During our initial phylogenetic study of the monocot genus Erythronium (Liliaceae), we observed peculiar eudicot-type internal transcribed spacer (ITS) sequences in a dataset derived from genomic DNA of Erythronium dens-canis. This raised the possibility of horizontal transfer of a eudicot alien ribosomal DNA (rDNA) into the Erythronium genome. In this work we aimed to support this hypothesis by carrying out genomic, molecular, and cytogenetic analyses. Genome skimming coupled by PacBio HiFi sequencing of a bacterial artificial chromosome clone derived from flow-sorted nuclei was used to characterise the alien 45S rDNA. Integration of alien rDNA in the recipient genome was further proved by Southern blotting and fluorescence in situ hybridization using specific probes. Alien rDNA, nested among Potentilla species in phylogenetic analysis, likely entered the Erythronium lineage in the common ancestor of E. dens-canis and E. caucasicum. Transferred eudicot-type rDNA preserved its tandemly arrayed feature on a single chromosome and was found to be transcribed in the monocot host, albeit much less efficiently than the native counterpart. This study adds a new example to the rarely documented nuclear-to-nuclear jumps of DNA between eudicots and monocots while holding the scientific community continually in suspense about the mode of DNA transfer.

Central European Institute of Technology Masaryk University 625 00 Brno Czech Republic

Centre of Systems Biology Biodiversity and Bioresources Babeş Bolyai University 400006 Cluj Napoca Romania

Department of Aquatic Microbial Ecology Institute of Hydrobiology Biology Centre of the Academy of Sciences of the Czech Republic 370 05 České Budějovice Czech Republic

Department of Molecular Biology and Biotechnology Faculty of Biology and Geology Babeş Bolyai University 400006 Cluj Napoca Romania

French Plant Genomic Resource Center INRAE CNRGV 31320 Castanet Tolosan France

Hungarian Department of Biology and Ecology Babeş Bolyai University 400006 Cluj Napoca Romania

Institute of Botany Czech Academy of Sciences 25243 Průhonice Czech Republic

Institute of Experimental Botany of the Czech Academy of Sciences Centre of the Region Haná for Biotechnological and Agricultural Research 779 00 Olomouc Czech Republic

Laboratory of Molecular Epigenetics Institute of Biophysics Academy of Sciences of the Czech Republic 61265 Brno Czech Republic

Molecular Biology Center Interdisciplinary Research Institute on Bio Nano Sciences Babeş Bolyai University 400271 Cluj Napoca Romania

Zobrazit více v PubMed

Allen GA, Soltis DE, Soltis PS. 2003. Phylogeny and biogeography of Erythronium (Liliaceae) inferred from chloroplast matK and nuclear rDNA ITS sequences. Systematic Botany 28: 512-523.

Aubin E, El Baidouri M, Panaud O. 2021a. Horizontal gene transfers in plants. Life 11: 857.

Aubin E, Llauro C, Garrigue J, Mirouze M, Panaud O, El Baidouri M. 2021b. Characterization of interspecific gene flows at the genome-wide level in a natural ecosystem the Massane Forest reveals new insights into horizontal transfer in plants. bioRxiv doi: 10.1101/2021.12.19.471934.

El Baidouri M, Carpentier M-C, Cooke R, Gao D, Lasserre E, Llauro C, Mirouze M, Picault N, Jackson SA, Panaud O. 2014. Widespread and frequent horizontal transfers of transposable elements in plants. Genome Research 24: 831-838.

Baldwin BG, Sanderson MJ, Porter JM, Wojciechowski MF, Campbell CS, Donoghue MJ. 1995. The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. Annals of the Missouri Botanical Garden 82: 247-277.

Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology 19: 455-477.

Bartha L, Sramkó G, Volkova PA, Surina B, Ivanov AL, Banciu HL. 2015a. Patterns of plastid DNA differentiation in Erythronium (Liliaceae) are consistent with allopatric lineage divergence in Europe across longitude and latitude. Plant Systematics and Evolution 301: 1747-1758.

Bartha L, Stepanov NV, Rukšāns J, Banciu HL, Keresztes L. 2015b. Non-monophyly of Siberian Erythronium (Liliaceae) leads to the recognition of the formerly neglected Erythronium sajanense. Journal of Plant Research 128: 721-729.

Bergthorsson U, Adams KL, Thomason B, Palmer JD. 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: 197-201.

Bourque G, Burns KH, Gehring M, Gorbunova V, Seluanov A, Hammell M, Imbeault M, Izsvák Z, Levin HL, Macfarlan TS et al. 2018. Ten things you should know about transposable elements. Genome Biology 19: 199.

Bushnell B. 2016. BBMap: a fast, accurate, splice-aware aligner. [WWW document] URL https://sourceforge.net/projects/bbmap/ [accessed 20 April 2020].

Bushnell B, Rood J, Singer E. 2017. BBMerge - accurate paired shotgun read merging via overlap. PLoS ONE 12: e0185056.

Christin P-A, Edwards Erika J, Besnard G, Boxall Susanna F, Gregory R, Kellogg Elizabeth A, Hartwell J, Osborne CP. 2012. Adaptive evolution of C4 photosynthesis through recurrent lateral gene transfer. Current Biology 22: 445-449.

Clennett JCB, Chase MW, Forest F, Maurin O, Wilkin P. 2012. Phylogenetic systematics of Erythronium (Liliaceae): morphological and molecular analyses. Botanical Journal of the Linnean Society 170: 504-528.

Davis CC, Anderson WR, Wurdack KJ. 2005. Gene transfer from a parasitic flowering plant to a fern. Proceedings of the Royal Society B: Biological Sciences 272: 2237-2242.

Dhillon B, Feau N, Aerts AL, Beauseigle S, Bernier L, Copeland A, Foster A, Gill N, Henrissat B, Herath P et al. 2015. Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen. Proceedings of the National Academy of Sciences, USA 112: 3451-3456.

Diao X, Freeling M, Lisch D. 2006. Horizontal transfer of a plant transposon. PLoS Biology 4: e5.

Dobeš C, Paule J. 2010. A comprehensive chloroplast DNA-based phylogeny of the genus Potentilla (Rosaceae): implications for its geographic origin, phylogeography and generic circumscription. Molecular Phylogenetics and Evolution 56: 156-175.

Dunning LT, Olofsson JK, Parisod C, Choudhury RR, Moreno-Villena JJ, Yang Y, Dionora J, Quick WP, Park M, Bennetzen JL et al. 2019. Lateral transfers of large DNA fragments spread functional genes among grasses. Proceedings of the National Academy of Sciences, USA 116: 4416-4425.

Van Etten J, Bhattacharya D. 2020. Horizontal gene transfer in eukaryotes: not if, but how much? Trends in Genetics 36: 915-925.

Feng T, Moore MJ, Yan M-H, Sun Y-X, Zhang H-J, Meng A-P, Li X-D, Jian S-G, Li J-Q, Wang H-C. 2017. Phylogenetic study of the tribe Potentilleae (Rosaceae), with further insight into the disintegration of Sibbaldia. Journal of Systematics and Evolution 55: 177-191.

Fukuda T, Nakamura S. 1987. Biotic interaction between a rust fungus, Uromyces erythronii Pass., and its host plant, Erythronium japonicum Decne. (Liliaceae). Plant Species Biology 2: 75-83.

Garcia LE, Edera AA, Palmer JD, Sato H, Sanchez-Puerta MV. 2021. Horizontal gene transfers dominate the functional mitochondrial gene space of a holoparasitic plant. New Phytologist 229: 1701-1714.

Graham LA, Davies PL. 2021. Horizontal gene transfer in vertebrates: a fishy tale. Trends in Genetics 37: 501-503.

Helfer S. 2005. Overview of the rust fungi (Uredinales) occurring on Rosaceae in Europe. Nova Hedwigia 81: 325-370.

Hibdige SGS, Raimondeau P, Christin P-A, Dunning LT. 2021. Widespread lateral gene transfer among grasses. New Phytologist 230: 2474-2486.

Huang J. 2013. Horizontal gene transfer in eukaryotes: the weak-link model. BioEssays 35: 868-875.

Jain R, Rivera MC, Lake JA. 1999. Horizontal gene transfer among genomes: the complexity hypothesis. Proceedings of the National Academy of Sciences, USA 96: 3801-3806.

Kado T, Innan H. 2018. Horizontal gene transfer in five parasite plant species in Orobanchaceae. Genome Biology and Evolution 10: 3196-3210.

Kechaykin AA, Shmakov AI, Gregor T, Paule J, German DA. 2021. (2820) Proposal to conserve the name Potentilla (Rosaceae: Potentilleae) with a conserved type. Taxon 70: 680-681.

Kitahara K, Miyazaki K. 2013. Revisiting bacterial phylogeny: natural and experimental evidence for horizontal gene transfer of 16S rRNA. Mobile Genetic Elements 3: e24210.

Kohany O, Gentles AJ, Hankus L, Jurka J. 2006. Annotation, submission and screening of repetitive elements in Repbase: Repbase submitter and censor. BMC Bioinformatics 7: 474.

Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research 27: 722-736.

Kovařík A, Matyášek R, Lim KY, Skalická K, Koukalová B, Knapp S, Chase MW, Leitch AR. 2004. Concerted evolution of 18-5.8-26S rDNA repeats in Nicotiana allotetraploids. Biological Journal of the Linnean Society 82: 615-625.

Kovařík A, Pires JC, Leitch AR, Lim KY, Sherwood AM, Matyášek R, Rocca J, Soltis DE, Soltis PS. 2005. Rapid concerted evolution of nuclear ribosomal DNA in two Tragopogon allopolyploids of recent and recurrent origin. Genetics 169: 931-944.

Kumar S, Stecher G, Suleski M, Hedges SB. 2017. TimeTree: a resource for timelines, timetrees, and tivergence times. Molecular Biology and Evolution 34: 1812-1819.

Lengyel S, Gove AD, Latimer AM, Majer JD, Dunn RR. 2010. Convergent evolution of seed dispersal by ants, and phylogeny and biogeography in flowering plants: a global survey. Perspectives in Plant Ecology, Evolution and Systematics 12: 43-55.

Li F-W, Villarreal JC, Kelly S, Rothfels CJ, Melkonian M, Frangedakis E, Ruhsam M, Sigel EM, Der JP, Pittermann J et al. 2014. Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns. Proceedings of the National Academy of Sciences, USA 111: 6672-6677.

Lim KY, Kovařík A, Matyášek R, Bezděk M, Lichtenstein CP, Leitch AR. 2000. Gene conversion of ribosomal DNA in Nicotiana tabacum is associated with undermethylated, decondensed and probably active gene units. Chromosoma 109: 161-172.

Mahelka V, Krak K, Kopecký D, Fehrer J, Šafář J, Bartoš J, Hobza R, Blavet N, Blattner FR. 2017. Multiple horizontal transfers of nuclear ribosomal genes between phylogenetically distinct grass lineages. Proceedings of the National Academy of Sciences, USA 114: 1726-1731.

Mahelka V, Krak K, Fehrer J, Caklová P, Nagy Nejedlá M, Čegan R, Kopecký D, Šafář J. 2021. A Panicum-derived chromosomal segment captured by Hordeum a few million years ago preserves a set of stress-related genes. The Plant Journal 105: 1141-1164.

Mandáková T, Lysak MA. 2016a. Chromosome preparation for cytogenetic analyses in Arabidopsis. Current Protocols in Plant Biology 1: 43-51.

Mandáková T, Lysak MA. 2016b. Painting of Arabidopsis chromosomes with chromosome-specific BAC clones. Current Protocols in Plant Biology 1: 359-371.

Martinez-Seidel F, Beine-Golovchuk O, Hsieh Y-C, Kopka J. 2020. Systematic review of plant ribosome heterogeneity and specialization. Frontiers in Plant Science 11: 948.

Minh BQ, Nguyen MAT, von Haeseler A. 2013. Ultrafast approximation for phylogenetic Bootstrap. Molecular Biology and Evolution 30: 1188-1195.

Mower JP, Stefanović S, Young GJ, Palmer JD. 2004. Gene transfer from parasitic to host plants. Nature 432: 165-166.

Nagy T, Pfliegler WP, Takács A, Tökölyi J, Molnár VA. 2019. Distribution, infection rates and DNA barcoding of Uromyces erythronii (Pucciniaceae), a parasite of Erythronium (Liliaceae) in Europe. Willdenowia 49: 13-20.

Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. 2014. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution 32: 268-274.

Park M, Christin P-A, Bennetzen JL. 2021. Sample sequence analysis uncovers recurrent horizontal transfers of transposable elements among grasses. Molecular Biology and Evolution 38: 3664-3675.

Pellicer J, Hidalgo O, Dodsworth S, Leitch IJ. 2018. Genome size diversity and its impact on the evolution of land plants. Genes 9: 88.

Persson NL, Toresen I, Andersen HL, Smedmark JEE, Eriksson T. 2020. Detecting destabilizing species in the phylogenetic backbone of Potentilla (Rosaceae) using low-copy nuclear markers. AoB Plants 12: plaa017.

Phansopa C, Dunning LT, Reid JD, Christin P-A. 2020. Lateral gene transfer acts as an evolutionary shortcut to efficient C4 biochemistry. Molecular Biology and Evolution 37: 3094-3104.

Pustahija F, Bašić N, Siljak-Yakovlev S. 2018. Chromosome numbers and genome size data for some Balkan species. In: Kamari G, Blanché C, Siljak-Yakovlev S, eds. Flora Mediterranea 28. Palermo, Italy: International Foundation pro Herbario Mediterraneo, 420-428.

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. The Plant Journal 53: 950-959.

Šafář J, Noa-Carrazana JC, Vrána J, Bartoš J, Alkhimova O, Sabau X, Šimková H, Lheureux F, Caruana M-L, Doležel J et al. 2004. Creation of a BAC resource to study the structure and evolution of the banana (Musa balbisiana) genome. Genome 47: 1182-1191.

Sato M, Miyazaki K. 2017. Phylogenetic network analysis revealed the occurrence of horizontal gene transfer of 16S rRNA in the genus Enterobacter. Frontiers in Microbiology 8: 2225.

Siljak-Yakovlev S, Pustahija F, Šolić EM, Bogunić F, Muratović E, Bašić N, Catrice O, Brown SC. 2010. Towards a genome size and chromosome number database of Balkan Flora: C-values in 343 taxa with novel values for 242. Advanced Science Letters 3: 190-213.

Sochorová J, Coriton O, Kuderová A, Lunerová J, Chèvre A-M, Kovařík A. 2016. Gene conversion events and variable degree of homogenization of rDNA loci in cultivars of Brassica napus. Annals of Botany 119: 13-26.

Tavares S, Ramos AP, Pires AS, Azinheira HG, Caldeirinha P, Link T, Abranches R, Silva Mdo C, Voegele RT, Loureiro J et al. 2014. Genome size analyses of Pucciniales reveal the largest fungal genomes. Frontiers in Plant Science 5: 422.

Tian R-M, Cai L, Zhang W-P, Cao H-L, Qian P-Y. 2015. Rare events of intragenus and intraspecies horizontal transfer of the 16S rRNA gene. Genome Biology and Evolution 7: 2310-2320.

Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK et al. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9: e112963.

Wang W, Ma L, Becher H, Garcia S, Kovarikova A, Leitch IJ, Leitch AR, Kovarik A. 2016. Astonishing 35S rDNA diversity in the gymnosperm species Cycas revoluta Thunb. Chromosoma 125: 683-699.

White TJ, Bruns T, Lee S, Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Shinsky JJ, White TJ, eds. PCR protocols: a guide to methods and applications. San Diego, CA, USA: Academic Press, 315-322.

Wicke S, Costa A, Muñoz J, Quandt D. 2011. Restless 5S: the re-arrangement(s) and evolution of the nuclear ribosomal DNA in land plants. Molecular Phylogenetics and Evolution 61: 321-332.

Xia J, Guo Z, Yang Z, Han H, Wang S, Xu H, Yang X, Yang F, Wu Q, Xie W et al. 2021. Whitefly hijacks a plant detoxification gene that neutralizes plant toxins. Cell 184: 1693-1705.e1617.

Xiao L-Q, Möller M, Zhu H. 2010. High nrDNA ITS polymorphism in the ancient extant seed plant Cycas: incomplete concerted evolution and the origin of pseudogenes. Molecular Phylogenetics and Evolution 55: 168-177.

Xie J, Fu Y, Jiang D, Li G, Huang J, Li B, Hsiang T, Peng Y. 2008. Intergeneric transfer of ribosomal genes between two fungi. BMC Evolutionary Biology 8: 87.

Xu Z, Wang H. 2007. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Research 35: W265-W268.

Yabuki A, Toyofuku T, Takishita K. 2014. Lateral transfer of eukaryotic ribosomal RNA genes: an emerging concern for molecular ecology of microbial eukaryotes. ISME Journal 8: 1544-1547.

Yang Z, Wafula EK, Kim G, Shahid S, McNeal JR, Ralph PE, Timilsena PR, Yu W-B, Kelly EA, Zhang H et al. 2019. Convergent horizontal gene transfer and cross-talk of mobile nucleic acids in parasitic plants. Nature Plants 5: 991-1001.

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

Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between?