Fig S1 Distribution of 17-mer frequency in Portunus trituberculatus genome. The volume of K-mer is plotted against the frequency at which they occur. The left-hand peak at low frequency and high volume represented K-mer containing essentially random sequencing errors. The main volume peak of K-mer was 41. The genome size was estimated as 1.2 Gb by the formula ’Genome size=total_kmer_num/kmer_depth’

Fig S2 Comparison of gene features among P trituberculatus ,Tetranychus urticae , Drosophila melanogaster ,Daphnia pulex , Ixodes scapularis , Parasteatoda tepidariorum , Penaeus vannamei , Tribolium castaneum .

Fig S3 Distribution of divergence rate of each type of TEs in theP.trituberculatus genome. The divergence rate was calculated between the identified TE elements in the genome and the consensus sequence in the de novo library we used.

Fig S4 The distribution of genes in different species

Fig S5 The statistics of KEGG pathway enrichment of expanded families

Fig S6 The statistics of KEGG pathway enrichment of identified specific families

Fig S7 the expression of genes in ribosome pathway in different stages of development, molting stage, low salt stress and pathogen infection

Fig S8 Trend of DEGs during salinity stress

Fig S9 KEGG enrichment of down-regulated expanded and specific DEGs during salt stress

Fig S10 KEGG enrichment of up-regulated expanded and specific DEGs during salt stress

Fig S11 KEGG enrichment analysis of growth-related genes

Fig S12 RT-PCR of Ptdmrt in male and female tissues of P. trituberculatus

Table S1 Primers used in this study.xlsx

Table S2 General statistics of SNP in P.trituberculatus genome