FIGURE LEGENDS
FIGURE 1 Morphological and genomic comparison between FCDK and FCSH. (a) Adult female FCDK. (b) FCDK furca with 1 well-developed apical seta. (c) Four ventral setae on the third thoracic segment of FCDK. (d) Adult female FCSH. (e) Adult male FCSH. (f-g) FCSH furca with 3 or 2 well-developed apical setae. (h) Seven ventral setae on the third thoracic segment of FCSH. (i) Circos graph of the genome characteristics of FCDK and FCSH. Element distributions in 100 kb sliding windows from outer to inner circles: chromosome length, GC content, density of protein-coding genes, DNA transposons, SINE/LINE/LTR retrotransposons, unclassified (other) transposons and simple repeats. Hox gene clusters are masked on chromosome 5. For collinear blocks, reddish links are intraspecific, and links of other colours are interspecific. (j) Comparison of chromosome lengths of both strains. The number of protein-coding genes on chromosomes is shown in brackets. (k) Comparison of major expanded repeat families between the two strains. Only repeat families larger than 100 kb are shown.
FIGURE 2 Chromosomal synteny, gene enrichment and Ks frequency distributions. (a) Syntenic links among chromosomes, arrows indicate nonhomologous regions; (b)–(c) GO (b) and KEGG pathways (c) of protein-coding genes located in nonhomologous regions of FCDK chromosomes 1, 3, 4 and 7. (d) Ks frequency distributions in the FCDK and FCSH genomes.
FIGURE 3 Phylogeny and gene family evolution. (a) Dating tree and orthologue statistics. Node values represent the 95% highest probability densities of divergence times (unit, 100 Mya). Numbers of significantly expanded and contracted gene families are labelled at terminals. ‘1:1:1’ represents shared single-copy orthologues, ‘N:N:N’ represents multicopy orthologues shared by all species, ‘Collembola’ represents orthologues unique to Collembola, ‘Others’ represents unclassified orthologues, and ‘Unassigned’ represents orthologues that cannot be assigned to any orthogroups. (b)‒(c) Significantly expanded gene families and corresponding orthologue numbers in FCDK (b) and FCSH (c).
FIGURE 4 Massive expansion of Folsomia ABC (a) and CYP gene families (b). Ultrafast bootstrap values are indicated at the nodes. Dk, FCDK (red name); Sh, FCSH (blue name); Dm, Drosophila melanogaster (green name).
FIGURE 5 Gene organizations and alignment of two mitochondrial genomes. (a) FCDK (15,177 bp). (b) FCSH (15,141 bp). CDS, tRNA, rRNA and rep_origin sequences are shown in the figure. The names of the majority-strand-encoded genes are labelled in the outer circle, the minority-strand-encoded genes are labelled in the inner circle, and the gene order, GC content, and GC skew of both strand tracks are located between labels. (c) Mauve alignment with a horizontal track to show the global similarity of the two mitochondrial genomes. The degree of DNA sequence similarity is indicated by the height of the red-coloured regions. The box-like diagrams show the annotation of coding regions (white boxes), tRNA genes (green), and rRNA genes (red).
FIGURE 6 Comparison of the miRNA distribution between FCDK and FCSH. (a) Distribution of miRNA genes and families. (I) Conserved miRNAs in both strains; (II) FCDK-specific miRNAs; (III) FCSH-specific miRNAs. (b) The chromosomal distribution of miRNAs in FCDH (red bars) and FCSH (blue bars). The serial numbers of chromosomes (chr1-chr7) are shown on the top of each chromosome. The miRNAs are labelled to the right of the bar, corresponding to their gene locations on the chromosomes. Brown lines indicate miRNAs shared by the two strains (black names). Red names represent FCDK-specific miRNAs, and blue names represent FCSH-specific miRNAs.