ArticleBMC genomics2009
Insertion sequence content reflects genome plasticity in strains of the root nodule actinobacterium Frankia.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 40 citations in OpenAlex.
- Gamma Ray-induced Mutations in pyrEF Genes in Frankia casuarinae Strain CcI3.Microbes and environments · 2025Article
- Large genomic differences between Moraxella bovoculi isolates acquired from the eyes of cattle with infectious bovine keratoconjunctivitis versus the deep nasopharynx of asymptomatic cattle.Veterinary research · 2016Article
- Dynamics of bacterial insertion sequences: can transposition bursts help the elements persist?BMC evolutionary biology · 2015Article
- Local hopping mobile DNA implicated in pseudogene formation and reductive evolution in an obligate cyanobacteria-plant symbiosis.BMC genomics · 2015Article
- Article
- Elucidation of insertion elements carried on plasmids and in vitro construction of shuttle vectors from the toxic cyanobacterium Planktothrix.Applied and environmental microbiology · 2014Article
- Different dynamics of genome content shuffling among host-specificity groups of the symbiotic actinobacterium Frankia.BMC genomics · 2014Article
- Bacterial genome instability.Microbiology and molecular biology reviews : MMBR · 2014Review
- What stories can the Frankia genomes start to tell us?Journal of biosciences · 2013Article
- Characterization of pseudogenes in members of the order Frankineae.Journal of biosciences · 2013Article
- The Nocardia cyriacigeorgica GUH-2 genome shows ongoing adaptation of an environmental Actinobacteria to a pathogen's lifestyle.BMC genomics · 2013Article
- Mobile genetic elements in the bacterial phylum Acidobacteria.Mobile genetic elements · 2012Article
- A novel human-infection-derived bacterium provides insights into the evolutionary origins of mutualistic insect-bacterial symbioses.PLoS genetics · 2012Article
- Transcriptomes of Frankia sp. strain CcI3 in growth transitions.BMC microbiology · 2011Article
- Genomic insights into bifidobacteria.Microbiology and molecular biology reviews : MMBR · 2010Review
- Coriander bornePathogens and global healthArticle
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenome analysis of three Frankia sp. strains has revealed a high number of transposable elements in two of the strains. Twelve out of the 20 major families of bacterial Insertion Sequence (IS) elements are represented in the 148 annotated transposases of Frankia strain HFPCcI3 (CcI3) comprising 3% of its total coding sequences (CDS). EAN1pec (EAN) has 183 transposase ORFs from 13 IS families comprising 2.2% of its CDS. Strain ACN14a (ACN) differs significantly from the other strains with only 33 transposase ORFs (0.5% of the total CDS) from 9 IS families.
resultsInsertion sequences in the Frankia genomes were analyzed using BLAST searches, PHYML phylogenies and the IRF (Inverted Repeat Finder) algorithms. To identify putative or decaying IS elements, a PSI-TBLASTN search was performed on all three genomes, identifying 36%, 39% and 12% additional putative transposase ORFs than originally annotated in strains CcI3, EAN and ACN, respectively. The distribution of transposase ORFs in each strain was then analysed using a sliding window, revealing significant clustering of elements in regions of the EAN and CcI3 genomes. Lastly the three genomes were aligned with the MAUVE multiple genome alignment tool, revealing several Large Chromosome Rearrangement (LCR) events; many of which correlate to transposase clusters.
conclusionAnalysis of transposase ORFs in Frankia sp. revealed low inter-strain diversity of transposases, suggesting that the majority of transposase proliferation occurred without recent horizontal transfer of novel mobile elements from outside the genus. Exceptions to this include representatives from the IS3 family in strain EAN and seven IS4 transposases in all three strains that have a lower G+C content, suggesting recent horizontal transfer. The clustering of transposase ORFs near LCRs revealed a tendency for IS elements to be associated with regions of chromosome instability in the three strains. The results of this study suggest that IS elements may help drive chromosome differences in different Frankia sp. strains as they have adapted to a variety of hosts and environments.
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