Sequencing and Assembly of the Salix purpurea L. Genome and Transcriptome to Improve Shrub Willow for Biomass Production

Sequencing of the Salix genome will facilitate the development of tools for faster breeding and selection of willow cultivars as woody biomass feedstock for conversion to biofuels and bioenergy. Due to the close similarity between Salix and Populus, comparative genomics will allow cross-species translation of QTL and regulatory networks controlling key traits for biomass yield and quality. Previous analyses have shown macrosynteny and overall colinearity between Salix and Populus, but there are key morphological and physiological differences between the genera. To develop a reference genome for the genus Salix, we conducted whole-genome shotgun sequencing of a wild diploid, female accession Salix purpurea complemented by Illumina sequencing of transcript libraries. In total, JGI completed sequencing 900 Mb with 454 and ~500X coverage with Illumina sequencing of paired-end and 4.5 kb, 5.3 kb, 6.5 kb mate-pair libraries. ALLPATHs was used to assemble sequences representing 140X coverage of paired-end reads and reads from all of the mate-pair libraries, producing contigs with L50=46 kb and scaffolds with L50=191 kb, and a total assembled size of 348 Mb. The new assembly was evaluated by comparison with the full-length sequence of 10 BACs. Illumina sequencing was also conducted on eight transcript libraries from five tissues: leaves, stems, roots, shoot tips and catkins. The Salix transcriptome was assembled using CLC Bio resulting in 201,926 assembled transcripts with N50=871 bp. Using BLAT, 84.6% of the S. purpurea transcriptome assembly aligned with the ALLPATHs assembly. We will present an alignment of the S. purpurea transcriptome with the P. trichocarpa v3.0 genome assembly and elaborate on similarities and differences between the expressed genes in each taxon.