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. 2024 May 2;19(5):e0301172.
doi: 10.1371/journal.pone.0301172. eCollection 2024.

Investigating the nature of prokaryotic genomic island locations within a genome

Reem Aldaihani  1   2 , Lenwood S Heath  2
Affiliations

Investigating the nature of prokaryotic genomic island locations within a genome

Reem Aldaihani et al. PLoS One. .

Abstract

Horizontal gene transfer (HGT) is a powerful evolutionary force that considerably shapes the structure of prokaryotic genomes and is associated with genomic islands (GIs). A GI is a DNA segment composed of transferred genes that can be found within a prokaryotic genome, obtained through HGT. Much research has focused on detecting GIs in genomes, but here we pursue a new course, which is identifying possible preferred locations of GIs in the prokaryotic genome. Here, we identify the locations of the GIs within prokaryotic genomes to examine patterns in those locations. Prokaryotic GIs were analyzed according to the genome structure that they are located in, whether it be a circular or a linear genome. The analytical investigations employed are: (1) studying the GI locations in relation to the origin of replication (oriC); (2) exploring the distances between GIs; and (3) determining the distribution of GIs across the genomes. For each of the investigations, the analysis was performed on all of the GIs in the data set. Moreover, to void bias caused by the distribution of the genomes represented, the GIs in one genome from each species and the GIs of the most frequent species are also analyzed. Overall, the results showed that there are preferred sites for the GIs in the genome. In the linear genomes, these sites are usually located in the oriC region and terminus region, while in the circular genomes, they are located solely in the terminus region. These results also showed that the distance distribution between the GIs is almost exponential, which proves that GIs have preferred sites within genomes. The oriC and termniuns are preferred sites for the GIs and a possible natural explanation for this could be connected to the content of the oriC region. Moreover, the content of the GIs in terms of its protein families was studied and the results demonstrated that the majority of frequent protein families are close to identical in each section.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Genomic island overlap.
Fig 2
Fig 2. Complete genome of the Acidovorax.
The circle shows the complete genome of the Acidovorax sp. (strain JS42) and the resulting GIs that come from IslandPick (Green), SIGI-HMM (Orange), and IslandPath-DIMOB (blue) [16]. The horizontal plot shows the part of the genome shaded in gray between the two black dots in the lower part of the circle. The blue triangle represents the GIs predicted by the IslandPath-DIMOB method, and the rest of the GIs are represented by the color of the predicted method. The distance between GIs is the length of space between every two GIs.
Fig 3
Fig 3. GIs location in relation to oriC (All GIs).
The location of the GIs in relation to the oriC using all of the GIs in the data set; (a) GIs in circular genomes. (b) GIs in linear genomes.
Fig 4
Fig 4. GIs location in relation to oriC (Species).
The location of the GIs in relation to the oriC using the GIs in one genome from each species in the data set; (a) GIs in circular genomes. (b) GIs in linear genomes.
Fig 5
Fig 5. GIs location in relation to oriC (Most frequent species).
The location of the GIs of the most frequent species in the data set in relation to the origin of replication in circular genomes; (a) Escherichia coli. (b) Salmonella enterica. (c) Klebsiella pneumoniae. (d) Bordetella pertussis. (e) Pseudomonas aeruginosa.
Fig 6
Fig 6. Circular genome.
A circular genome divided into two equal size arcs; oriC arc (from 0.0 to 0.25 and from 0.75 to 1.0) and terminus arc (from 0.25 to 0.75).
Fig 7
Fig 7. Circular genomes with a range of 0 to 0.5.
The location of the GIs in relation to the origin of replication in circular genomes with a range of 0 to 0.5; (a) All of the GIs in the data set, (b) The GIs in one genome from each species.
Fig 8
Fig 8. Circular genomes with a range of 0 to 0.5 (Most frequent species).
The location of the GIs in relation to the origin of replication in circular genomes ranges from 0 to 0.5; (a) Escherichia coli. (b) Salmonella enterica. (c) Klebsiella pneumoniae. (d) Bordetella pertussis. (e) Pseudomonas aeruginosa.
Fig 9
Fig 9. The distance between the GIs using all of the GIs in the data set.
(a) GIs in circular genomes. (b) GIs in linear genomes.
Fig 10
Fig 10. Distance between the GIs (Species).
The distance between the GIs using the GIs in one genome from each species in the data set; (a) GIs in circular genomes. (b) GIs in linear genomes.
Fig 11
Fig 11. Distance between the GIs (Most frequent species).
The distance between the GIs in the most frequent species in the data set (Circular genomes); (a) Escherichia coli. (b) Salmonella enterica. (c) Klebsiella pneumoniae. (d) Bordetella pertussis. (e) Pseudomonas aeruginosa.
Fig 12
Fig 12. The distribution of GIs.
Using (a) All of the GIs in the data set. (b) The GIs in one genome from each species.
Fig 13
Fig 13. The distribution of GIs using the most frequent species in the data set.
See this image and copyright information in PMC

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