3.3 Gene family identification and phylogeny analysis
Finally, 9,636 gene families were identified in assembled genome, covering 13,039 genes. Among these, thirteen gene families containing 106 genes were unique to S. peregrina . Besides, 2,662 unclustered genes were identified (Fig. 2c , Additional file 1: Table S20). We then identified 5,622 single-copy orthologs to construct phylogenetic trees (Additional file 1: Figure S7 and Table S21). Phylogenetic analysis indicated that eight fly species were clustered together into a large branch and strongly supported (ML bootstrap percentage, BP = 100), whilst S. peregrina and S. bullata were clustered more closely than other species. As an outgroup taxon, A. aegypti and A. gambiae (Diptera: Culicidae) are clustered together and clearly separated (Additional file 1: Figure S8). Moreover, the family Sarcophagidae is more closely related to Calliphoridae than to other family, and estimated divergence time between them was 32.53 Mya (95% HPD: 25.38–40.06 Mya) within the Late Paleogene epoch. This is likely consistent with that both of them constitute the main part of insect faunal succession on decomposed remains (Byrd& Castner 2010). Moreover, within the family Sarcophagidae, the diversification of S. peregrina and S. bullata took place 7.14 Mya (95% HPD: 4.99–9.43 Mya) (Additional file 1: Figure S9).