ArticleGenome biology2007
Genetic flux over time in the Salmonella lineage.
Article in Genome biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 74 citations in OpenAlex.
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- MTGIpick allows robust identification of genomic islands from a single genome.Briefings in bioinformatics · 2018Article
- xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria.BMC bioinformatics · 2018Article
- Transmission in the Origins of Bacterial Diversity, From Ecotypes to Phyla.Microbiology spectrum · 2017Article
- Inferring horizontal gene transfer.PLoS computational biology · 2015Article
- The extent of genome flux and its role in the differentiation of bacterial lineages.Genome biology and evolution · 2014Article
- Genome analysis and CRISPR typing of Salmonella enterica serovar Virchow.BMC genomics · 2014Article
- Evolution of pan-genomes of Escherichia coli, Shigella spp., and Salmonella enterica.Journal of bacteriology · 2013Article
- The adaptation of temperate bacteriophages to their host genomes.Molecular biology and evolution · 2013Article
- The dynamics of gut-associated microbial communities during inflammation.EMBO reports · 2013Review
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Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
backgroundDNA sequences that are shared between closely related organisms while being absent from their common ancestor and from sister lineages of that ancestor are likely to have been acquired by horizontal gene transfer. Over time, the composition of those sequences tends to become more similar to the compositional signature of their host (amelioration).
resultsFrom a whole-genome comparative analysis of eleven Salmonella, three Escherichia coli and one Shigella strain, we inferred the relative time of insertion of putative horizontally acquired (PHA) genes in three Salmonella strains on different branches of the S. enterica phylogenetic tree. Compositional analysis suggests that most of the PHA genes are still undergoing an amelioration process and shows a clear correlation between time of insertion and the level of amelioration.
conclusionThe results show that older insertions include almost all functional classes. However, very recent horizontal transfer events in the Salmonella lineage involve primarily prophage elements that are shared only between very recently diverged lineages; despite this, the prophage sequence composition is close to that of the host, indicating that host adaptation, rather than amelioration, is likely to be the source of the compositional similarity. Almost half of the PHA genes were acquired at the base of the Salmonella lineage, whereas nearly three-quarters are shared between most S. enterica subspecies. The numerical distribution of PHA genes in the Salmonella tree topology correlates well with the divergence of the major Salmonella species, highlighting the major impact of horizontal transfer on the evolution of the salmonellae.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.