Mining and comparative survey of EST–SSR markers among members of Euphorbiaceae family
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.
KeywordsESTs 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.
- 1.Oldfield S (1997) Cactus and succulent plants—status survey and conservation action plan. IUCN, CambridgeGoogle Scholar
- 4.Kapoor LD (1989) Handbook of ayurvedic medicinal plants: herbal reference library. CRC Press, Boca RatonGoogle Scholar
- 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.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
- 9.Benavides A, Benjumea P, Pashova V (2007) Castor oil biodiesel as an alternative fuel for diesel engines. Dyna 74:141–150Google Scholar
- 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
- 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. https://gephi.org/publications/gephi-bastian-feb09.pdf. Accessed 20 Mar 2017
- 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