Abstract

IN SILICO MINING OF SSRS AND AN INSIGHT INTO CANDIDATE GENES RESPONSIBLE FOR ADAPTATION IN THREE RANUNCULUS SPECIES

Samapti Swagatika and Krishna Kumar Das*

ABSTRACT

Adaptations of organisms to changing environment are a fundamental topic in modern evolutionary ecology. The advances in genomic technology or Next generation sequencing (NGS) makes it more feasible than ever to identify genetic loci responsible for adaptive evolution in non- model organisms. The family Ranunculaceae comprises numerous species that inhabit a wide range of habitats and climatic conditions, including one species Ranuculus bungei, which is adapted to aquatic habitats and 2 close relatives to R. bungei are Ranuculus brotherusii, Ranuculus cantoniensis which have adaptation to terrestrial habitats. To explore the molecular mechanism of adaptation from terrestrial to aquatic habitat the transcriptome of 3 Ranuculus species were downloaded from SRA database and revealed candidates genes for adaptation to aquatichabitats. De novo assembly resulted in generation of 198, 810, 201, 767, 186 and 609 contigs. Using these contigs 20,093, 26,543, and 24,637 numbers of novel microsatellite simple sequence repeat (SSR) markers were developed from R. brotherusii, R. cantoniensis and R. bungei respectively. By comparing these results 58 SSR markers were identified associated with 24 unique genes putatively involved in the adaptive transition from terrestrial to aquatic habitats. A total of 84 primer pairs were designed out of 112 SSR transcripts. Some of the homologs to these genes in model plants are involved in resistance towards abiotic stresses like salt tolerance, low or high light level, low water level / drought condition and others were found to be associated with nucleolar protein, vacuolar protein, microtubular protein, chaperon protein etc.

Keywords: Microsatellite; SSR marker; Ranunculus; De novo; Transcriptome.