Patterns and architecture of genomic islands in marine bacteria

BMC Genomics

Table 1 Comparison of the GIs of eight marine bacteria referred to as Control Genomes where GIs were available in previous studies and the GIs predicted by this study for the same genomes by IslandViewer

Bacterial strain	Previous studies GIs		IslandViewer GIs				Comparison analyses (Previous vs. IslandViewer GIs)
Bacterial strain	Number of GIs	Total GIs length detected in control genomes (kb)	#GIs present (+)	Extra GIs^b(+)	#GIs absent (−)	Total GIs length with IslandViewer prediction (kb)*	(% overlap)^a(kb)	Recall^b(sensitivity)(%)	Precision^c(%)
P. marinus str. MIT9312¹	5	233	3^d	0	3	44.9	19.3	50	100
S. sp. RCC307²	15	271	9	1	6	56.9	18.7	60	90
S. sp. WH7803²	11	344	3	2	8	73.7	20.3	27	60
S. sp. CC9605²	20	505.3	18	4	2	300.4	54.3	90	82
S. sp. CC9311²	24	578.6	9	2	15	125.9	16.9	38	82
A. macleodii “deep ecotype”³	13	480	6	5	7	272.7	69.6	46	55
S. ruber DSM13855⁴	3	221.8	3	1	0	168.2	41.1	100	75
S. ruber M8⁴	2	265.9	2	3	0	144.9	44.5	100	40
Average							35.58	64	73

¹Coleman et al., 2006. Method used to detect GIs: Comparative genomics using 2 Prochlorococcus marinus genomes.
²Dufresne et al., 2008. Method used to detect GIs in Synechococcus genomes: Modified protocols published by Hsiao[15] and Rusch et al.[36] specifically deviations of tetranucleotide frequency, presence of MGE, tRNAs and the occurrence of core genome gene blocks.
³Ivars-Martínez et al., 2008. Method used to detect GIs: Comparative genomics using 2 Alteromonas macleodii strains genomes.
⁴Peña et al., 2010. Method used to detect GIs: Comparative genomics using 2 Salinibacter ruber genomes.
a)% overlap between GIs of previous studies and this study.
b) Recall (sensitivity): GIs present (+)/ [GIs present (+) plus GIs absent (−)].
c) Precision: GIs present (+)/[GIs present (+) plus Extra GIs (+)].
d) Two of these three GIs detected by IslandViewer match different sections of the biggest GI of Prochlorococcus marinus str. MIT9312 (see in Figure1).
* All GIs detected by IslandViewer/IslandPick included some small genomic islets (<9.5 kb) that are not included in Additional file3: Table S3.

ISSN: 1471-2164