Five libraries including the single species genomic DNA were constructed, namely the individual species library. Approximately 1 Gbp raw data were generated for the individual species library. In addition, seven libraries included multiple species, namely the multiplex sample library. Besides the sequenced leaf beetle species, other 20 distantly related species with equimolar amounts of DNA were pooled into a library, respectively. Approximately 20 Gbp raw data were generated for each of the library including multiple species. For both kinds of libraries, genomic DNA was sonicated to 300 bp using Covaris S220 focused-ultrasonicator (Covaris Inc.), according to Illumina’s protocol. Genomic libraries were constructed using an Illumina TruSeq TM DNA Sample Prep Kit (Illumina, San Diego, CA, USA). Genome sequencing was performed on an Illumina HiSeq 2500 platform (Beijing Novogene Bioinformatics Technology Co., Ltd, China), using 150 bp paired-end run.
The raw reads were demultiplexed and concatenated. The low-quality reads, low-quality ends, and adapter sequences were trimmed using NGS QC Toolkit [45 (link)]. The clean reads were used in the genome assembly. We used IDBA-tran [46 (link)] to conduct the de novo assembly. The parameters are set to the minimum size of contig of 200, an initial k-mer size of 41, an iteration size of 10, and a maximum k-mer size of 91.
The raw reads were demultiplexed and concatenated. The low-quality reads, low-quality ends, and adapter sequences were trimmed using NGS QC Toolkit [45 (link)]. The clean reads were used in the genome assembly. We used IDBA-tran [46 (link)] to conduct the de novo assembly. The parameters are set to the minimum size of contig of 200, an initial k-mer size of 41, an iteration size of 10, and a maximum k-mer size of 91.
Free full text: Click here
