Low coverage genome sequencing of maize weevil Sitophilus zeamais to analyse the repeatome
Twenty pairs of ovaries were dissected from females S. oryzae, S. zeamais, S. granarius and S. linearis. Ovaries were homogenized in 100 mM NaCl, 1 mM EDTA pH 8, 10 mM Tris-HCl pH 8 using a small piston. Proteinase K digestion followed in the presence of SDS for 2h at 55C with shaking and for 1h at 37C with RNAse A. A typical phenol chloroform extraction was then performed and genomic DNA was isopropanol precipitated. Eight whole genome sequencing libraries with a median insert size of 550 bp were constructed using the Illumina TruSeq DNA PCR-free sample preparation kit, according to manufacturer's protocols. Briefly, 2 ug of each gDNA were sheared using a Covaris M220 Focused-ultrasonicator, end-repaired, A-tailed, and adapter ligated. Library quality control was performed using the 2100 Bioanalyzer System with the Agilent High Sensitivity DNA Kit. The libraries were individually quantified via qPCR using a KAPA Library Quantification Kits for Illumina platforms, then they were pooled together in equimolar quantities and sequenced in a MiSeq sequencing system (Illumina). 2x300 paired-end reads were obtained using a MiSeq Reagent Kits (600-cycles).