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Massive Horizontal Transfer of Transposable Elements in Insects

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Massive Horizontal Transfer of Transposable Elements in Insects Massive horizontal transfer of transposable elements in insects Jean Peccouda,1, Vincent Loiseaua, Richard Cordauxa, and Clément Gilberta,1 aUMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, Poitiers F-86073, France Edited by Nancy L. Craig, Johns Hopkins University School of Medicine, Baltimore, MD, and approved March 20, 2017 (received for review December 22, 2016) Horizontal transfer (HT) of genetic material is central to the architec- Results and Discussion ture and evolution of prokaryote genomes. Within eukaryotes, the To detect HTT in insects, we de novo characterized TEs in all majority of HTs reported so far are transfers of transposable elements reference genome assemblies available in GenBank as of May (TEs). These reports essentially come from studies focusing on specific 2016 (n = 195 species; Dataset S1 and Fig. S1) which represent lineages or types of TEs. Because of the lack of large-scale survey, the 123 genera and 13 of the 28 insect orders. To minimize detection amount and impact of HT of TEs (HTT) in eukaryote evolution, as well biases, we did not rely on established genome annotations that as the trends and factors shaping these transfers, are poorly known. are available for only a subset of the species included in our Here, we report a comprehensive analysis of HTT in 195 insect study, and instead treated every species’ genome equally. This genomes, representing 123 genera and 13 of the 28 insect orders. We automatic characterization was performed with the Repeat- found that these insects were involved in at least 2,248 HTT events Modeler pipeline (18) and led to the identification of 53,452 TE that essentially occurred during the last 10 My. We show that DNA families assigned to 98 superfamilies (Dataset S2). These exclude transposons transfer horizontally more often than retrotransposons, 3,417 families whose consensus sequences were found to include and unveil phylogenetic relatedness and geographical proximity as genes that may not belong to TEs (SI Materials and Methods), as major factors facilitating HTT in insects. Even though our study is well as all short interspersed element (SINE) consensus se- restricted to a small fraction of insect biodiversity and to a recent quences, which might correspond to RNA pseudogenes (19). For evolutionary timeframe, the TEs we found to be horizontally trans- each species, the consensus sequences of TE families were used ferred generated up to 24% (2.08% on average) of all nucleotides of to locate TE copies in genomic contigs. TE copies >100 base insect genomes. Together, our results establish HTT as a major force pairs were compared by pairwise reciprocal homology searches shaping insect genome evolution. between every two species. After filtering out short and low- score alignments, and alignments between TEs from different horizontal transfer | transposable elements | insects | genome evolution | superfamilies, we retained a total of ∼5.9 million hits, each of biogeography which indicated TE homology between two genomes. TEs inherited from a recent common ancestor by descendent orizontal transfer (HT) is the transmission of genetic ma- species, rather than horizontally transferred between these spe- EVOLUTION Hterial between organisms through a mechanism other than cies, may present homology passing our filters. We identified reproduction. In prokaryotes, HT is pervasive, its mechanisms clades of related insect species for which this situation may are well understood, and it is now viewed as one of the main happen, by relying on the common assumption that inherited forces shaping genome architecture and evolution (1, 2). In TEs evolve neutrally and similarly to synonymous sites of protein contrast, the study of HT in eukaryotes is less documented, but coding genes (20). This assumption implies that TEs showing has been increasingly investigated. The majority of genes hori- higher interspecific homology than the synonymous sites of zontally acquired by eukaryotes come from bacteria, but the orthologous genes should share a more recent ancestor than the extent to which these transfers have contributed to eukaryote host species, and hence be the result of HT (16, 21). Conversely, evolution is still unclear (3, 4). Gene transfers from eukaryote to eukaryote appear to be largely limited to filamentous organisms, Significance such as oomycetes and fungi (5, 6). In animals and plants, very few cases of such horizontal gene Eukaryotes normally receive their genetic material from their transfers (HGTs) have been reported so far (7, 8). In fact, most parents but may occasionally, like prokaryotes do, acquire DNA of the genetic material that is horizontally transferred in animals from unrelated organisms through horizontal transfer (HT). In and plants consists of transposable elements (TEs) (9–11), which animals and plants, HT mostly concerns transposable elements are pieces of DNA able to move from a chromosomal locus to (TEs), probably because these pieces of DNA can move within another (12). The greater ability of TEs to move between or- genomes. Assessing the impact of HTs on eukaryote evolution ganisms certainly relates to their intrinsic ability to transpose and the factors shaping the dynamics of these HTs requires within genomes, which genes cannot do. HT of TEs (HTT) may large-scale systematic studies. We have analyzed the genomes allow these elements to enter naive genomes, which they invade from 195 insect species and found that no fewer than by making copies of themselves, and then escape before they 2,248 events of HT of TEs occurred during the last 10 My, become fully silenced by anti-TE defenses (13). A growing – particularly between insects that were closely related and number of studies have identified such HTT (11, 14 16). How- geographically close. These results suggest that HT of TEs plays ever, a common drawback of these studies has been the inclusion a major role in insect genome evolution. of a limited set of TEs (11) or organisms (16), which hampers our understanding of the breadth of HTT, its contribution to genome Author contributions: J.P., R.C., and C.G. designed research; J.P., V.L., and C.G. performed evolution, and of the factors and barriers shaping these transfers research; J.P. and V.L. analyzed data; and J.P., R.C., and C.G. wrote the paper. in eukaryotes (13). In this study, we overcame these limitations The authors declare no conflict of interest. by performing a large-scale, comprehensive analysis of HTT in This article is a PNAS Direct Submission. insects. We focused on insects because a large number of whole- 1To whom correspondence may be addressed. Email: [email protected] or genome sequences are publicly available for this group and be- [email protected]. cause insect genomes are known to harbor diverse and highly This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. dynamic TE landscapes (17). 1073/pnas.1621178114/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1621178114 PNAS | May 2, 2017 | vol. 114 | no. 18 | 4721–4726 Downloaded by guest on October 1, 2021 TEs whose divergence is similar to the synonymous divergence of copies. These two rounds of clustering yielded 4,499 HTT events orthologous genes may be vertically inherited. We thus collapsed for all pairs of insect lineages (Fig. 1), after discarding transfers a clade of insect species into a lineage if (i) a fraction (>0.3%) of that involved fewer than five TE copies per lineage. Taking pairs its core orthologous genes showed lower synonymous divergence of lineages separately, each of these transfers represents an in- than the highest nucleotide divergence of TEs or (ii) these dependent HTT event. species diverged in the last 40 My (Materials and Methods and To infer the minimum number of HTT events across all 81 in- Fig. S2). This collapsing resulted in the delineation of 81 line- sect lineages, we considered that any HTT inferred in a pair of ages. We ignored all homologies within these lineages and con- lineages might not reflect a direct transfer from one to the other, sidered the ∼1.46 million hits between species from distinct but separate acquisitions of TEs from other sources, which may lineages to essentially result from HT. already be counted as HTTs in other lineage pairs. There is no To translate these hits into a minimum number of HTT events, method that can discriminate between direct transfer and such it must be considered that many hits may result from a single TE “indirect” transfers. However, it is possible to avoid counting in- that transferred between two lineages and transposed into mul- direct HTTs, by constructing networks of insect species sharing tiple similar copies. The resulting hits have a distinct feature: similar TEs, in which the minimum number of HTT events is the The copies they involve diverged within the recipient lineage number of lineages minus one. This parsimonious count resulted after the transfer; hence, they should be more similar to each in 2,248 HTT events among the 81 insect lineages considered in other than to copies from the other lineage. We applied a heu- our study (Fig. 2 and Dataset S2). This unprecedented figure is ristic approach based on this principle (Materials and Methods)to more than four times higher than the total number of HTT events cluster hits within each pair of lineages and TE superfamily into reported so far in metazoans, plants, and fungi combined (10). candidate HTT events. We also considered that a transferred TE Such a high number is still not unexpected, given that studies might have degraded into nonoverlapping parts that share no focusing on one or a few TEs often found one or more HTT sequence homology. To avoid counting these parts as several events between multiple, distantly related taxa (11, 14–16, 22).
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