Multiple paired-end and mate-pair libraries were constructed with a spanning size that ranged from 180 bp to 20 kb. Sequencing was conducted on an Illumina HiSeq 2500 platform. In total, 179.1 Gb raw sequencing reads were produced (Supplementary Table 1). Raw sequencing reads were subjected to filtering to remove (1) low quality reads with low quality bases (>50% bases with Q-value ≤8); (2) reads with Ns >10% of the read length; (3) reads with adapter contamination; and (4) duplicated reads caused by PCR during library construction. Filtered data were assembled using ALLpaths-LG (version 44080)32, where overlapping paired-end reads with an insert size of 230 nucleotides were used as fragment libraries, and all other libraries (>230 nucleotide insert size) were used as jumping libraries. The Allpaths-LG assembly was run with default settings, then a gap filling step was carried out using GapCloser based on the paired-end information of the paired-end reads that had one end mapped to the unique contig and the others located in the gap region (http://sourceforge.net/projects/soapdenovo2/files/GapCloser).