Applied RNA-seq in crustaceans: Promises and challenges

Abstract

High-throughput sequencing technology (usually referred to as Next Generation Sequencing; NGS) has dramatically changed the way biological research is being conducted in the post-genomic era. Although only been made available in the last decade, NGS has been widely utilized across many non-model crustacean species, predominantly by sequencing the transcriptome of different tissues and life stages. In addition, NGS can provide a rapid, cost-effective solution for discovery of genetic markers crucial for many applications that would have otherwise been taking years to develop. Sequencing of the entire transcriptome (referred to as RNA sequencing ;RNA-seq) is among the most utilized NGS tool. RNA-Seq has proven useful in rapidly identifying the transcript sequences encoding for proteins that are at the core of developmental biology, growth and reproduction, immune & stress response and in some cases, propel the elucidation of pathways and novel groups of genes. The vast and rapid expansion in sequencing output that has been made publicly available to some extent enables bridging the gaps between crustaceans and other arthropod groups and perhaps even ecdysozoans. With that, we posit that a large gap exists between the exponential rate at which new datasets are being generated and the painstakingly slow process of functional annotation. To meet this gap, high-throughput functional annotation approaches must be considered and adopted from other taxa