Role of Horizontal Gene Transfer in Evolution of the Plant Genome

  • Nageswara Rao Reddy Neelapu
  • Malay Ranjan Mishra
  • Titash Dutta
  • Surekha ChallaEmail author


Horizontal gene transfer (HGT) transmits genetic material across species via more than ten possible mechanisms in nature. HGT is well studied, and accumulated evidence shows that HGT has contributed to transfer of genetic material and the evolution of the plant genome. This evolution in the plant genome aids plants in adapting to changing environment conditions. In this chapter we focus on the mechanism of contacts between two species, vectors, and acquisition of genetic elements, and also discuss the possible impacts on the evolution of plants.


Horizontal gene transfer Genome evolution Adaptation Plant genome Genetic material Donor Recipient 



C.S., M.R.M., T.D., and N.N.R. are grateful to GITAM (Deemed to be University) for providing necessary facilities to carry out the research work and for extending constant support.

Authors’ Contribution

C.S., M.R.M., T.D., and N.N.R. initiated the review, participated in writing, and revised the manuscript.

Conflict of Interest Statement

The authors declare that there is no potential conflict of interest.


  1. Alcázar R, Altabella T, Marco F, Bortolotti C, Reymond M, Koncz C, Carrasco P, Tiburcio A (2010) Polyamines: molecules with regulatory functions in plant abiotic stress tolerance. Planta (Berl) 231(6):1237–1249CrossRefGoogle Scholar
  2. Anderson MT, Seifert HS (2011) Opportunity and means: horizontal gene transfer from the human host to a bacterial pathogen. MBio 2(1):5–11CrossRefGoogle Scholar
  3. Andersson JO (2005) Lateral gene transfer in eukaryotes. CMLS (Cell Mol Life Sci) 62(11):1182–1197CrossRefGoogle Scholar
  4. Andersson JO, Sjögren ÅM, Davis LA, Embley TM, Roger AJ (2003) Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers affecting eukaryotes. Curr Biol 13(2):94–104PubMedCrossRefPubMedCentralGoogle Scholar
  5. Andika IB, Wei S, Cao C, Salaipeth L, Kondo H, Sun L (2017) Phytopathogenic fungus hosts a plant virus: a naturally occurring cross-kingdom viral infection. Proc Natl Acad Sci 114(46):12267–12272PubMedCrossRefPubMedCentralGoogle Scholar
  6. Arber W (2008) Molecular mechanisms driving darwinian evolution. Math Comput Model 47(7–8):666–674CrossRefGoogle Scholar
  7. Archibald JM, Richards TA (2010) Gene transfer: anything goes in plant mitochondria. BMC Biol 8(1):147PubMedPubMedCentralCrossRefGoogle Scholar
  8. Ayliffe MA, Agostino A, Clarke BC, Furbank R, von Caemmerer S, Pryor AJ (2009) Suppression of the barley uroporphyrinogen III synthase gene by a ds activation tagging element generates developmental photosensitivity. Plant Cell 21(3):814–831PubMedPubMedCentralCrossRefGoogle Scholar
  9. Babić A, Lindner AB, Vulić M, Stewart EJ, Radman M (2008) Direct visualization of horizontal gene transfer. Science 319(5869):1533–1536PubMedCrossRefPubMedCentralGoogle Scholar
  10. Bansal AK, Meyer TE (2002) Evolutionary analysis by whole-genome comparisons. J Bacteriol 184(8):2260–2272PubMedPubMedCentralCrossRefGoogle Scholar
  11. Bergthorsson U, Adams KL, Thomason B, Palmer JD (2003) Wide spread horizontal transfer of mitochondrial genes in flowering plants. Nature 424(6945):197–201PubMedCrossRefPubMedCentralGoogle Scholar
  12. Bock R (2010) The give-and-take of DNA: horizontal gene transfer in plants. Trends Plant Sci 15(1):11–22PubMedCrossRefPubMedCentralGoogle Scholar
  13. Bonen L (2006) Mitochondrial genes leave home. New Phytol 172(3):379–381PubMedCrossRefPubMedCentralGoogle Scholar
  14. Brennicke A, Grohmann L, Hiesel R, Knoop V, Schuster W (1993) The mitochondrial genome on its way to the nucleus: different stages of gene transfer in higher plants. FEBS Lett 325(1–2):140–145PubMedCrossRefPubMedCentralGoogle Scholar
  15. Broothaerts W, Mitchell HJ, Weir B, Kaines S, Smith LMA, Yang W, Mayer JE, Roa-Rodriguez C, Jefferson RA (2005) Gene transfer to plants by diverse species of bacteria. Nature 433(7026):629–633PubMedCrossRefPubMedCentralGoogle Scholar
  16. Buell CR, Yuan Q, Ouyang S, Liu J, Zhu W, Wang A, Maiti R, Haas B, Wortman J, Pertea M, Jones KM, Kim M, Overton L, Tsitrin T, Fadrosh D, Bera J, Weaver B, Jin S, Johri S, Reardon M, Webb K, Hill J, Moffat K, Tallon L, Van Aken S, Lewis M, Utterback T, Feldblyum T, Zismann V, Iobst S, Hsiao J, de Vazeille AR, Salzberg SL, White O, Fraser C, Yu Y, Kim H, Rambo T, Currie J, Collura K, Kernodle-Thompson S, Wei F, Kudrna K, Ammiraju JS, Luo M, Goicoechea JL, Wing RA, Henry D, Oates R, Palmer M, Pries G, Saski C, Simmons J, Soderlund C, Nelson W, de la Bastide M, Spiegel L, Nascimento L, Huang E, Preston R, Zutavern T, Palmer L, O’Shaughnessy A, Dike S, WR MC, Minx P, Cordum H, Wilson R, Jin W, Lee HR, Jiang J, Jackson S, Rice Chromosome 3 Sequencing Consortium (2005) Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. Genome Res 15(9):1284–1291PubMedCrossRefPubMedCentralGoogle Scholar
  17. Bukhalid RA, Takeuchi T, Labeda D, Loria R (2002) Horizontal transfer of the plant virulence gene, nec1, and flanking sequences among genetically distinct Streptomyces strains in the diastatochromo genes cluster. Appl Environ Microbiol 68(2):738–744PubMedPubMedCentralCrossRefGoogle Scholar
  18. Burger G, Lang BF (2003) Parallels in genome evolution in mitochondria and bacterial symbionts. IUBMB Life 55(4–5):205–212PubMedCrossRefPubMedCentralGoogle Scholar
  19. Capy P, Loreto ELS, Carareto CMA (2008) Revisiting horizontal transfer of transposable elements in Drosophila. Heredity 100(6):545PubMedCrossRefPubMedCentralGoogle Scholar
  20. Cheng Y, Dai X, Zhao Y (2006) Auxin biosynthesis by the YUCCA flavin monooxygenases controls the formation of floral organs and vascular tissues in Arabidopsis. Genes Dev 20(13):1790–1799PubMedPubMedCentralCrossRefGoogle Scholar
  21. Christin PA, Edwards EJ, Besnard G, Boxall SF, Gregory R, Kellogg EA, Hartwell J, Osborne CP (2012) Adaptive evolution of C4 photosynthesis through recurrent lateral gene transfer. Curr Biol 22(5):445–449PubMedCrossRefPubMedCentralGoogle Scholar
  22. Copley SD, Dhillon JK (2002) Lateral gene transfer and parallel evolution in the history of glutathione biosynthesis genes. Genome Biol Res 3(5):0025–0021Google Scholar
  23. Cullis CA, Vorster BJ, Van Der Vyver C, Kunert KJ (2008) Transfer of genetic material between the chloroplast and nucleus: how is it related to stress in plants? Ann Bot 103(4):625–633PubMedPubMedCentralCrossRefGoogle Scholar
  24. Czislowski E, Fraser-Smith S, Zander M, O’Neill WT, Meldrum RA, Tran-Nguyen LTT, Batley J, Aitken EAB (2018) Investigation of the diversity of effector genes in the banana pathogen, Fusarium oxysporum f. sp. cubense, reveals evidence of horizontal gene transfer. Mol Plant Pathol 19(5):1155–1171PubMedCrossRefPubMedCentralGoogle Scholar
  25. Danchin EG, Rosso MN, Vieira P, de Almeida-Engler J, Coutinho PM, Henrissat B, Abad P (2010) Multiple lateral gene transfers and duplications have promoted plant parasitism ability in nematodes. Proc Natl Acad Sci 107(41):17651–17656PubMedCrossRefPubMedCentralGoogle Scholar
  26. Dante RA, Neto GC, Leite A, Yunes JA, Arruda P (1999) The DapA gene encoding the lysine biosynthetic enzyme dihydrodipicolinate synthase from Coix lacryma-jobi: cloning, characterization, and expression analysis. Plant Mol Biol 41(4):551–561PubMedCrossRefPubMedCentralGoogle Scholar
  27. Davidsen T, Rødland EA, Lagesen K, Seeberg E, Rognes T, Tønjum T (2004) Biased distribution of DNA uptake sequences towards genome maintenance genes. Nucleic Acids Res 32(3):1050–1058PubMedPubMedCentralCrossRefGoogle Scholar
  28. Davis CC, Wurdack KJ (2004) Host-to-parasite gene transfer in flowering plants: phylogenetic evidence from malpighiales. Science 305(5684):676–678PubMedCrossRefPubMedCentralGoogle Scholar
  29. Davis CC, Anderson WR, Wurdack KJ (2005) Gene transfer from a parasitic flowering plant to a fern. Proc R Soc Lond B Biol Sci 272(1578):2237–2242CrossRefGoogle Scholar
  30. de Wit PJ, Mehrabi R, Bahkali AH (2011) Horizontal gene and chromosome transfer in plant pathogenic fungi affecting host range. FEMS Microbiol Rev 35(3):542–554PubMedCrossRefPubMedCentralGoogle Scholar
  31. Diao X, Freeling M, Lisch D (2005) Horizontal transfer of a plant transposon. PLoS Biol 4(1):e5PubMedCentralCrossRefGoogle Scholar
  32. Diao Y, Qi Y, Ma Y, Xia A, Sharakhov I, Chen X, Biedler J, Ling E, Jake Tu Z (2011) Next-generation sequencing reveals recent horizontal transfer of a DNA transposon between divergent mosquitoes. PLoS One 6(2):16743CrossRefGoogle Scholar
  33. Doolittle WF (1998) You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends Genet 14(8):307–311PubMedCrossRefPubMedCentralGoogle Scholar
  34. Dotto BR, Carvalho EL, Silva AF (2015) HTT-DB: horizontally transferred transposable elements database. Bioinformatics 31(17):2915–2917PubMedCrossRefPubMedCentralGoogle Scholar
  35. El Baidouri M, Carpentier MC, Cooke R (2014) Widespread and frequent horizontal transfers of transposable elements in plants. Genome Res 24(5):831–838PubMedPubMedCentralCrossRefGoogle Scholar
  36. Emmermann M, Braun HP, Schmitz UK (1991) The ADP/ATP translocator from potato has a long amino-terminal extension. Curr Genet 20(5):405–410PubMedCrossRefPubMedCentralGoogle Scholar
  37. Feder ME (2007) Evolvability of physiological and biochemical traits: evolutionary mechanisms including and beyond single-nucleotide mutation. J Exp Biol 210(9):1653–1660PubMedCrossRefPubMedCentralGoogle Scholar
  38. Feschotte C, Wessler SR (2002) Mariner-like transposases are widespread and diverse in flowering plants. Proc Natl Acad Sci 99(1):280–285PubMedCrossRefPubMedCentralGoogle Scholar
  39. Feschotte C, Gilbert C, Schaack S, Pace JK, Brindley PJ (2010) A role for host–parasite interactions in the horizontal transfer of transposons across phyla. Nature 464(7293):1347–1350PubMedPubMedCentralCrossRefGoogle Scholar
  40. Fortune PM, Roulin A, Panaud O (2008) Horizontal transfer of transposable elements in plants. Commun Integr Biol 1(1):74–77PubMedPubMedCentralCrossRefGoogle Scholar
  41. Fournier PE, Moliner C, Raoult D (2009) Evidence of horizontal gene transfer between amoeba and bacteria. Clin Microbiol Infect 15:178–180PubMedCrossRefPubMedCentralGoogle Scholar
  42. Franck AR, Cochrane BJ, Garey JR (2013) Phylogeny, biogeography, and infrageneric classification of Harrisia (Cactaceae). Syst Bot 38(1):210–223CrossRefGoogle Scholar
  43. Freist W, Logan DT, Gauss DH (1996) Glycyl-tRNA synthetase. Biol Chem Hoppe Seyler 377(6):343–356PubMedPubMedCentralGoogle Scholar
  44. Gao C, Ren X, Mason AS (2014) Horizontal gene transfer in plants. Funct Integr Genomics 14(1):23–29PubMedCrossRefPubMedCentralGoogle Scholar
  45. Garcia-Vallve S, Romeu A, Palau J (2000) Horizontal gene transfer of glycosyl hydrolases of the rumen fungi. Mol Biol Evol 17(3):352–361PubMedCrossRefPubMedCentralGoogle Scholar
  46. Giulotto E, Nergadze SG, Lupotto M, Pellanda P, Santagostino M, Vitelli V (2010) Mitochondrial DNA insertions in the nuclear horse genome. Anim Genet 41:176–185PubMedCrossRefPubMedCentralGoogle Scholar
  47. Gogarten JP, Doolittle WF, Lawrence JG (2002) Prokaryotic evolution in light of gene transfer. Mol Biol Evol 19(12):2226–2238PubMedCrossRefPubMedCentralGoogle Scholar
  48. Goldenfeld N, Woese C (2007) Biology’s next revolution. Nature 445(7126):369PubMedCrossRefPubMedCentralGoogle Scholar
  49. Goremykin VV, Salamini F, Velasco R, Viola R (2008) Mitochondrial DNA of Vitis vinifera and the issue of rampant horizontal gene transfer. Mol Biol Evol 26(1):99–110PubMedCrossRefPubMedCentralGoogle Scholar
  50. Goremykin VV, Lockhart PJ, Viola R (2012) The mitochondrial genome of Malus domestica and the import driven hypothesis of mitochondrial genome expansion in seed plants. Plant J 71(4):615–626PubMedCrossRefPubMedCentralGoogle Scholar
  51. Gribaldo S, Emiliani G, Fondi M, Fani R, Gribaldo S (2009) A horizontal gene transfer at the origin of phenylpropanoid metabolism: a key adaptation of plants to land. Biol Direct 4(1):7PubMedPubMedCentralCrossRefGoogle Scholar
  52. Guljamow A, Jenke-Kodama H, Saumweber H (2007) Horizontal gene transfer of two cytoskeletal elements from a eukaryote to a cyanobacterium. Curr Biol 17(17):R757–R759PubMedCrossRefPubMedCentralGoogle Scholar
  53. Hall C, Brachat S, Dietrich FS (2005) Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae. Eukaryot Cell 4(6):1102–1115PubMedPubMedCentralCrossRefGoogle Scholar
  54. Hayes R, Kudla J, Schuster G, Gabay L, Maliga P, Gruissem W (1996) Chloroplast mRNA 3′-end processing by a high molecular weight protein complex is regulated by nuclear encoded RNA binding proteins. EMBO J 15(5):1132–1141PubMedPubMedCentralCrossRefGoogle Scholar
  55. Hotopp JCD (2011) Horizontal gene transfer between bacteria and animals. Trends Genet 27(4):157–163CrossRefGoogle Scholar
  56. Hotopp JCD, Clark ME, Oliveira DC (2007) Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science 317(5845):1753–1756CrossRefGoogle Scholar
  57. Huang J (2013) Horizontal gene transfer in eukaryotes: the weak link model. BioEssays 35(10):868–875PubMedPubMedCentralGoogle Scholar
  58. Huang J, Gogarten JP (2006) Ancient horizontal gene transfer can benefit phylogenetic reconstruction. Trends Genet 22(7):361–366PubMedCrossRefPubMedCentralGoogle Scholar
  59. Huang J, Gogarten JP (2008) Concerted gene recruitment in early plant evolution. Genome Biol 9(7):R109PubMedPubMedCentralCrossRefGoogle Scholar
  60. Intrieri MC, Buiatti M (2001) The horizontal transfer of Agrobacterium rhizogenes genes and the evolution of the genus Nicotiana. Mol Phylogenet Evol 20(1):100–110PubMedCrossRefPubMedCentralGoogle Scholar
  61. Kazazian HH (2004) Mobile elements: drivers of genome evolution. Science 303(5664):1626–1632PubMedCrossRefPubMedCentralGoogle Scholar
  62. Keeling PJ, Palmer JD (2001) Lateral transfer at the gene and subgenic levels in the evolution of eukaryotic enolase. Proc Natl Acad Sci 98(19):10745–10750PubMedCrossRefPubMedCentralGoogle Scholar
  63. Kidwell MG, Lisch DR (2001) Perspective: transposable elements, parasitic DNA, and genome evolution. Evolution 55(1):1–24PubMedCrossRefPubMedCentralGoogle Scholar
  64. Klasson L, Kambris Z, Cook PE et al (2009) Horizontal gene transfer between Wolbachia and the mosquito Aedes aegypti. BMC Genomics 10(1):33PubMedPubMedCentralCrossRefGoogle Scholar
  65. Kondo N, Nikoh N, Ijichi N (2002) Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect. Proc Natl Acad Sci 99(22):14280–14285PubMedCrossRefPubMedCentralGoogle Scholar
  66. Koonin EV (2009) Darwinian evolution in the light of genomics. Nucleic Acids Res 37:1011–1034PubMedPubMedCentralCrossRefGoogle Scholar
  67. Koulintchenko M, Konstantinov Y, Dietrich A (2003) Plant mitochondria actively import DNA via the permeability transition pore complex. EMBO J 22(6):1245–1254PubMedPubMedCentralCrossRefGoogle Scholar
  68. Kusano T, Berberich T, Tateda C, Takahashi Y (2008) Polyamines: essential factors for growth and survival. Planta (Berl) 228(3):367–381CrossRefGoogle Scholar
  69. Kyndt T, Quispe D, Zhai H, Jarret R, Ghislain M, Liu Q, Gheysen G, Kreuze JF (2015) The genome of cultivated sweet potato contains Agrobacterium T-DNAs with expressed genes: an example of a naturally transgenic food crop. Proc Natl Acad Sci 112(18):5844–5849PubMedCrossRefPubMedCentralGoogle Scholar
  70. Lacroix B, Citovsky V (2016) Transfer of DNA from bacteria to eukaryotes. MBio 7(4):00863–00816CrossRefGoogle Scholar
  71. Lacroix B, Citovsky V (2018) Beyond Agrobacterium-mediated transformation: horizontal gene transfer from bacteria to eukaryotes. Curr Top Microbiol Immunol 418:443–462PubMedPubMedCentralGoogle Scholar
  72. Laten HM, Havecker ER, Farmer LM (2003) SIRE1, an endogenous retrovirus family from Glycine max, is highly homogeneous and evolutionarily young. Mol Biol Evol 20(8):1222–1230PubMedCrossRefPubMedCentralGoogle Scholar
  73. Lerat E, Daubin V, Ochman H (2005) Evolutionary origins of genomic repertoires in bacteria. PLoS Biol 3(5):e130PubMedPubMedCentralCrossRefGoogle Scholar
  74. Liang D, White RG, Waterhouse PM (2012) Gene silencing in Arabidopsis spreads from the root to the shoot, through a gating barrier, by template-dependent, nonvascular, cell–cell movement. Plant Physiol 159(3):984–1000PubMedPubMedCentralCrossRefGoogle Scholar
  75. Ling HQ, Zhao S, Liu D, Wang J, Sun H, Zhang C, Fan H, Li D, Dong L, Tao Y, Gao C, Wu H, Li Y, Cui Y, Guo X, Zheng S, Wang B, Yu K, Liang Q, Yang W, Lou X, Chen J, Feng M, Jian J, Zhang X, Luo G, Jiang Y, Liu J, Wang Z, Sha Y, Zhang B, Wu H, Tang D, Shen Q, Xue P, Zou S, Wang X, Liu X, Wang F, Yang Y, An X, Dong Z, Zhang K, Zhang X, Luo MC, Dvorak J, Tong Y, Wang J, Yang H, Li Z, Wang D, Zhang A, Wang J (2013) Draft genome of the wheat A-genome progenitor Triticum urartu. Nature 496(7443):87PubMedCrossRefPubMedCentralGoogle Scholar
  76. Liu H, Fu Y, Jiang D (2010) Wide spread horizontal gene transfer from double-stranded RNA viruses to eukaryotic nuclear genomes. J Virol 84(22):11876–11887PubMedPubMedCentralCrossRefGoogle Scholar
  77. Liu X, Liu Y, Huang P, Ma Y, Qing Z, Tang Q, Cao H, Cheng P, Zheng Y, Yuan Z, Zhou Y, Liu J, Tang Z, Zhuo Y, Zhang Y, Yu L, Huang J, Yang P, Peng Q, Zhang J, Jiang W, Zhang Z, Lin K, Ro DK, Chen X, Xiong X, Shang Y, Huang S, Zeng J (2017) The genome of medicinal plant Macleaya cordata provides new insights into benzylisoquinoline alkaloids metabolism. Mol Plant 10(7):975–989PubMedCrossRefPubMedCentralGoogle Scholar
  78. Lucas WJ, Ham BK, Kim JY (2009) Plasmodesmata: bridging the gap between neighboring plant cells. Trends Cell Biol 19(10):495–503PubMedCrossRefPubMedCentralGoogle Scholar
  79. Marienfeld J, Unseld M, Brennicke A (1999) The mitochondrial genome of Arabidopsis is composed of both native and immigrant information. Trends Plant Sci 4(12):495–502PubMedCrossRefPubMedCentralGoogle Scholar
  80. Martin W, Brinkmann H, Savonna C, Cerff R (1993) Evidence for a chimeric nature of nuclear genomes: eubacterial origin of eukaryotic glyceraldehyde-3-phosphate dehydrogenase genes. Proc Natl Acad Sci 90(18):8692–8696PubMedCrossRefPubMedCentralGoogle Scholar
  81. Matveeva TV, Lutova LA (2014) Horizontal gene transfer from Agrobacterium to plants. Front Plant Sci 5:326PubMedPubMedCentralCrossRefGoogle Scholar
  82. Matveeva TV, Bogomaz DI, Pavlova OA, Nester EW, Lutova LA (2012) Horizontal gene transfer from genus Agrobacterium to the plant Linaria in nature. Mol Plant Microbe Interact 25(12):1542–1551PubMedCrossRefPubMedCentralGoogle Scholar
  83. Maumus F, Epert A, Nogué F, Blanc G (2014) Plant genomes enclose footprints of past infections by giant virus relatives. Nat Commun 5:5268CrossRefGoogle Scholar
  84. Maurel C, Barbier-Brygoo H, Spena A, Spena A, Tempé J, Guern J (1991) Single rol genes from the Agrobacterium rhizogenes TL-DNA alter some of the cellular responses to auxin in Nicotiana tabacum. Plant Physiol 97(1):212–216PubMedPubMedCentralCrossRefGoogle Scholar
  85. Mayer WE, Schuster LN, Bartelmes G (2011) Horizontal gene transfer of microbial cellulases into nematode genomes is associated with functional assimilation and gene turnover. BMC Evol Biol 11(1):13PubMedPubMedCentralCrossRefGoogle Scholar
  86. McGinty SE, Rankin DJ, Brown SP (2011) Horizontal gene transfer and the evolution of bacterial cooperation. Evol Int J Org Evol 65(1):21–32CrossRefGoogle Scholar
  87. Mitsui T, Yamaguchi J, Akazawa T (1996) Physicochemical and serological characterization of rice [α]-amylase isoforms and identification of their corresponding genes. Plant Physiol 110(4):1395–1404PubMedPubMedCentralCrossRefGoogle Scholar
  88. Mohr KI, Tebbe CC (2007) Field study results on the probability and risk of a horizontal gene transfer from transgenic herbicide-resistant oilseed rape pollen to gut bacteria of bees. Appl Microbiol Biotechnol 75(3):573–582PubMedCrossRefPubMedCentralGoogle Scholar
  89. Moran NA, Jarvik T (2010) Lateral transfer of genes from fungi underlies carotenoid production in aphids. Science 328(5978):624–627PubMedCrossRefPubMedCentralGoogle Scholar
  90. Mower JP, Stefanovic S, Young GJ, Palmer JD (2004) Plant genetics: gene transfer from parasitic to host plants. Nature 432(7014):165–166PubMedCrossRefPubMedCentralGoogle Scholar
  91. Mower JP, Stefanović S, Hao W (2010) Horizontal acquisition of multiple mitochondrial genes from a parasitic plant followed by gene conversion with host mitochondrial genes. BMC Biol 8(1):150PubMedPubMedCentralCrossRefGoogle Scholar
  92. Nedelcu AM, Miles IH, Fagir AM (2008) Adaptive eukaryote to eukaryote lateral gene transfer: stress related genes of algal origin in the closest unicellular relatives of animals. J Evol Biol 21(6):1852–1860PubMedCrossRefPubMedCentralGoogle Scholar
  93. Neelapu NRR, Titash D, Surekha C (2018) Quorum sensing and its role in Agrobacterium mediated gene transfer. In: Veera Bramhachari P (ed) Implication of quorum sensing system in biofilm formation and virulence. Springer Nature, Switzerland, pp 259–275CrossRefGoogle Scholar
  94. Nerva L, Varese GC, Falk BW, Turina M (2017) Mycoviruses of an endophytic fungus can replicate in plant cells: evolutionary implications. Sci Rep 7(1908):1–11Google Scholar
  95. Neuteboom LW, Veth-Tello LM, Clijdesdale OR, Hooykaas PJJ, Zaal EJ, der v (1999) A novel subtilisin-like protease gene from Arabidopsis thaliana is expressed at sites of lateral root emergence. DNA Res 6(1):13–19PubMedCrossRefPubMedCentralGoogle Scholar
  96. Ni T, Yue J, Sun G (2012) Ancient gene transfer from algae to animals: mechanisms and evolutionary significance. BMC Evol Biol 12(1):83PubMedPubMedCentralCrossRefGoogle Scholar
  97. Notsu Y, Masood S, Nishikawa T (2002) The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants. Mol Gen Genomics 268(4):434–445CrossRefGoogle Scholar
  98. Novick P, Smith J, Ray D, Boissinot S (2010) Independent and parallel lateral transfer of DNA transposons in tetrapod genomes. Gene (Amst) 449(1):85–94CrossRefGoogle Scholar
  99. O’Malley MA, Boucher Y (2005) Paradigm change in evolutionary microbiology. Stud Hist Philos Biol Biomed Sci 36(1):183–208PubMedCrossRefPubMedCentralGoogle Scholar
  100. Ogata H, Monier A, Claverie JM (2007) Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses. BMC Genomics 8(1):456PubMedPubMedCentralCrossRefGoogle Scholar
  101. Panaud O (2016) Horizontal transfers of transposable elements in eukaryotes: the flying genes. C R Biol 339(7-8):296–299PubMedCrossRefPubMedCentralGoogle Scholar
  102. Park JM, Manen JF, Schneeweiss GM (2007) Horizontal gene transfer of a plastid gene in the non-photosynthetic flowering plants Orobanche and Phelipanche (Orobanchaceae). Mol Phylogenet Evol 43(3):974–985PubMedCrossRefPubMedCentralGoogle Scholar
  103. Peccoud J, Loiseau V, Cordaux R (2017) Massive horizontal transfer of transposable elements in insects. Proc Natl Acad Sci 114(18):4721–4726PubMedCrossRefPubMedCentralGoogle Scholar
  104. Peng M, Gao Y, Chen W, Wang W, Shen S, Shi J, Wang C, Zhang Y, Zou L, Wang S, Wan J, Liu X, Gong L, Luo J (2016) Evolutionarily distinct BAHD N-acyltransferases are responsible for natural variation of aromatic amine conjugates in rice. Plant Cell 28:1528–1554Google Scholar
  105. Piskurek O, Okada N (2007) Poxviruses as possible vectors for horizontal transfer of retroposons from reptiles to mammals. Proc Natl Acad Sci 104(29):12046–12051PubMedCrossRefPubMedCentralGoogle Scholar
  106. Pontiroli A, Rizzi A, Simonet P, Daffonchio D, Vogel TM, Monier JM (2009) Visual evidence of horizontal gene transfer between plants and bacteria in the phytosphere of transplastomic tobacco. Appl Environ Microbiol 75(10):3314–3322PubMedPubMedCentralCrossRefGoogle Scholar
  107. Price DC, Chan CX, Yoon HS (2012) Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants. Science 335(6070):843–847PubMedCrossRefPubMedCentralGoogle Scholar
  108. Quispe-Huamanquispe DG, Gheysen G, Kreuze JF (2017) Horizontal gene transfer contributes to plant evolution: the case of Agrobacterium T-DNAs. Front Plant Sci 8:2015PubMedPubMedCentralCrossRefGoogle Scholar
  109. Richards TA, Hirt RP, Williams BA, Embley TM (2003) Horizontal gene transfer and the evolution of parasitic protozoa. Protist 154(1):17PubMedCrossRefPubMedCentralGoogle Scholar
  110. Richards TA, Dacks JB, Campbell SA (2006) Evolutionary origins of the eukaryotic shikimate pathway: gene fusions, horizontal gene transfer, and endosymbiotic replacements. Eukaryot Cell 5(9):1517–1531PubMedPubMedCentralCrossRefGoogle Scholar
  111. Richards TA, Soanes DM, Foster PG, Leonard G, Thornton CR, Talbot NJ (2009) Phylogenomic analysis demonstrates a pattern of rare and ancient horizontal gene transfer between plants and fungi. Plant Cell 21(7):1897–1911PubMedPubMedCentralCrossRefGoogle Scholar
  112. Richardson AO, Palmer JD (2006) Horizontal gene transfer in plants. J Exp Bot 58(1):1–9PubMedCrossRefPubMedCentralGoogle Scholar
  113. Rolland T, Neuvéglise C, Sacerdot C, Dujon B (2009) Insertion of horizontally transferred genes within conserved syntenic regions of yeast genomes. PLoS One 4(8):6515CrossRefGoogle Scholar
  114. Roney JK, Khatibi PA, Westwood JH (2007) Cross-species translocation of mRNA from host plants into the parasitic plant dodder. Plant Physiol 143(2):1037–1043PubMedPubMedCentralCrossRefGoogle Scholar
  115. Roossinck MJ (2019) Evolutionary and ecological links between plant and fungal viruses. New Phytol 221(1):86–92PubMedCrossRefPubMedCentralGoogle Scholar
  116. Rosewich UL, Kistler HC (2000) Role of horizontal gene transfer in the evolution of fungi. Annu Rev Phytopathol 38(1):325–363PubMedCrossRefPubMedCentralGoogle Scholar
  117. Roulin A, Piegu B, Wing RA, Panaud O (2008) Evidence of multiple horizontal transfers of the long terminal repeat retrotransposon RIRE1 within the genus Oryza. Plant J 53(6):950–959PubMedCrossRefPubMedCentralGoogle Scholar
  118. Roulin A, Piegu B, Fortune PM, Sabot F, D'Hont A, Manicacci D, Panaud O (2009) Whole genome surveys of rice, maize and sorghum reveal multiple horizontal transfers of the LTR-retrotransposon Route66 in Poaceae. BMC Evol Biol 9(1):58PubMedPubMedCentralCrossRefGoogle Scholar
  119. Salanoubat M, Lemcke K, Rieger M, Ansorge W, Unseld M, Fartmann B, Valle G, Blöcker H, Perez-Alonso M, Obermaier B, Delseny M, Boutry M, Grivell LA, Mache R, Puigdomènech P, De Simone V, Choisne N, Artiguenave F, Robert C, Brottier P, Wincker P, Cattolico L, Weissenbach J, Saurin W, Quétier F, Schäfer M, Müller-Auer S, Gabel C, Fuchs M, Benes V, Wurmbach E, Drzonek H, Erfle H, Jordan N, Bangert S, Wiedelmann R, Kranz H, Voss H, Holland R, Brandt P, Nyakatura G, Vezzi A, D’Angelo M, Pallavicini A, Toppo S, Simionati B, Conrad A, Hornischer K, Kauer G, Löhnert TH, Nordsiek G, Reichelt J, Scharfe M, Schön O, Bargues M, Terol J, Climent J, Navarro P, Collado C, Perez-Perez A, Ottenwälder B, Duchemin D, Cooke R, Laudie M, Berger-Llauro C, Purnelle B, Masuy D, de Haan M, Maarse AC, Alcaraz JP, Cottet A, Casacuberta E, Monfort A, Argiriou A, Flores M, Liguori R, Vitale D, Mannhaupt G, Haase D, Schoof H, Rudd S, Zaccaria P, Mewes HW, Mayer KF, Kaul S, Town CD, Koo HL, Tallon LJ, Jenkins J, Rooney T, Rizzo M, Walts A, Utterback T, Fujii CY, Shea TP, Creasy TH, Haas B, Maiti R, Wu D, Peterson J, Van Aken S, Pai G, Militscher J, Sellers P, Gill JE, Feldblyum TV, Preuss D, Lin X, Nierman WC, Salzberg SL, White O, Venter JC, Fraser CM, Kaneko T, Nakamura Y, Sato S, Kato T, Asamizu E, Sasamoto S, Kimura T, Idesawa K, Kawashima K, Kishida Y, Kiyokawa C, Kohara M, Matsumoto M, Matsuno A, Muraki A, Nakayama S, Nakazaki N, Shinpo S, Takeuchi C, Wada T, Watanabe A, Yamada M, Yasuda M, Tabata S, European Union Chromosome 3 Arabidopsis Sequencing Consortium, Institute for Genomic Research, Kazusa DNA Research Institute (2000) Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana. Nature 408(6814):820–822PubMedCrossRefPubMedCentralGoogle Scholar
  120. Schaack S, Gilbert C, Feschotte C (2010) Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends Ecol Evol 25(9):537–546PubMedPubMedCentralCrossRefGoogle Scholar
  121. Schaller A, Stintzi A, Graff L (2012) Subtilases–versatile tools for protein turnover, plant development, and interactions with the environment. Physiol Plant 145(1):52–66PubMedCrossRefPubMedCentralGoogle Scholar
  122. Schlüter K, Fütterer J, Potrykus I (1995) Horizontal gene transfer from a transgenic potato line to a bacterial pathogen (Erwinia chrysanthemi) occurs—if at all—at an extremely low frequency. Nat Biotechnol 13(10):1094CrossRefGoogle Scholar
  123. Schmidt SM, Houterman PM, Schreiver I, Ma L, Amyotte S, Chellappan B, Boeren S, Takken FL, Rep M (2013) MITEs in the promoters of effector genes allow prediction of novel virulence genes in Fusarium oxysporum. BMC Genomics 14(1):119PubMedPubMedCentralCrossRefGoogle Scholar
  124. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326(5956):1112–1115PubMedCrossRefPubMedCentralGoogle Scholar
  125. Scholl EH, Bird DM (2011) Computational and phylogenetic validation of nematode horizontal gene transfer. BMC Biol 9(1):9PubMedPubMedCentralCrossRefGoogle Scholar
  126. Schönknecht G, Weber AP, Lercher MJ (2014) Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution. BioEssays 36(1):9–20PubMedCrossRefPubMedCentralGoogle Scholar
  127. Screen SE, Leger RJS (2000) Cloning, expression, and substrate specificity of a fungal chymotrypsin: evidence for lateral gene transfer from an Actinomycete bacterium. J Biol Chem 275(9):6689–6694PubMedCrossRefPubMedCentralGoogle Scholar
  128. Seehausen O (2004) Hybridization and adaptative radiation. Trends Ecol Evol 1:198–207CrossRefGoogle Scholar
  129. Serrato-Capuchina A, Matute DR (2018) The role of transposable elements in speciation. Genes (Basel) 9(5):254CrossRefGoogle Scholar
  130. Shimojima M, Ohta H, Iwamatsu A, Masuda T, Shioi Y, Takamiya K (1997) Cloning of the gene for monogalactosyldiacylglycerol synthase and its evolutionary origin. Proc Natl Acad Sci 94(1):333–337PubMedCrossRefPubMedCentralGoogle Scholar
  131. Silva JC, Loreto EL, Clark JB (2004) Factors that affect the horizontal transfer of transposable elements. Curr Issues Mol Biol 6:57–71PubMedPubMedCentralGoogle Scholar
  132. Slot JC, Rokas A (2011) Horizontal transfer of a large and highly toxic secondary metabolic gene cluster between fungi. Curr Biol 21(2):134–139PubMedCrossRefPubMedCentralGoogle Scholar
  133. Sormacheva I, Smyshlyaev G, Mayorov V, Blinov A, Novikov A, Novikova O (2012) Vertical evolution and horizontal transfer of CR1 non-LTR retrotransposons and Tc1/mariner DNA transposons in Lepidoptera species. Mol Biol Evol 29(12):3685–3702PubMedCrossRefPubMedCentralGoogle Scholar
  134. Stegemann S, Bock R (2009) Exchange of genetic material between cells in plant tissue grafts. Science 324(5927):649–651PubMedCrossRefPubMedCentralGoogle Scholar
  135. Stegemann S, Keuthe M, Greiner S, Bock R (2012) Horizontal transfer of chloroplast genomes between plant species. Proc Natl Acad Sci 109(7):2434–2438PubMedCrossRefPubMedCentralGoogle Scholar
  136. Sun S, Zhou Y, Chen J, Shi J, Zhao H, Zhao H, Song W, Zhang M, Cui Y, Dong X, Liu H, Ma X, Jiao Y, Wang B, Wei X, Stein JC, Glaubitz JC, Lu F, Yu G, Liang C, Fengler K, Li B, Rafalski A, Schnable PS, Ware DH, Buckler ES, Lai J (2018) Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. Nat Genet 50(9):1289PubMedCrossRefPubMedCentralGoogle Scholar
  137. Suzuki K, Yamashita I, Tanaka N (2002) Tobacco plants were transformed by Agrobacterium rhizogenes infection during their evolution. Plant J 32(5):775–787PubMedCrossRefPubMedCentralGoogle Scholar
  138. Tanaka H, Onouchi H, Kondo M, Hara-Nishimura I, Nishimura M, Machida C, Machida Y (2001) A subtilisin-like serine protease is required for epidermal surface formation in Arabidopsis embryos and juvenile plants. Development (Camb) 128(23):4681–4689Google Scholar
  139. Thyssen G, Svab Z, Maliga P (2012) Cell-to-cell movement of plastids in plants. Proc Natl Acad Sci 109(7):2439–2443PubMedCrossRefPubMedCentralGoogle Scholar
  140. Timmis JN, Ayliffe MA, Huang CY, Martin W (2004) Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet 5(2):123PubMedCrossRefPubMedCentralGoogle Scholar
  141. Trobridge GD (2009) Foamy virus vectors for gene transfer. Expert Opin Biol Ther 9(11):1427–1436PubMedPubMedCentralCrossRefGoogle Scholar
  142. Turano FJ, Weisemann JM, Matthews BF (1992) Identification and expression of a cDNA clone encoding aspartate aminotransferase in carrot. Plant Physiol 100(1):374–381PubMedPubMedCentralCrossRefGoogle Scholar
  143. Veronico P, Jones J, Di Vito M, De Giorgi C (2001) Horizontal transfer of a bacterial gene involved in polyglutamate biosynthesis to the plant parasitic nematode Meloidogyne artiellia. FEBS Lett 508(3):470–474PubMedCrossRefPubMedCentralGoogle Scholar
  144. Wallau GL, Ortiz MF, Loreto ELS (2012) Horizontal transposon transfer in Eukarya: detection, bias, and perspectives. Genome Biol Evol 4(8):801–811PubMedCentralCrossRefGoogle Scholar
  145. Wang D, Lloyd AH, Timmis JN (2012) Environmental stress increases the entry of cytoplasmic organellar DNA into the nucleus in plants. Proc Natl Acad Sci 109(7):2444–2448PubMedCrossRefPubMedCentralGoogle Scholar
  146. Watkins RF, Gray MW (2006) The frequency of eubacterium-to-eukaryote lateral gene transfers shows significant cross-taxa variation within amoebozoa. J Mol Evol 63(6):801–814PubMedCrossRefPubMedCentralGoogle Scholar
  147. Watts RA, Hunt PW, Hvitved AN, Hargrove MS, Peacock WJ, Dennis ES (2001) A hemoglobin from plants homologous to truncated hemoglobins of microorganisms. Proc Natl Acad Sci 98(18):10119–10124PubMedCrossRefPubMedCentralGoogle Scholar
  148. Werner AK, Sparkes IA, Romeis T, Witte CP (2008) Identification, biochemical characterization, and subcellular localization of allantoate amidohydrolases from Arabidopsis and soybean. Plant Physiol 146(2):418–430PubMedPubMedCentralCrossRefGoogle Scholar
  149. Wiszniewski AA, Zhou W, Smith SM, Bussell JD (2009) Identification 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(5):503PubMedCrossRefPubMedCentralGoogle Scholar
  150. Wolf YI, Koonin EV (2001) Origin of an animal mitochondrial DNA polymerase subunit via lineage-specific acquisition of a glycyl-tRNA synthetase from bacteria of the Thermus–Deinococcus group. Trends Genet 17(8):431–433PubMedCrossRefPubMedCentralGoogle Scholar
  151. Won H, Renner SS (2003) Horizontal gene transfer from flowering plants to gnetum. Proc Natl Acad Sci 100(19):10824–10829PubMedCrossRefPubMedCentralGoogle Scholar
  152. Woodson JD, Chory J (2008) Coordination of gene expression between organellar and nuclear genomes. Nat Rev Genet 9(5):383PubMedPubMedCentralCrossRefGoogle Scholar
  153. Yoshida S, Maruyama S, Nozaki H, Shirasu K (2010) Horizontal gene transfer by the parasitic plant Striga hermonthica. Science 328(5982):1128–1128PubMedCrossRefPubMedCentralGoogle Scholar
  154. Yue J, Hu X, Sun H, Yang Y, Huang J (2012) Widespread impact of horizontal gene transfer on plant colonization of land. Nat Commun 3:1152PubMedPubMedCentralCrossRefGoogle Scholar
  155. Yue J, Hu X, Huang J (2014) Origin of plant auxin biosynthesis. Trends Plant Sci 19(12):764–770PubMedCrossRefPubMedCentralGoogle Scholar
  156. Zambryski P, Crawford K (2000) Plasmodesmata: gatekeepers for cell-to-cell transport of developmental signals in plants. Annu Rev Cell Dev Biol 16(1):393–421PubMedCrossRefPubMedCentralGoogle Scholar
  157. Zardoya R, Ding X, Kitagawa Y, Chrispeels MJ (2002) Origin of plant glycerol transporters by horizontal gene transfer and functional recruitment. Proc Natl Acad Sci 99(23):14893–14896PubMedCrossRefPubMedCentralGoogle Scholar
  158. Zhao C, Johnson BJ, Kositsup B, Beers EP (2000) Exploiting secondary growth in Arabidopsis. Construction of xylem and bark cDNA libraries and cloning of three xylem endopeptidases. Plant Physiol 123(3):1185–1196PubMedPubMedCentralCrossRefGoogle Scholar
  159. Zhu B, Lou MM, Xie GL, Zhang GQ, Zhou XP, Li B, Jin GL (2011) Horizontal gene transfer in silkworm, Bombyx mori. BMC Genomics 12(1):248PubMedPubMedCentralCrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Nageswara Rao Reddy Neelapu
    • 1
  • Malay Ranjan Mishra
    • 2
  • Titash Dutta
    • 1
  • Surekha Challa
    • 1
    Email author
  1. 1.Department of Biochemistry and BioinformaticsInstitute of Science, Gandhi Institute of Technology and Management (GITAM Deemed to be University)VisakhapatnamIndia
  2. 2.Department of BiotechnologyInstitute of Technology, Gandhi Institute of Technology and Management (GITAM Deemed to be University)VisakhapatnamIndia

Personalised recommendations