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Table 2 Anchoring into chromosomes using previously known sequences

From: High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing

Sequence Location Canu contig size Falcon contig size Reference
DNA puff II/9A Chr II locus 9A 13.1 Mb 28.5 Mb [124,125,126,127]
RNA Puff III/9B Chr III locus 9B 5.4 Mb 12.5 Mb [126, 128]
Ecdysone receptor Chr IV locus 12A 3.8 Mb 9.6 Mba [129]
Ultraspiracle Chr IV locus 10A 9.3 Mb 5.5 Mb [129]
Hsp70 Chr IV
locus 4A or 12C
5.4 Mb 13 Mb [130]
Hsp70 Chr IV
locus 4A or 12C
6.8 Mb 2.6 Mb [130]
ScoHet1 Chr IV locus 5A 15.2 Mb (9.6 Mb)a [57]
ScoHet2 Chr IV
locus 12C-13A
5.9 Mb 4 Mb [57]
rDNA Chr X locus 1A 5 primary contigs and 11 associated contigs
(Σ 1.3 Mb)
2 primary contigs and 41 associated contigs
(Σ 1.7 Mb)
[3, 131,132,133]
Microclone B4 Chr X locus 1A 69.8 kb 59 kb [23]
Microclone F7 Near centromere of Chr Xb, non-centromeric Chr IV, L chromosomes 3 associated contigs
(Σ 66.8 kb)
1 primary and 1 associated contig
(Σ 161.6 kb)
Microclone G2 (Sccr) Centromeres of all chromosomes 20 primary and 85 associated contigs
(Σ 1.3 Mb)
6 primary and 42 associated contigs
(Σ 604 kb)
  1. aEcdysone receptor (EcR) and ScoHet1 identified the same 9.6 Mb contig in Falcon. The locus inconsistency may represent a misassembly in Falcon or misannotation from Greciano et al. [57]. Nevertheless, both EcR and ScoHet1 results agree it is from chromosome IV
  2. b Coverage analyses confirm contigs with F7 as chromosome X sequence