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. 2007 Feb 8;7 Suppl 1(Suppl 1):S8.
doi: 10.1186/1471-2148-7-S1-S8.

The role of laterally transferred genes in adaptive evolution

Pradeep Reddy Marri  1 , Weilong Hao, G Brian Golding
Affiliations

The role of laterally transferred genes in adaptive evolution

Pradeep Reddy Marri et al. BMC Evol Biol. .

Abstract

Background: Bacterial genomes develop new mechanisms to tide them over the imposing conditions they encounter during the course of their evolution. Acquisition of new genes by lateral gene transfer may be one of the dominant ways of adaptation in bacterial genome evolution. Lateral gene transfer provides the bacterial genome with a new set of genes that help it to explore and adapt to new ecological niches.

Methods: A maximum likelihood analysis was done on the five sequenced corynebacterial genomes to model the rates of gene insertions/deletions at various depths of the phylogeny.

Results: The study shows that most of the laterally acquired genes are transient and the inferred rates of gene movement are higher on the external branches of the phylogeny and decrease as the phylogenetic depth increases. The newly acquired genes are under relaxed selection and evolve faster than their older counterparts. Analysis of some of the functionally characterised LGTs in each species has indicated that they may have a possible adaptive role.

Conclusion: The five Corynebacterial genomes sequenced to date have evolved by acquiring between 8-14% of their genomes by LGT and some of these genes may have a role in adaptation.

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Figures

Figure 1
Figure 1
Bayesian tree obtained for the concatenated sequence of fusA, gltS, infB, lysS, rplB, rpoB, secY, serS and ychF genes. The abbreviations are: Cje (Corynebacterium jeikeium), Cdi (C. diphtheriae), Cgl1 (C. glutamicum ATCC 13032, NCBI accession No. NC_006958), Cgl2 (C. glutamicum ATCC 13032, NCBI accession No. NC_006958), Cef (C. efficiens), and Mbo (Mycobacterium bovis) as the outgroup. All branches are supported by posterior probability values of 100%. At least 80% of the trees for the commonly present single copy genes (534 genes in total) support branches 7 (with 82%) and 8 (with 86%), and trees for all genes support the remaining branches. Model I: Constant insertion/deletion rate on all branches. μ = μ1 = μ2 = μ3 = μ4 = μ5 = μ6 = μ7 = μ8. Model II: Branches separated into external and internal branches. External: μ1 = μ2 = μ3 = μ4 = μ5 = μ6; Internal: μ7 = μ8 Model III: Different insertion/deletion rate on each branch.
Figure 2
Figure 2
Non-synonymous change of different group-specific genes. Data is measured using the genes present in Cgl and Cef; genes present only in Cgl and Cef (A); genes present only in Cgl, Cef, and Cdi (B); genes present in only Cgl, Cef, Cdi, and Cje (C); genes present in all Corynebacterium taxa and Mbo (D).
Figure 3
Figure 3
Synonymous change of different group-specific genes. Data is measured using the genes present in Cgl and Cef; genes present only in Cgl and Cef (A); genes present only in Cgl, Cef, and Cdi (B); genes present in only Cgl, Cef, Cdi, and Cje (C); genes present in all Corynebacterium taxa and Mbo (D).
Figure 4
Figure 4
Ka/Ks ratio of different group-specific genes. Data is measured using the genes present in Cgl and Cef; genes present only in Cgl and Cef (A); genes present only in Cgl, Cef, and Cdi (B); genes present in only Cgl, Cef, Cdi, and Cje (C); genes present in all Corynebacterium taxa and Mbo (D).
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