Gap-filling, assembly correction and quantitative assessment of genome scaffold assembly

Post-processing of the resulting scaffolds was done using the gap-filling function of the PBJelly software package (English et al. 2012). The PacBio SMRT sequence data were used to anchor and further improve the contiguity of the scaffolds and reduce the number of ambiguous base ‘N’. Further correction was achieved using PILON automated genome assembly improvement tool (Walker et al. 2014). The binary alignment map (BAM) file was generated using Bowtie2 (Langmead and Salzberg 2012) by mapping the pre-processed Illumina Miseq PE reads to the scaffold assembly; output of which was input data for PILON assembly correction. The quality of the resulting assembly was assessed through a local Perl script as previously described, as well as TopHat2 (Kim et al. 2013) alignment of quality trimmed (Trimmomatic v0.36; SLIDINGWINDOW: 5:30; LEADING:5; TRAILING:5; MINLEN:100; Bolger et al. 2014) RNA-seq reads (SRR1173229). The quality is further evaluated with the Benchmarking Universal Single Copy Ortholog (BUSCO) program using the plant-specific database OrthoDB consisting of 1440 genes (Simão et al. 2015).