Annotation of the Salix purpurea L. Genome and Gene Families Important for Biomass Production

Sequence assembly and functional annotation of the Salix genome will provide a useful resource for efficient breeding of shrub willow as a biomass feedstock for conversion to biofuels and bioenergy. Whole genome shotgun Illumina sequence data from Salix purpurea was assembled into scaffolds using ALLPATHs. Using a genetic map based on 8,272 GBS markers from a full-sib, F₂ population, scaffolds were assembled into 19 pseudomolecules. Genomic sequences were complemented by Illumina sequencing of eight transcript libraries from five tissues; producing  ~125M paired-end reads and assembled with PERTRAN, resulting in 70,393 transcripts. Structural annotation of the S. purpurea genome was completed by homology based predictors using GenomeScan, FGENESH+, and FGENESH_EST. Gene predictions were improved by a PASA assembly of EST sequences and subjected to protein homology analysis, resulting in 37,864 protein-coding loci with primary transcripts having a median exon length of 162 bp with an average of 5.2 exons per gene. Approximately 25,000 of these gene models have ≥95% of their lengths supported by EST sequence and ~27,000 with ≥95% known peptide homology. Overall, alternative transcripts are identified in 62% of gene models. Additionally, GBrowse resources have been developed from the S. purpurea reference genome. Initial sequence comparisons show high sequence conservation (~92% sequence identity in coding regions and 88% overall) and synteny with Populus trichocarpa. Comparative gene family analysis between Populus and Salix will offer clues about the molecular evolutionary bases for contrasting characteristics of these species, including crown architecture, pollination mode, and wood composition traits important for biomass production.