Molecular evolution of silkworm SPs.

(A) Phylogenetic tree of insect Storage proteins based on Bayesian inference analyses. Full-length amino acid sequences were aligned to generate a phylogenetic tree. Bayesian posterior probability was shown for each node. Cf, Choristoneura fumiferana; Bm, Bombyx mori; Hc, Hyalophora cecropia; Sr, Samia ricini; Ms, Manduca sexta; Ob, Operophtera brumata; Hyc, Hyphantria cunea; Sl, Spodoptera litura; Sn, Sesamia nonagrioides; Cs, Chilo suppressalis; Pi, Plodia interpunctella; Px, Plutella xylostella; Ad, Anopheles darlingi; Ca, Corethrella appendiculata; Dm, Drosophila melanogaster; Pm, Perla marginata; Td, Thermobia domestica. Accession number for each protein is indicated ahead of abbrevation of each species. (B-C). Selection signatures of the silkworm SPs. Signature index—Population divergence coefficient (Fst) between the Chinese local trimoulting (CHN_L_M3) domestic silkworm group and the wild silkworms and nucleic acid diversity (π) in the silkworm populaton is shown along the genomic regions covering the SP genes. Dashed lines represent the top 5% Fst cutoff. The red square represents SP1 region which is located in Chromosome 23 and the blue squares represents the other SPs which are clustered in Chromosome 3. (D) Plotting of frequency of reference genotype for each SNP position in the upstream 2 kb region of SP1, indicating many mutant alleles with fairly high allelic frequency in the wild silkworm population. (E) Expression level indicated as FPKM of SP1 in the ova of domestic and wild silkworms. The three data pot indicate the highest value with 95% confidence, the average and the lowest value with 95% confidence, respectively. ***, FDR corrected p <0.001. Dome, the domestic silkworm. Wild, the wild silkworm.