Widespread impact of horizontal gene transfer on plant colonization of land

Nature Communications

Volumn 3, Issue , 2012, Pages

  Yue, Jipei ^a,b   Hu, Xiangyang ^a,c   Sun, Hang ^a   Yang, Yongping ^a,c   Huang, Jinling ^b  

^a KUNMING INSTITUTE OF BOTANY   (China)

^b EAST CAROLINA UNIVERSITY   (United States)

^c INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

GLUTATHIONE; NITROGEN; PHYTOHORMONE; POLYAMINE; STARCH;

COLONIZATION; EUKARYOTE; GENE TRANSFER; GENOME; HORMONE; NITROGEN CYCLE; PLANT DEFENSE; STARCH; XYLEM;

ARTICLE; BIOSYNTHESIS; ENZYME ACTIVITY; GENOME ANALYSIS; HORIZONTAL GENE TRANSFER; MOSS; NONHUMAN; PHYSCOMITRELLA PATENS; PLANT GENETICS;

BIOLOGICAL EVOLUTION; BRYOPSIDA; GENE TRANSFER, HORIZONTAL; GENES, PLANT; MULTIGENE FAMILY; PHYLOGENY; PLANT DEVELOPMENT; PLANT PHYSIOLOGICAL PHENOMENA; PLANTS; SEQUENCE ALIGNMENT;

ANIMALIA; BRYOPHYTA; EMBRYOPHYTA; EUKARYOTA; FUNGI; PHYSCOMITRELLA PATENS; PROKARYOTA; TRACHEOPHYTA;

EID: 84869409983     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms2148     Document Type: Article

References (59)

1. Gogarten, J. P., Doolittle, W. F. & Lawrence, J. G. Prokaryotic evolution in light of gene transfer. Mol. Biol Evol. 19, 2226-2238 (2002). (Pubitemid 35440456)
2. Andersson, J. O. Gene transfer and diversifcation of microbial eukaryotes. Annu. Rev. Microbiol 63, 177-193 (2009).
3. Belbahri, L., Calmin, G., Mauch, F. & Andersson, J. O. Evolution of the cutinase gene family: evidence for lateral gene transfer of a candidate Phytophthora virulence factor. Gene 408, 1-8 (2008).
4. Sun, G., Yang, Z., Kosch, T., Summers, K. & Huang, J. Evidence for acquisition of virulence efectors in pathogenic chytrids. BMC Evol Biol. 11, 195 (2011).
5. Danchin, E. G. et al. Multiple lateral gene transfers and duplications have promoted plant parasitism ability in nematodes. Proc. Natl Acad. Sci. USA 107, 17651-17656 (2010).
6. Ricard, G. et al. Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment. BMC Genomics 7, 22 (2006).
7. Andersson, J. O., Sjogren, A. M., Davis, L. A., Embley, T. M. & Roger, A. J. Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers afecting eukaryotes. Curr. Biol. 13, 94-104 (2003). (Pubitemid 36154336)
8. Ochman, H., Lawrence, J. G. & Groisman, E. A. Lateral gene transfer and the nature of bacterial innovation. Nature 405, 299-304 (2000). (Pubitemid 30337055)
9. Andersson, J. O. Lateral gene transfer in eukaryotes. Cell Mol. Life Sci. 62, 1182-1197 (2005). (Pubitemid 40880124)
10. Keeling, P. J. & Palmer, J. D. Horizontal gene transfer in eukaryotic evolution. Nat Rev. Genet 9, 605-618 (2008).
11. Bock, R. The give-and-take of DNA: horizontal gene transfer in plants. Trends Plant Sci. 15, 11-22 (2010).
12. Klasson, L., Kambris, Z., Cook, P. E., Walker, T. & Sinkins, S. P. Horizontal gene transfer between Wolbachia and the mosquito Aedes aegypti. BMC Genomics 10, 33 (2009).
13. Yoshida, S., Maruyama, S., Nozaki, H. & Shirasu, K. Horizontal gene transfer by the parasitic plant Striga hermonthica. Science 328, 1128 (2010).
14. Bergthorsson, U., Adams, K. L., Tomason, B. & Palmer, J. D. Widespread horizontal transfer of mitochondrial genes in fowering plants. Nature 424, 197-201 (2003). (Pubitemid 36858687)
15. Richardson, A. O. & Palmer, J. D. Horizontal gene transfer in plants. J. Exp. Bot. 58, 1-9 (2007). (Pubitemid 46026245)
16. Moran, N. A. & Jarvik, T. Lateral transfer of genes from fungi underlies carotenoid production in aphids. Science 328, 624-627 (2010).
17. Christin, P. A. et al. Adaptive evolution of C(4) photosynthesis through recurrent lateral gene transfer. Curr. Biol. 22, 445-449 (2012).
18. Ni, T. et al. Ancient gene transfer from algae to animals: mechanisms and evolutionary signifcance. BMC Evol. Biol. 12, 83 (2012).
19. Huang, J. & Gogarten, J. P. Ancient horizontal gene transfer can beneft phylogenetic reconstruction. Trends Genet. 22, 361-366 (2006). (Pubitemid 44015971)
20. Sanderson, M. J., Torne, J. L., Wikstrom, N. & Bremer, K. Molecular evidence on plant divergence times. Am. J. Bot. 91, 1656-1665 (2004). (Pubitemid 43193724)
21. Graham, L. E., Cook, M. E. & Busse, J. S. The origin of plants: body plan changes contributing to a major evolutionary radiation. Proc. Natl Acad. Sci. USA 97, 4535-4540 (2000). (Pubitemid 30238593)
22. Syvanen, M. Horizontal gene transfer: evidence and possible consequences. Annu. Rev. Genet 28, 237-261 (1994).
23. Copley, S. D. & Dhillon, J. K. Lateral gene transfer and parallel evolution in the history of glutathione biosynthesis genes. Genome Biol 3, research0025 (2002).
24. Emiliani, G., Fondi, M., Fani, R. & Gribaldo, S. A horizontal gene transfer at the origin of phenylpropanoid metabolism: a key adaptation of plants to land. Biol Direct 4, 7 (2009).
25. Richards, T. A. et al. Phylogenomic analysis demonstrates a pattern of rare and ancient horizontal gene transfer between plants and fungi. Plant Cell 21, 1897-1911 (2009).
26. Pisani, D., Cotton, J. A. & McInerney, J. O. Supertrees disentangle the chimerical origin of eukaryotic genomes. Mol. Biol. Evol. 24, 1752-1760 (2007). (Pubitemid 47236695)
27. Martin, W. et al. Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc. Natl Acad. Sci. USA 99, 12246-12251 (2002).
28. Hackett, J. D. et al. Migration of the plastid genome to the nucleus in a peridinin dinofagellate. Curr. Biol. 14, 213-218 (2004). (Pubitemid 38215348)
29. Esser, C. et al. A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol. Biol. Evol. 21, 1643-1660 (2004). (Pubitemid 39096881)
30. Wang, B. et al. Presence of three mycorrhizal genes in the common ancestor of land plants suggests a key role of mycorrhizas in the colonization of land by plants. New Phytol 186, 514-525 (2010).
31. Huang, J. & Gogarten, J. P. Concerted gene recruitment in early plant evolution. Genome Biol. 9, R109 (2008).
32. Price, D. C. et al. Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants. Science 335, 843-847 (2012).
33. Huang, J. & Gogarten, J. P. Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids? Genome Biol. 8, R99 (2007).
34. Tian, J. et al. AlienG: an efective computational tool for phylogenetic identifcation of horizontally transferred genes The third International Conference on Bioinformatics and Computational Biology (BICoB): New Orleans, Lousiana (2011).
35. Philippe, H. & Douady, C. J. Horizontal gene transfer and phylogenetics. Curr. Opin Microbiol. 6, 498-505 (2003). (Pubitemid 37345416)
36. Andersson, J. O. Evolution of patchily distributed proteins shared between eukaryotes and prokaryotes: Dictyostelium as a case study J. Mol. Microbiol. Biotechnol. 20, 83-95 (2011).
37. Sun, G., Yang, Z., Ishwar, A. & Huang, J. Algal genes in the closest relatives of animals. Mol. Biol. Evol. 27, 2879-2889 (2010).
38. Schaller, A., Stintzi, A. & Graf, L. Subtilases-versatile tools for protein turnover, plant development, and interactions with the environment. Physiol. Plant 145, 52-66 (2012).
39. Cheng, Y., Dai, X. & Zhao, Y. Auxin biosynthesis by the YUCCA favin monooxygenases controls the formation of foral organs and vascular tissues in Arabidopsis. Genes Dev. 20, 1790-1799 (2006). (Pubitemid 43992887)
40. Wiszniewski, A. A., Zhou, W., Smith, S. M. & Bussell, J. D. Identifcation of two Arabidopsis genes encoding a peroxisomal oxidoreductase-like protein and an acyl-CoA synthetase-like protein that are required for responses to pro-auxins. Plant Mol. Biol. 69, 503-515 (2009).
41. Flores, T. et al. Arginase-negative mutants of Arabidopsis exhibit increased nitric oxide signaling in root development. Plant Physiol. 147, 1936-1946 (2008). (Pubitemid 352844233)
42. Noctor, G. et al. Glutathione in plants: an integrated overview. Plant Cell Environ. 35, 454-484 (2012).
43. Werner, A. K., Romeis, T. & Witte, C. P. Ureide catabolism in Arabidopsis thaliana and Escherichia coli. Nat Chem. Biol. 6, 19-21 (2010).
44. Goremykin, V. V., Salamini, F., Velasco, R. & Viola, R. Mitochondrial DNA of Vitis vinifera and the issue of rampant horizontal gene transfer. Mol. Biol. Evol. 26, 99-110 (2009).
45. Koulintchenko, M., Konstantinov, Y & Dietrich, A. Plant mitochondria actively import DNA via the permeability transition pore complex. EMBO J. 22, 1245-1254 (2003). (Pubitemid 36362688)
46. Zhu, B. et al. Horizontal gene transfer in silkworm, Bombyx mori. BMC Genomics 12, 248 (2011).
47. Lowry, B., Lee, D. & Hébant, C. The Origin of Land Plants: A New Look at an Old Problem 29 (1980).
48. Cove, D. The moss Physcomitrella patens. Annu Rev Genet 39, 339-358 (2005). (Pubitemid 43011119)
49. Brundrett, M. C. Coevolution of roots and mycorrhizas of land plants. New Phytol 154, 275-304 (2002). (Pubitemid 34458302)
50. Neuteboom, L. W., Veth-Tello, L. M., Clijdesdale, O. R., Hooykaas, P. J. & van der Zaal, B. J. A novel subtilisin-like protease gene from Arabidopsis thaliana is expressed at sites of lateral root emergence. DNA Res. 6, 13-19 (1999). (Pubitemid 129705125)
51. Tanaka, H. et al. A subtilisin-like serine protease is required for epidermal surface formation in Arabidopsis embryos and juvenile plants. Development 128, 4681-4689 (2001). (Pubitemid 33138579)
52. Zhao, C., Johnson, B. J., Kositsup, B. & Beers, E. P. Exploiting secondary growth in Arabidopsis. Construction of xylem and bark cDNA libraries and cloning of three xylem endopeptidases. Plant Physiol. 123, 1185-1196 (2000). (Pubitemid 30466870)
53. Alcazar, R. et al. Polyamines: molecules with regulatory functions in plant abiotic stress tolerance. Planta 231, 1237-1249 (2010).
54. Kusano, T., Berberich, T., Tateda, C. & Takahashi, Y Polyamines: essential factors for growth and survival. Planta 228, 367-381 (2008).
55. Davidsen, T. et al. Biased distribution of DNA uptake sequences towards genome maintenance genes. Nucleic Acids Res. 32, 1050-1058 (2004). (Pubitemid 38854705)
56. Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307-321 (2010).
57. Felsenstein, J. PHYLIP (Phylogeny Inference Package) Version 3.65. Distributed by the Author, Department of Genome Sciences, University of Washington: Seattle (WA), (2005).
58. Keane, T. M., Creevey, C. J., Pentony, M. M., Naughton, T. J. & McLnerney, J. O. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justifed. BMC Evol. Biol. 6, 29 (2006).
59. Schmidt, H. A., Strimmer, K., Vingron, M. & von Haeseler, A. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18, 502-504 (2002). (Pubitemid 34284960)