In silico mining and characterization of simple sequence repeats (SSRs) from Euphorbia esula expressed sequence tags (ESTs): A potential crop for biofuel

Abstract

Euphorbia esula (leafy spurge) is a perennial noxious weed native to Eurasia, which can also be potentially useful as a biofuel, medicine, or a pest control agent. In this study, we analysed publicly available ESTs of 'NCBI dbEST' (http://www.ncbi.nlm.nih.gov/dbEST) using in silico tools to have an insight into the genetic makeup of the plant. Mining of simple sequence repeats (SSRs) was performed by MISA, primer designing by Primer3 while functional annotation, gene ontology and enrichment analysis were performed by Blast2GO. SSR mining from 47543 ESTs revealed a total 3248 SSRs, of which di-, tri-and hexa-nucleotide repeats were 352 (10.83%), 822 (25.30%), 17 (0.52%) respectively. A total of 527 primer pairs were designed for the annotated SSR-Contigs. About 77.07% SSR-ESTs could be assigned a significant match to the protein database. 210 unique SSR-FDM (Functional Domain Markers) were assigned for significant functional domains by InterProScan. The gene ontology (GO) analysis provided 1213 number of unique GO terms which were subjected to enrichment analysis to obtain 95 statistically significant GO terms mapped to the SSR containing ESTs. Most frequent enriched GO terms were GO:0005886 for cellular component, GO:0003677 for molecular function and GO:0044255 in case of biological process, indicating the potential of the species as a fuel crop. Many SSR markers were functionally annotated to various biotic and abiotic stress responsive genes. Further studies may help us to understand these traits of extreme adaptive features. This will provide opportunity to genetically manage and modify crops for resistance to these stresses.

In Silico Comparative Analysis of Simple Sequence Repeats in Chloroplast Genomes of Genus Nymphaea

“…Earlier, SSRs were identified in various plants including Citrus sinensis (Shanker et al, 2007), Gracilaria tenuistipitata (Song et al, 2014), Cocos nucifera (Srivastava & Shanker, 2015), Glycine species (Ozyigit et al, 2015), Magnoliids (Srivastava & Shanker, 2016), Euphorbia esula (Sen et al, 2017), Arabidopsis (Kumar & Shanker, 2018), and Triticum (Kapil et al, 2018). However, the trend to detect common, polymorphic, and unique cpSSRs is relatively new (Kabra et al, 2016;Kapil et al, 2018) and no such information is available for genus Nymphaea.…”