Host-to-parasite gene transfer in flowering plants: Phylogenetic evidence from Malpighiales

Science

Volumn 305, Issue 5684, 2004, Pages 676-678

  Davis, Charles C ^a   Wurdack, Kenneth J ^b  

^a UNIVERSITY OF MICHIGAN   (United States)

^b SMITHSONIAN INSTITUTION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GENE TRANSFER; VIRUSES;

HORIZONTAL GENE TRANSFER (HGT); PARASITIC RELATIONSHIPS; PHYLOGENETIC;

PLANTS (BOTANY);

RIBOSOME DNA; MITOCHONDRIAL DNA; MITOCHONDRIAL PROTEIN; VEGETABLE PROTEIN;

ANGIOSPERM; GENETICS;

ANGIOSPERM; ARTICLE; CELL NUCLEUS; CLADISTICS; ENDOPHYTE; FLOWERING; HORIZONTAL GENE TRANSFER; HOST PARASITE INTERACTION; MALPIGHIACEAE; MITOCHONDRION; MULTIGENE FAMILY; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; CLASSIFICATION; FLOWER; GENE; GENETICS; PARASITOLOGY; VITACEAE;

CLUSIACEAE; DNA VIRUSES; EMBRYOPHYTA; MAGNOLIOPHYTA; MALPIGHIACEAE; MALPIGHIALES; OCHNACEAE; RAFFLESIACEAE; TETRASTIGMA; VITACEAE;

ANGIOSPERMS; CELL NUCLEUS; DNA, MITOCHONDRIAL; FLOWERS; GENE TRANSFER, HORIZONTAL; GENES, PLANT; MITOCHONDRIA; MITOCHONDRIAL PROTEINS; PHYLOGENY; PLANT PROTEINS; VITACEAE;

EID: 3442897333     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.1100671     Document Type: Article

References (17)

1. The Angiosperm Phylogeny Group, Bot. J. Linn. Soc. 141, 399 (2003).
2. A. Cronquist, An Integrated System of Classification of Flowering Plants (Columbia Univ. Press, New York, 1981).
3. P. F. Stevens, Angiosperm Phylogeny Website, ed. 4 (2001 onward) (www.mobot.org/MOBOT/research/ Apweb).
4. T. J. Barkman, S.-K. Lim, K. Mat Salleh, J. Nais, Proc. Natl. Acad. Sci. U.S.A. 101, 787 (2004).
5. R. S. Beaman, P. J. Decker, J. H. Beaman, Am. J. Bot. 75, 1148 (1988).
6. For primer and GenBank information see the supporting online material (SOM) on Science Online.
7. C. C. Davis, M. W. Chase, Am. J. Bot. 91, 262 (2004).
8. For detailed information on materials and methods, data sets, phylogenetic analyses, and complete annotated figures see the SOM. We were unable to sample PHYC from all families of Malpighiales because it is probably absent from some clades (7). Hence, we analyzed these data in combination with 18S to ensure that all families were represented for the nuclear genome. We also examined the placement of Rafflesiaceae with 18S in two ways. First, we excluded the most divergent domains, V2 and V4, from the analysis (14) (322 of 1813 base pairs)] across all taxa. Second, we treated these domains as missing data only for Raflesiaceae. Both approaches yielded congruent topologies, with the latter (shown here) being much better resolved. The spurious placement of Rafflesiaceae as sister to all angiosperms when 18S is used (4) may be attributable to high divergence in these small domains and suggests that 185 may not be as useless for placing problematic taxa as previously suggested (4).
9. We took several precautions to avoid and detect contamination. First, our results were independently corroborated in the laboratories of each author. Second, Rafflesiaceae data were acquired before starting any work on Vitaceae. Third, if our DNA were cross-contaminated we would not expect such strongly conflicting results regarding the placement of Rafflesiaceae, given the same DNA. Nor would we expect such a high degree of sequence divergence of nad1B-C between Rafflesiaceae and Tetrastigma (or other Vitaceae we sampled). If contamination occurred, we would expect sequences to be nearly identical to those of other sampled Vitaceace, especially given the relatively low amount of sequence divergence between all accessions of Vitaceae in nad1B-C (0.51 to 0.95% sequence divergence). Not only is nad1B-C divergent within Rafflesiaceae (6.2%), but it is also highly divergent from other phylogenetically diverse Vitaceae (15) included here (2.5 to 3.3%).
10. Taxa in the combined analysis of 18S, PHYC, and matR were included if they were sampled for matR plus at least one of the two nuclear loci. We believe this analysis to represent the best estimate of Malpighiales phylogeny. Similar approaches combining multiple genes have provided powerful insights into angiosperm phylogeny where single gene studies have failed (16).
11. H. Won, S. S. Renner, Proc. Natl. Acad. Sci. U.S.A. 100, 10824 (2003).
12. U. Bergthorsson, K. L. Adams, B. Thomason, J. D. Palmer, Nature 424, 197 (2003).
13. J. Kuijt, The Biology of Parasitic Flowering Plants (Univ. of California Press, Berkeley, CA, 1969).
14. D. L Nickrent, E. H. Starr, J. Mol. Evol. 39, 62 (1994).
15. M. J. Ingrouille et al., Bot. J. Linn. Soc. 138, 421 (2002).
16. Y.-L. Qiu et al., Nature 402, 404 (1999).
17. We thank W. Anderson, D. Boufford, Y.-L. Qiu, and P. Stevens. C.C.D. was supported by grants from the University of Michigan, NSF AToL 0431266, and the Michigan Society of Fellows. This paper is dedicated to V. Morrison.