Project description:Leaves of the potatoes grown for 3 and 8 weeks at NT and HT were harvested for total RNA extraction. Total RNA was extracted from 100 mg of ground leaves using the Trizol reagent (MRC) following the manufacturer’s instructions. Five micro gram of each RNA sample were generated for a strand-specific library as previously described. The library was containing inserts of 150-200 bp. For RNA sequencing, paired-end 150 nt sequencing was performed using a HiSeq 4000 platform (Illumina, USA) at Microgen (Korea).
Project description:St (common potato) is a freezing sensitive species unable to cold acclimate. The close wild relative Sc is freezing tolerant and able to cold acclimate. Here we compare the cold transcriptome of these two species with different levels of freezing tolerance. We also identify the putative CBF regulons by comparing the transcriptomes of wild type plants with that of 35S::AtCBF3 transgenic lines in both species. Plants were grown in 16:8 photoperiod. Eight hours after dawn, plants were either transfered to cold or kept in the warn. Wild type S. tuberosum and S. commersonii were grown at 2oC for 2h, 24h and 7 days. Wild type plants grown under warm temperatures for 2h was used as control for 2h cold samples; wild type warm grown plants for 24h were used as controls for 24h and 7 days cold samples. Under warm conditions, S. commersonii 35S::AtCBF3 lines were compared to S. commersonii wild type plants (same thing was done for S. tuberosum).
Project description:St (common potato) is a freezing sensitive species unable to cold acclimate. The close wild relative Sc is freezing tolerant and able to cold acclimate. Here we compare the cold transcriptome of these two species with different levels of freezing tolerance. We also identify the putative CBF regulons by comparing the transcriptomes of wild type plants with that of 35S::AtCBF3 transgenic lines in both species.
Project description:Solanum lycopersicum and Solanum tuberosum are agriculturally important crop species as they are rich sources of starch, protein, antioxidants, lycopene, beta-carotene, vitamin C, and fiber. The genomes of S. lycopersicum and S. tuberosum are currently available. However the linear strings of nucleotides that together comprise a genome sequence are of limited significance by themselves. Computational and bioinformatics approaches can be used to exploit the genomes for fundamental research for improving their varieties. The comparative genome analysis, Pfam analysis of predicted reviewed paralogous proteins was performed. It was found that S. lycopersicum proteins belong to more families, domains and clans in comparison with S. tuberosum. It was also found that mostly intergenic regions are conserved in two genomes followed by exons, intron and UTR. This can be exploited to predict regions between genomes that are similar to each other and to study the evolutionary relationship between two genomes, leading towards the development of disease resistance, stress tolerance and improved varieties of tomato.
