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In silico mining of ssrs and an insight into candidate gene responsible for adaptation in 3 RANUNCULUS species

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Title In silico mining of ssrs and an insight into candidate gene responsible for adaptation in 3 RANUNCULUS species
 
Creator Swagatika, Samapti
 
Contributor Sen, P
 
Subject Microsatellite; SSR marker; Ranunculus; De novo, Transcriptome; Adaptation; Primer
 
Description Adaptation of organisms to changing environment is 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 Ranunculus species were
downloaded from SRA database and revealed candidates genes for adaptation to aquatic habitats.
De novo assembly resulted in generation of 198, 810, 201, 767, 186,609 contigs. Using these
contigs, 20,093, 26,543, 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.
 
Date 2017-01-04T12:40:46Z
2017-01-04T12:40:46Z
2016
 
Type Thesis
 
Identifier http://krishikosh.egranth.ac.in/handle/1/94403
 
Language en
 
Relation Th;4642
 
Format application/pdf