Whole Genome, Transcriptome and Metagenomic Applications: Successful Sample Preparation and Experimental Designs

During the past decade, next-generation sequencing technologies have been instrumental in advancing plant and animal research. Regular improvements in protocols, techniques and instruments constantly spawn new opportunities for enhancing genomic exploration.

Here, we discuss recent advancements and their application to support a diverse portfolio of research projects in animal health and behavior, plant breeding and development, and host-microbiome interactions.  We present the latest library construction techniques for de novo assembly and resequencing of a variety of organisms, from simple bacteria through large complex polyploid genomes.  This includes strategies for library preparation of genomic DNA, stranded RNASeq, mate-pair, synthetic long reads, small RNA and ChIP-Seq and applying these libraries across the span of current next-generation DNA sequencing platforms to bolster genomic research. 

Notably, metagenomics and microbial community profiling have been tremendously empowered by these technologies. We have developed unique capabilities that go well beyond 16S studies by using a combined approach of Fluidigm plus Illumina platforms to generate a broad profile of microbial communities.  This is accomplished by employing a flexible collection of primer sets covering not just 16S, but also 18S, archaea, ITS, gene-specific targets, and functional genes to develop a comprehensive understanding of the community profiles and metabolic activities at a fraction of the cost of full metagenomic sequencing.  These protocols can also be readily applied to high-throughput multi-loci screening on any plant or animal species of interest.