Evolution of Ty1 copy number control in yeast by horizontal transfer and recombination

Summary

Transposable elements constitute a large fraction of most eukaryotic genomes. Insertion of mobile DNA sequences typically has deleterious effects on host fitness, and thus diverse mechanisms have evolved to control mobile element proliferation. Mobility of the Ty1 retrotransposon in Saccharomyces yeasts is regulated by copy number control (CNC) mediated by a self-encoded restriction factor derived from the Ty1 gag capsid gene that inhibits virus-like particle function. Here, we survey a panel of wild and human-associated strains of S. cerevisiae and S. paradoxus to investigate how genomic Ty1 content influences variation in Ty1 mobility. We observe high levels of mobility for a tester element with a gag sequence from the canonical Ty1 subfamily in permissive strains that either lack full-length Ty1 elements or only contain full-length copies of the Ty1’ subfamily that have a divergent gag sequence. In contrast, low levels of canonical Ty1 mobility are observed in restrictive strains carrying full-length Ty1 elements containing a canonical gag sequence. Phylogenomic analysis of full-length Ty1 elements revealed that Ty1’ is the ancestral subfamily present in wild strains of S. cerevisiae, and that canonical Ty1 in S. cerevisiae is a derived subfamily that acquired gag from S. paradoxus by horizontal transfer and recombination. Our results provide evidence that variation in the ability of S. cerevisiae and S. paradoxus strains to repress canonical Ty1 transposition via CNC is regulated by the genomic content of different Ty1 subfamilies, and that self-encoded forms of transposon control can spread across species boundaries by horizontal transfer.

Keywords:

Transposable elements – Saccharomyces cerevisiae – Sequence analysis – Sequence alignment – Phylogenetics – Phylogenetic analysis – Multiple alignment calculation – Gag genes

Introduction

Retrotransposons are mobile genetic elements that transpose via an RNA intermediate and impact genome size, structure, function and molecular evolution in diverse eukaryotic lineages [1,2]. The budding yeast Saccharomyces cerevisiae is a powerful model organism for studying retrovirus-like long terminal repeat (LTR) retrotransposons, with many fundamental aspects of retrotransposon biology initially characterized in this species [3–5]. The complete sequencing of the yeast genome provided the first insight into organization and evolution of retrotransposons at the genomic scale [6–10]. More recently, advances in sequencing technologies and bioinformatics have provided unprecedented opportunities to investigate the evolutionary dynamics and consequences of transposition across yeast populations and species [11–20].

The current assembly of the S. cerevisiae S288c reference strain contains sequences from six families of LTR retrotransposons, four that are active (Ty1, Ty2, Ty3, and Ty4) and two that are inactive (Ty5 and Ty3_1p) [7,13]. At least 50 complete and over 400 partial Ty elements comprise 3.3% of the S288c reference assembly [7,13]. The abundance of complete or partial Ty elements and their solo LTR derivatives varies significantly between S. cerevisiae strains, where relatively high Ty content is observed in lab strains such as S288c relative to wild strains [12–14,21,22]. In general, full-length Ty element insertions are strain-specific or shared by only a few strains, while most solo LTR insertions and a few truncated “relic” elements are found at high allele frequency [13,14]. Additionally, some Ty elements in S. cerevisiae have distinct subfamilies (e.g. the Ty1’ and Ty1/2 subfamilies of Ty1) [7,8,23] or show evidence of recent horizontal transmission from other species (e.g. Ty2 and Ty3_1p) [13,22].

Ty1 is the most abundant retrotransposon family in the S. cerevisiae reference strain S288c (>30 full-length copies), and is both actively transcribed and transpositionally competent (reviewed in [4]). The structure and replication of Ty1 elements resembles that of retroviruses. Ty1 consists of two partially overlapping open reading frames–gag (TYA) and pol (TYB)–flanked by LTRs. mRNA from full-length Ty1 elements serves as a template for both reverse transcription and translation of the proteins necessary for retrotransposition: the Gag capsid protein, protease, integrase, and reverse transcriptase. Ty1 RNA is specifically packaged into virus-like particles (VLPs) and serves as the template for reverse transcription into linear cDNA, which subsequently is imported into the nucleus as a protein/DNA complex using a nuclear localization signal present on integrase. Ty1 preferentially integrates near genes transcribed by RNA Polymerase III through an association between integrase and Pol III-complexes [24,25].

Because of the deleterious effects of most transposition events, eukaryotic hosts have evolved effective mechanisms to restrict the mobility or expression of transposons including RNAi, DNA methylation, and APOBEC proteins [26,27]. Importantly, none of those systems operate natively in S. cerevisiae or its sister species S. paradoxus [28], two species that diverged 4–5 million years ago [29]. Instead, Ty1 mobility in S. cerevisiae and S. paradoxus is limited by a novel retroelement-directed restriction mechanism termed Copy Number Control (CNC) [21,30–33]. CNC is defined as a decrease in Ty1 mobility when additional copies of the Ty1 element are present in the genome. CNC is mediated by the Ty1 restriction protein p22, which is a truncated version of Gag encoded by internally-initiated Ty1 transcripts [32]. p22 interferes with a central function of the Ty1 capsid during VLP assembly and maturation, and thus is a potent self-encoded trans-dominant negative inhibitor of Ty1 retrotransposition [32,34,35]. Ty1 inhibition by p22 bears striking similarities to host-encoded restriction factors that inhibit retrovirus assembly or capsid uncoating [36].

To date, Ty1 CNC has been studied in a very limited number of genetic backgrounds: first in S. paradoxus strain 337 [30,32,37,38] and more recently in S. cerevisiae strain DJ12 [33]. Thus, it remains an open question at what level CNC operates in diverse lineages of S. cerevisiae and S. paradoxus that vary in their endogenous genomic Ty1 content. Here we use well-developed methods to measure mobility of a Ty1 tester element (called Ty1-H3) with a gag sequence from the “canonical” Ty1 subfamily in S. cerevisiae [39–41] across a diverse panel of S. cerevisiae and S. paradoxus strains. Our results reveal that Ty1-H3 mobility varies substantially among strains in both species. We show that “permissive” strains with high Ty1-H3 mobility can be converted to “restrictive” strains with low Ty1-H3 mobility by experimentally introducing multiple Ty1-H3 elements into permissive genomes, implying that permissive strains are competent to express Ty1 CNC. Additionally, we investigated the genomic basis of variation in Ty1-H3 mobility using whole genome PacBio long-read assemblies that yield complete sequence information of transposable elements in their native chromosomal locations [18,42,43]. By comparing Ty1 copy number and sequence composition with mobility frequency, we infer that restrictive strains in both S. cerevisiae and S. paradoxus contain full-length Ty1 elements with a canonical form of gag. In contrast, permissive strains either lack full-length Ty1 elements or only contain full-length elements from the Ty1’ subfamily that have a divergent gag sequence. Surprisingly, the reconstructed evolutionary history of full-length Ty1 elements in S. cerevisiae and S. paradoxus shows that the Ty1’ subfamily is the ancestral subfamily in S. cerevisiae found in wild lineages, while the canonical Ty1 family used in most functional studies is a highly-derived element found in human-associated strains. Furthermore, we discovered that the gag region of the canonical S. cerevisiae Ty1 element was acquired by horizontal transfer from an Old-World lineage of S. paradoxus followed by recombination onto a pre-existing ancestral Ty1’-like element. Our results demonstrate that intraspecific variation in the ability to repress transposition of elements from the canonical Ty1 subfamily in S. cerevisiae is a consequence of horizontal transfer of a CNC-competent gag gene from a closely-related yeast species.

Results

Ty1 restriction varies across diverse isolates of S. cerevisiae and S. paradoxus

Because Ty1 CNC is mediated by a self-encoded factor (p22) and dependent on Ty1 genomic copy number, we hypothesized that variation in endogenous Ty1 genomic content may influence the strength of Ty1 CNC across Saccharomyces strains. To address this possibility, we used Southern analysis to screen a set of genetically-tractable haploid derivatives of 25 S. cerevisiae strains and 27 S. paradoxus strains from the Saccharomyces Genome Resequencing Project (SGRP) for variation in their Ty1 content [12,44]. The probe for hybridization experiments in both species is derived from the gag region of the Ty1-H3 element (S1A Fig). Ty1-H3 is a full-length competent Ty1 element used in many pioneering studies on Ty1 structure and function that was isolated in S. cerevisiae as a His⁺ reversion mutant [45–47]. Because Ty1-H3 has played an important role in defining our understanding of Ty1 structure and function, we designate it as the “canonical” form of Ty1. However, as detailed below, Ty1-H3 shows evidence of recombination with the Ty1’ subfamily in its pol region and thus the Ty1-H3 is not a “pure” representative of the canonical Ty1 subfamily. Southern analysis revealed substantial diversity across both S. cerevisiae and S. paradoxus strains in the number of Ty1 elements that share strong sequence similarity to Ty1-H3 gag (S1B Fig and S1C Fig), with most strains having fewer Ty1 elements than the S. cerevisiae reference strain S288c. These results also revealed several strain genomes where we failed to detect hybridization with the Ty1-H3 gag probe, consistent with the existence of multiple “Ty1-less” strains that lack full-length elements in S. cerevisiae and S. paradoxus [16,18,21,37].

Next, we selected a diverse panel of seven S. cerevisiae and three S. paradoxus SGRP strains with distinct Ty1 hybridization patterns (S1B Fig and S1C Fig) to test for variation in the frequency of mobility using a Ty1-H3 tester element marked with a his3-AI indicator gene [39]. We performed Ty1 mobility assays in the seven S. cerevisiae strains (S288c, Y12, DBVPG6044, UWOPS83-787.3, YPS606, UWOPS05-227.2, L-1374) by introducing a URA3-based centromere plasmid containing a competent Ty1his3-AI element (pOy1) into haploid MATα ho::HygroMX ura3::KanMX his3-Δ200hisG SGRP strains. The frequency of His⁺ colony formation in this assay detects Ty1 mobility events from either de novo retrotransposition events or insertion events from a minor pathway where Ty1 cDNA undergoes homologous recombination with genomic or plasmid-borne Ty1 sequences [48]. For the three S. paradoxus strains tested (CBS432, N-44, YPS138), deletion of HIS3 could not be achieved efficiently and thus Ty1 mobility assays were performed by first replacing the KanMX gene inserted at the URA3 locus with NatMX in haploid MATα SGRP strains, then introducing a reporter plasmid containing Ty1neo-AI (pBDG954) into the resulting MATα ho::HygroMX ura3::NatMX strains. The appearance of G418-resistant colonies in these S. paradoxus strains is a readout for retromobility that can be monitored by qualitative or quantitative assays similar to Ty1his3-AI reporter system [39–41]. These experiments revealed >50-fold differences in the mobility of Ty1-H3 across strains within both S. cerevisiae and S. paradoxus (Table 1). In both species, we observed “restrictive” strains with very low levels of Ty1-H3 mobility (S. cerevisiae: S288c, Y12, and DBVPG6044; S. paradoxus: CBS432, N-44). Likewise, we observed “permissive” strains in both species with Ty1-H3 mobility frequencies which were more than an order of magnitude higher than restrictive strains (S. cerevisiae: UWOPS05-787.3, YPS606, UWOPS05-227.2, and L1374; S. paradoxus: YPS138).

Variation in Ty1 mobility across Saccharomyces strains could result from variation in the strength of CNC conferred by endogenous Ty1 elements or other differences in host genetic background that render some strains incapable of expressing Ty1 CNC. To determine whether Ty1 mobility in permissive strains is due to host backgrounds that are unable to manifest Ty1 CNC, we over-expressed Ty1-H3 from a plasmid to “populate” the genomes of three permissive S. cerevisiae strains (UWOPS05-227.2, L1374, and YPS606) with >8 Ty1-H3 elements, as estimated by Southern analysis (see Materials and Methods for details). As shown previously for S. paradoxus strain 337 [30], we observed a >60-fold decrease in Ty1-H3 mobility in three S. cerevisiae strains populated with multiple Ty1-H3 elements when compared with their respective native parental strains (Table 2), with Ty1-H3 mobility in populated strains being on the same order as other native strains with restrictive phenotypes. We note that mobility data for native strains in Table 2 were from an independent set of experiments done in parallel with populated strains and thus differ slightly from the data in Table 1 for the same native strains. The ability for all three permissive strains tested to become restrictive with the addition of full-length copies of Ty1-H3 indicates that the genetic background of permissive strains is competent to express canonical Ty1 CNC and is consistent with the hypothesis that genomic Ty1 content plays an important role in shaping variation in Ty1 mobility among yeast strains.

The presence of full-length Ty1 elements is not sufficient to restrict Ty1-H3 mobility

To determine if variation in Ty1 mobility is influenced by the copy number or sequence of endogenous Ty1 elements, we generated ~100x whole-genome shotgun PacBio datasets and assembled genome sequences for the seven S. cerevisiae strains assayed for Ty1 mobility. We integrated data from our S. cerevisiae PacBio assemblies with similar high quality PacBio genome assemblies from Yue et al. [18] for the three strains of S. paradoxus with mobility data in our study (CBS432, N-44, YPS138). PacBio assemblies typically reconstructed complete chromosomes in single contigs (with the exception of chromosome XII which was broken at the highly repeated rDNA locus) and thus provide an essentially-complete catalogue of Ty content in yeast genomes. We identified Ty elements in these ten PacBio assemblies using a RepeatMasker-based strategy that classifies Ty elements as full-length, truncated, or solo LTR sequences based on the completeness of internal sequences in each predicted element (see Materials and Methods for details). Although our focus is on Ty1, we annotated all Ty families in these genomes to avoid potential misidentification, and because the similarity of solo LTRs from Ty1 and Ty2 does not allow their unambiguous assignment to either family (see also Yue et al. [18]). Predicted numbers of full-length, truncated, or solo LTR sequences for Ty1 can be found in Table 3 and for all Ty families in S1 File. We focused on full-length elements in our analysis since they are most likely to have the complete set of functional sequences required for Ty1 gene expression and transposition.

The total number of full-length Ty1 elements varies substantially across the ten yeast strains with mobility data in our sample (Table 3). S. cerevisiae strains can have high (S288c), intermediate (DBVPG6044 and Y12), or low (UWOPS05-787.3, and YPS606) Ty1 copy number, or are Ty1-less (UWOPS05-227.2 and L1374). S. paradoxus strains either have low copy number (CBS432 and N-44) or are Ty1-less (YPS138). All strains contain truncated Ty1 elements and Ty1-like solo LTRs, indicating that Ty1 was present in the ancestor of all strains in both species and that Ty1-less strains arose by multiple independent losses of full-length Ty1 elements, presumably by LTR-LTR recombination. Integrating genomic Ty1 content with mobility data, we observe that all restrictive strains contain multiple full-length copies of Ty1 elements (S. cerevisiae: S288c, Y12, DBVPG6044; S. paradoxus: CBS432, N-44), consistent with the expectation that repression of Ty1 mobility is mediated by Ty1 CNC. Also consistent with predictions of the Ty1 CNC mechanism, Ty1-less strains are permissive (S. cerevisiae: UWOPS05-227.2, L1374; S. paradoxus: YPS138). However, we observed two permissive strains in S. cerevisiae that unexpectedly contained full-length Ty1 elements (UWOPS83-787.3, YPS606). These results indicate that variation in the frequency of Ty1 mobility across strains cannot be explained by a simple model whereby the presence of a full-length Ty1 element in the genome is sufficient to confer a restrictive phenotype.

Recombination occurs among canonical Ty1 and Ty1’ subfamilies in S. cerevisiae

The two exceptional S. cerevisiae permissive strains that had full-length Ty1 elements detected in their PacBio assemblies (UWOPS05-787.3 and YPS606) displayed multiple bands with weak hybridization to the Ty1 gag probe by Southern blot analysis (Fig 1A). Some, but not all, of these weak Ty1 bands could be explained by cross-hybridization with Ty2 (Fig 1B). This observation suggested the possibility of divergent Ty1 sequences in these genomes such as the Ty1’ subfamily that is known to differ from the canonical Ty1 subfamily in its gag region [7]. To determine if the presence of a variant Ty1 subfamily could potentially explain the observation of permissive strains with full-length Ty1 elements, we extracted and aligned all full-length Ty1 elements from the PacBio assemblies of the ten S. cerevisiae and S. paradoxus strains for which we had mobility data, then clustered full-length Ty1 elements based on sequence similarity. We included the Ty1-H3 tester element used in our mobility assays and used a distance-based clustering approach (Neighbor Joining) in this analysis, since our goal was to identify potential Ty1 subfamilies that could explain variation in Ty1-H3 mobility across strains, not to infer the detailed evolutionary history of Ty1 in these species.

Clustering of complete Ty1 sequences revealed a well-supported long branch separating S. cerevisiae elements from those in S. paradoxus (Fig 2A). In S. cerevisiae, two major clusters of Ty1 elements are observed. One cluster corresponds to the canonical Ty1 subfamily as defined by the presence of the Ty1-H3 tester element in this cluster (green background, Fig 2A). Two strains have full-length elements in the canonical Ty1 cluster (S288c and DBVPG6044). The other major S. cerevisiae cluster (found in S288c, Y12, UWOPS83-787.3, and YPS606) contains three elements previously defined as the Ty1’ subfamily in S288c by Kim et al. [7] (orange background, Fig 2A). The canonical Ty1 and Ty1’ clusters are separated by a long internal branch containing multiple short branches leading to individual Ty1 elements or small groups of closely-related Ty1 elements from Y12 and S288c. Inspection of our multiple sequence alignment revealed that one of these elements (Y12_f109; single asterisk, Fig 2A) is in fact a recombinant element derived from an exchange event between canonical Ty1 and Ty1’ sequences within the gag region (S2A Fig). A second recombinant in gag between canonical Ty1 and Ty1’ sequences was also found in our dataset (S288c_f486; double asterisk, Fig 2A; S2B Fig), which previously was classified as a divergent Ty1’ element by Kim et al. [7] (SGD: YNLCTy1-1). Sliding window analysis showed that these two recombinant elements are essentially Ty1’ elements with fragments of canonical Ty1 sequence in their gag regions (S2A Fig and S2B Fig). Full-length elements from the canonical Ty1 or Ty1’ subfamilies are not found in S. paradoxus, implying that both of these subfamilies are specific to S. cerevisiae.

Because previous work shows that Ty1 gag and pol genes have different evolutionary histories in S. cerevisiae [14,23], we next clustered full-length Ty1 elements on the basis of their gag (Fig 2B) and pol (Fig 2C) sequences separately. Clustering of elements based on Ty1 gag revealed a discordant topology relative to that from complete sequences, with no long branch separating S. paradoxus and S. cerevisiae and essentially no elements on the long internal branch separating the canonical Ty1 and Ty1’ clusters (except the recombinant S288c_f486 element noted above). In the gag tree, S. paradoxus elements unexpectedly clustered closely with S. cerevisiae canonical Ty1 elements, indicating a previously-unreported similarity between S. paradoxus Ty1 gag and S. cerevisiae canonical Ty1 gag (see below). Y12 and S288c elements found on the long branch between canonical Ty1 and Ty1’ clusters in the complete sequence tree (Fig 2A) cluster in the canonical group in the gag tree (Fig 2B), indicating that these elements all have a canonical Ty1 type gag gene. The recombinant Y12_f109 element noted above clusters with the canonical Ty1 group (single asterisk, Fig 2B) since the majority of its gag gene is canonical Ty1 but is found on a very long unique branch due to the presence of Ty1’ sequences in the 5’ part of its gag (S2A Fig). Aside from these two elements with evidence of recombination in gag, all full-length Ty1 elements are found in two main groups separated by substantial sequence divergence in their gag region: (i) elements with a canonical Ty1 type gag found in S. cerevisiae and S. paradoxus, and (ii) elements with a Ty1’ type gag found only in S. cerevisiae.

Clustering of Ty1 pol (Fig 2C) revealed a topology similar to that of complete Ty1 sequences (Fig 2A) with two notable exceptions. First, the two elements that are recombinant in gag (Y12_f109 and S288c_f486) are both found within the Ty1’ cluster in their pol regions, consistent with these elements being predominantly Ty1’ except for parts of their gag genes (S2A Fig and S2B Fig). Second, the seven closely-related Y12 elements found on the long internal branch in the complete tree (arrowhead, Fig 2A) cluster in the Ty1’ group in the pol tree (arrowhead, Fig 2C). This observation, in addition to the fact that these seven Y12 elements have a canonical Ty1 gag (arrowhead, Fig 2B), implies that they are recombinants between the canonical Ty1 and Ty1’ subfamilies with an exchange event somewhere near the boundary of gag and pol (see below). Phylogenetic network analysis revealed that the remaining S288c elements on the long internal branch in the pol tree, plus additional elements in the canonical Ty1 cluster (including the Ty1-H3 tester element), are recombinants between the canonical Ty1 and Ty1’ subfamilies within the pol region (S3 Fig). Canonical Ty1 elements from DBVPG6044, however, show no evidence of recombination in pol (or gag) and therefore best represent “pure” canonical Ty1 elements. Thus, all S. cerevisiae elements found on the long internal branch between canonical Ty1 and Ty1’ subfamilies in the complete sequence tree exhibit recombination between subfamilies within gag, near the boundary of the gag and pol, or within pol.

Saccharomyces strains that restrict Ty1-H3 mobility encode full-length elements with canonical Ty1 gag

We next attempted to interpret variation in Ty1-H3 mobility at the strain level with genomic Ty1 content partitioned by the type of gag–canonical Ty1 or Ty1’–encoded by full-length elements. The rationale for this analysis is based on p22 being encoded in the C-terminal half of gag, and recombination between the canonical Ty1 and Ty1’ subfamilies precluding straightforward classification at the complete element level. We classified S. paradoxus Ty1 elements as having canonical Ty1 type gag because of the close clustering with S. cerevisiae canonical Ty1 sequences (Fig 2B). This analysis revealed that restrictive strains from both S. cerevisiae and S. paradoxus contain one or more full-length elements that encode a canonical Ty1 type gag (S. cerevisiae: S288c, DBVPG6044 and Y12; S. paradoxus: CBS432 and N-44) (Table 3). Conversely, permissive strains only have full-length elements that encode Ty1’ gag (S. cerevisiae: UWOPS83-787.3 and YPS606) or lack full-length Ty1 elements altogether (S. cerevisiae: UWOPS05-227.2, L1374; S. paradoxus: YPS138). These results suggest that the ability to restrict mobility of the Ty1-H3 tester element requires a full-length Ty1 element in the genome with sufficient sequence similarity to canonical Ty1 gag. Because the two restrictive strains with recombinants between canonical Ty1 and Ty1’ in gag (Y12 and S288c) each also have full-length elements with a complete canonical Ty1 gag gene, the presence of these two recombinants does not alter this general conclusion. The dependency of Ty1-H3 mobility on the presence of full-length Ty1 elements with canonical gag appears to hold quantitatively as well. Ty1-H3 mobility and the number of full-length Ty1 elements that have a canonical Ty1 gag are negatively correlated across S. cerevisiae strains (rho = -0.8669214; p-value = 0.01154), consistent with the general hypothesis that increasing genomic canonical Ty1 gag content increases the strength of canonical Ty1 CNC [30].

One confounding factor to the interpretation that having a full-length element with a canonical Ty1 gag is required to confer the restrictive phenotype is that there is substantial sequence divergence between canonical Ty1 and Ty1’ not only in gag (red, Fig 3A) but also in parts of both LTRs and pol (blue and purple, Fig 3A). The impact of divergence in gag can be separated from other changes between canonical Ty1 and Ty1’ using data from the restrictive strain Y12. Full-length elements in Y12 are either “pure” Ty1’ (elements from the Ty1’ subfamily that show no evidence of recombination with the canonical Ty1 subfamily) or “mosaic” Ty1 (elements that are divergent from Ty1’ in gag like pure canonical elements but are otherwise nearly identical to Ty1’ in their LTRs and pol regions) (Fig 3B). Remarkably, mosaic Ty1 elements in Y12 have recombination breakpoints that coincide almost precisely with the gag open reading frame (ORF) (Fig 3B), which explains the discordant placement of these elements when clustered by gag versus pol (arrowheads, Fig 2B vs. Fig 2C). Thus, the main difference in Ty1 content between Y12 and other strains that carry only pure Ty1’ elements (i.e. UWOPS83-787.3 and YPS606) is the presence of mosaic Ty1 elements in Y12 that encode a canonical Ty1 gag. Given that other S. cerevisiae strains carrying only pure Ty1’ elements have a permissive phenotype (i.e. UWOPS83-787.3 and YPS606), the restrictive phenotype in Y12 suggests that having canonical Ty1 gag in mosaic Ty1 elements is sufficient (and that canonical LTRs and pol are not required) to restrict Ty1-H3 mobility.

How genomic Ty1 content influences mobility phenotypes is also complicated by the existence of truncated Ty1 elements which may contain functional p22 sequences. To address this, we aligned truncated Ty1 elements to the Ty1-H3 tester element to identify truncated elements that have the potential to code for p22. All S. cerevisiae strains with mobility data contain truncated Ty1 elements that span the p22 region of gag (Table 3, S4 Fig). Two S. cerevisiae strains (S288c, L-1374) share a truncated Ty1 element found on chromosome IV that includes all of gag plus the 5’ LTR and some of pol. Likewise, five S. cerevisiae strains (DBVPG6044, Y12, UWOPS83-787.3, YPS606, UWOPS05-227.2) share a common truncated Ty1 element found at a different location on chromosome IV that includes nearly all of gag but no other parts of Ty1. Additionally, two S. cerevisiae strains (S288c and DBVPG6044) have strain-specific truncated elements that also span the p22 region of gag. By integrating these truncated elements into the multiple sequence alignment of gag sequences from a diverse panel of yeast strains reported in Bleykastens-Grosshans et al. [14], we confirmed that the two different truncated Ty1 loci found on chromosome IV shared by multiple S. cerevisiae strains are the same as two high-frequency “relics” related to the Ty1’ subfamily reported by Bleykastens-Grosshans et al. [14]. The remaining two strain-specific S. cerevisiae truncated Ty1 elements that span the p22 region are derived from the canonical Ty1 lineage. All truncated Ty1 elements that span the p22 region in S. cerevisiae have the capacity to encode an ORF for p18, the proteolytically processed form of p22 that is also capable of restricting Ty1 transposition [32]. In S. paradoxus, only one strain (CBS432) has a truncated element with gag sequences that span the p22 region, but the truncated Ty1 element in this strain does not encode a complete ORF for p18/p22. From these data, we conclude that presence of truncated elements with canonical Ty1 gag may contribute to the restrictive mobility phenotypes of S288c and DBVPG6044, and that the presence of truncated elements with Ty1’ gag does not inhibit the restrictive phenotypes in S288c, DBVPG6044, and Y12. Conversely, four permissive S. cerevisiae strains that lack full-length elements with canonical Ty1 gag (UWOPS83-787.3, YPS606, UWOPS05-227.2 and L-1374) only contain truncated elements from the Ty1’ subfamily, and thus our conclusion that having full-length elements with a canonical Ty1 gag is required to confer the restrictive phenotype is unaltered by the presence of truncated elements with Ty1’ gag sequences in the genomes of these strains.

Canonical S. cerevisiae Ty1 gag was recently acquired from S. paradoxus by horizontal transfer

Clustering of Ty1 sequences from strains with mobility data revealed a surprising similarity between the gag sequences of full-length elements from the S. cerevisiae canonical Ty1 cluster and S. paradoxus (Fig 2B). Sliding window divergence analysis revealed that the regions of high divergence between canonical S. cerevisiae Ty1 and S. cerevisiae Ty1’ in gag (red, Fig 3A) and the middle part of pol (purple, Fig 3A) correspond exactly to regions of high sequence similarity between canonical S. cerevisiae Ty1 and S. paradoxus Ty1 (Fig 3C). High sequence similarity is not observed in the corresponding regions between S. cerevisiae Ty1’ and S. paradoxus Ty1 (Fig 3D). These results suggest that the extreme divergence between canonical Ty1 and Ty1’ in gag may have resulted from horizontal transfer of a S. paradoxus Ty1 element and recombination with an ancestor of the S. cerevisiae canonical Ty1 subfamily after divergence of the canonical Ty1 and Ty1’ lineages and that the Ty1’ subfamily represents the ancestral state in S. cerevisiae.

To further investigate this putative horizontal transfer event and the ancestral state of the Ty1 family in S. cerevisiae, we reconstructed the phylogenetic history of gag and pol sequences from full-length Ty1 elements using an expanded set of S. cerevisiae and S. paradoxus strains with essentially-complete PacBio assemblies. This expanded dataset includes the ten strains analyzed above, plus six S. cerevisiae strains with diverse geographic origins (SK1, YPS128, UWOPS03-461.4, DBVPG6765, Sb-biocodex, Sb-unique28) and two New World S. paradoxus strains (UFRJ50816, UWOPS91-917.1) that have publicly-available PacBio data [18,42]. Additionally, we generated and included PacBio assemblies for three S. cerevisiae strains isolated from ancestral oak habitats in North America, Europe and Japan (SDO2s1, ZP568s1, ZP655.1A) to better sample Ty1 content in geographically-diverse wild S. cerevisiae lineages [49,50]. Ty1 sequences from PacBio assemblies of two S. jurei strains (NCYC 3947, NCYC 3962) reported in Naseeb et al. [43] were used to root trees and polarize changes on the S. cerevisiae and S. paradoxus lineages. Ty elements in these genomes were detected as described above and Ty content for all strains can be found in S1 File. Several strains in the expanded dataset in addition to those noted above were found to be Ty1-less and therefore are not represented in these trees: S. cerevisiae Wine/European (DBVPG6765, Sb-biocodex, Sb-unique28), S. cerevisiae Malaysian (UWOPS05-227.2, UWOPS03-461.4) and S. paradoxus N. America (YPS138). For this analysis, trees were generated using maximum likelihood so that ancestral states could be reconstructed for the gag gene. Two recombinants in gag noted above (S288c_f486 and Y12_f109) were excluded from this analysis since their inclusion distorted ancestral state reconstruction. Annotated trees for gag and pol with element identifiers can be found in S6 Fig, and tree files for gag and pol can be found in S2 and S3 Files, respectively.

Analysis of maximum likelihood phylogenetic trees from this expanded set of strains revealed strikingly discordant histories for Ty1 gag (Fig 4A) and pol (Fig 4B). Importantly, the phylogenetic history of the gag gene is not compatible with the accepted species tree for these taxa [51]. In the gag tree, S. cerevisiae Ty1 sequences are found in two well-supported monophyletic groups (brown background, Fig 4A). One S. cerevisiae gag clade is the sister group to the ancestor of all S. paradoxus Ty1 gag sequences and contains only elements with Ty1’ type gag. The other S. cerevisiae gag clade–which includes the Ty1-H3 tester element carrying canonical gag–is discordantly placed as being derived from the Old World clade of S. paradoxus Ty1 elements (black arrow, Fig 4A), with the closest affinity to elements from the European lineage of S. paradoxus represented by CBS432 (S6A Fig). The discordant placement and monophyly of the canonical Ty1 gag lineage in S. cerevisiae are most parsimoniously explained by a single horizontal transfer event from S. paradoxus. Importantly, all S. cerevisiae strains isolated from wild sources only contain elements from the Ty1’ clade, despite being sampled from diverse geographic regions around the globe: the Caribbean (UWOPS83-787.3), North America (YPS606, YPS128, SDO2s1), Asia (ZP655.1A), and Europe (ZP568s1) (Fig 4A, S6A Fig). In contrast, human-associated S. cerevisiae strains have only Ty1 elements with canonical gag (DBVPG6044, SK1) or have both types of elements (with canonical Ty1 gag or with Ty1’ gag) plus their recombinants (S288C, Y12) (Fig 4A, S6 Fig). The Ty1’ gag lineage found in human-associated strains is a monophyletic lineage nested within the wild Ty1’ diversity, suggesting a single origin for the introduction of Ty1’ into human-associated strains of S. cerevisiae (grey arrow, Fig 4A). With the exception of the European S. paradoxus lineage unexpectedly containing sequences from the S. cerevisiae canonical Ty1 subfamily, the phylogeny of S. paradoxus Ty1 gag sequences follows the accepted population structure for this species [12]: S. paradoxus Ty1 elements form an Old World clade comprised of subclades of elements from European (CBS432) and Far Eastern (N-44) lineages, plus a New World clade comprised subclades of elements from S. American (UFRJ50816) and Hawaiian (UWOPS91-917.1) lineages (Fig 4A, S6A Fig).

In contrast to the gag phylogeny, the pol tree shows the expected species-specific clustering of Ty1 sequences for both S. cerevisiae and S. paradoxus (Fig 4B). Within S. cerevisiae, pol sequences form two major groups corresponding generally to the Ty1’ and canonical Ty1 gag clades (Fig 4B), but whose coherence and bootstrap support is obscured by recombination in pol between the canonical Ty1 and Ty1’ subfamilies (as shown above for the mobility dataset in Fig 2C). The first major S. cerevisiae pol clade contains all elements that have a Ty1’ gag, plus several other recombinant Ty1 elements that have a canonical Ty1 gag (e.g. the mosaic Ty1 elements from Y12). The second major S. cerevisiae pol clade contains elements that have a canonical Ty1 gag and includes the Ty1-H3 tester element. Similar to gag, all wild strains have a Ty1’ type pol and all elements with a canonical Ty1 type pol are from human-associated strains. Divergence between the two major S. cerevisiae groups in pol is primarily caused by the regions of pol in canonical Ty1 that were acquired by recombination with S. paradoxus Ty1 (purple region, Fig 3A) or with S. cerevisiae Ty2 ([8,23]; blue region, Fig 3A), since phylogenetic analysis of a smaller region of pol (nucleotides 1700–3000 in Ty1-H3; GenBank: M17806) outside of the regions affected by these recombination events generates a single clade for all S. cerevisiae strains (S7 Fig, S4 File). As observed for S. paradoxus Ty1 gag sequences, S. paradoxus Ty1 pol sequences cluster by strain according to the accepted global biogeographic relationships for this species [12] (Fig 4B, S6B Fig).

Together, these results suggest that Ty1’ is the ancestral subfamily of Ty1 in S. cerevisiae, as reflected by its deep divergence from S. paradoxus in both gag and pol, and by the unique presence of only pure Ty1’ elements (that have both Ty1’ type gag and pol) in S. cerevisiae strains isolated from wild habitats around the world. The conclusion that the Ty1’ subfamily is ancestral in S. cerevisiae is further supported by the fact that the two truncated Ty1 relics found at high frequency in strains from geographically diverse regions are both from the Ty1’ subfamily (see S4 Fig). These results also suggest that the canonical Ty1 subfamily in S. cerevisiae is a highly-derived subfamily that acquired a complete S. paradoxus Ty1 gag sequence (as well as parts of pol from S. paradoxus and parts of both LTRs and pol from Ty2; purple and blue regions in Fig 3, see also [8,23]) by recombination onto a pre-existing S. cerevisiae Ty1’-like element, most likely in a human-associated environment. Furthermore, the placement of the S. cerevisiae canonical Ty1 gag clade within the Old World (European) S. paradoxus clade but sister to the New World S. paradoxus clade indicates the horizontal transfer involving the gag gene event occurred in the Old World, after S. cerevisiae and S. paradoxus speciated from one another and divergence of the major worldwide S. paradoxus lineages had occurred.

Divergence between canonical Ty1 and Ty1’ Gag occurs outside functionally-characterized residues

Comparison of Ty1 genomic content with mobility phenotypes above revealed that strains encoding only Ty1’ gag cannot strongly repress mobility of a Ty1-H3 tester element (Table 1). These mobility assays imply that sequence divergence between canonical Ty1 and Ty1’ in Gag may affect the ability of Ty1’ elements to confer CNC on a canonical Ty1 element. To understand how molecular evolution along the branch separating the canonical Ty1 and Ty1’ subfamilies relates to potential functional divergence in gag, we reconstructed ancestral gag sequences for all canonical Ty1 elements and Ty1’ elements, respectively. Codon-based alignment of ancestral canonical Ty1 and Ty1’ gag sequences revealed 93 amino acid and three insertion/deletion substitutions across Gag, 40 of which are in the p22 region (Fig 5). Consistent with the extensive divergence in gag occurring along functional Ty1 lineages evolving in distinct species rather than rapid sequence evolution within species due to positive selection, we found that purifying selection was the prevailing mode of molecular evolution across both the entire gag gene (dN = 0.125; dS = 0.252; dN/dS = 0.496) and the p22 region (dN = 0.128; dS = 0.289; dN/dS = 0.443) (see also Kim et al. [7]). Moreover, the two alternative start codons for p22 are conserved between canonical Ty1 and Ty1’ ancestors [32,34], as are the ten CNC^R residues shown to provide resistance to p22 [35], the seven amino acids shown to be important for Ty1 protein maturation [35], and the seven nucleotides required for +1 frameshifting to create the Gag-Pol fusion protein [52]. Amino acid substitutions differentiating canonical Ty1 and Ty1’ occur at similar proportions in the p22 region versus the non-p22 portions of Gag (P = 0.907; Fisher’s Exact Test) as well as in the nine predicted helical regions relative to remaining non-helical regions of Gag (P = 0.123; Fisher’s Exact Test). Similarly, nucleotide substitutions between canonical Ty1 and Ty1’ occur at similar proportions in the regions of gag that produce anti-sense RNAs [53] relative to regions that do not produce anti-sense RNAs (P = 0.745; Fisher’s Exact Test). These results suggest that the Ty1’ subfamily has the capacity to code for a p22-like molecule and that potential functional divergence between canonical Ty1 and Ty1’ Gag occurs outside residues currently known to affect Ty1 protein function, maturation or resistance to p22.

Discussion

Here we combine in vivo transposition assays with high-resolution phylogenomics to show that variation in the ability to repress mobility of a Ty1 element carrying a canonical gag in S. cerevisiae is a consequence of horizontal transfer of a gag gene from a closely related yeast species, S. paradoxus. Additionally, our results indicate that canonical Ty1 CNC is likely to be widespread in both species and vary in strength as a function of the genomic content of specific Ty1 subfamilies. The correlation of the presence of canonical Ty1 gag in full-length elements with the restrictive Ty1-H3 mobility phenotype–demonstrated most clearly by the restrictive Y12 strain–also provides compelling and independent evolutionary genomic evidence to support functional studies showing that canonical Ty1 CNC is mediated by sequences within the Ty1 gag region [30,32].

Our work reveals that, while the presence of the Ty1 family is ancestral to both species, the ability of S. cerevisiae strains to strongly repress Ty1-H3 mobility was likely acquired after speciation through horizontal transfer. Acquisition of a S. paradoxus gag gene by S. cerevisiae canonical Ty1 explains the surprising similarity between S. cerevisiae and S. paradoxus Ty1 gag sequences first reported here, as well as the ability of S. paradoxus strains with full-length Ty1 elements to restrict mobility of a heterospecific S. cerevisiae Ty1 tester element shown here and in previous studies [30,37]. Our observation of restrictive strains in S. paradoxus with full-length Ty1 elements from both European and Far Eastern lineages (Table 1) suggests that canonical Ty1 CNC was present in the ancestor of all Old World S. paradoxus lineages. However, Ty1 mobility assays in American and Hawaiian S. paradoxus strains with full-length Ty1 elements are needed to establish if canonical Ty1 CNC is also present in New World S. paradoxus lineages, which would suggest it was present in the common ancestor of all S. paradoxus lineages prior to colonizing worldwide habitats. Further studies on Ty1 from other species in the Saccharomyces genus and related Ty elements are also needed to understand where and when canonical Ty1 CNC first evolved. Previous work indicates that S. cerevisiae Ty2 is not under a self-encoded form of CNC nor is Ty2 responsive to p22 based Ty1 CNC [35]. These results suggest that Ty1 CNC could have evolved after the divergence of Ty1 and Ty2, however the complex history of the Ty1/Ty2 superfamily in the Saccharomyces genus [13,22,54] currently leaves open many other possibilities as to when canonical Ty1 CNC ultimately originated.

Our findings raise a number of intriguing questions about the p22-based mechanism of Ty1 CNC that can be explored in future studies. The inability of S. cerevisiae strains containing only Ty1’ gag to strongly repress Ty1-H3 mobility implies potential functional divergence in the gag genes of the canonical and Ty1’ subfamilies. While sequence analysis suggests Ty1’ is potentially capable of manifesting p22-based CNC (Fig 5), further work is needed to address whether this is indeed the case. If it can be shown that Ty1’ is capable of producing a functional p22 that exerts CNC on other Ty1’ elements, it will be important to evaluate which sequences in gag/p22 outside of currently functionally-characterized residues are responsible for this potential functional divergence. If Ty1’ does exert CNC via a p22-based mechanism, it is also possible that the different truncated Ty1’ relics found in multiple S. cerevisiae strains [14] may represent domesticated Ty1 restriction factors that repress Ty1’ mobility, similar to domesticated gag genes that inhibit murine or sheep retrovirus replication [36,55,56]. Potential functional divergence in the ability of Ty1’ to repress canonical Ty1 also raises questions about possible regulatory interactions among these two subfamilies. At this point, it is clear that strains containing elements with both canonical Ty1 and Ty1’ gag (e.g. native S288c, native Y12, and populated YPS606) restrict Ty1-H3, and thus Ty1’ elements do not dominantly inhibit CNC mediated by canonical Ty1 p22. If one assumes similar levels of Ty1his3-AI expression and RNA splicing in different strains, there is also some indication that permissive strains containing full-length Ty1’ elements (UWOPS83-787.3 and YPS606) have lower Ty1-H3 mobility than permissive strains that lack any full-length Ty1 elements (UWOPS05-227.2 and L-1374). This observation raises the possibility that Ty1’ can limit Ty1-H3 mobility to some degree through a CNC-like mechanism. Additionally, many questions remain about the basis of quantitative variation in Ty1-H3 mobility across strains, including why Ty1-H3 mobility is similar for genomes that vary two-fold in the number of canonical Ty1 elements (S288c and DBVP6044). The expression level of individual Ty1 insertions has previously been shown to differ substantially as a function of genomic location [57], and thus the genomic context of Ty1 insertions (in addition to overall copy number) likely contributes to variation in Ty1-H3 mobility among strains. To address these questions, future functional studies on Ty1 CNC in S. cerevisiae will require development and application of robust genetic techniques to characterize the mobility and CNC competence of a wider range of native Ty1 elements (including members of the Ty1’ subfamily) in a diverse panel of natural isolates and isogenic strains derived from natural strains populated with various Ty1 elements.

Results presented here extend our understanding of the evolution of Ty1 in S. cerevisiae and S. paradoxus. Combined with previous work by Jordan and McDonald [8,23], our results suggest that the Ty1-H3 element used in most studies on Ty1 expression or function is a highly-derived element that acquired sequences from both S. paradoxus Ty1 and S. cerevisiae Ty2, most likely in a human-associated environment. How and when these events happened remain to be determined, although the importance of homologous recombination in both events is clear. Decoding the history of the canonical Ty1 subfamily will need to explain the somewhat paradoxical observation that this subfamily confers strong repression against itself but also apparently has high fitness, as reflected by its high copy number in strains that carry this subfamily. Understanding the history of these events may be challenging since the lack of overlap in the sequences acquired from S. paradoxus and Ty2 prevents their relative ordering, and the ongoing effects of recombination between canonical Ty1 and Ty1’ in strains that carry both subfamilies may obscure efforts to reconstruct the original sequences involved. Regardless, the highly-derived nature of the Ty1 element should caution against naively interpreting the structure, function or evolution of transposable elements isolated in domesticated lab strains as being reflective of the natural genome biology in yeast or other species.

Our results also provide evidence that horizontal transfer events may not always lead to the transfer of complete transposable element sequences, and that recombination after horizontal transfer may lead to the evolution of novel hybrid transposable elements. The presence of S. paradoxus sequences in canonical Ty1 in both the gag (red, Fig 3A) and pol (purple, Fig 3A) regions could either reflect independent recombination events of horizontally transferred Ty1 sequences from S. paradoxus or indicate that a larger fragment of S. paradoxus was originally transferred onto the ancestor of canonical Ty1 (with the sequence between gag and pol subsequently converted back to a Ty1’-like state by recombination). Given the relatively common occurrence of introgression of nuclear genes from S. paradoxus into S. cerevisiae [20,58–62], multiple horizontal transfer or recombination events may have occurred in the Old World to create the canonical Ty1 lineage, and additional horizontal transfer events of Ty1 are yet to be discovered in other geographic areas where these two species coexist in nature. Horizontal transfer of Ty1 sequences from S. paradoxus into S. cerevisiae may have occurred by transmission of a Ty1 VLP or RNA during mating between S. paradoxus and S. cerevisiae. Alternatively, S. paradoxus Ty1 sequences may have entered S. cerevisiae by introgression of a segment of the nuclear genome carrying one or more S. paradoxus Ty1 elements.

Finally, the evolution of Ty1 in S. cerevisiae described here may inform aspects of the history of domestication and biogeography of this species. Recent work proposed that S. cerevisiae beer strains have genetic contributions from European and Asian lineages [63]. The acquisition by canonical Ty1 of sequences related to both European S. paradoxus Ty1 and Ty2 (which is proposed to have arisen in S. cerevisiae by horizontal transfer from the Asian species S. mikatae [13,22]) in human-associated strains supports this model. Likewise, the inference that Ty1’ is the ancestral lineage in S. cerevisiae and that wild strains of S. cerevisiae lack canonical Ty1 suggests that Ty1’ may be a useful marker for studying biogeography in this species. For example, if the “out-of-China” origin proposed for the ancestral range of wild S. cerevisiae is correct [20,64], our findings predict that that only the Ty1’ subfamily should be found in ancestral woodland strains of S. cerevisiae from China. Answers to these and other questions should be facilitated by advances in the assembly of noisy long-read datasets [16], and development of computational techniques to resolve the presence of canonical Ty1 and Ty1’ sequences from abundant short-read datasets for S. cerevisiae [20,49,60,61,63,65–72].

Materials and methods

Strains, plasmids, and genetic techniques

All strains used in this study are listed in S5 File. Strains used for Southern analysis, mobility assays and the majority of genome sequencing experiments (S288c, Y12, DBVPG6044, UWOPS83-787.3, YPS606, UWOPS05-227.2, L-1374, CBS432, N-44 and YPS138) are MATα haploid derivatives of S. cerevisiae and S. paradoxus strains from the SGRP [44]. Additional monosporic wild-type S. cerevisiae strains used for genome sequencing (SDO2s1, ZP568s1, ZP655.1A) were reported previously [49]. For the S. cerevisiae SGRP strains used in mobility experiments, the HIS3 universal gene blaster pBDG652 digested with EcoRI and SphI was used to generate his3-Δ200hisG deletion alleles in SGRP strains [30,73]. For the S. paradoxus strains used in mobility experiments, KanMX was replaced by NatMX by homologous recombination as previously described [74]. For S. cerevisiae strains YPS606, UWOPS05-227.2 and L-1374, his3-Δ200hisG deletion strains were subsequently “populated” with canonical Ty1 elements following galactose-induced expression of pGTy1-H3 [45], and copy number estimates were determined by Southern analysis as described previously [30]. To generate strains for determining the level of Ty1 mobility, native or populated haploid MATα his3-Δ200hisG S. cerevisiae strains were transformed with a Ty1his3-AI URA3 centromere plasmid pOY1 (pBDG633) [75]. Likewise, native haploid MATα NatMX S. paradoxus strains were transformed with a Ty1neo-AI plasmid (pBDG954) constructed by subcloning a BstE II–Eag I fragment from pGTy1-H3PtefKAN-AI [41] into pBDG633. Restriction endonucleases, Phusion DNA polymerase, and T4 DNA ligase were purchased from New England Biolabs (Ipswich MA). Plasmids were verified by restriction analysis and DNA sequencing. Standard yeast genetic and microbiological procedures were used in this work, including media preparation and DNA transformation [76–78].

Southern blot hybridization

A single colony from each strain was inoculated in 10 ml of YEPD medium and grown to saturation at 30°C, and total DNA was isolated as described previously [45]. Approximately 10 μg of DNA was digested with BglII and resolved on a 0.6% agarose gel for 16 hours at 30V. DNA fragments were transferred via capillary action to Hybond-N membrane (GE Healthcare, Aurora OH) and UV-crosslinked according to the supplier’s specifications (Spectroline, Westbury NY). ³²P-labeled DNA probes containing gag sequences were made by randomly primed DNA synthesis with Amersham Megaprime DNA labeling System (GE Healthcare). The gag sequences were amplified by PCR from plasmids pGTy1-H3 (GenBank: M18706; nucleotides 335–1496) and pGTy2-917 (GenBank: KT203716; nucleotides 333–1490) [79]. DNA for the Ty1 probe was amplified with primers 5’-TGGTAGCGCCTGTGCTTCGGTTAC-3' and 5'-CATGTTTCCTCGAGTTAGTGAGCCCTGGCTGTTTCG-3' and Phusion DNA polymerase (New England Biolabs). DNA for the Ty2 probe was generated with primers 5’-TGGTAGCGCCTATGCTTCGGTTAC-3’ and 5’-GCAATATTGTGAGCTTTTGCTGCTCTTGG-3’. Hybridization was performed at 68°C overnight in a buffer containing buffer containing 6X SSC, 5X Denhardt’s solution, 0.5% SDS, and 100 μg/μl single-strand salmon sperm DNA. Blots were washed at 68°C, twice with 2X SSC + 0.1% SDS for 30 min, followed by two washes with 1X SSC + 0.1% SDS for 15 min. Membranes were exposed to storage phosphor screens followed by scanning with Molecular Dynamics Storm PhosphorImager (GE Healthcare).

Ty1 mobility

The frequency of Ty1his3-AI and Ty1neo-AI mobility was determined as described previously with minor modifications [30,39,41]. Briefly, a single colony from a SC-Ura plate incubated at 30°C was resuspended in 1 ml of water and 5 μl of cells was added to quadruplicate one-ml cultures of SC-Ura liquid medium. The cultures were grown for 3 days at 22°C, washed, diluted, and spread onto SC-Ura, and SC-His-Ura (for Ty1his3-AI) or YEPD + Geneticin (G418; 200 μg/ml for Ty1neo-AI) (ThermoFisher, Waltham MA) plates. To minimize flocculence, 0.25 M NaCl was used for cell washes and dilutions prior to plating [80]. The frequency of Ty1 mobility is defined as the number His⁺ Ura⁺ or G418^R colonies divided by the number of Ura⁺ colonies per ml of culture. Standard deviations were calculated from the number Ty1 mobility events detected per 1 ml culture. To determine the fraction of colonies on YEPD +/- Geneticin that retain pBDG954, we analyzed strain YPS138 (DG3912, Table 1, Sup File 5). Over 95% of the mobility events obtained on YEPD + G418 remain Ura⁺ (86/90), and over 98% (377/382) retain pBDG954 after growth in SC-Ura liquid medium. Thus, the same events are revealed in Ty1 mobility assays using his3-AI or neo-AI indicator genes and slightly different plating schemes, because pBDG954 retention remains very high on YEPD +/- G418 following growth in SC-Ura.

Isolation of genomic DNA for PacBio sequencing

Genomic DNA was extracted using the Wizard Genomic DNA purification kit (Promega, Madison WI) according to the manufacturer’s instructions for yeast with minor modifications (https://dx.doi.org/10.17504/protocols.io.rved63e). A single colony of each strain was inoculated in 7 ml of YPD media and cultured for 20–24 hours at 30°C. Approximately 6 ml of culture for each strain was transferred to 4, 1.5 ml tubes and centrifuged at 16,162 relative centrifugal force (RCF) for 2 min at room temperature. The resulting cell pellet was resuspended in 293 μl of 50mM EDTA, pH 8.0 and incubated with 100 units of Lyticase (Sigma-Aldrich, Saint Louis MO) at 37°C for 21 hours. The resulting spheroplasts were centrifuged at 16,162 RCF for 2 min, resuspended in 300 μl of Promega Nuclei Lysis Solution, followed by adding 100 μl of Promega Protein Precipitation Solution, and incubated on ice for 5 min. Lysates were centrifuged at 16,162 RCF for 10 min. The supernatant was transferred to a 1.5 ml tube containing 300 μl of isopropanol and tubes were inverted 50 times to facilitate DNA precipitation. DNA was pelleted by centrifugation at 16,162 RCF for 10 min. The DNA pellet was washed with 300 μl of 70% ethanol, centrifuged at 16,162 RCF for 5 min and air dried for 15 min. The DNA pellet was resuspended in 50 μl of Promega DNA rehydration solution by gentle pipetting. Samples were treated with 5.25 units of RNAse A (Qiagen, Hilden Germany) at 37°C for 1 hour. Samples were incubated at 65°C for 45 min and stored at 4°C. DNA was centrifuged at 16,162 RCF for 10 min and supernatants of the four extracts were pooled, and additional purification steps were performed as follows. Qiagen DNA Hydration solution was added to bring the final volume from ~180 μl to 200 μl/strain. Three microliters of Qiagen RNase A Solution was added to each tube followed by incubation at 37°C for 1 hour. The sample was transferred on ice and 0.5 volume of Qiagen Protein Precipitation Solution was added, followed by 2 volumes of cold 100% ethanol. Tubes were mixed by inversion 50 times and incubated on ice for 15 min. Precipitated DNA was pelleted at 16,162 RCF for 10 min and washed with 70% ethanol followed by short spin 16,162 RCF for 3 min. The supernatant was removed, and the DNA pellet was air dried for 15 min. The DNA pellet was resuspended in 110 μl of Qiagen DNA hydration Solution by gentle pipetting, followed by incubation at 37°C for 1.5 hours to fully dissolve the DNA. An additional spin at 16,162 RCF for 10 min was performed in order to pellet any impurities. Supernatants were transferred to fresh tubes and stored at 4°C or -20°C prior to making PacBio libraries.

Genome sequencing and assembly

PacBio sequences were generated for S. cerevisiae using the PacBio RS II platform [81]. For S. cerevisiae genomes, total DNA was purified with 1x cleaned AMPure beads (Beckman Coulter, Pasadena CA) and the quantity and quality were assessed using Nanodrop and Qubit assays. Five micrograms of purified DNA samples were sheared to approximately 20 Kb using gTubes (Covaris, Woburn MA) at 1000 x g. Sheared DNA was recovered by purification with 1:1 vol ratio of AMPure beads. Sheared DNA was treated with Exonuclease V11 (New England Biolabs), at 37°C for 15 min. The ends of the DNA were repaired by first incubating for 20 min at 37°C with damage repair mix supplied in the SMRTbell library kit (Pacific Biosciences, Menlo Park CA). This was followed by a 5-minute incubation at 25°C with end repair mix in the SMRTbell library kit. End-repaired DNA was then cleaned using 1:1 volume ratio of AMPure beads and 70% ethanol washes. End-repaired DNA was ligated to SMRTbell adapter overnight at 25°C. Ligation was terminated by incubation at 65°C for 10 min followed by exonuclease treatment for 1 hour at 37°C. The SMRTbell library was purified with 1:1 volume ratio of AMPure beads. The quantity of library and therefore the recovery was determined by Qubit assay and the average fragment size determined by Fragment Analyzer. Size-selection was performed on Sage Blue Pippin Prep using 0.75% agarose cassette and S1 marker. The size-selected SMRT bell was recovered using 1:1 volume ratio of AMPure beads and quantified by Qubit. The final average size was between 17–23 Kb. SMRTbell libraries were annealed to sequencing primer at values predetermined by the Binding Calculator (Pacific Biosciences) and a complex made with the DNA Polymerase (P6/C4 chemistry). The complexes were bound to Magbeads and this was used to set up the required number of SMRT cells for each sample. SMRT sequencing was performed using the PacBio RS II system with a movie time 360 min. Genome assembly was performed using the RS_HGAP_Assembly.3 protocol in the SMRT Analysis package version 2.3.0. Assembly statistics and quality were determined using Quast (version 4.2) [82] and Mummerplot (version 3.23) [83] relative to the UCSC sacCer3 reference assembly. Raw PacBio reads and assemblies were submitted to ENA under accession PRJEB33725.

Annotation of Ty elements

HGAP assemblies for the genomes reported here plus a complementary set of HGAP assemblies from S. cerevisiae, S. paradoxus, and the outgroup species S. jurei [18,43] were used to identify Ty elements using a modified strategy similar to Carr et al. [13]. RepeatMasker (version 4.0.5; options: -e wublast -s -xsmall -nolow -no_is) (http://repeatmasker.org) was used to find all Ty fragments with similarity to a custom database of canonical Ty sequences derived from those reported in Carr et al. [13] that was updated to fix several small errors and include a version of the Tsu4 element from S. paradoxus [19] (S6 File). Inspection of raw RepeatMasker results identified a number of false positive matches to divergent sequences, LTR fragments from full-length or truncated elements were labeled as the incorrect family, tandem duplications of Ty elements that share a common LTR sequence that were incorrectly joined, and fusion of nearby solo LTRs fragments to full or truncated Ty elements. To fix these errors, we applied a series of automated filtering and editing operations to the raw RepeatMasker .out files: (i) false positive Ty predictions were filtered out of the RepeatMasker .out file by removing all matches to fragments with >20% divergence to the canonical Ty internal or LTR sequence; (ii) LTR fragments from full-length Ty1 and Ty2 elements were modified to match the name of the internal region found in contiguous clusters of Ty fragments with the same RepeatMasker id; (iii) tandemly-arrayed Ty elements that share an internal LTR sequence were split into distinct copies with shared LTR sequences being represented in each component copy; and (iv) flanking solo LTRs that were incorrectly joined to a complete or truncated element were split into distinct, non-overlapping copies. The final modified RepeatMasker .out file was converted to BED12 format with all fragments having the same RepeatMasker ID joined into a single BED12 record. Each Ty element in the BED12 file was categorized structurally as full-length (f, internal region present and total length >95% of canonical length), truncated (t, internal region present and total length <95% of canonical length), or solo LTRs (s, LTR present but no match to internal region). BED12 files for each strain (S7 File) were then used to summarize counts of all Ty element structural classes. Following Yue et al. [18], counts of solo LTRs for Ty1 and Ty2 were pooled because of the similarity of their LTR sequences.

Alignment and sequence analysis of Ty1 elements

BED12 files were used to extract fasta sequences oriented relative to the positive strand of each full-length Ty element using BEDtools getfasta (version 2.26.0; options: -name -s) [84]. Fasta files of full-length Ty1 sequences from all strains were concatenated together with the Ty1-H3 and Ty2 canonical elements and aligned using mafft (version 7.273) [85] (S8 File). gag and pol regions were annotated based on Ty1-H3 coordinates in the resulting multiple alignment. For sliding window analysis, a subset of aligned fasta sequences was extracted and gap-only sites were removed using Seaview (version 4.7) [86]. Sequence divergence between pairs of Ty1 elements was estimated using Kimura’s 2-parameter substitution model was calculated for 50 bp windows with a 10 bp step size in R (version 3.5.2) using the spider (version 1.5) and phangorn (version 2.4) packages [87,88]. For clustering analysis, complete sequence and region-specific alignments (for gag and pol) from the subset of strains with mobility data plus Ty1-H3 were extracted and gap-only sites were removed using Seaview (version 4.7) [86]. Aligned sequences were then clustered using the BIONJ algorithm with a Kimura 2-parameter substitution model in Seaview (version 4.7) [86,89] and resulting trees were visualized in R (version 3.5.2) using the APE package (version 5.2) [90]. Phylogenetic networks of sequences from the mobility dataset plus Ty1-H3 were generated using uncorrected P-distance and the Neighbor Net algorithm in SplitsTree 4.15.1 [91,92]. For maximum-likelihood phylogenetic analysis, region-specific alignments for the expanded dataset plus Ty1-H3 (excluding one recombinant element each from S288c and Y12) was performed using raxmlHPC-PTHREADS-AVX (version 8.2.4; options -T 28 -x 12345 -p 12345 -b 12345 -N 100 -m GTRGAMMA) [93]. Resulting phylogenetic trees were visualized in FigTree 1.4.4. Ancestral states for gag nucleotide sequences in the maximum likelihood tree were reconstructed using raxmlHPC-PTHREADS-AVX (version 8.2.4; options -T 28 -f A -m GTRGAMMA) [93]. Fasta sequences for the ancestors of all canonical Ty1 and Ty1’ gag sequences, respectively, were extracted and re-aligned using PRANK (v.170427; options: -codon -F) [94]. Codon-aligned ancestral gag sequences were used to estimate dN, dS, and dN/dS ratios under PAML model M0 using ETE3 [95,96]. Codon-based nucleotide alignments were converted to amino acids and visualized in Seaview (version 4.7) [86]. Regions of Ty1 retained in truncated elements were determined by aligning individual truncated elements to the Ty1-H3 reference sequence using minimap2 (version 2.17: options -x spliced -a) [97], converting to BAM format with SAMtools (version 1.8) [98], projecting aligned fragments onto the Ty1-H3 reference sequence using BEDtools bamtobed (version 2.28.0; options: -splitD) [84], and visualizing using ggplot2 [99].

Supporting information

S1 Fig [a]
Southern blots of canonical Ty1-H3 hybridized with total DNA from Genome Resequencing Project (SGRP) strains.

S2 Fig [a]
Sequence divergence between Ty1’ and elements with recombination between canonical Ty1 and Ty1’ in the .

S3 Fig [a]
Phylogenetic networks Ty1 sequences from . strains with Ty1-H3 mobility phenotypes.

S4 Fig [tif]
Truncated Ty1 elements in strains with Ty1-H3 mobility phenotypes.

S5 Fig [a]
Sequence divergence between subfamilies of Ty1 and Ty2.

S6 Fig [a]
Strain-labelled phylogeny of and genes from full-length Ty1 elements in . and . .

S7 Fig [tif]
Strain-labelled phylogeny of non-recombinant region from full-length Ty1 elements in . and . .

S1 File [txt]
Assembly statistics and Ty content in PacBio assemblies of species.

S2 File [txt]
Maximum likelihood tree for the complete Ty1 region.

S3 File [txt]
Maximum likelihood tree for the complete Ty1 region.

S4 File [txt]
Maximum likelihood tree for the non-recombinant region of Ty1 .

S5 File [xlsx]
List of strains used in this study.

S6 File [txt]
Database of Ty element query sequences.

S7 File [zip]
BED files of Ty element coordinates.

S8 File [txt]
Full-length Ty1 element nucleotide sequences.