Gene fragmentation in bacterial draft genomes: extent, consequences and mitigation

BMC Genomics

Table 2 Efficacy of partial ORF linkage^a

Strain	True matching fragments linked (%)	False matching fragments linked (%)^b
S. albus J1074	127 (22.1)	2 (0.4)
S. clavuligerus ATCC27064 (#1)	58 (31.2)	0 (0)
S. clavuligerus ATCC27064 (#2)	40 (9.3)	0 (0)
S. clavuligerus ATCC27064 (#3)	12 (20.7)	2 (3.5)
S. ghanaensis ATCC14672	182 (28.04	0 (0)
S. griseoflavus Tü4000	326 (27.5)	2 (0.2)
S. hygroscopicus ATCC53653	220 (20.2)	1 (0.1)
S. lividans TK24	117 (27.9)	2 (0.5)
S. pristinaespiralis ATCC25486	207 (20.7)	0 (0)
S. roseosporus NRRL11379	182 (46.2)	7 (1.8)
S. roseosporus NRRL15998	192 (41.6)	8 (1.7)
Streptomyces sp. XylebKG-1	0 (0)	0 (0)
Streptomyces sp. C	146 (17.9)	9 (1.1)
Streptomyces sp. e14	158 (17.7)	2 (0.2)
Streptomyces sp. Mg1	46 (12.0)	0 (0)
Streptomyces sp. PP-C42	887 (10.6)	No scaffolds
Streptomyces sp. SPB74	145 (15.8)	12 (1.3)
Streptomyces sp. SPB78	109 (12.8)	6 (0.7)
S. sviceus ATCC29083	200 (28.1)	7 (1.0)
S. viridochromogenes DSM40736	102 (31.1)	8 (2.4)

^aAll Streptomyces genomes except Streptomyces sp. PP-C42 and each query genome were used to link partial ORFs in that query genome. The parameters used were: ≥ 20% identity to and ≥ 60% coverage between the query and reference sequence and ≥ 50% similarity between the identities of each partial fragment to the reference sequence.
^bFalse positive linkages were identified from their incongruencies with the scaffold information

ISSN: 1471-2164