FIGURE LEGENDS
Fig. 1 Genomic landscape of S. peregrina . From outer to inner: (I) sizes of 6 pseudochromosomes; (II) DNA transposon content; (III) LTR transposon content; (IV) GC content (%); (V) gene density. Densities are calculated in 500 Kb windows. The photo in the circle shows an adult female.
Fig. 2 Chromosome-level de novo genome assembly S. peregrina and comparative genome analysis with other species.a Contig contact matrix of the assembled genome. The color bar on the right shows the density of Hi-C interactions from red (high) to white (low), which are indicated number of contact links at the 100-kb resolution. b Chromosome collinear blocks between S. peregrina and D. melanogaster genomes. The best match across the two species is linked by lines with the same color. Chromosomes ofS. peregrina are marked as “Chr1-6”, “X, 2L, 2R, 3L, 3R, 4” respectively represents pseudochromosomes of D. melanogaster .c Venn diagram shows the distribution of orthologous clusters between S. peregrina and other flies (for clarity, only five species with the close evolutionary relationship to S. peregrinawere shown). The numbers indicate gene families identified among all selected species.
Fig. 3 Comparative genomic analyses among S. peregrinaand nine other species. The number on the branch shows the number of expanded (blue) and contracted (red) gene families for each clade. The number near each branch indicates the number of significantly expanded (red) and contracted (blue) gene families for each clade. The black numbers show the divergence times, and two red circles indicate the calibration nodes.