Assembly Based on NGS Platform

The genomes sequenced on the NGS platform were de novo assembled into contigs by using a pipeline that combined the Fermi package (Li 2012) and Phusion assembler (Mullikin and Ning 2003) for 500/800 bp paired-end libraries. For the 3/5 Kb mate-pair libraries, we used SOAPdenovo (Li et al. 2010) with 77 kmers to build contigs. Furthermore, SSPACE (Boetzer et al. 2011) was used to build scaffolds, and the contigs assembled by Fermi and Phusion were used for the substitution of sequences and bases and for further rectifying to rectify the local assembly error. After the inspection of the initial scaffolds, gaps were closed using Gap5 (Bonfield and Whitwham 2010) software.