Horizontal transfer of OC1 transposons in the Tasmanian devil
© Gilbert et al.; licensee BioMed Central Ltd. 2013
Received: 21 September 2012
Accepted: 18 January 2013
Published: 27 February 2013
There is growing recognition that horizontal DNA transfer, a process known to be common in prokaryotes, is also a significant source of genomic variation in eukaryotes. Horizontal transfer of transposable elements (HTT) may be especially prevalent in eukaryotes given the inherent mobility, widespread occurrence, and prolific abundance of these elements in many eukaryotic genomes.
Here, we provide evidence for a new case of HTT of the transposon family OposCharlie1 (OC1) in the Tasmanian devil, Sarcophilus harrisii. Bioinformatic analyses of OC1 sequences in the Tasmanian devil genome suggest that this transposon infiltrated the common ancestor of the Dasyuridae family ~17 million years ago. This estimate is corroborated by a PCR-based screen for the presence/absence of this family in Tasmanian devils and closely-related species.
This case of HTT is the first to be reported in dasyurids. It brings the number of animal lineages independently invaded by OC1 to 12, and adds a fourth continent to the pandemic-like pattern of invasion of this transposon. In the context of these data, we discuss the evolutionary history of this transposon family and its potential impact on the diversification of marsupials.
KeywordsHorizontal transfer Transposable element Tasmanian devil Sarcophilus harrisii
Much like horizontal gene transfer (HGT), the frequency, mechanisms and evolutionary impact of the horizontal transfer of transposable elements (HTT) have been well characterized in prokaryotes [1, 2]. In eukaryotes, the number of fully sequenced genomes is now sufficient to reveal that HTT has also had a significant impact on the evolution of genomes in this group, but many aspects of the phenomenon remain largely mysterious [3, 4]. Among metazoans, and in particular vertebrates, HTT can be examined on a geological timescale because these taxa are characterized by large, slow-evolving genomes in which vast numbers of transposable elements (TEs) can persist for many millions of years. In a series of recent studies, we and others reported numerous cases of Class II TEs (cut-and-paste DNA transposons) transferred horizontally among vertebrate and invertebrate species, between multiple continents, over a period stretching from ~45 to ~15 My ago [5–8]. These HTT events are notable because they are geographically widespread, implicate several transposon families, and affect a wide range of tetrapods, as well as a blood-sucking parasitic insect (Rhodnius prolixus) as a possible vector . One of the transposon families, OposCharlie1 (OC1), achieved a particularly high level of promiscuity, as it was found to have infiltrated the genomes of 11 deeply diverged species on both Old and New World continents at the time of transfer.
Results and discussion
Sequence homology-based searches (BLASTn) using the OC1_Et consensus sequence as a query (reconstructed in ) yielded many significant hits in the genome of the Tasmanian devil (Sarcophilus harrisii). Majority-rule consensus sequences were reconstructed for an autonomous element (2,571 bp) encoding a 602-amino acid transposase and for a major family of non-autonomous elements (192 bp) based on an alignment of 25 representative copies of each type (Additional file 1). We called this autonomous element family OC1_Das to reflect the fact that, in addition to the Tasmanian devil, it is present in several other members of the family Dasyuridae (see below). In addition, non-autonomous partners of OC1_Das are called OC1_Das_NA. They form a high copy number, homogenous family of non-autonomous elements (also called miniature terminal inverted-repeat transposable elements, or MITEs), which likely result from amplification of an internally-deleted autonomous copy (deletion breakpoints occur at position 36 and 2337 of the consensus OC1_Das), a process typical of Class II transposons . Further sequence mining using BLASTn and RepeatMasker  revealed that the Tasmanian devil’s genome contains 5,208 copies (or fragments of copies longer than 100 bp) of OC1_Das; of these, 387 are full length or slightly truncated autonomous elements and the rest correspond to short non-autonomous elements. Two studies recently produced whole genome sequence (WGS) data for several Tasmanian devil individuals [11, 12]. The results presented here are based on analyses of the WGS produced by Miller et al.  only, but analyses (not shown) carried out on the other WGS data  yield very similar numbers.
An alignment of the OC1_Das autonomous consensus sequence with those reconstructed previously for vertebrate and invertebrate taxa known to harbor OC1  revealed a very high level of nucleotide identity across the entire length of the elements (90 to 95%). Phylogenetic analyses of 30 randomly-selected copies of OC1_Das yielded a star topology and a lack of subfamily structure, indicating that OC1_Das amplified through a single major burst of transposition, followed by the accumulation of private mutations in its copies. This pattern is consistent with a scenario of neutral evolution after insertion in the genome (Additional file 2: Figure S1). In further support for the neutral evolution of OC1_Das transposase sequences, we found that dN/dS values calculated between the consensus OC1_Das and each of the 30 copies examined were all above 0.5 (mean = 0.88; SD = 0.22). In addition, a codon-based Z-test revealed no evidence of purifying selection acting on OC1_Das transposase genes after their insertion in the Tasmanian devil genome (p-values > 0.05 for 27 pairwise comparisons and p-values between 0.027 and 0.042 for the three other pairwise comparisons). Thus, as concluded in previous studies [5, 6], the level of sequence conservation between OC1_Das and OC1 elements previously identified in other species is incompatible with vertical inheritance from the most recent common ancestor (dating between 80 My and 500 My ago [13, 14]. For example, the level of nucleotide identity (95%) between OC1_Das and OC1_Md from the opposum (the closest species to Dasyuridae known to harbor OC1) is significantly higher (88%) than that of RAG1, a gene known to evolve under strong functional constraint in vertebrates (dN/dS = 0.1 between Tasmanian devil and opossum RAG1 sequences; codon Z-test p-value = 0). Thus, the presence of OC1 in the Tasmanian devil’s genome is best explained by the horizontal transfer of this element into this lineage. This discovery brings the total number of animal lineages independently infiltrated by OC1 to twelve.
Genome-wide characterization of OC1 elements based on WGS for various metazoans 1
Amount of DNA (kb)
Average distance from consensus (%)
Two scenarios can explain the patterns we observe. First, OC1_Das was horizontally transferred into a common ancestor of the dunnart and Tasmanian devil, and the absence of orthologous copies at the three loci that we tested is due to the fact that the element continued actively transposing after the split of the species, and/or to the differential fixation of ancestrally polymorphic insertions in the two species. The second possibility is that OC1 was transferred independently in the dunnart and Tasmanian devil lineages. Our molecular estimate of the timing of OC1_Das amplification (17 My) falls within the range of proposed divergence times for dunnart/Tasmanian devil (14 – 23 My; [14, 17, 18]), which supports the idea that OC1_Das was active during the speciation event that separated the Tasmanian devil from its dasyurid sister group that includes about 40 species from four genera (Sminthopsis, Dasyurus, Antechinus and Phascogale; [14, 18]). Whether the amplification of OC1_Das played a role in this speciation event, as proposed for other transposition bursts , is an interesting question that deserves further investigation.
It is also noteworthy that we found one full-length OC1_Das transposase that is free of premature stop codons and frameshift mutations (contig AEFK01150217; ). While it is unclear whether this transposase is part of a complete autonomous element (it lies within a short 1975-bp contig), it may be a source of functional protein capable of mobilizing other OC1 copies. The question of whether this family of element is still active in Dasyuridae warrants further assessment, as to the best of our knowledge no active Class II transposon has yet been reported in marsupials.
Several hypotheses have been proposed to explain how transposable elements might be transferred between eukaryotic hosts, including transmission by contact of bodily fluids, feeding, or via some kind of vector such as a parasite [22–24], reviewed in [3, 25]. None of these routes can be favored at present in the case of the Dasyuridae. The location of OC1_Das in the Old World Clade of the OC1 phylogeny (Figure 2) does not help resolve this issue. However OC1 is an especially interesting case of HTT in that alignment of the 5′ subterminal region of the otherwise nearly identical consensus sequences from all taxa previously found to harbor horizontally-transferred copies of the element reveals two geographically distinct signatures (either Old or New World). Surprisingly, this subterminal region in OC1_Das is made of a 382-bp fragment that is unique among all OC1 elements so far described (Position 66 to 447 on the OC1_Das autonomous consensus provided in Additional file 1). Taxa that are found to share this region may provide evidence for concurrent HTT and open the possibility that this region of the transposon could be used to identify direct donor or vector species in the future.
We provide evidence for a new case of HTT of the transposon family OposCharlie1 (OC1) based on WGS of the Tasmanian devil, Sarcophilus harrisii, and molecular screening of closely-related marsupials. Our bioinformatic analysis and PCR results indicate the HTT event occurred ~17 My ago. This finding expands one of the most widespread case of HTT identified in eukaryotes to include another deeply diverged vertebrate lineage (the dasyurid marsupials) and an additional continent (Australia). Intriguingly, our estimated dating of this episode of HTT coincides with a series of speciation events that have led to the diversification of this lineage of marsupials.
Searches for the presence of OposCharlie1 (OC1) in eukaryote genomes were performed using BLASTn and the OC1_Et consensus sequence reconstructed for the tenrec (Echinops telfairi) in . Phylogenetic analyses of OC1 consensus sequences were reconstructed using PhyML 3.0 . The best fitting nucleotide substitution model (TPM3uf + G) was chosen using jModeltest 0.1.1 . The robustness of the nodes was assessed by a bootstrap analysis involving 1000 pseudo replicates of the original matrix. To examine the pattern of evolution of OC1 after horizontal transfer in the Tasmanian devil’s genome, dN/dS analyses were performed as follows: all non-sense mutations were removed from the transposase sequences of the 30 full (or nearly full) length copies aligned as described above and we then tested whether the dynamics of evolution between each copy and the consensus (an estimate of the ancestral founder element) was significantly different from what is expected if the sequence is evolving neutrally using the codon-based Z-test in MEGA 4.0 (Nei-Gojobori method; Jukes-Cantor correction; 1000 bootstrap replicates).
PCR of OC1_Das using internal primers and primers designed on flanking regions were conducted using the following temperature cycling: initial denaturation at 94°C for 5 min, followed by 30 cycles of denaturation at 94°C for 30 s, annealing between 48–54°C based on element-specific gradients (for 30 s), and elongation at 72°C for 1 min, ending with a 10 min elongation step at 72°C. Fragments from the PCR were visualized on a 1–2% agarose gel, cloned and sequenced.
The authors would like to acknowledge the following organizations for funding portions of this work: NIH-R01 GM077582 (CF), M.J. Murdock Charitable Trust (SS) and NSF-MCB-1150213 (SS).
- Frost LS, Leplae R, Summers AO, Toussaint A: Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol. 2005, 3: 722-732. 10.1038/nrmicro1235.View ArticlePubMed
- Bichsel M, Barbour AD, Wagner A: The early phase of a bacterial insertion sequence infection. Theor Popul Biol. 2010, 78 (4): 278-288. 10.1016/j.tpb.2010.08.003.View ArticlePubMed
- Schaack S, Gilbert C, Feschotte C: Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends Ecol Evol. 2010, 25: 537-546. 10.1016/j.tree.2010.06.001.PubMed CentralView ArticlePubMed
- Wallau GL, Ortiz MF, Silva Loreto EL: Horizontal transposon transfer in Eukarya: detection, bias and perspectives. Genome Biol Evol. 2012, Available online Jul 12
- Pace JK, Gilbert C, Clark MS, Feschotte C: Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods. Proc Natl Acad Sci U S A. 2008, 105: 17023-17028. 10.1073/pnas.0806548105.PubMed CentralView ArticlePubMed
- Gilbert C, Schaack S, Pace JK, Brindley PJ, Feschotte C: A role for host-parasite interactions in the horizontal transfer of transposons across phyla. Nature. 2010, 464: 1347-1350. 10.1038/nature08939.PubMed CentralView ArticlePubMed
- Novick P, Smith J, Ray D, Boissinot S: Independent and parallel lateral transfer of DNA transposons in tetrapod genomes. Gene. 2010, 449: 85-94. 10.1016/j.gene.2009.08.017.View ArticlePubMed
- Gilbert C, Hernandez SS, Flores-Benabib J, Smith EN, Feschotte C: Rampant horizontal transfer of SPIN transposons in squamate reptiles. Mol Biol Evol. 2012, 29: 503-515. 10.1093/molbev/msr181.PubMed CentralView ArticlePubMed
- Feschotte C, Zhang X, Wessler SR: Miniature inverted-repeat transposable elements (MITEs) and their relationship with established DNA transposons. Mobile DNA II. Edited by: Craig N, Craigie R, Gellert M, Lambowitz A. 2002, Washington D.C: American Society of Microbiology Press
- Smit AFA, Hubley R, Green P: RepeatMasker Open-3.0 (1996–2004). http://www.repeatmasker.org,
- Miller W, Hayes VM, Ratan A, Petersen DC, Wittekindt NE, Miller J, Walenz B, Knight J, Qi J, Zhao F, Wang Q, Bedoya-Reina OC, Katiyar N, Tomsho LP, Kasson LM, Hardie RA, Woodbridge P, Tindall EA, Bertelsen MF, Dixon D, Pyecroft S, Helgen KM, Lesk AM, Pringle TH, Patterson N, Zhang Y, Kreiss A, Woods GM, Jones ME, Schuster SC: Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil). Proc Natl Acad Sci U S A. 2011, 108: 12348-12353. 10.1073/pnas.1102838108.PubMed CentralView ArticlePubMed
- Murchison EP, Murchison EP, Schulz-Trieglaff OB, Ning Z, Alexandrov LB, Bauer MJ, Fu B, Hims M, Ding Z, Ivakhno S, Stewart C, Ng BL, Wong W, Aken B, White S, Alsop A, Becq J, Bignell GR, Cheetham RK, Cheng W, Connor TR, Cox AJ, Feng ZP, Gu Y, Grocock RJ, Harris SR, Khrebtukova I, Kingsbury Z, Kowarsky M, Kreiss A, Luo S: Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer. Cell. 2012, 148: 780-791. 10.1016/j.cell.2011.11.065.PubMed CentralView ArticlePubMed
- Peterson KJ, Cotton JA, Gehling JG, Pisani D: The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records. Philosophical Transactions of the Royal Society Series B. 2008, 363 (1496): 1435-1443. 10.1098/rstb.2007.2233.View Article
- Meredith RW, Westerman M, Case JA, Springer MS: A phylogeny and timescale for marsupial evolution based on sequences for five nuclear genes. J Mammal Evol. 2008, 15: 1-36. 10.1007/s10914-007-9062-6.View Article
- Le Rouzic A, Capy P: The first steps of transposable elements invasion: parasitic strategy vs. genetic drift. Genetics. 2005, 169: 1033-1043. 10.1534/genetics.104.031211.PubMed CentralView ArticlePubMed
- Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, Belov K, Rens W, Waters PD, Pharo EA, Shaw G, Wong ES, Lefèvre CM, Nicholas KR, Kuroki Y, Wakefield MJ, Zenger KR, Wang C, Ferguson-Smith M, Nicholas FW, Hickford D, Yu H, Short KR, Siddle HV, Frankenberg SR, Chew KY, Menzies BR, Stringer JM, Suzuki S, Hore TA, Delbridge ML: Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biol. 2011, 12: R81-10.1186/gb-2011-12-8-r81.PubMed CentralView ArticlePubMed
- Meredith RW, Westerman M, Springer MS: A phylogeny of Diprotodontia (Marsupialia) based on sequences for five nuclear genes. Mol Phylogenet Evol. 2009, 51: 554-571. 10.1016/j.ympev.2009.02.009.View ArticlePubMed
- Krajewski C, Wroe S, Westerman M: Molecular evidence for the pattern and timing of cladogenesis in dasyurid marsupials. Zool J Linn Soc. 2000, 130: 375-404. 10.1111/j.1096-3642.2000.tb01635.x.View Article
- Jurka J, Bao W, Kojima KK: Families of transposable elements, population structure and the origin of species. Biol Direct. 2011, 6: 44-10.1186/1745-6150-6-44.PubMed CentralView ArticlePubMed
- Brown OJF: Tasmanian devil (Sarcophilus harrisii) extinction on the Australian mainland in the mid-Holocene: multicausality and ENSO intensification. Alcheringa. 2006, 30: 49-57. 10.1080/03115510609506855.View Article
- Lambeck K, Chappell J: Sea level change through the last glacial cycle. Science. 2001, 292: 679-686. 10.1126/science.1059549.View ArticlePubMed
- Houck MA, Clark JB, Peterson KR, Kidwell MG: Possible horizontal transfer of Drosophila genes by the mite Proctolaelaps regalis. Science. 1991, 253: 1125-1128. 10.1126/science.1653453.View ArticlePubMed
- Schubbert R, Hohlweg U, Renz D, Doerfler W: On the fate of orally ingested foreign DNA in mice: chromosomal association and placental transmission to the fetus. Mol Gen Genet. 1998, 259: 569-576. 10.1007/s004380050850.View ArticlePubMed
- Yoshiyama M, Tu Z, Kainoh Y, Honda H, Shono T, Kimura K: Possible horizontal transfer of a transposable element from host to parasitoid. Mol Biol Evol. 2001, 18: 1952-1958. 10.1093/oxfordjournals.molbev.a003735.View ArticlePubMed
- Loreto EL, Carareto CM, Capy P: Revisiting horizontal transfer of transposable elements in Drosophila. Heredity (Edinb). 2008, 100: 545-554. 10.1038/sj.hdy.6801094.View Article
- Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O: New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010, 59: 307-321. 10.1093/sysbio/syq010.View ArticlePubMed
- Posada D: jModelTest: phylogenetic model averaging. Mol Biol Evol. 2008, 25: 1253-1256. 10.1093/molbev/msn083.View ArticlePubMed
- Hall T: BioEdit version 5.8. 2004, http://www.mbio.ncsu.edu/BioEdit/bioedit.html/,
- Tamura K, Dudley J, Nei M, Kumar S: MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 2007, 24: 1596-1599. 10.1093/molbev/msm092.View ArticlePubMed
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.