Additional file 2 of Unraveling the complex evolutionary history of lepidopteran chromosomes through ancestral chromosome reconstruction and novel chromosome nomenclature

Additional file 2: Fig. S1. The heat map of collinear genes. The number of collinear genes between any two species detected by MCScanX. Fig. S2. Chromosome rearrangement is associated with LTR insertion. Similar to Fig. 3. Histograms show the distribution of TE counts (by class) in 10,000 randomized sets of chromosomal regions. Red lines indicate real observed values for each TE class within autosomal synteny breakpoint regions which shows that long terminal repeat retrotransposons (LTR) are significantly enriched in the breakpoint regions. The DNA transposons (DNA), unidentified transposons (Unknown), rolling-circle Helitron transposons (RC), and long and short interspersed nuclear elements (LINE and SINE) are not enriched. The time of the burst of LTRs is later than the divergence time between the two species. Histograms showing the age distribution of LTRs located on the corresponding genome. Red lines indicate the divergence time between the two species. The Y axis shows the LTR content (bp) of the corresponding genome. A. LTRs are enriched within C. croceus and A. crataegi synteny breakpoint regions in the A. crataegi genome. The time of the burst of LTRs on A. crataegi genome is later than the divergence time between A. crataegi and C. croceus. B. LTRs are enriched within C. croceus and P. brassicae synteny breakpoint regions in the A. crataegi genome. The time of the burst of LTRs on P. brassicae genome is later than the divergence time between P. brassicae and C. croceus. C. LTRs are enriched within C. croceus and P. rapae synteny breakpoint regions in the A. crataegi genome. The time of the burst of LTRs on P. rapae genome is later than the divergence time between P. rapae and C. croceus. Fig. S3. Synteny between Wolbachia and two W chromosomes. There were six synteny blocks between Wolbachia and the W chromosome of L. populi. There were five synteny blocks between Wolbachia and the W chromosome of L. camilla. Fig. S4. Expression of Geminin in three species. A. Expression level of two Geminins in Monarch butterfly. The average FPKM of biological repeats is shown in the figures. B. Expression level of Geminin in Fall armyworm. The average FPKM of biological repeats is shown in the figures. C. Analysis of transcription levels of Geminin in silkworm by qRT-PCR. Data are shown as means ± SD of three experiments (**P < 0.01).