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

Table 2 Anchoring into chromosomes using previously known sequences

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 Mb^a	[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 X^b, non-centromeric Chr IV, L chromosomes	3 associated contigs (Σ 66.8 kb)	1 primary and 1 associated contig (Σ 161.6 kb)	[23]
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)	[23]

^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
^b Coverage analyses confirm contigs with F7 as chromosome X sequence

ISSN: 1471-2164