Genome assembly and Iso-Seq transcriptome sequencing of tetraploid cotton

Whole genome reference sequences are very important tools to identify genes controlling traits in a wide variety of species. Yet the generation of reference genomes in complex organisms including many commercial crops is technically challenging and costly. This is particularly true for polyploid crops. The long-read capability of the PacBio RSII provides unparalleled power to assemble genomes of plants de novo and to characterize transcriptome diversity. We present genome sequencing strategies and de novo sequencing of tetraploid cotton (Gossipium hirsutum; 2n = 4x = 52), which has an estimated genome size of 2.5 Gbp. We also show transcriptome diversity based on IsoSeq sequencing of cotton  root, leaf and stem tissues and visualization of these resources in a  <cotton>Pedia. This genome encyclopedia is the perfect tool to securely integrate public and private plant data, understand data set relationships, extract knowledge and to centralize and share breeding data.