Horizontally transferred genes cluster spatially and metabolically

Biology Direct

Alexander Dilthey²  Martin J. Lercher¹ 

[1] Institute for Computer Science, Heinrich Heine University, Düsseldorf, 40225, Germany

[2] Present address: The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK

关键词: Flux balance analysis;    Metabolic clustering;    Spatial clustering;    Benchmark;    Co-transfer;    Lateral gene transfer;    Horizontal gene transfer;   

Others  :  1235127
DOI  :  10.1186/s13062-015-0102-5

 received in 2015-09-22, accepted in 2015-12-14,  发布年份 2015

【 摘 要 】

Background

Genomic uptake of DNA by prokaryotes often encompasses more than a single gene. In many cases, several horizontally transferred genes may be acquired together. Accordingly, we expect that horizontally transferred genes cluster spatially in the genome more often than expected if transfers were independent. Further, genes that depend on each other functionally may be unlikely to have beneficial fitness effects when taken up individually by a foreign genome. Hence, we also expect the co-acquisition of functionally related genes, resulting in the clustering of horizontally transferred genes in functional networks.

Results

Analysing spatial and metabolic clustering of recent horizontal (or lateral) gene transfers among 21 γ-proteobacteria, we confirm both predictions. When comparing two datasets of predicted transfers that differ in their expected false-positive rate, we find that the more stringent dataset shows a stronger enrichment of clustered pairs.

Conclusions

The enrichment of interdependent metabolic genes among predicted transfers supports a biologically significant role of horizontally transferred genes in metabolic adaptation. Our results further suggest that spatial and metabolic clustering may be used as a benchmark for methods that predict recent horizontal gene transfers.

Reviewers

This article was reviewed by Peter Gogarten in collaboration with Luiz Thiberio Rangel, and by Yuri Wolf.

【 授权许可】

   
2015 Dilthey and Lercher.

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