Innovations in de novo Whole Genome, Transcriptome and Metagenomic Sequencing

The last decade has delivered non-stop advancement in next-generation sequencing technologies, which in turn has spurred continuous improvement in next-generation library construction techniques and strategies to utilize these advances. These strategies can be applied ubiquitously across all areas of research, from de novo whole genome sequencing, to transcriptome sequencing, to metagenomic sequencing.

Here, we present novel approaches for utilization of the most recent technologies, combining the array of Illumina sequencing platforms and 10X Genomics to generate robust sequencing data that supports research in both plant and animal health, breeding, and development. These systems can also be used to support microbial studies ranging from waste water treatment to soil and gut compositions and beyond. We discuss the latest advancement in library construction with strategies for genomic DNA, stranded RNASeq for both eukaryotic and bacterial samples, mate-pair libraries, ChIP-Seq and small RNAs.

In addition, we showcase a novel approach to the study of microbial communities that allows simultaneous amplification and sequencing of not just the 16S microbial gene target, but also archaea, 18S, ITS, eukaryotic specific, and functional gene targets, all at a much reduced workload and cost. While used mostly for microbial community profiling, this unique approach can also be used to screen multiple loci on any animal or plant of interest. This unique Fluidigm plus Illumina streamlined approach has been demonstrated on hundreds of different sample types to date. It allows for a much more comprehensive view of the microbial community profiles and functional gene activity at a significantly reduced cost compared to full metagenomic DNA sequencing.