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Read mapping to reference whole genome
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A series of data analyses was processed using CLC Genomics Workbench 12 (Qiagen, Hilden, Germany). After adapter trimming and quality filtering, the clean read data were mapped to the reference genome of T. castaneum (Tcas5.2) that was obtained from the NCBI genome database (https://www.ncbi.nlm/nih.gov/). The mapping parameters were as follows: mismatch cost = 2, insertion cost = 3, deletion cost = 3, length fraction = 0.9, and similarity fraction = 0.9. After local realignment of the mapped reads, duplicate PCR reads were discarded.
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