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Background  Horizontal gene transfer (HGT) to the plant mitochondrial genome has recently been shown to occur at a surprisingly high rate; however, little evidence has been found for HGT to the plastid genome, despite extensive sequencing. In this study, we analyzed all genes from sequenced plastid genomes to unearth any neglected cases of HGT and to obtain a measure of the overall extent of HGT to the plastid.    Results  Although several genes gave strongly supported conflicting trees under certain conditions, we are confident of HGT in only a single case beyond the rubisco HGT already reported. Most of the conflicts involved near neighbors connected by long branches (e.g. red algae and their secondary hosts), where phylogenetic methods are prone to mislead. However, three genes –  clpP ,  ycf2 , and  rpl36  – provided strong support for taxa moving far from their organismal position. Further taxon sampling of  clpP  and  ycf2  resulted in rejection of HGT due to long-branch attraction and a serious error in the published plastid genome sequence of  Oenothera elata , respectively. A single new case, a bacterial  rpl36  gene transferred into the ancestor of the cryptophyte and haptophyte plastids, appears to be a true HGT event. Interestingly, this  rpl36  gene is a distantly related paralog of the  rpl36  type found in other plastids and most eubacteria. Moreover, the transferred gene has physically replaced the native  rpl36  gene, yet flanking genes and intergenic regions show no sign of HGT. This suggests that gene replacement somehow occurred by recombination at the very ends of  rpl36 , without the level and length of similarity normally expected to support recombination.    Conclusion  The  rpl36  HGT discovered in this study is of considerable interest in terms of both molecular mechanism and phylogeny. The plastid acquisition of a bacterial  rpl36  gene via HGT provides the first strong evidence for a sister-group relationship between haptophyte and cryptophyte plastids to the exclusion of heterokont and alveolate plastids. Moreover, the bacterial gene has replaced the native plastid  rpl36  gene by an uncertain mechanism that appears inconsistent with existing models for the recombinational basis of gene conversion.

bmc biology

An exceptional horizontal gene transfer in plastids: gene replacement by a distant bacterial paralog and evidence that haptophyte and cryptophyte plastids are sisters