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.