Contribution of plant–bacteria interactions to horizontal gene transfer in plants

References

• Newman ME. A model of mass extinction. J Theor Biol. 1997;189(3):235–252.
   PubMed Web of Science ®Google Scholar
• Baltrus DA. Exploring the costs of horizontal gene transfer. Trends Ecol Evol. 2013;28(8):489–495.
   PubMed Web of Science ®Google Scholar
• Wickell DA, Li FW. On the evolutionary significance of horizontal gene transfers in plants. New Phytol. 2020;225(1):113–117.
   PubMed Web of Science ®Google Scholar
• Danchin EG. Lateral gene transfer in eukaryotes: tip of the iceberg or of the ice cube? BMC Biol. 2016;14(1):101.
   PubMedGoogle Scholar
• Ku C, Martin WF . A natural barrier to lateral gene transfer from prokaryotes to eukaryotes revealed from genomes: the 70 % rule. BMC Biol. 2016;14(1):89.
   PubMedGoogle Scholar
• Rossoni AW, Price DC, Seger M, et al. The genomes of polyextremophilic cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions. eLife. 2019;8:e45017.
   PubMed Web of Science ®Google Scholar
• Blesa A, Berenguer J. Methods to identify and analyze vesicle-protected DNA Transfer. Methods Mol Biol. 2020;2075:209–221.
   PubMedGoogle Scholar
• Blokesch M. Natural competence for transformation. Curr Biol. 2016;26(21):R1126–R1130.
   PubMed Web of Science ®Google Scholar
• Hall RJ, Whelan FJ, McInerney JO, et al. Horizontal gene transfer as a source of conflict and cooperation in prokaryotes. Frontier in Microbiology. 2020;11:1569.
   PubMed Web of Science ®Google Scholar
• Vos M, Hesselman MC, Te Beek TA, et al. Rates of lateral gene transfer in prokaryotes: High but why? Trends Microbiol. 2015;23(10):598–605.
   PubMed Web of Science ®Google Scholar
• Bock R. The give-and-take of DNA: horizontal gene transfer in plants. Trends Plant Sci. 2010;15(1):11–22.
   PubMed Web of Science ®Google Scholar
• Dunning Hotopp JC. Horizontal gene transfer between bacteria and animals. Trends Genet. 2011;27(4):157–163.
   PubMed Web of Science ®Google Scholar
• Dunning Hotopp JC, Clark ME, Oliveira DCSG, et al. Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science (New York, NY). 2007;317(5845):1753–1756.
   Google Scholar
• Kyndt T, Quispe D, Zhai H, et al. 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 U S A. 2015;112(18):5844–5849.
   PubMed Web of Science ®Google Scholar
• Quispe-Huamanquispe DG, Gheysen G, Kreuze JF. Horizontal gene transfer contributes to plant evolution: the case of agrobacterium T-DNAs. Front Plant Sci. 2017;8:2015.
   PubMed Web of Science ®Google Scholar
• Husnik F, McCutcheon JP. Functional horizontal gene transfer from bacteria to eukaryotes. Nat Rev Microbiol. 2018;16(2):67–79.
   PubMed Web of Science ®Google Scholar
• Cai H, Bai Y, Guo C. Comparative genomics of 151 plant-associated bacteria reveal putative mechanisms underlying specific interactions between bacteria and plant hosts. Genes Genomics. 2018;40(8):857–864.
   PubMed Web of Science ®Google Scholar
• Davis CC, Wurdack KJ. Host-to-parasite gene transfer in flowering plants: phylogenetic evidence from malpighiales. Science. 2004;305(5684):676–678.
   PubMed Web of Science ®Google Scholar
• Yue J, Hu X, Sun H, et al. Widespread impact of horizontal gene transfer on plant colonization of land. Nat Commun. 2012;3:1152.
   PubMed Web of Science ®Google Scholar
• Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 2015;16:157.
   PubMed Web of Science ®Google Scholar
• Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792–1797.
   PubMed Web of Science ®Google Scholar
• Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312–1313.
   PubMed Web of Science ®Google Scholar
• Yang Z, Zhang Y, Wafula EK, et al. Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation. Proc Natl Acad Sci U S A. 2016;113(45):E7010–E7019.
   PubMed Web of Science ®Google Scholar
• Huerta-Cepas J, Serra F, Bork P. ETE 3: reconstruction, analysis, and visualization of phylogenomic data. Mol Biol Evol. 2016;33(6):1635–1638.
   PubMed Web of Science ®Google Scholar
• Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol. 2011;7(10):e1002195.
   PubMed Web of Science ®Google Scholar
• Ravenhall M, Skunca N, Lassalle F, et al. Inferring horizontal gene transfer. PLoS Comput Biol. 2015;11(5):e1004095.
   PubMed Web of Science ®Google Scholar
• Hruz T, Laule O, Szabo G, et al. Genevestigator v3: a reference expression database for the Meta-analysis of transcriptomes. Adv Bioinformatics. 2008;2008:420747.
   PubMedGoogle Scholar
• Ronquist F, Teslenko M, van der Mark P, et al. MrBayes 3.2: efficient bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012;61(3):539–542.
   PubMed Web of Science ®Google Scholar
• Kaur C, Vishnoi A, Ariyadasa TU, et al. Episodes of horizontal gene-transfer and gene-fusion led to co-existence of different metal-ion specific glyoxalase I. Sci Rep. 2013;3:3076.
   PubMed Web of Science ®Google Scholar
• Gao JG. Tracking the evolutionary innovations of plant terrestrialization. Gene. 2021;769:145203.
   PubMed Web of Science ®Google Scholar
• Cheng S, Xian W, Fu Y, et al. Genomes of subaerial zygnematophyceae provide insights into land plant evolution. Cell. 2019;179(5):1057–1067 e1014.
   PubMed Web of Science ®Google Scholar
• Lacroix B, Citovsky V. Transfer of DNA from bacteria to eukaryotes. MBio. 2016;7(4):e00863–16.
   PubMed Web of Science ®Google Scholar
• Danchin EG, Guzeeva EA, Mantelin S, et al. Horizontal gene transfer from bacteria has enabled the plant-parasitic nematode Globodera pallida to feed on host-derived sucrose. Mol Biol Evol. 2016;33(6):1571–1579.
   PubMed Web of Science ®Google Scholar
• Kikuchi T, Eves-van den Akker S, Jones JT. Genome evolution of plant-parasitic nematodes. Annu Rev Phytopathol. 2017;55:333–354.
   PubMed Web of Science ®Google Scholar