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).

附加文件2：补充图S1。共线性基因热图：展示通过MCScanX检测得到的任意两个物种间的共线性基因数量。
补充图S2：染色体重排与长末端重复序列（long terminal repeat, LTR）插入相关。同图3，直方图展示了10000组随机染色体区域中转座因子（transposable element, TE）按类别的计数分布。红色线条代表常染色体共线性断裂区域内每一类转座因子的实际观测值，结果表明长末端重复反转录转座子（LTR）在断裂区域中显著富集；而DNA转座子（DNA）、未分类转座子（Unknown）、滚环式Helitron转座子（RC）以及长、短散在核元件（LINE和SINE）均无显著富集。长末端重复序列的爆发时间晚于两个物种的分化时间。直方图展示了对应基因组中长末端重复序列的年龄分布，红色线条代表两个物种的分化时间，纵轴代表对应基因组的长末端重复序列含量（单位：碱基对，bp）。
A. 在山楂粉蝶（A. crataegi）基因组中，长末端重复序列在橙黄粉蝶（C. croceus）与山楂粉蝶的共线性断裂区域内富集。山楂粉蝶基因组中的长末端重复序列爆发时间晚于山楂粉蝶与橙黄粉蝶的分化时间。
B. 在山楂粉蝶基因组中，长末端重复序列在橙黄粉蝶与欧洲粉蝶（P. brassicae）的共线性断裂区域内富集。欧洲粉蝶基因组中的长末端重复序列爆发时间晚于欧洲粉蝶与橙黄粉蝶的分化时间。
C. 在山楂粉蝶基因组中，长末端重复序列在橙黄粉蝶与菜粉蝶（P. rapae）的共线性断裂区域内富集。菜粉蝶基因组中的长末端重复序列爆发时间晚于菜粉蝶与橙黄粉蝶的分化时间。
补充图S3：沃尔巴克氏体（Wolbachia）与两条W染色体的共线性关系。沃尔巴克氏体与杨叶甲（L. populi）的W染色体之间存在6个共线性区块；沃尔巴克氏体与L. camilla的W染色体之间存在5个共线性区块。
补充图S4：Geminin在三个物种中的表达情况。
A. 帝王蝶中两种Geminin的表达水平，图中展示了生物学重复的平均FPKM值。
B. 草地贪夜蛾中Geminin的表达水平，图中展示了生物学重复的平均FPKM值。
C. 通过定量实时反转录PCR（quantitative real-time reverse transcription PCR, qRT-PCR）分析家蚕中Geminin的转录水平，数据以三次实验的平均值±标准差表示（**P < 0.01）。