Fig. 2
![Fig. 2](http://media.springernature.com/full/springer-static/image/art%3A10.1186%2Fs13059-016-1049-2/MediaObjects/13059_2016_1049_Fig2_HTML.gif)
C. capitata genome scaffold map based on scaffold linkage of annotated genes and microsatellite (Medflymic) sequences previously localized to map banding positions by in situ hybridization to autosomal polytene chromosomes (chromosomes 2 to 6). The larval salivary gland polytene chromosome map [193] presented includes left (L) and right (R) autosomal chromosome arms linked at a centromeric region (K). Arrows with adjacent scaffold numbers point to mapped loci positions of designated genes/microsatellites, with bracketed positions used for less precise mapping. See Additional file 2: Table S6 for sequence and scaffold accession numbers and sizes, in addition to map positions for sex-linked (chromosome 1; X and Y) genes/sequences mapped to undefined loci on mitotic non-polytenized chromosome spreads [20, 21]