Horizontal transfer of expressed genes in a parasitic flowering plant

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Xi, Zhenxiang ^a   Bradley, Robert K ^b   Wurdack, Kenneth J ^c   Wong, KM ^d   Sugumaran, M ^e   Bomblies, Kirsten ^a   Rest, Joshua S ^f   Davis, Charles C ^a  

^a HARVARD UNIVERSITY   (United States)

^b Fred Hutchinson Cancer Research Center   (United States)

^c SMITHSONIAN INSTITUTION   (United States)

^d SINGAPORE BOTANIC GARDENS   (Singapore)

^e UNIVERSITY OF MALAYA   (Malaysia)

^f STONY BROOK UNIVERSITY   (United States)

Author keywords

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

Indexed keywords

TRANSCRIPTOME;

ANGIOSPERM; ARTICLE; CODON USAGE; GENE EXPRESSION; GENE TRANSFER; GENETIC TRANSCRIPTION; HORIZONTAL GENE TRANSFER; HOST PARASITE INTERACTION; NONHUMAN; PARASITE; PARASITIC PLANT; PHYLOGENOMICS; RAFFLESIA CANTLEYI; TETRASTIGMA RAFFLESIAE; VERTICAL GENE TRANSFER; VITACEAE;

ANGIOSPERMS; CODON; DNA, PLANT; GENE TRANSFER, HORIZONTAL; HOST-PARASITE INTERACTIONS; PHYLOGENY; TRANSCRIPTOME;

MAGNOLIOPHYTA; RAFFLESIA; TETRASTIGMA;

EID: 84861935738     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-227     Document Type: Article

References (45)

1. Keeling PJ, Palmer JD. Horizontal gene transfer in eukaryotic evolution. Nat Rev Genet 2008, 9:605-618. 10.1038/nrg2386, 18591983.
2. Richardson AO, Palmer JD. Horizontal gene transfer in plants. J Exp Bot 2007, 58:1-9.
3. Stegemann S, Keuthe M, Greiner S, Bock R. Horizontal transfer of chloroplast genomes between plant species. Proc Natl Acad Sci USA 2012, 109:2434-2438. 10.1073/pnas.1114076109, 3289295, 22308367.
4. Stegemann S, Bock R. Exchange of genetic material between cells in plant tissue grafts. Science 2009, 324:649-651. 10.1126/science.1170397, 19407205.
5. Bock R. The give-and-take of DNA: horizontal gene transfer in plants. Trends Plant Sci 2010, 15:11-22. 10.1016/j.tplants.2009.10.001, 19910236.
6. Christin P-A, Edwards EJ, Besnard G, Boxall SF, Gregory R, Kellogg EA, Hartwell J, Osborne CP. Adaptive evolution of C4 photosynthesis through recurrent lateral gene transfer. Curr Biol 2012, 22:445-449. 10.1016/j.cub.2012.01.054, 22342748.
7. Davis CC, Wurdack KJ. Host-to-parasite gene transfer in flowering plants: phylogenetic evidence from Malpighiales. Science 2004, 305:676-678. 10.1126/science.1100671, 15256617.
8. Mower JP, Stefanovic S, Young GJ, Palmer JD. Gene transfer from parasitic to host plants. Nature 2004, 432:165-166.
9. Barkman TJ, McNeal JR, Lim SH, Coat G, Croom HB, Young ND, dePamphilis CW. Mitochondrial DNA suggests at least 11 origins of parasitism in angiosperms and reveals genomic chimerism in parasitic plants. BMC Evol Biol 2007, 7:248. 10.1186/1471-2148-7-248, 2234419, 18154671.
10. Nickrent DL, Blarer A, Qiu Y-L, Vidal-Russell R, Anderson FE. Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer. BMC Evol Biol 2004, 4:40. 10.1186/1471-2148-4-40, 528834, 15496229.
11. Park JM, Manen JF, Schneeweiss GM. Horizontal gene transfer of a plastid gene in the non-photosynthetic flowering plants Orobanche and Phelipanche (Orobanchaceae). Mol Phylog Evol 2007, 43:974-985.
12. Davis CC, Anderson WR, Wurdack KJ. Gene transfer from a parasitic flowering plant to a fern. Proc R Soc B 2005, 272:2237-2242. 10.1098/rspb.2005.3226, 1560187, 16191635.
13. Davis CC, Latvis M, Nickrent DL, Wurdack KJ, Baum DA. Floral gigantism in Rafflesiaceae. Science 1812, 2007:315.
14. Barkman TJ, Lim S-K, Mat Salleh K, Nais J. Mitochondrial DNA sequences reveal the photosynthetic relatives of Rafflesia, the world's largest flower. Proc Natl Acad Sci USA 2004, 101:787-792. 10.1073/pnas.0305562101, 321759, 14715901.
15. Goodstein DM, Shu SQ, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 2012, 40:D1178-D1186. 10.1093/nar/gkr944, 3245001, 22110026.
16. Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 2006, 313:1596-1604. 10.1126/science.1128691, 16973872.
17. Chan AP, Crabtree J, Zhao Q, Lorenzi H, Orvis J, Puiu D, Melake-Berhan A, Jones KM, Redman J, Chen G, et al. Draft genome sequence of the oilseed species Ricinus communis. Nat Biotechnol 2010, 28:951-956. 10.1038/nbt.1674, 2945230, 20729833.
18. Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 2007, 449:463-467. 10.1038/nature06148, 17721507.
19. Wikström N, Savolainen V, Chase MW. Evolution of the angiosperms: calibrating the family tree. Proc R Soc Lond B 2001, 268:2211-2220.
20. Novaes E, Drost DR, Farmerie WG, Pappas GJ, Grattapaglia D, Sederoff RR, Kirst M. High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 2008, 9:312. 10.1186/1471-2164-9-312, 2483731, 18590545.
21. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008, 456:53-59. 10.1038/nature07517, 2581791, 18987734.
22. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437:376-380. 1464427, 16056220.
23. Veldkamp JF. The correct name for the Tetrastigma (Vitaceae) host of Rafflesia (Rafflesiaceae) in Malesia and a (not so) new species. Reinwardtia 2008, 12(4):261-265.
24. Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H, Li D, Meyer T, Muller R, Ploetz L, et al. The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res 2008, 36:D1009-D1014. 2238962, 17986450.
25. Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud- Nissen F, Malek RL, Lee Y, Zheng L, et al. The TIGR Rice Genome Annotation Resource: Improvements and new features. Nucleic Acids Res 2007, 35:D883-D887. 10.1093/nar/gkl976, 1751532, 17145706.
26. APG An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Bot J Linn Soc 2009, 161:105-121. APG.
27. Felsenstein J. Inferring phylogenies 2004, Massachusetts: Sinauer Associates, Sunderland.
28. Ochman H, Lawrence JG, Groisman EA. Lateral gene transfer and the nature of bacterial innovation. Nature 2000, 405:299-304. 10.1038/35012500, 10830951.
29. David-Schwartz R, Runo S, Townsley B, Machuka J, Sinha N. Long-distance transport of mRNA via parenchyma cells and phloem across the host-parasite junction in Cuscuta. New Phytol 2008, 179:1133-1141. 10.1111/j.1469-8137.2008.02540.x, 18631294.
30. Kitamura-Abe S, Itoh H, Washio T, Tsutsumi A, Tomita M. Characterization of the splice sites in GT-AG and GC-AG introns in higher eukaryotes using full-length cDNAs. J Bioinform Comput Biol 2004, 2:309-331. 10.1142/S0219720004000570, 15297984.
31. Yoshida S, Maruyama S, Nozaki H, Shirasu K. Horizontal gene transfer by the parasitic plant Striga hermonthica. Science 2010, 328:1128. 10.1126/science.1187145, 20508124.
32. Lawrence JG, Ochman H. Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol 1997, 44:383-397. 10.1007/PL00006158, 9089078.
33. Medrano-Soto A, Moreno-Hagelsieb G, Vinuesa P, Christen JA, Collado-Vides J. Successful lateral transfer requires codon usage compatibility between foreign genes and recipient genomes. Mol Biol Evol 2004, 21:1884-1894. 10.1093/molbev/msh202, 15240837.
34. Chantawannakul P, Cutler RW. Convergent host-parasite codon usage between honeybee and bee associated viral genomes. J Invertebr Pathol 2008, 98:206-210. 10.1016/j.jip.2008.02.016, 18397791.
35. de Felipe KS, Pampou S, Jovanovic OS, Pericone CD, Ye SF, Kalachikov S, Shuman HA. Evidence for acquisition of Legionella Type IV secretion substrates via interdomain horizontal gene transfer. J Bacteriol 2005, 187:7716-7726. 10.1128/JB.187.22.7716-7726.2005, 1280299, 16267296.
36. Garavaglia BS, Thomas L, Gottig N, Zimaro T, Garofalo CG, Gehring C, Ottado J. Shedding light on the role of photosynthesis in pathogen colonization and host defense. Commun Integr Biol 2010, 3:382-384. 10.4161/cib.3.4.12029, 2928325, 20798833.
37. Nickrent DL, Duff RJ, Colwell AE, Wolfe AD, Young ND, Steiner KE, dePamphilis CW. Molecular phylogenetic and evolutionary studies of parasitic plants. Molecular systematics of plants II: DNA sequencing 1998, 211-241. Boston: Kluwer, Soltis DE, Soltis PS, Doyle JJ, 2.
38. Wasmuth JD, Blaxter ML. prot4EST: translating expressed sequence tags from neglected genomes. BMC Bioinforma 2004, 5:187.
39. Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, Seaver E, Rouse GW, Obst M, Edgecombe GD, et al. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 2008, 452:745-749. 10.1038/nature06614, 18322464.
40. Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 2008, 57:758-771. 10.1080/10635150802429642, 18853362.
41. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
42. Kim D, Salzberg SL. TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol 2011, 12:R72. 10.1186/gb-2011-12-8-r72, 3245612, 21835007.
43. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
44. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5:621-628. 10.1038/nmeth.1226, 18516045.
45. Médigue C, Rouxel T, Vigier P, Hénaut A, Danchin A. Evidence for horizontal gene transfer in Escherichia coli speciation. J Mol Biol 1991, 222:851-856. 10.1016/0022-2836(91)90575-Q, 1762151.