title: Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers affecting eukaryotes.
abstract: BACKGROUND
  Lateral gene transfer (LGT) is an important evolutionary mechanism among prokaryotes. The situation in eukaryotes is less clear; the human genome sequence failed to give strong support for any recent transfers from prokaryotes to vertebrates, yet a number of LGTs from prokaryotes to protists (unicellular eukaryotes) have been documented. Here, we perform a systematic analysis to investigate the impact of LGT on the evolution of diplomonads, a group of anaerobic protists.
  
  
  RESULTS
  Phylogenetic analyses of 15 genes present in the genome of the Atlantic Salmon parasite Spironucleus barkhanus and/or the intestinal parasite Giardia lamblia show that most of these genes originated via LGT. Half of the genes are putatively involved in processes related to an anaerobic lifestyle, and this finding suggests that a common ancestor, which most probably was aerobic, of Spironucleus and Giardia adapted to an anaerobic environment in part by acquiring genes via LGT from prokaryotes. The sources of the transferred diplomonad genes are found among all three domains of life, including other eukaryotes. Many of the phylogenetic reconstructions show eukaryotes emerging in several distinct regions of the tree, strongly suggesting that LGT not only involved diplomonads, but also involved other eukaryotic groups.
  
  
  CONCLUSIONS
  Our study shows that LGT is a significant evolutionary mechanism among diplomonads in particular and protists in general. These findings provide insights into the evolution of biochemical pathways in early eukaryote evolution and have important implications for studies of eukaryotic genome evolution and organismal relationships. Furthermore, "fusion" hypotheses for the origin of eukaryotes need to be rigorously reexamined in the light of these results.
authors.affiliation: The Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Biochemistry, Dalhousie University, B3H 4H7, Halifax, Nova Scotia, Canada. joanders@is.dal.ca
authors.forename: Jan O
authors.initials: JO
authors.lastname: Andersson
authors.forename: Asa M
authors.initials: AM
authors.lastname: Sjögren
authors.forename: Lesley A M
authors.initials: LA
authors.lastname: Davis
authors.forename: T Martin
authors.initials: TM
authors.lastname: Embley
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Roger
mesh_terms: D000222:Adaptation, Physiological; D000445:Aldehyde Oxidoreductases / Q000235:genetics; D000446:Aldehyde-Lyases / Q000235:genetics; D000604:Amino Acyl-tRNA Synthetases / Q000235:genetics; D000693:Anaerobiosis; D000818:Animals; D016054:DNA, Protozoan / Q000235:genetics; D016828:Diplomonadida / Q000201:enzymology / Q000235:genetics* / Q000502:physiology; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D017125:Genes, Protozoan; D016829:Giardia lamblia / Q000201:enzymology / Q000235:genetics* / Q000502:physiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D015800:Protozoan Proteins / Q000235:genetics; D013913:Threonine Dehydratase / Q000235:genetics; D000637:Transaminases / Q000235:genetics
chemical_list: D016054:DNA, Protozoan; D015800:Protozoan Proteins; C020145:formaldehyde dehydrogenase (glutathione); D000445:Aldehyde Oxidoreductases; D000637:Transaminases; C019798:branched-chain-amino-acid transaminase; D000446:Aldehyde-Lyases; C020019:deoxyribose-phosphate aldolase; D013913:Threonine Dehydratase; D000604:Amino Acyl-tRNA Synthetases