Comparison of genomic islands in cyanobacteria: Evidence of bacteriophage-mediated horizontal gene transfer from eukaryotes

• Published in: Microbiological research Vol. 211; pp. 31 - 46
• Main Authors: Godde, James S., Baichoo, Shakuntala, Mungloo-Dilmohamud, Zahra, Jaufeerally-Fakim, Yasmina
• Format: Journal Article
• Language: English
• Published: Germany Elsevier GmbH 01.06.2018
• Subjects: Bacteriophages - genetics; Base Composition; Chlorophyta - genetics; Cyanobacteria - genetics; Eukaryota - genetics; Evolution, Molecular; Fructose-Bisphosphate Aldolase - genetics; Gene Transfer, Horizontal; Genes, Bacterial - genetics; Genomic Islands; Genomics; Horizontal gene transfer; Microbial evolution; Microsatellite Repeats; Phylogeny; Prochlorococcus - genetics; Rhodophyta - genetics; Sequence Analysis, Protein; Sulfate Adenylyltransferase - classification; Sulfate Adenylyltransferase - genetics; Trans-domain lateral gene transfer; GI; Genomic islands; HGT; Microbial evolution; Trans-domain lateral gene transfer; Horizontal gene transfer
• ISSN: 0944-5013; 1618-0623; 1618-0623
• DOI: 10.1016/j.micres.2018.03.005

A number of examples of putative eukaryote-to-prokaryote horizontal gene transfer (HGT) have been proposed in the past using phylogenetic analysis in support of these claims but none have attempted to map these gene transfers to the presence of genomic islands (GIs) in the host. Two of these cases have been examined in detail, including an ATP sulfurylase (ATPS) gene and a class I fructose bisphosphate aldolase (FBA I) gene that were putatively transferred to cyanobacteria of the genus Prochlorococcus from either green or red algae, respectively. Unlike previous investigations of HGT, parametric methods were initially used to detect genomic islands, then more traditional phylogenomic and phylogenetic methods were used to confirm or deny the HGT status of these genes. The combination of these three methods of analysis- detection of GIs, the determination of genomic neighborhoods, as well as traditional phylogeny, lends strong support to the claim that trans-domain HGT has occurred in only one of these cases and further suggests a new insight into the method of transmission of FBA I, namely that cyanophage-mediated transfer may have been responsible for the HGT event in question. The described methods were then applied to a range of prochlorococcal genomes in order to characterize a candidate for eukaryote-to-prokaryote HGT that had not been previously studied by others. Application of the same methodology used to confirm or deny HGT for ATPS and FBA I identified a ⊗12 fatty acid desaturase (FAD) gene that was likely transferred to Prochlorococcus from either green or red algae.