2.4 Dickeya solani population genomics
Total DNA was purified from each of 56 D. solani isolates (their
characteristics in Figure S2 ) using MasterPure complete DNA and
RNA purification kit (Epicentre, Illumina). After quantity and quality
controls of extracted DNA using a NanoDrop (ND 1000) device and agarose
gel electrophoresis at 1.0 % (w/v), paired-end libraries were
constructed for each strain and then sequenced using High Output
Sequencing kit with 75 × 2 cycles on and Illumina NextSeq500 sequencer
(CNRS, Gif-sur-Yvette, France). For each strain, 2.4 to 18 million reads
were obtained, corresponding to an average coverage ranging from 37× to
270×. Paired-end reads were trimmed (quality score threshold 0.05) and
mapped against the D. solani reference genome, from the 3337
strain, at mild stringency threshold (80% identity on 50% read length)
using CLC Genomics Workbench version 10.1.3 (Khayi et al. 2015).
The mapping was used for the detection of SNPs and InDels using the
variant calling tool from CLC genomic workbench version 10.1.3. Only
SNPs and InDels (1 to 9 nucleotides) with a high occurrence (≥ 99 % of
the reads) in the mapping step were retained. The representation of
allelic variants in D. solani population was performed using
PHYLOViZ (Francisco et al., 2012).