Rusli I, Meon S, Abdullah SNA, Rahim HA, Latif MA (2012) SSRs for marker-assisted selection for blast resistance in rice (Oryza sativa L.). Plant Mol Biol Rep 30:79–86CrossRefGoogle Scholar
  20. 20.
    Kalia RK, Rai MK, Kalia S, Singh R, Dhawan AK (2011) Microsatellite markers: an overview of the recent progress in plants. Euphytica 177:309–334CrossRefGoogle Scholar
  21. 21.
    Sraphet S, Boonchanawiwat A, Thanyasiriwat T, Boonseng O, Tabata S, Sasamoto S, Shirasawa K, Isobe S, Lightfoot DA, Tangphatsornruang S, Triwitayakorn K (2011) SSR and EST-SSR-based genetic linkage map of cassava (Manihot esculenta Crantz). Theor Appl Genet 122:1161–1170CrossRefPubMedGoogle Scholar
  22. 22.
    Andersen JR, Lubberstedt T (2003) Functional markers in plants. Trends Plant Sci 8:554–560CrossRefPubMedGoogle Scholar
  23. 23.
    Arnold C, Rossetto M, McNally J, Henry RJ (2002) The application of SSRs characterized for grape (Vitis vinifera) to conservation studies in Vitaceae. Am J Bot 89:22–28CrossRefPubMedGoogle Scholar
  24. 24.
    Saha S, Karaca M, Jenkins JN, Zipf AE, Reddy OUK, Kantety RV (2003) Simple sequence repeats as useful resources to study transcribed genes of cotton. Euphytica 130:355–364CrossRefGoogle Scholar
  25. 25.
    Masoudi-Nejad A, Tonomura K, Kawashima S, Moriya Y, Suzuki M, Itoh M, Kanehisa M, Endo T, Goto S (2006) EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. Nucleic Acids Res 34:W459–W462CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9:868–877CrossRefPubMedPubMedCentralGoogle Scholar
  27. 27.
    Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365–386PubMedGoogle Scholar
  28. 28.
    Kalendar R, Lee D, Schulman A (2014) FastPCR software for PCR, in silico PCR, and oligonucleotide assembly and analysis. In: Valla S, Lale R (eds) DNA cloning and assembly methods, methods in molecular biology, vol. 1116. Humana Press, New York, pp 271–302CrossRefGoogle Scholar
  29. 29.
    Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676CrossRefPubMedGoogle Scholar
  30. 30.
    Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19:1639–1645CrossRefPubMedPubMedCentralGoogle Scholar
  31. 31.
    Bastian M, Heymann S, Jacomy M (2009) Gephi: an open source software for exploring and manipulating networks. In: International AAAI conference on weblogs and social media. Accessed 20 Mar 2017
  32. 32.
    Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with non-repetitive DNA in plant genomes. Nat Genet 30:194–200CrossRefPubMedGoogle Scholar
  33. 33.
    Varshney RK, 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 7:537–546PubMedGoogle Scholar
  34. 34.
    Kumpatla SP, Mukhopadhyay S (2005) Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species. Genome 48:985–998CrossRefPubMedGoogle Scholar
  35. 35.
    Poncet V, Rondeau M, Tranchant C, Cayrel A, Hamon S, deKochko A, Hamon P (2006) SSR mining in coffee tree EST databases: potential use of EST-SSRs as markers for the Coffea genus. Mol Genet Genom 276:436–449CrossRefGoogle Scholar
  36. 36.
    Scaglione D, Acquadro A, Portis E, Taylor CA, Lanteri S, Knapp SJ (2009) Ontology and diversity of transcript-associated microsatellites mined from a globe artichoke EST database. BMC Genom 10:454CrossRefGoogle Scholar
  37. 37.
    Varshney VK, Dayal R, Bhandari RS, Jyoti KN, Prasuna AL, Prasad AR, Yadav JS (2005) Behavioral response of the borer beetle Hoplocerambyx spinicornis to volatile compounds of the tree Shorea robusta. Chem Biodivers 2:785–791CrossRefPubMedGoogle Scholar
  38. 38.
    Fraser LG, Harvey CF, Crowhurst RN, De Silva HN (2004) EST-derived microsatellites from Actinidia species and their potential for mapping. Theor Appl Genet 108:1010–1016CrossRefPubMedGoogle Scholar
  39. 39.
    Sahu J, Sarmah R, Dehury B, Sarma K, Sahoo S, Sahu M, Barooah M, Modi MK, Sen P (2012) Mining for SSRs and FDMs from expressed sequence tags of Camellia sinensis. Bioinformation 8:260–266CrossRefPubMedPubMedCentralGoogle Scholar
  40. 40.
    Rungis D, Bérubé Y, Zhang J, Ralph S, Ritland CE, Ellis BE, Douglas C, Bohlmann J, Ritland K (2004) Robust simple sequence repeat markers for spruce (Picea spp.) from expressed sequence tags. Theor Appl Genet 109:1283–1294CrossRefPubMedGoogle Scholar
  41. 41.
    Sahu J, Sen P, Choudhury MD, Dehury B, Barooah M, Modi MK, Talukdar AD (2014) Rediscovering medicinal plants’ potential with OMICS: microsatellite survey in expressed sequence tags of eleven traditional plants with potent antidiabetic properties. OMICS 18:298–309CrossRefPubMedPubMedCentralGoogle Scholar
  42. 42.
    Nicot N, Chiquet V, Gandon B, Amilhat L, Legeai F, Leroy P, Bernard M, Sourdille P (2004) Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs). Theor Appl Genet 109:800–805CrossRefPubMedGoogle Scholar
  43. 43.
    L´opez CE, Quesada-Ocampo LM, Boh´orquez A, Duque MC, Vargas J, Tohme J, Verdier V (2007) Mapping EST-derived SSRs and ESTs involved in resistance to bacterial blight in Manihot esculenta. Genome 50:1078–1088CrossRefGoogle Scholar
  44. 44.
    Zou M, Xia Z, Ling P, Zhang Y, Chen X, Wei Z, Bo W, Wang W (2011) Mining EST-derived SSR markers to assess genetic diversity in cassava (Manihot esculenta Crantz). Plant Mol Biol Rep 29:961–971CrossRefGoogle Scholar
  45. 45.
    Low ETL, Alias H, Boon SH, Shariff EM, Tan CYA, Ooi LCL, Cheah SC, Raha AR, Wan KL, Singh R (2008) Oil palm (Elaeis guineensis Jacq.) tissue culture ESTs: identifying genes associated with callogenesis and embryogenesis. BMC Plant Biol 8:62CrossRefPubMedPubMedCentralGoogle Scholar
  46. 46.
    Victoria FC, da Maia LC, de Oliveira AC (2011) In silico comparative analysis of SSR markers in plants. BMC Plant Biol 11:15CrossRefPubMedPubMedCentralGoogle Scholar
  47. 47.
    Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R (2000) Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 156:847–854PubMedPubMedCentralGoogle Scholar
  48. 48.
    Metzgar D, Bytof J, Wills C (2000) Selection against frame shift mutations limits microsatellite expansion in coding DNA. Genome Res 10:72–80PubMedPubMedCentralGoogle Scholar
  49. 49.
    Toth G, Gaspari Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10:967–981CrossRefPubMedPubMedCentralGoogle Scholar
  50. 50.
    Wren JD, Forgacs E, Fondon JW 3rd, Pertsemlidis A, Cheng SY, Gallardo T, Williams RS, Shohet RV, Minna JD, Garner HR (2000) Repeat polymorphisms within gene regions: phenotypic and evolutionary implications. Am J Hum Genet 67:345–356CrossRefPubMedPubMedCentralGoogle Scholar
  51. 51.
    Bull LN, Pabo´n-Pen˜a CR, Freimer NB (1999) Compound microsatellite repeats: practical and theoretical features. Genome Res 9:830–838CrossRefPubMedPubMedCentralGoogle Scholar
  52. 52.
    Kofler R, Schlo¨tterer C, Luschu¨tzky E, Lelley T (2008) Survey of microsatellite clustering in eight fully sequenced species sheds light on the origin of compound microsatellites. BMC Genom 9:612–626CrossRefGoogle Scholar
  53. 53.
    Ellis JR, Burke JM (2007) EST-SSRs as a resource for population genetic analyses. Heredity 99:125–132CrossRefPubMedGoogle Scholar
  54. 54.
    Decroocq V, Favé MG, Hagen L, Bordenave L, Decroocq S (2003) Development and transferability of apricot and grape EST microsatellite markers across taxa. Theor Appl Genet 106:912–922CrossRefPubMedGoogle Scholar
  55. 55.
    Zhang LY, Bernard M, Leroy P, Feuillet C, Sourdille P (2005) High transferability of bread wheat EST-derived SSRs to other cereals. Theor Appl Genet 111:677–687CrossRefPubMedGoogle Scholar
  56. 56.
    Heesacker A, Kishore VK, Gao W, Tang S, Kolkman JM, Gingle A, Matvienko M, Kozik A, Michelmore RM, Lai Z, Rieseberg LH, Knapp SJ (2008) SSRs and INDELs mined from the sunflower EST database: abundance, polymorphisms, and cross-taxa utility. Theor Appl Genet 117:1021–1029CrossRefPubMedGoogle Scholar
  57. 57.
    Gupta S, Prasad M (2009) Development and characterization of genic SSR markers in Medicago truncatula and their transferability in leguminous and non-leguminous species. Genome 52:761–771CrossRefPubMedGoogle Scholar
  58. 58.
    Barbará T, Palma-Silva C, Paggi GM, Bered F, Fay MF, Lexer C (2007) Cross-species transfer of nuclear microsatellite markers: potential and limitations. Mol Ecol 16:3759–3767CrossRefPubMedGoogle Scholar
  59. 59.
    Figueiredo AC, José JB, Luis GP, Johannes JCS (2008) Factors affecting secondary metabolite production in plants: volatile components and essential oils. Flavour Fragr J 23:213–226CrossRefGoogle Scholar
  60. 60.
    Koricheva J, Larsson S, Haukioja E, Keinanen M (1998) Regulation of woody plant secondary metabolism by resource availability: hypothesis testing by means of meta-analysis. Oikos 83:212–226CrossRefGoogle Scholar
  61. 61.
    Wink M (2003) Evolution of secondary metabolites from an ecological and molecular phylogenetic perspective. Phytochemistry 64:3–19CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  1. 1.Centre for Biotechnology and BioinformaticsDibrugarh UniversityDibrugarhIndia
  2. 2.Biomedical Informatics CentreICMR-Regional Medical Research CentreBhubaneswarIndia
  3. 3.Distributed Information Center, Department of Agricultural BiotechnologyAssam Agricultural UniversityJorhatIndia
  4. 4.Department of Biochemistry and Agricultural ChemistryAssam Agricultural UniversityJorhatIndia
  5. 5.Department of Life SciencesDibrugarh UniversityDibrugarhIndia

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