Figure legends
Fig. 1 Eggs (A), larva (B), cocoons (C) and adult (D) of the peach fruit moth Carposina sasakii (A-D) and the damage symptoms to apple (E-G). The hatched larva bores into apple usually near the calyx with white secreta near the boring hole (E); the damaged apple showing shrinkage (F); damage from larvae boring and developing in the apple (G).
Fig. 2 Genome features of Carposina sasakii. (a) GenomeScope analysis of genome size, heterozygosity and duplicate rate using k-mers (K = 17) count histogram, indicating a genome size of 338.52 Mb, a heterozygosity of 1.06%, and a duplication rate of 2.06%; (b) Genome-wide all-by-all Hi-C interaction identified 32 linkage groups; (c) Synteny between Carposina sasakii (Csas) andCydia pomonella (Cpom) and Spodoptera litura (Slit) genomes reveal highly conserved gene order and chromosomal fusion or split events in the three moths.
Fig. 3 Comparative genomics of Carposina sasakii. (a) Phylogenetic tree of PFM with 15 insect genomes including 11 other Lepidoptera. The phylogeny was inferred from 947 single-copy genes with 364,262 reliable sites by an approximately-maximum-likelihood method. All nodes received bootstrap support of 100. (b) Orthogroups shared by five Lepidoptera species of Carposina sasakii ,Cydia pomonella , Bombyx mori , Ostrinia furnacalis and Helicoverpa armigera.
Fig. 4 Schematic arrangement of the domains of five circadian genes including period (PER), timeless (TIM), Clock(CLK), cycle (CYC) and cryptochrome (CRY-m, CRY-d) inCarposina sasakii and other 15 insects. Boxes in different color show different domains, while numbers under boxes show the postion of domains on protein sequences. Species and their taxonomic status are shown on the left: Tcas, Tribolium castaneum ; Agla,Anoplophora glabripennis ; Agam, Anopheles gambiae ; Dmel,Drosophila melanogaster ; Pxy, Plutella xylostella ; Cpom,Cydia pomonella ; Csas, Carposina sasakii ; Dple,Danaus plexippus ; Tni, Trichoplusia ni ; Slit,Spodoptera litura ; Harm, Helicoverpa armigera ; Bmor,Bombyx mori ; Bman, Bombyx mandarina ; Msex, Manduca sexta ; Gmel, Galleria mellonella ; Ofur, Ostrinia furnacalis .
Fig. 5 Phylogenetic relationships of two PAS domains in three circadian genes: period (per), Clock (clk) andcycle (cyc). Each tip is labeled by the name of domain, gene and species. Abbreviations of species are same as in Fig. 4. Six clades shaded in different color reveal two domains of three genes, while one domain of clk gene has two different type among species. Tips in red show the position of Carposina sasakii .