De novo transcriptome analysis and development of novel EST-SSR markers in Bergenia ciliata (Haw.) Sternb. (Saxifragaceae) through Illumina sequencing

Abstract

Bergenia ciliata (Haw.) Sternb. is an important herb predominantly found in Indian Himalayan Region (IHR). It is widely used in medicines and healthcare system, cosmetics, food, fodder, and ornamental purposes. Illumina sequencing and de novo transcriptome assembly were carried out in B. ciliata to develop and identify simple sequence repeat markers for genetic diversity and conservation studies. The assembled data generated a total of 65,010 unigenes that showed significant similarities when compared with seven functional databases including 53,577 (Non-Redundant Protein Sequence Database: 82.41%), 44,297 (Nucleotide Sequence Database: 68.14%), 42,287 (Swiss Prot: 65.05%), 15,027 (Eukaryotic Orthologous Groups: 23.11%), 22,540 (KEGG Orthology: 34.67%), 29,477 (Gene Ontology: 45.34%) and 20,609 (Pfam: 31.7%) unigenes. In this study, a total of 18,226 SSRs and 14,497 SSR containing sequences were identified. Dinucleotides were found to be abundant (47.88%) in B. ciliata followed by mononucleotides (35.04%), and trinucleotides repeat (15.90%). AG/CT was the most common di-nucleotide repeat (40.33%). A total of 11,839 EST-SSR primers were designed, of which 96 primer pairs were synthesized randomly. Finally, 18 primer pairs were selected that revealed clear, distinct polymorphic bands when examined in eight diverse B. ciliata accessions. Furthermore, the transcriptome data and the EST-SSR markers will be an important resource for investigating genetic diversity in B. ciliata and other species of the family Saxifragaceae.