Strategies and Tools for Next Generation Sequencing
Next Generation Sequencing (NGS) technologies have accelerated the process of whole-genome sequencing. It provided a faster and easier way to sequence whole genomes at a fraction of cost and time. With the availability of multiple technologies; choices still needs to be made when planning a genome sequencing project in order to maximize assembly quality versus cost. For neem genome sequencing we have used Illumina and Roche sequencing technologies. To sequence and assemble neem genome, we isolated high-quality genome DNA from neem leaves and library was prepared for paired end DNA sequencing using Illumina HiSeq 1000. Library was also prepared for Roche 454 sequencer to generate long reads from genome. Transcriptome sequence from RNA of various tissues and seedlings was also generated to assess the expressed genes and support the gene prediction and annotation process.
KeywordsNGS Whole genome Illumina Roche 454 Transcriptome sequencing
We acknowledge Genomics facility (BT/PR3481/INF/22/140/2011) at Centre for Cellular and Molecular Platforms, Bangalore for sequencing of Neem genomes. We acknowledge Pradeep H, Aarati Karaba, Manojkumar S and Annapurna for their help in NGS library preparation and sequencing. We thank Ashmita G and Divya S for their help in manual curation of SSR markers. We are grateful to Rajanna, National Botanical Garden, University of Agricultural Sciences, GKVK campus, Bangalore for his help during neem sample collection.