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

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Abstract

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.

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Authors and Affiliations

  1. Centre for Biotechnology and Bioinformatics, Dibrugarh University, Dibrugarh, Assam, India

    Surojit Sen

  2. Biomedical Informatics Centre, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India

    Budheswar Dehury

  3. Distributed Information Center, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India

    Jagajjit Sahu

  4. Department of Biochemistry and Agricultural Chemistry, Assam Agricultural University, Jorhat, Assam, 785013, India

    Sunayana Rathi

  5. Department of Life Sciences, Dibrugarh University, Dibrugarh, Assam, 786004, India

    Raj Narain Singh Yadav

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Sen, S., Dehury, B., Sahu, J. et al. Mining and comparative survey of EST–SSR markers among members of Euphorbiaceae family. Mol Biol Rep 45, 453–468 (2018). https://doi.org/10.1007/s11033-018-4181-0

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