Genome-to-phenome research in rats: progress and perspectives.

Because of their relatively short lifespan (<4 years), rats have become the second most used model organism to study health and diseases in humans who may live for up to 120 years. First-, second- and third-generation sequencing technologies and platforms have produced increasingly greater sequencing depth and accurate reads, leading to significant advancements in the rat genome assembly during the last 20 years. In fact, whole genome sequencing (WGS) of 47 strains have been completed.

Alternative polyadenylation analysis in animals and plants: newly developed strategies for profiling, processing and validation.

Alternative polyadenylation is an essential RNA processing event that contributes significantly to regulation of transcriptome diversity and functional dynamics in both animals and plants. Here we review newly developed next generation sequencing methods for genome-wide profiling of alternative polyadenylation (APA) sites, bioinformatics pipelines for data processing and both wet and dry laboratory approaches for APA validation. The library construction methods LITE-Seq (Low-Input 3'-Terminal sequencing) and PAC-seq (PolyA Click sequencing) tag polyA cDNA, while BAT-seq (BArcoded, three-prime specific sequencing) and PAPERCLIP (oly() binding rotein-mediated mRNA 3'nd etrieval by rossinking mmunorecipitation) enrich polyA RNA.