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

Table 2 Chromosome anchoring statistics compared to the previous reference assembly

	Bcop_v1 (Urban et al. 2021)	Bcop_v2 (This paper)	Expected size based on Gabrusewycz-Garcia (1964)^a	Expected size based on Crouse (1943)	Gabrusewycz-Garcia (1964) Size Relationships	Crouse 1943 Size Relationships
Total primary length classified as autosomal	223.8–232.8 Mb	226.5 Mb	218–231 Mb	214–231 Mb
Total length classified as X	62–71 Mb	70.5 Mb	48.9–62.2 Mb	65.8–71.0 Mb ^b	Shortest and similar to II	Similar length as III
Total length classified as II	13.1–28.5 Mb	58.3 Mb	62.2–66 Mb	54.9–59.2 Mb	Shortest and similar to X	Shortest
Total length classified as III	5.4–12.5 Mb	71.0 Mb	66.6–70.7 Mb	65.8–71.0 Mb	Longer than X and II	Similar length as X
Total length classified as IV	34.7–46.4 Mb	Mb	88.8–94.2 Mb	93.3–100.6	Longest	Longest

^a Expected size calculations based on Gabrusewycz-Garcia (1964) [31] are from Supplemental Table S1 in Urban et al. 2021 [9], and are based on genome size estimates from Rasch (2006) [33]. Chromosome lengths were predicted according to the number of polytene zones for each chromosome assigned by Gabrucewycz-Garcia 1964 (14, 14, 15, and 20 for X, II, III, and IV, respectively) [31]. Rasch estimated the X to be 48.9 Mb [33], which is reflected in the range given. Autosomal size ranges reflect calculations using the estimated size of the entire genome (279.789 Mb) [9] or just the autosomal complement after subtracting out Rasch’s expected size of the X (230.889)
^b Chromosome length calculations were predicted according to the number of polytene sections for each chromosome assigned by Crouse (1943) (12, 10, 12, and 17 for X, II, III, and IV, respectively) [30]. The size range of X is kept identical to that of III based on Crouse’s expectation that they are the same length [30], although the range could go as low as 48.9 Mb given Rasch’s estimate [33]

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