3.1 A high-quality, chromosome-scale S. scabiei reference genome
A total of 33.4 Gb of sequence data (670.28-fold genome coverage based on an estimated genome size of 49.83Mb) was generated (Table S2; Figure S1) . We obtained a high-quality chromosome-scale reference genome of S . scabiei var. cuniculi , with contig N50 size of 5.92 Mb and total assembled length of 57.30 Mb (Table 1 ), of which 100% was anchored to nine chromosomes (Figure 1; Table S3 ). The high accuracy and completeness was represented by the normal GC content (33.23% of genome) (Figure S2 ), the mapping rate of 97.27% of short sequencing reads, 0.001472% of homozygous SNPs (Table S4 ), and the 97.98% and 89.0% of genome completeness assessed by the Core Eukaryotic Genes Mapping Approach (CEGMA)(Parra et al. , 2007) and Benchmarking Universal Single-Copy orthologues (BUSCOs) (Simao et al. , 2015) strategies (Tables S5-6 ).
Genome-wide searching and homology prediction results showed 12.65% of the scabies mite genome belongs to transposable element (TE) families (7,247,159 bp, Figure S3; Tables S7–8 ). We annotated the genes using combination methods of homology searching, ab initioprediction, and direct mRNA sequencing evidence. In total, 9,333 protein-coding genes were identified (Table S9; Figure S4 ), and approximately 99.30% of these genes were functional annotated either in Kyoto Encyclopedia of Genes and genomes (KEGG) pathway database (Kanehisa & Goto, 2000), InterPro (Mulder et al. , 2007) and Gene Ontology (GO) (Ashburner, 2000) (Table S10 ).