Additional file 1:
Figure S1 . A female adult specimen of S. peregrina .
Figure S2 . GC content distributions of the assembled genome.
Figure S3 . The GC depth distribution of S. peregrinagenome.
Figure S4. Depth distribution of S. peregrina genome.
Figure S5 . Frequency of the 17 -mer depth distribution curve in the error-corrected reads used to the genome size estimation.
Figure S6 . Comparetive analysis of predicted annotation of gene structure characteristics between S. peregrina and other five dipteran species.
Figure S7 . A comparative representation of orthologous and paralogous genes aligned with other nine insect genomes.
Figure S8 . The maximum likelihood (ML) phylogenetic tree amongS. peregrina and other nine insects.
Figure S9 . Divergence time estimation across 10 insect species.
Table S1. Evaluation for genome sequencing samples.
Table S2. Transcriptome sequencing statistics from the Illumina HiSeq to assist protein coding genes annotation.
Table S3. Genome size and heterozygosity estimation using17 -mer analysis.
Table S4. The heterozygosity of assembled genome was estimated using SNP calling.
Table S5. Statistic of raw sequencing data based on the PacBio platform.
Table S6. Statistic of the genome assembly.
Table S7 . The completeness of the draft assembled genome was assessed using BUSCO.
Table S8. Construction of library and the Hi-C raw data from Illumina HiSeq Xten.
Table S9. Statistical analysis of Hi-C raw data after quality control.
Table S10 . Genome size of the clustered contigs in six chromosomes.
Table S11 . The completeness of the Hi-C assembled genome was assessed using BUSCO.
Table S12. Summary of protein-coding genes annotation of the genome assembly.
Table S13. Comparative statistics of the genome with other species.
Table S14. Statistic of functional annotation for predicted genes.
Table S15. Classification of repetitive sequences in the genome assembly.
Table S16. Annotation of repetitive sequences in assembled genome.
Table S17. Statistic of SSR distribution.
Table S18. Summary of SSR classification.
Table S19. Statistic of annotation for non-protein-coding genes in the genome assembly.
Table S20. Statistic of gene families among 10 insect species.
Table S21. Statistic of Single-copy orthologous genes aligned with other nine insect genomes.
Table S22. Statistic of expanded and contracted gene families among 10 insect species.
Table S23. Versions and main parameters of the software used in this study.