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EVOLUTION
Direct phylogenetic evidence for lateral transfer of elongation factor-like gene

Ryoma Kamikawa^*, Yuji Inagaki^,, and Yoshihiko Sako^*

*Laboratory of Marine Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan; and Center of Computational Sciences and Institute of Biological Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan

Edited by W. Ford Doolittle, Dalhousie University, Halifax, NS, Canada, and approved March 18, 2008 (received for review November 26, 2007)

Abstract

Genes encoding elongation factor-like (EFL) proteins, which show high similarity to elongation factor-1 (EF-1), have been found in phylogenetically distantly related eukaryotes. The sporadic distribution of "EFL-containing" lineages within "EF-1-containing" lineages indirectly, but strongly, suggests lateral gene transfer as the principal driving force in EFL evolution. However, one of the most critical aspects in the above hypothesis, the donor lineages in any putative cases of lateral EFL gene transfer, remained unclear. In this study, we provide direct evidence for lateral transfer of an EFL gene through the analyses of 10 diatom EFL genes. All diatom EFL homologues tightly clustered in phylogenetic analyses, suggesting acquisition of the exogenous EFL gene early in diatom evolution. Our survey additionally identified Thalassiosira pseudonana as a eukaryote bearing EF-1 and EFL genes and secondary EFL gene loss in Phaeodactylum tricornutum, the complete genome of which encodes only the EF-1 gene. Most importantly, the EFL phylogeny recovered a robust grouping of homologues from diatoms, the cercozoan Bigelowiella natans, and the foraminifer Planoglabratella opecularis, with the diatoms nested within the Bigelowiella plus Planoglabratella (Rhizaria) grouping. The particular relationships recovered are further consistent with two characteristic sequence motifs. The best explanation of our data analyses is an EFL gene transfer from a foraminifer to a diatom, the first case in which the donor–recipient relationship was clarified. Finally, based on a reverse transcriptase quantitative PCR assay and the genome information of Thalassiosira and Phaeodactylum, we propose the loss of elongation factor function in Thalassiosira EF-1.

EF-1 | EFL | eukaryotic phylogeny

Author contributions: R.K., Y.I., and Y.S. designed research; R.K. and Y.I. performed research; R.K. and Y.I. analyzed data; and R.K., Y.I., and Y.S. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

To whom correspondence should be addressed. E-mail: yuji{at}ccs.tsukuba.ac.jp

© 2008 by The National Academy of Sciences of the USA

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