Convergent horizontal gene transfer and cross-talk of mobile nucleic acids in parasitic plants

Abstract

Horizontal gene transfer (HGT), the movement and genomic integration of DNA across species boundaries, is commonly associated with bacteria and other microorganisms, but functional HGT (fHGT) is increasingly being recognized in heterotrophic parasitic plants that obtain their nutrients and water from their host plants through direct haustorial feeding. Here, in the holoparasitic stem parasite Cuscuta, we identify 108 transcribed and probably functional HGT events in Cuscuta campestris and related species, plus 42 additional regions with host-derived transposon, pseudogene and non-coding sequences. Surprisingly, 18 Cuscuta fHGTs were acquired from the same gene families by independent HGT events in Orobanchaceae parasites, and the majority are highly expressed in the haustorial feeding structures in both lineages. Convergent retention and expression of HGT sequences suggests an adaptive role for specific additional genes in parasite biology. Between 16 and 20 of the transcribed HGT events are inferred as ancestral in Cuscuta based on transcriptome sequences from species across the phylogenetic range of the genus, implicating fHGT in the successful radiation of Cuscuta parasites. Genome sequencing of C. campestris supports transfer of genomic DNA—rather than retroprocessed RNA—as the mechanism of fHGT. Many of the C. campestris genes horizontally acquired are also frequent sources of 24-nucleotide small RNAs that are typically associated with RNA-directed DNA methylation. One HGT encoding a leucine-rich repeat protein kinase overlaps with a microRNA that has been shown to regulate host gene expression, suggesting that HGT-derived parasite small RNAs may function in the parasite–host interaction. This study enriches our understanding of HGT by describing a parasite–host system with unprecedented gene exchange that points to convergent evolution of HGT events and the functional importance of horizontally transferred coding and non-coding sequences.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Fig. 1: Identification and characterization of HGT genes and donors.
Fig. 2: Convergent evolution of expressed HGTs in two independent parasitic lineages.
Fig. 3: C. campestris HGT events are a frequent source of small RNAs.
Fig. 4: HGT is both ancestral and an ongoing process in Cuscuta.
Fig. 5: HGT pathways in light of interaction with mobile mRNAs and mobile small RNAs.

Data availability

Publicly available data sources are as given in the Methods section of the manuscript. Web links for publicly available datasets are indicated in Supplementary Table 22. C. campestris genome assembly and annotations are available from http://ppgp.huck.psu.edu/cuscuta.html. The raw sequence reads for the eight Cuscuta taxa sampled in this study (Cuscuta species RNA sequencing datasets), C. campestris HGT sequences, all multiple sequence alignments and HGT tree files, as well as the supporting trees and alignments for selective constraint analyses (C. campestris HGT gene sequences, alignments and phylogenies), are given as supporting data at http://ppgp.huck.psu.edu/data/Cuscuta_HGT_Manuscript_Data/. All HGT sequences extracted from these assemblies are included as supporting data in the posted multiple sequence alignments and as described below. The raw data for Fig. 1a are in Supplementary Table 2 (column C); Fig. 1b in Supplementary Table 3; Fig. 1d in Supplementary Figs. 11 and 12; Fig. 2a,c,d in Supplementary Table 11; Fig. 2b on http://ppgp.huck.psu.edu/data/Cuscuta_HGT_Manuscript_Data/; Fig. 3a,b in Supplementary Tables 13 and 14; Fig. 3c in Supplementary Table 2; Fig. 3g on http://ppgp.huck.psu.edu/data/Cuscuta_HGT_Manuscript_Data/; Fig. 4 in Supplementary Table 15; and Fig. 5 in Supplementary Tables 2, 13 and 14.

Code availability

The customized code and pipeline associated with data analysis are available from https://github.com/dePamphilis/Cuscuta_HGT_ms_code.

References

  1. 1.

    Davies, J. & Davies, D. Origins and evolution of antibiotic resistance. Microbiol. Mol. Biol. Rev. 74, 417–433 (2010).

  2. 2.

    Davis, C. C. & Xi, Z. Horizontal gene transfer in parasitic plants. Curr. Opin. Plant Biol. 26, 14–19 (2015).

  3. 3.

    Gao, C. et al. Horizontal gene transfer in plants. Funct. Integr. Genom. 14, 23–29 (2014).

  4. 4.

    Kado, T. & Innan, H. Horizontal gene transfer in five parasite plant species in Orobanchaceae. Genome Biol. Evol. 10, 3196–3210 (2018).

  5. 5.

    Sun, T. et al. Two hAT transposon genes were transferred from Brassicaceae to broomrapes and are actively expressed in some recipients. Sci. Rep. 6, 30192 (2016).

  6. 6.

    Xi, Z. et al. Horizontal transfer of expressed genes in a parasitic flowering plant. BMC Genom. 13, 227 (2012).

  7. 7.

    Yang, Z. et al. Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation. Proc. Natl Acad. Sci. USA 113, E7010–E7019 (2016).

  8. 8.

    Yoshida, S., Maruyama, S., Nozaki, H. & Shirasu, K. Horizontal gene transfer by the parasitic plant Striga hermonthica. Science 328, 1128 (2010).

  9. 9.

    Zhang, D. et al. Root parasitic plant Orobanche aegyptiaca and shoot parasitic plant Cuscuta australis obtained Brassicaceae-specific strictosidine synthase-like genes by horizontal gene transfer. BMC Plant Biol. 14, 19 (2014).

  10. 10.

    Zhang, Y. et al. Evolution of a horizontally acquired legume gene, albumin 1, in the parasitic plant Phelipanche aegyptiaca and related species. BMC Evol. Biol. 13, 48 (2013).

  11. 11.

    Kim, G. & Westwood, J. H. Macromolecule exchange in Cuscuta-host plant interactions. Curr. Opin. Plant Biol. 26, 20–25 (2015).

  12. 12.

    Vogel, A. et al. Footprints of parasitism in the genome of the parasitic flowering plant Cuscuta campestris. Nat. Commun. 9, 2515 (2018).

  13. 13.

    Mower, J. P. et al. Horizontal acquisition of multiple mitochondrial genes from a parasitic plant followed by gene conversion with host mitochondrial genes. BMC Biol. 8, 150 (2010).

  14. 14.

    Kim, G., LeBlanc, M. L., Wafula, E., dePamphilis, C. W. & Westwood, J. H. Genomic-scale exchange of mRNA between a parasitic plant and its hosts. Science 345, 808–811 (2014).

  15. 15.

    Shahid, S. et al. MicroRNAs from the parasitic plant Cuscuta campestris target host messenger RNAs. Nature 553, 82–85 (2018).

  16. 16.

    Hepburn, N. J., Schmidt, D. W. & Mower, J. P. Loss of two introns from the Magnolia tripetala mitochondrial cox2 gene implicates horizontal gene transfer and gene conversion as a novel mechanism of intron loss. Mol. Biol. Evol. 29, 3111–3120 (2012).

  17. 17.

    Ranjan, A. et al. De novo assembly and characterization of the transcriptome of the parasitic weed dodder identifies genes associated with plant parasitism. Plant Physiol. 166, 1186–1199 (2014).

  18. 18.

    Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007).

  19. 19.

    Gene Ontology Consortium. Gene Ontology Consortium: going forward. Nucleic Acids Res. 43, D1049–D1056 (2015).

  20. 20.

    Park, C. J., Caddell, D. F. & Ronald, P. C. Protein phosphorylation in plant immunity: insights into the regulation of pattern recognition receptor-mediated signaling. Front. Plant Sci. 3, 177 (2012).

  21. 21.

    Cho, Y., Qiu, Y. L., Kuhlman, P. & Palmer, J. D. Explosive invasion of plant mitochondria by a group I intron. Proc. Natl Acad. Sci. USA 95, 14244–14249 (1998).

  22. 22.

    Barkman, T. J. et al. Mitochondrial DNA suggests at least 11 origins of parasitism in angiosperms and reveals genomic chimerism in parasitic plants. BMC Evol. Biol. 7, 248 (2007).

  23. 23.

    Cho, Y., Mower, J. P., Qiu, Y. L. & Palmer, J. D. Mitochondrial substitution rates are extraordinarily elevated and variable in a genus of flowering plants. Proc. Natl Acad. Sci. USA 101, 17741–17746 (2004).

  24. 24.

    Li, F. et al. MicroRNA regulation of plant innate immune receptors. Proc. Natl Acad. Sci. USA 109, 1790–1795 (2012).

  25. 25.

    Fei, Q., Xia, R. & Meyers, B. C. Phased, secondary, small interfering RNAs in posttranscriptional regulatory networks. Plant Cell 25, 2400–2415 (2013).

  26. 26.

    Arikit, S. et al. An atlas of soybean small RNAs identifies phased siRNAs from hundreds of coding genes. Plant Cell 26, 4584–4601 (2014).

  27. 27.

    Law, J. A. & Jacobsen, S. E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 11, 204–220 (2010).

  28. 28.

    ten Hove, C. A. et al. SCHIZORIZA encodes a nuclear factor regulating asymmetry of stem cell divisions in the Arabidopsis root. Curr. Biol. 20, 452–457 (2010).

  29. 29.

    Mylona, P., Linstead, P., Martienssen, R. & Dolan, L. SCHIZORIZA controls an asymmetric cell division and restricts epidermal identity in the Arabidopsis root. Development 129, 4327–4334 (2002).

  30. 30.

    Bustillo-Avendano, E. et al. Regulation of hormonal control, cell reprogramming, and patterning during de novo root organogenesis. Plant Physiol. 176, 1709–1727 (2018).

  31. 31.

    Liu, M. J. et al. The complex jujube genome provides insights into fruit tree biology. Nat. Commun. 5, 5315 (2014).

  32. 32.

    Becher, H. et al. Endogenous pararetrovirus sequences associated with 24 nt small RNAs at the centromeres of Fritillaria imperialis L. (Liliaceae), a species with a giant genome. Plant J. 80, 823–833 (2014).

  33. 33.

    Costea, M., García, M. A., Baute, K. & Stefanović, S. Entangled evolutionary history of Cuscuta pentagona clade: a story involving hybridization and Darwin in the Galapagos. Taxon 64, 1225–1242 (2015).

  34. 34.

    Costea, M., García, M. A. & Stefanović, S. A phylogenetically based infrageneric classification of the parasitic plant genus Cuscuta (Dodders, Convolvulaceae). Syst. Bot. 40, 269–285 (2015).

  35. 35.

    McNeal, J. R., Kuehl, J. V., Boore, J. L. & dePamphilis, C. W. Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta. BMC Plant Biol. 7, 57 (2007).

  36. 36.

    Westwood, J. H., Yoder, J. I., Timko, M. P. & dePamphilis, C. W. The evolution of parasitism in plants. Trends Plant Sci. 15, 227–235 (2010).

  37. 37.

    Weiss-Schneeweiss, H., Greilhuber, J. & Schneeweiss, G. M. Genome size evolution in holoparasitic Orobanche (Orobanchaceae) and related genera. Am. J. Bot. 93, 148–156 (2006).

  38. 38.

    Zonneveld, B. J. M. New record holders for maximum genome size in eudicots and monocots. J. Bot. 2010, 527357 (2010).

  39. 39.

    Fultz, D., Choudury, S. G. & Slotkin, R. K. Silencing of active transposable elements in plants. Curr. Opin. Plant Biol. 27, 67–76 (2015).

  40. 40.

    Sun, T. et al. Two hAT transposon genes were transferred from Brassicaceae to broomrapes and are actively expressed in some recipients. Sci. Rep. 6, 30192 (2016).

  41. 41.

    Iseli, C., Jongeneel, C. V. & Bucher, P. ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. In Proc. Int. Conf. Intell. Syst. Mol. Biol. 138–148 (1999).

  42. 42.

    Hirakawa, H. et al. Survey of genome sequences in a wild sweet potato, Ipomoea trifida (H. B. K.) G. Don. DNA Res. 22, 171–179 (2015).

  43. 43.

    Denoeud, F. et al. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science 345, 1181–1184 (2014).

  44. 44.

    Sollars, E. S. et al. Genome sequence and genetic diversity of European ash trees. Nature 541, 212–216 (2017).

  45. 45.

    Wang, L. et al. Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis. Genome Biol. 15, R39 (2014).

  46. 46.

    Huang, S. et al. Draft genome of the kiwifruit Actinidia chinensis. Nat. Commun. 4, 2640 (2013).

  47. 47.

    Scaglione, D. et al. The genome sequence of the outbreeding globe artichoke constructed de novo incorporating a phase-aware low-pass sequencing strategy of F1 progeny. Sci. Rep. 6, 19427 (2016).

  48. 48.

    Sierro, N. et al. The tobacco genome sequence and its comparison with those of tomato and potato. Nat. Commun. 5, 3833 (2014).

  49. 49.

    Iorizzo, M. et al. A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution. Nat. Genet. 48, 657–666 (2016).

  50. 50.

    Yang, Z. et al. Comparative transcriptome analyses reveal core parasitism genes and suggest gene duplication and repurposing as sources of structural novelty. Mol. Biol. Evol. 32, 767–790 (2015).

  51. 51.

    Matasci, N. et al. Data access for the 1,000 Plants (1KP) project. Gigascience 3, 17 (2014).

  52. 52.

    Duvick, J. et al. PlantGDB: a resource for comparative plant genomics. Nucleic Acids Res. 36, D959–D965 (2008).

  53. 53.

    Zhu, Q., Kosoy, M. & Dittmar, K. HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers. BMC Genom. 15, 717 (2014).

  54. 54.

    Campbell, M. S., Holt, C., Moore, B. & Yandell, M. Genome annotation and curation using MAKER and MAKER-P. Curr. Protoc. Bioinformatics 48, 4.11.1–4.11.39 (2014).

  55. 55.

    Felsenstein, J. PHYLIP (Phylogenetic Inference Package), Version 3.6 Vol. 5 (Department of Genome Sciences, Univ. of Washington, 2005).

  56. 56.

    Belfort, M. & Bonocora, R. P. Homing endonucleases: from genetic anomalies to programmable genomic clippers. Methods Mol. Biol. 1123, 1–26 (2014).

  57. 57.

    Edgell, D. R. Selfish DNA: homing endonucleases find a home. Curr. Biol. 19, R115–R117 (2009).

  58. 58.

    Maglott, D., Ostell, J., Pruitt, K. D. & Tatusova, T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res. 39, D52–D57 (2011).

  59. 59.

    Goodstein, D. M. et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 40, D1178–D1186 (2012).

  60. 60.

    Fernandez-Pozo, N. et al. The Sol Genomics Network (SGN)–from genotype to phenotype to breeding. Nucleic Acids Res. 43, D1036–D1041 (2015).

  61. 61.

    Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

  62. 62.

    Johnson, N. R., Yeoh, J. M., Coruh, C. & Axtell, M. J. Improved placement of multi-mapping small RNAs. G3 (Bethesda) 6, 2103–2111 (2016).

Download references

Acknowledgements

Sequence data are archived at National Center for Biotechnology Information BioProject ID SRP001053, and at http://ppgp.huck.psu.edu. This research was supported by award No. IOS-1238057 to J.H.W. and C.W.deP. from the NSF Plant Genome Research Program; No. 2018-05102 to M.J.A., J.H.W. and C.W.deP. from the United States Department of Agriculture, with additional support to Z.Y. from the Plant Biology and Biology Department graduate programmes at Penn State; and by the National Institute of Food and Agriculture Project (No. 131997) to J.H.W. The authors thank I. Ko for help with PCR experiments and E. Bellis, Y. Zheng and three anonymous reviewers for helpful comments and suggestions.

Author information

C.W.deP., J.H.W. and Z.Y. conceived this project. Z.Y. performed major analyses, with additional analyses by E.K.W., S.S., G.K., J.R.M., P.R.T, W.-b.Y. and T.N.P. G.K. and P.E.R. performed experiments. E.A.K. and H.Z. performed RT–PCR. J.R.M. generated transcriptome samples for ancestral inference. M.J.A. and S.S. contributed small RNA analyses. N.S.A. supervised the statistical analyses and conception of HGTpropor. Z.Y. and C.W.deP. wrote the manuscript with contributions from E.K.W., J.H.W., P.E.R., S.S. and M.J.A. All authors read and approved the final manuscript.

Correspondence to James H. Westwood or Claude W. dePamphilis.

Additional information

Peer review information: Nature Plants thanks David Hannapel, Fay-Wei Li, Jianqiang Wu and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary Figs. 1–17.

Reporting Summary

Supplementary Tables

Supplementary Tables 1–23.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark