3.5 Selection signature analysis
A total of 447.23 Gb clean resequencing data of 42 shrimps (21 wild and 21 cultured) was obtained, which were mapped to the assembled genome. Fixation index (F ST) between wild shrimp and cultured shrimp and nucleotide diversity (π) in both populations were calculated in 40 kb windows across the genome (Figure 3a). A total of 534 outlier genes were identified according to theF ST-π conjoint analysis. Most of these genes were involved in metabolic process (Figure S4). In addition, the phototransduction-fly pathway and neuroactive ligand-receptor interaction pathway were enriched by the target genes (Figure 3b).