A Comprehensive Guide to Potato Transcriptome Assembly.

We have witnessed a rapid advancement in high-throughput genome sequencing and the maturation of long-read technologies. However, an accurate assembly of polyploid potato genomes still remains challenging. Sequencing the double-monoploid genome of Solanum tuberosum Group Phureja (Xu et al., Nature 475:189-195, 2011) has enabled functional studies of polyploid potato cultivars using RNA sequencing (RNA-Seq) technologies, although with the limitation of not covering cultivar-specific gene expression. The accumulated RNA-Seq datasets from these cultivars can be leveraged to assemble tetraploid potato transcriptomes that enable the analysis of genes that are not limited to reference genome annotations. To increase transcriptomes' quality, short-read assemblies are nowadays complemented with full-length transcriptome sequencing using Pacific Biosciences or Oxford Nanopore platforms. In this chapter we give a detailed guide on a pipeline for de novo transcriptome assembly of polyploid potato genotypes and their integration into a pan-transcriptome.