Creevey, Christopher J. and Doerks, Tobias and Fitzpatrick, David A. and Raes, Jeroen and Bork, Peer (2011) Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer. PLoS ONE, 6 (8). ISSN 1932-6203

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Abstract

Single copy genes, universally distributed across the three domains of life and encoding mostly ancient parts of the translation machinery, are thought to be only rarely subjected to horizontal gene transfer (HGT). Indeed it has been proposed to have occurred in only a few genes and implies a rare, probably not advantageous event in which an ortholog displaces the original gene and has to function in a foreign context (orthologous gene displacement, OGD). Here, we have utilised an automatic method to identify HGT based on a conservative statistical approach capable of robustly assigning both donors and acceptors. Applied to 40 universally single copy genes we found that as many as 68 HGTs (implying OGDs) have occurred in these genes with a rate of 1.7 per family since the last universal common ancestor (LUCA). We examined a number of factors that have been claimed to be fundamental to HGT in general and tested their validity in the subset of universally distributed single copy genes. We found that differing functional constraints impact rates of OGD and the more evolutionarily distant the donor and acceptor, the less likely an OGD is to occur. Furthermore, species with larger genomes are more likely to be subjected to OGD. Most importantly, regardless of the trends above, the number of OGDs increases linearly with time, indicating a neutral, constant rate. This suggests that levels of HGT above this rate may be indicative of positively selected transfers that may allow niche adaptation or bestow other benefits to the recipient organism.

Item Type:	Article
Keywords:	Universally Distributed Single-Copy Genes; Constant Rate of Horizontal Transfer;
Academic Unit:	Faculty of Science and Engineering > Biology
Item ID:	2761
Identification Number:	https://doi.org/10.1371/journal.pone.0022099
Depositing User:	David Fitzpatrick
Date Deposited:	10 Oct 2011 11:12
Journal or Publication Title:	PLoS ONE
Publisher:	PLoS ONE
Refereed:	Yes
Funders:	EU 7th Framework Programme (number: HEALTH-F4-2007-201052), Science Foundation Ireland (SFI) Stokes Lecturer Scheme (number: 07/SK/B1236A)
URI:
Use Licence:	This item is available under a Creative Commons Attribution Non Commercial Share Alike Licence (CC BY-NC-SA). Details of this licence are available here

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