Connecting genomic islands across prokaryotic and phage genomes via protein families.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
07 01 2023
07 01 2023
Historique:
received:
20
09
2022
accepted:
04
01
2023
entrez:
7
1
2023
pubmed:
8
1
2023
medline:
11
1
2023
Statut:
epublish
Résumé
Prokaryotic genomes evolve via horizontal gene transfer (HGT), mutations, and rearrangements. A noteworthy part of the HGT process is facilitated by genomic islands (GIs). While previous computational biology research has focused on developing tools to detect GIs in prokaryotic genomes, there has been little research investigating GI patterns and biological connections across species. We have pursued the novel idea of connecting GIs across prokaryotic and phage genomes via patterns of protein families. Such patterns are sequences of protein families frequently present in the genomes of multiple species. We combined the large data set from the IslandViewer4 database with protein families from Pfam while implementing a comprehensive strategy to identify patterns making use of HMMER, BLAST, and MUSCLE. we also implemented Python programs that link the analysis into a single pipeline. Research results demonstrated that related GIs often exist in species that are evolutionarily unrelated and in multiple bacterial phyla. Analysis of the discovered patterns led to the identification of biological connections among prokaryotes and phages. These connections suggest broad HGT connections across the bacterial kingdom and its associated phages. The discovered patterns and connections could provide the basis for additional analysis on HGT breadth and the patterns in pathogenic GIs.
Identifiants
pubmed: 36611105
doi: 10.1038/s41598-023-27584-6
pii: 10.1038/s41598-023-27584-6
pmc: PMC9825383
doi:
Substances chimiques
Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
344Informations de copyright
© 2023. The Author(s).
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