Chromosome-scale scaffolds of the fungus gnat genome reveal multi-Mb-scale chromosome-folding interactions, centromeric enrichments of retrotransposons, and candidate telomere sequences

Table 9 Nucleotide distances between FBRs and other features of the X chromosome are concordant with expectations

Locus 1	Locus 2	Approx. Polytene Map Distance (# sub-zones)	Expected Distance (Mb)	Observed Distance (Mb)
Centromere	FBR1	2	3.4	3.49
5’ X’ break point	FBR1	0.5	0.839	0.620
FBR1	FBR2	7	11.8	10.3
FBR2	FBR3	26	43.6	42.7
FBR3	3’ X’ break point	3	5.0	4.65
FBR3	3’ end of chromosome	6	10.1	12.3

The X polytene map [31] is organized into 14 zones of similar lengths, each with 3 subzones (A, B, and C) for a total of 42 sub-zones. Assuming nucleotide lengths are also similar, the ~ 70.5 Mb X-scaffold would indicate zone lengths of ~ 5 Mb (5.036276) and an average sub-zone length of ~ 1.68 Mb (1.678759), which we used to compute expected nucleotide distances

ISSN: 1471-2164