Comparative transcriptomic assessment and landscape genetic analysis of endangered Himalayan gymnosperm Taxus Contorta Griffith

Abstract

Taxus contorta is an important medicinal plant currently listed as endangered in IUCN newlineRed Data List. It is almost unexplored at the genomic and transcriptomic level. This newlinestudy was therefore aimed to explore T. contorta by using massively parallel RNAseq newlinetechnology to generate a reference transcriptome which would bridge the gap in the newlinegenomic field to a greater extent, if not completely. The transcriptomic sequences can newlinethen be used to address a myriad of scientific problems in T. contorta. Although not newlinelimited to, this study through the utility of the transcriptomic sequences addressed to newlinedecipher and explore T. contorta in the context of four problems viz generation of newlineSSR marker resource and their use in population and landscape genetic analysis, newlineassessment of codon usage bias, expressional variation under changing environment newlineand resolving the taxonomic ambiguity of the family of T. contorta. The transcriptomic newlinesequences generated here have proven useful to answer these problems. newlineThe reference transcriptome constituted around 129869 unigenes. Functional newlineannotation resulted into 35752 transcripts with assigned 5971 unique GO terms. newlineAround 40386 transcripts were found to have 2163 unique Pfam Ids. Pathway newlineanalysis against KEGG database yielded 3721 unique enzyme numbers. Screening newlineof the transcripts for microsatellite regions yielded 7041 SSRs. Among the 100 SSRs newlineselected for characterization on 30 genotypes, 37 were found polymorphic. A set of newline20 polymorphic SSR markers were used in population and landscape genetic newlineanalysis on 241 samples constituting 17 populations in Western Himalayas. The newlinegenetic bottleneck, low heterozygosity and enhanced homozygosity was observed. newlineThe genetic diversity hot spots were identified through interpolation technique. newlineEcological niche modelling based analysis revealed stable/improved climatic patches newlinefor T. contorta in future. The genetic diversity hot spots and stable/improve climatic newlinepatches were recommended for priority of conservation This integrative approach of newlinetranslating