Horizontal Transfer of Retrotransposons Between Bivalves and Other
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Horizontal transfer of retrotransposons between PNAS PLUS bivalves and other aquatic species of multiple phyla Michael J. Metzgera,b,c, Ashley N. Paynterd, Mark E. Siddalld, and Stephen P. Goffa,b,e,1 aDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10027; bHoward Hughes Medical Institute, Columbia University, New York, NY 10027; cPacific Northwest Research Institute, Seattle, WA 98122; dSackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY 10024; and eDepartment of Microbiology and Immunology, Columbia University, New York, NY 10027 Contributed by Stephen P. Goff, March 2, 2018 (sent for review October 2, 2017; reviewed by Cédric Feschotte and Welkin Johnson) The LTR retrotransposon Steamer is a selfish endogenous element We previously identified an LTR retrotransposon, Steamer,in in the soft-shell clam genome that was first detected because of its the genomes of soft-shell clams (Mya arenaria) that was highly dramatic amplification in bivalve transmissible neoplasia afflicting amplified in the transmissible cancer of that species (2–10 copies the species. We amplified and sequenced related retrotransposons per haploid genome in normal individuals vs. 100–300 copies in from the genomic DNA of many other bivalve species, finding neoplastic cells) (11, 12). Steamer is a 4,968-bp retrotransposon evidence of horizontal transfer of retrotransposons from the ge- in the Mag family of the Ty3 lineage of LTR retrotransposons, nome of one species to another. First, the phylogenetic tree of the with a single 1,335-aa gag-pol ORF. As with all other Mag ele- Steamer-like elements from 19 bivalve species is markedly discor- ments, it has no detectible env gene. The dramatically expanded dant with host phylogeny, suggesting frequent cross-species copy number of Steamer in the clonal cancer line may be re- transfer throughout bivalve evolution. Second, sequences nearly sponsible for the oncogenic phenotype or may contribute to the Steamer identical to were identified in the genomes of Atlantic continued evolution of this contagious cancer lineage. We also razor clams and Baltic clams, indicating recent transfer. Finally, a identified sequences of retroelements related to Steamer in sev- search of the National Center for Biotechnology Information se- eral bivalves susceptible to bivalve transmissible neoplasia, but quence database revealed that Steamer-like elements are present those specific retroelements were not amplified in the neoplasias in the genomes of completely unrelated organisms, including in those species (13). The identification of Steamer did, however, EVOLUTION zebrafish, sea urchin, acorn worms, and coral. Phylogenetic incon- gruity, a patchy distribution, and a higher similarity than would be prompt us to look further throughout the genomes of bivalves to expected by vertical inheritance all provide evidence for multiple understand the diversity of Steamer-like elements (SLEs) and to long-distance cross-phyla horizontal transfer events. These data determine if their phylogenetic relationships suggest vertical in- suggest that over both short- and long-term evolutionary time- heritance from a bivalve ancestor or more recent HTT between scales, Steamer-like retrotransposons, much like retroviruses, can species. We found SLEs in many, but not all, bivalve species and move between organisms and integrate new copies into new found evidence for multiple, frequent cross-species transfers, host genomes. including recent transfer of nearly identical elements between soft-shell clams, razor clams, and Baltic clams. We furthermore retrotransposons | transposable elements | horizontal transfer | bivalves | found evidence for widespread and frequent transfer throughout cross-phyla horizontal transfer bivalve evolutionary history and even cross-phyla transfer into ransposable elements (TEs) are selfish genetic elements that Significance Tgenerate new copies of themselves within the genomes of their host cells and are inherited vertically during replication of An LTR retrotransposon, Steamer, was previously identified by their hosts. TEs include both the DNA transposons, which usu- virtue of high expression and dramatic amplification in a ally replicate through cut-and-paste mechanisms, and the retro- transmissible cancer in soft-shell clams (Mya arenaria). Here, transposons, which replicate through reverse transcription of an we investigated genome sequences obtained from both phys- RNA transcribed from a DNA copy resident in the host genome ical collections of bivalves and genome databases and found Steamer (1). These TEs most often increase their copy number by in- evidence of horizontal transfer of -like transposons from one species to another, with jumps between bivalves and tracellular retrotransposition, leading to new insertions into the even between animals of completely different phyla. Some genome of the cell they inhabit. In somatic cells, these events can events were ancient, but some (in particular, those between cause mutations and lead to cancers, and, if they occur in germ bivalves) appear to be recent, as the elements are nearly cells or progenitors of germ cells, can result in increased copy identical in different species. These data show that horizontal number in the germ-line genome of the host species (2, 3). The transfer of LTR retrotransposons like Steamer has occurred and gag and pol genes of LTR retrotransposons are related to those continues to occur frequently and that the marine environment of retroviruses (4), and it appears very likely that the vertebrate may be particularly suitable for transfer of transposons. retrovirus lineage itself arose from an ancestral LTR retro- transposon which acquired an envelope gene (5). Despite this Author contributions: M.J.M. and S.P.G. designed research; M.J.M. and A.N.P. performed research; M.J.M., A.N.P., and M.E.S. contributed new reagents/analytic tools; M.J.M. and evolutionary relationship with retroviruses, LTR retrotransposons S.P.G. analyzed data; and M.J.M. and S.P.G. wrote the paper. and other TEs are not expected to transmit easily from cell to Reviewers: C.F., Cornell University; and W.J., Boston College. cell or from individual to individual. It is even harder to under- The authors declare no conflict of interest. stand how these elements can be transmitted from the germ line of Published under the PNAS license. one species to another. To do this, the TE must be released from a Data deposition: The sequences reported in this paper have been deposited in the GenBank cell in one individual and then transported into and integrated database (accession nos. MH012205–MH012241 and MH025768–MH025795). into the germ line of a different organism. While this is a rare 1To whom correspondence should be addressed. Email: [email protected]. event compared with intracellular transposition, with multiple This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. barriers, there are numerous reports of horizontal transfer of 1073/pnas.1717227115/-/DCSupplemental. TEs (HTT) from one organism to another (6–10). Published online April 18, 2018. www.pnas.org/cgi/doi/10.1073/pnas.1717227115 PNAS | vol. 115 | no. 18 | E4227–E4235 Downloaded by guest on September 29, 2021 many other marine organisms, including vertebrates, sea urchins, of multiple independent researchers, and from multiple commercial and coral. sources. The integrity of the genomic DNA and the species iden- tities were confirmed by amplification and sequencing of a region of Results the mitochondrial cytochrome c oxidase subunit I gene (COI). Se- Multiple Cross-Species Transfers Throughout Bivalve Evolution. To quences from this gene could be amplified from only 24 species search for SLEs across the bivalve class, we performed PCR using reported pan-invertebrate primers (14), but by using other primer amplification using degenerate primers in conserved positions in variants, mitochondrial COI DNA was amplified and sequenced the reverse transcriptase-integrase (RT-IN) region of the pol gene from all 37 species. in the genomic DNA of 36 bivalve species (and one gastropod) Using degenerate primers in conserved regions of Steamer, obtained from the Ambrose Monell Cryo Collection (AMCC) of the SLE sequences were amplified from 19 of the 37 species analyzed American Museum of Natural History (AMNH), from collections (Table S1). The DNAs were cloned from these 18 bivalves and one A B 2.5 3.5 3 2 2.5 1.5 2 1.5 1 1 0.5 0.5 SLE nucleotide sequence distance 0 SLE amino acid sequence distance 0 0 0.2 0.4 0.6 0.8 1 0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 COI nucleotide sequence distance COI amino acid sequence distance C COI SLE Retusa obtusa Barbatia candida 100 Cardites floridanus x Limaria pellucida 2 100 Placopecten magellanicus Placopecten magellanicus 2 70 Spondylus tenuis x Limaria pellucida Mytilus trossulus Pteria colymbus x Limaria pellucida 1 100 Anadara transversa x Geukensia demissa Barbatia candida Retusa obtusa 100 Crassostrea virginica Crassostrea virginica Crassostrea gigas 58 100 Mytilus trossulus Ischadium recurvum 100 Mytilus edulis Crassostrea gigas 92 Brachidontes exustus x Siliqua patula 94 Geukensia demissa Mya arenaria 65 100 Ischadium recurvum Ensis directus 1 70 61 Ctena orbiculata x 86 78 100 Gastrochaena ovata x Limecola balthica 99 Siliqua patula Mytilus edulis 100 97 68 Ensis directus Cerastoderma edule 1 100 Panopea generosa Panopea generosa 100 Donax variabili x Mercenaria mercenaria 2 Limecola balthica Cerastoderma edule 4 78 Mya arenaria 100 Dreissena polymorpha Venerupis philippinarum 100 Caryocorbula swiftiana x Polititapes aureus 1 62 Mulinia lateralis x Venerupis corrugata 2 84 75 55 Chama macerophylla x Dreissena polymorpha 96 66 Mercenaria mercenaria Cerastoderma edule 2 59 97 72 Chione elevata x 53 Venerupis philippinarum Venerupis corrugata 1 97 Polititapes aureus Mercenaria mercenaria 1 Venerupis corrugata Cerastoderma edule 3 100 Sphaerium fabale x Ensis directus 2 100 Cerastoderma glaucum x Placopecten magellanicus 1 Cerastoderma edule 66 Elliptio complanata x Mercenaria mercenaria 3 100 Lampsilis siliquoidea x Polititapes aureus 3 Lasmigona costata x Polititapes aureus 2 Fig.