Computational protocol: America's red gold: multiple lineages of cultivated cochineal in Mexico

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[…] A draft Dactylopius coccus genome assembly was constructed using JR-Assembler 1.02 (Chu et al. ; Table). The final assembly was 18.6 Mbp long with an N50 of 378,999 bp (Table). The quality-controlled merged sequence reads were aligned against the D. coccus assembly using BWA 0.7.5 (Li and Durbin , ) in order to identify sequence variants. A total of 1.99 Gbp of reads (106.8× mean depth) were aligned to the assembly. Analysis of the assembly using BEDTools 2.17.0 (Quinlan and Hall ), however, showed significant variation in coverage across the genome and between samples (per sample mean depth ± standard deviation: 9.4× ± 78.7×, 43.3× ± 26.9×, and 54.0× ± 34.0× for the Oaxacan small-scale farm, Mexican commercial, and Peruvian commercial samples, respectively). Genotypes were called using SAMtools 0.1.19 (Li et al. ). [...] To determine whether the cochineal genome was undergoing detectable natural or artificial selection, we predicted genic sequences using GeneMark-ES 2.3c (Borodovsky and Lomsadze ). The ratio of nonsynonymous to synonymous (N/S) SNPs was calculated using SnpEff 3.6a (Cingolani et al. ). Tajima's D was calculated using 500-bp windows with VCFtools 1.0.9 (Danecek et al. ). […]

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