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).