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Horizontal transfer of expressed genes in a parasitic flowering plant

Zhenxiang Xi1, Robert K Bradley23, Kenneth J Wurdack4, KM Wong5, M Sugumaran6, Kirsten Bomblies1, Joshua S Rest7* and Charles C Davis1*

Author affiliations

1 Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA, 02138, USA

2 Computational Biology Program, Public Health Sciences Division, Fred, Hutchinson Cancer Research Center, Seattle, WA, 98109, USA

3 Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA

4 Department of Botany, Smithsonian Institution, Washington, DC, 20013, USA

5 Singapore Botanic Gardens, Singapore, 259569, Singapore

6 Rimba Ilmu Botanic Garden, Institute of Biological Sciences, University of Malaya, 50603, Kuala Lumpur, Malaysia

7 Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, USA

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Citation and License

BMC Genomics 2012, 13:227  doi:10.1186/1471-2164-13-227

Published: 8 June 2012



Recent studies have shown that plant genomes have potentially undergone rampant horizontal gene transfer (HGT). In plant parasitic systems HGT appears to be facilitated by the intimate physical association between the parasite and its host. HGT in these systems has been invoked when a DNA sequence obtained from a parasite is placed phylogenetically very near to its host rather than with its closest relatives. Studies of HGT in parasitic plants have relied largely on the fortuitous discovery of gene phylogenies that indicate HGT, and no broad systematic search for HGT has been undertaken in parasitic systems where it is most expected to occur.


We analyzed the transcriptomes of the holoparasite Rafflesia cantleyi Solms-Laubach and its obligate host Tetrastigma rafflesiae Miq. using phylogenomic approaches. Our analyses show that several dozen actively transcribed genes, most of which appear to be encoded in the nuclear genome, are likely of host origin. We also find that hundreds of vertically inherited genes (VGT) in this parasitic plant exhibit codon usage properties that are more similar to its host than to its closest relatives.


Our results establish for the first time a substantive number of HGTs in a plant host-parasite system. The elevated rate of unidirectional host-to- parasite gene transfer raises the possibility that HGTs may provide a fitness benefit to Rafflesia for maintaining these genes. Finally, a similar convergence in codon usage of VGTs has been shown in microbes with high HGT rates, which may help to explain the increase of HGTs in these parasitic plants.

Rafflesia; Transcriptome; Phylogenomics; Horizontal gene transfer; Codon usage