Reference Genomes for Diploid and Tetraploid Panicum

The Department of Energy Joint Genome Institute, in collaboration with groups at the BioEnergy Research Centers, has been developing a genomic reference sequence for Panicum virgatum (switchgrass) genotype Alamo clone AP13. In January of 2012, we released a preliminary version 0.0 genome sequence consisting of unordered contigs that were sequenced with the Roche 454 platform and assembled using Newbler.  A minimal annotation using homology-based methods was provided as part of the version 0.0 release. Since that time, we have created a high-density subgenome specific AP13 genetic map and built a custom assembly pipeline that combines the mapping and sequencing data and utilizes several paired next-generation sequenced libraries for scaffolding. Version 1.0 of the P. virgatum genome positions about half of the sequence into the correct subgenomes, removes redundant sequence within the pseudomolecules, and orders the sequence based on syntenty with a related diploid Panicum genome (Panicum hallii var. filipes). We have recently completed an annotation of the version 1.0 genome using available genomic resources and dense newly created RNA-seq data sets across 5 tissues. In parallel, with Thomas Juenger at UT-Austin, we have been developing a reference genome for a model diploid grass, Panicum hallii to use as a comparator to the tetraploid.

We will present version 1.1 of the tetraploid genome sequence and annotation and the preliminary version 0.5 of the diploid genome reference sequence. We will also discuss ongoing directed improvement efforts based on next-generation sequencing of localized BAC clones and projects to improve the mapping and genomic resources for V2.0 of the tetraploid reference and ongoing work towards V1.0 of the diploid Panicum reference.