Assembly and correction of the Genome
De novo assembly was performed on the basis of PacBio long reads using FALCON v0.3.0 (https://github.com/PacificBiosciences/falcon). Error correction and pre-assembly were initially performed following the FALCON pipeline, with a length_cutoff of 28 kb and a length_cutoff_pr of 27 kb chosen for the assembly step. The draft assembly was corrected using Arrow, based on the mapping results of the PacBio reads to the assembled genome when following the BLASR pipeline (Chaisson & Tesler, 2012). Next, all filtered Illumina reads were mapped to the corrected contigs using BWA-mem (H. Li & Durbin, 2009), to polish the genome for 3-rounds of Pilon iteratively (Walker et al., 2014).