Fig. 4

Repeat regions, centromere locations, and terminal repeats across the B. coprophila chromosome-scale scaffolds. A Repeat densities in 100 kb bins across each chromosome, and locations of known locus markers. Sccr = Sciara coprophila centromeric repeat [32]. F4 = probe sequence for ScRTE [32]. hAT-Tag1 = a DNA transposon sub-family. RTE = a LINE sub-family. F4, RTE, LINE, and LTR are retrotransposon families. Helitron elements are DNA transposons thought to amplify through a rolling-circle mechanism. Unknown = repeats that were modeled but not classified as a known repeat class. All Repeats = all in comprehensive repeat library. Conserved Arthropod = matches to known Arthropod Repeats (excluding B. coprophila). Tandem Repeats were found with Tandem Repeats Finder [94]. Gaps = assembly gaps. (B) Dot plots corresponding to (i) the entirety of Bcop_v2, including all primary chromosome scaffolds as well as the associated contigs, and (ii) each individual chromosome mapped against itself. The locations of various loci markers are shown in the margins, are color-coded as shown in the legend, and are extended to axes. Gap locations are shown as white rectangles in the grey margins. Polytene chromosome maps were reproduced from plates 1, 2 and 3 of Gabrusewycz-Garcia [31] with permission from Springer Nature under permission number: 5490830617309. (C) Legend to help interpret D-J. D-G Pictorial models of the left termini for scaffolds corresponding to (D) chromosome II (II-L), (E) chromosome III (III-L), (F) chromosome IV (IV-L), and (G) chromosome X (X-L). H-I Pictorial models of the right termini for scaffolds corresponding to (H) chromosome X, and (I) chromosomes II, III, and IV. (J) Pictorial models of satellite sequences in centromeric and pericentromeric regions of each chromosome scaffold. Models represent the approximate positions and lengths of RTRS and satellite arrays. RTRS copy number is shown. Satellite copy number can be approximated by the total length divided by the satellite unit length