Horizontal transfer and the widespread presence of Galileo transposons in Drosophilidae (Insecta: Diptera)

Abstract

Galileo is a transposon notoriously involved with inversions in Drosophila buzzatii by ectopic recombination. Although widespread in Drosophila, little is known about this transposon in other lineages of Drosophilidae. Here, the abundance of the canonical Galileo and its evolutionary history in Drosophilidae genomes was estimated and reconstructed across genera within its two subfamilies. Sequences of this transposon were masked in these genomes and their transposase sequences were recovered using BLASTn. Phylogenetic analyses were employed to reconstruct their evolutionary history and compare it to that of host genomes. Galileo was found in nearly all 163 species, however, only 37 harbored nearly complete transposase sequences. In the remaining, Galileo was found highly fragmented. Copies from related species were clustered, however horizontal transfer events were detected between the melanogaster and montium groups of Drosophila, and between the latter and the Lordiphosa genus. The similarity of sequences found in the virilis and willistoni groups of Drosophila was found to be a consequence of lineage sorting. Therefore, the evolution of Galileo is primarily marked by vertical transmission and long-term inactivation, mainly through the deletion of open reading frames. The latter has the potential to lead copies of this transposon to become miniature inverted-repeat transposable elements.

Keywords:
DNA transposon; MITEs; P superfamily

Introduction

Transposable elements (TEs) belong to the repetitive fraction of genomes, and are linear sequences of DNA that have the ability to move within or between genomes (Wells and Feschotte, 2020). Classifications divide these sequences firstly into two classes, based on the intermediate molecule in their transposition process (Finnegan, 1989). Class I is composed of retrotransposons as their mobilization involves the synthesis of an RNA molecule, which are retrotranscribed into DNA and then inserted elsewhere in the genome (Wicker et al., 2007). On the other hand, the majority of Class II elements - or DNA transposons - are directly excised by their transposase (TPase), and then reinserted in another site in the genome (Wicker et al., 2007).

In addition, TEs can be either autonomous or nonautonomous (Wicker et al., 2007). The first are those that present their structures preserved, encoding all necessary enzymes to be transposed. The latter comprise defective TEs that no longer encode nor produce their own proteins, and move only if recognized by the enzymes of a closely related autonomous TE; such as the Miniature Inverted-repeat Transposable Elements (MITEs). MITEs are non-autonomous TEs, derived from autonomous Class II transposons, and present a few structural characteristics: (i) small size, ranging from 50 to 500 base pairs (bp); (ii) AT-rich sequences; and (iii) a lack of a functional TPase (Deprá et al., 2012; Fattash et al., 2013).

Transposable elements are often referred to as “parasites” (Colonna Romano and Fanti, 2022), given their ability to invade new genomes and increase their copy number (Loreto et al., 2008). Horizontal transposon transfer (HTT) is the phenomenon in which a given TE “jumps” to the genome of a non-closely related species, i.e., sexually isolated organisms (Panaud, 2016). The role of HTT in shaping diversity as an endogenous source of evolution is widely recognized (Pace et al., 2008; Gilbert and Feschotte, 2018; Carvalho et al., 2023), and its frequency is much higher than previously thought (Schaack et al., 2010; Panaud, 2016; Peccoud et al., 2017; Melo and Wallau, 2020).

In this sense, several evolutionary events have been proposed as a direct consequence of TEs mobilization and/or recombination. For instance, in several taxa the variation and evolution of genome size are directly related to the amplification or contraction in TEs copy number (Canapa et al., 2015; Antoniolli et al., 2023). Nucleotide polymorphisms are also frequently produced after transposition events (Bourque et al., 2018). Transposable elements are also known to be related to changes in gene expression, either by silencing or enhancing them (Finnegan, 1989), and chromosomal rearrangements - i.e., deletions, duplications, translocations and inversions by ectopic recombination (Kidwell and Lisch, 1997). In the latter, distant loci in a genome carry highly similar TE copies, which allows homologous recombination to occur (see review in Bourque et al., 2018), thus resulting in a drastic modification in the chromosome architecture (Ren et al., 2018). Documented cases of a TE as a mediator of ectopic recombination include the families of retrotransposons Bel-Pao, Doc, I element and roo, as well as the transposons foldback, Galileo and hobo (Lim and Simmons, 1994; Delprat et al., 2009).

Galileo is a family of Class II transposons, and encodes its own TPase flanked by terminal inverted repeats (TIRs). Initially described as a foldback-like element, its TIRs and THAP domains exhibit similarities with those of the P element, leading to the classification of Galileo within the P superfamily (Marzo et al., 2008). However, unlike the P element, Galileo does not present introns (Marzo et al., 2008). Galileo was discovered by Cáceres et al. (1999) due to its association with the breakpoints of the 2j inversion in wild specimens of Drosophila buzzatii. In fact, Galileo is the only TE known to induce chromosomal rearrangements in natural populations of Drosophila (Marzo et al., 2008), as most others have been observed in laboratory populations (Lim and Simmons, 1994). Besides the 2j inversion, Galileo was involved with two other rearrangements described in D. buzzatii (Casals et al., 2003; Delprat et al., 2009). This makes this transposon as one of the most well-documented examples of a natural TE-induced chromosomal rearrangement.

Studies have shown the widespread presence of Galileo in the Drosophila genus (Marzo et al., 2008; Acurio, 2015). The main focus of the present study was to characterize the evolutionary history of the Galileo family and evaluate its main transmission mode in Drosophilidae. This transposon was masked in genome assemblies of 163 species available at online databases, and TPase sequences found were employed for reconstructing a phylogeny and testing putative cases of HTT.

Material and Methods

Masking Galileo in the genome assemblies

Representative genome assemblies of 163 Drosophilidae species (see details on taxonomy and accession numbers in ^{Table S1}) were retrieved from GenBank (NCBI) with a Python package written by Blin (2021). These species belong to the Chymomyza, Drosophila, Lordiphosa, Scaptodrosophila, Scaptomyza, and Zaprionus genera of the Drosophilinae subfamily; and Leucophenga and Phortica of Steganinae subfamily (^{Table S1}). BUSCO v.5 (Manni et al., 2021) was employed to assess the completeness of each assembly with the Diptera orthologous database.

The nucleotide sequence of seven Galileo copies characterized by Marzo et al. (2008) in D. ananassae (Dana\Galileo - BK006363), D. buzzatii (Dbuz\Galileo - EU334682 and EU334685), D. mojavensis (Dmoj\Galileo - BK006357), D. persimilis (Dper\Galileo - BK006361), D. virilis (Dvir\Galileo - BK006359) and D. willistoni (Dwil\Galileo - BK006360) were downloaded from GenBank, and used as queries in our workflow. Firstly, the queries were input as the repeat library in RepeatMasker (Smit et al., 2023) for masking canonical Galileo sequences in each genome assembly. The script ‘One code to find them all’ (Bailly-Bechet et al., 2014) was then employed to parse the output, recovering the nucleotide sequence of each identified copy in an assembly with at least 80% identity to its best query and a minimum length of 80 base pairs.

Phylogenetic analysis of Galileo potentially autonomous copies

The complete nucleotide sequence encoding the transposase (TPase) of six copies (Dana\Galileo, Dbuz\Galileo, Dmoj\Galileo, Dper\Galileo, Dvir\Galileo, and Dwil\Galileo) served as queries for local BLASTn searches in each FASTA file containing the Galileo copies of each genome. Hits with at least 80% identity and coverage of at least 70% for any of the queries were used in downstream analyses. Additionally, a P element from the genome of Drosophila buzzatii (GenBank accession No. KC690135) and two copies of the 1360 element (GenBank accession Nos. AF533772 and AY138841) were included in the nucleotide matrix as outgroups. This matrix was aligned with MACSE v2 (Ranwez et al., 2018) in two steps: (i) using the option alignSequences, which aligns nucleotide sequences based on their underlying codon structure, accounting for frameshifts and stop codons; (ii) the resulting alignment was edited with the option exportAlignment, replacing codons containing frameshifts and internal stop codons with “N” (e.g., TG! was replaced by NNN). The codon alignment was then processed with Gblocks (Castresana, 2000) to remove poorly aligned regions, allowing the presence of gaps.

The final codon alignment was translated to amino acids and used for a Bayesian phylogenetic inference (BI) analysis, performed in MrBayes 3.2.7 (Ronquist et al., 2012). The majority-rule consensus tree was built under the best amino acid substitution model, as estimated by ModelTest-NG (Darriba et al., 2020). Metropolis-coupled Markov chain Monte Carlo (MCMCMC) analysis was run with two parallel runs with four chains each for 1,000,000 generations, sampling every 100. Convergence was reached when the average standard deviation of split frequencies was below 1%. A burn-in of 25% was applied to the sampled trees before obtaining the consensus tree. The tree was visualized and edited in FigTree (Rambaut, 2018).

Analysis of abundance and repeat profile

Forward short-reads of high-throughput whole genome sequencing were downloaded from the Sequence Read Archive of NCBI (see SRA accession No. in ^{Table S1}) for those species with positive hits for the TPase queries. These were submitted to the RepeatProfiler pipeline (Negm et al., 2021), an analysis in which sequencing reads are mapped against queries to build coverage graphs, allowing to infer which regions of a given query have a higher or lower abundance.

Quality trim was performed with fastp (Chen et al., 2018), when reads had their adaptor removed while keeping only reads with no N base. The total reads were downsampled to 3 million, achieving near 1x coverage for all genomes (assuming a genome size mean of 200 megabases for species of the family Drosophilidae). In addition, five single-copy genes were randomly selected in the Diptera orthologous genes dataset of BUSCO 5 (Manni et al., 2021) to normalize the results (^{Table S2}). The six complete copies of Galileo used in BLASTn searches were used as queries (Dbuz\Galileo - EU334685 was excluded because it was shorter than Dbuz\Galileo - EU334682). RepeatProfiler (Negm et al., 2021) was executed with default parameters.

Inference of HTT events

Possible cases of HTT were determined based on incongruences between the phylogeny of host genomes and the phylogeny of Galileo. Validation of such cases was performed with the vhica R package (Wallau et al., 2015), implemented on the HTT-DB platform (Dotto et al., 2015). This method relies on discrepancies in the evolutionary rates of synonymous positions (dS), which considers codon usage bias (CUB), between nuclear genes (vertically transmitted) and transposable elements (TEs). Wallau et al. (2015) demonstrated that dS and CUB are correlated, and low values for both are indicative of inconsistencies with vertical transmission.

Sequences of single-copy orthologous genes were searched in the assemblies with positive hits of Galileo using BUSCO 5 (Manni et al., 2021) and the Diptera orthologous database. Nucleotide sequences of 30 randomly selected genes (see ^{Table S3}) were aligned based on codons using the ClustalW algorithm (Thompson et al., 1994) implemented in MEGA 11 (Tamura et al., 2021). These alignments were used to compare the dS-CUB between the host nuclear genome and Galileo sequences. A substitution rate of 0.016 per million years (Sharp and Li, 1989) was applied to estimate the time of divergence between Galileo sequences.

To provide an evolutionary context for the results, a phylogenetic tree of the 37 host genomes was reconstructed using the entire set of BUSCO genes shared among them. Their amino acid sequences were aligned with MUSCLE (Edgar, 2004) and refined with trimAl (Capella-Gutiérrez et al., 2009), implemented in a pipeline written by McGowan (2020). Scaptodrosophila lebanonensis was included in this analysis as an outgroup. Their phylogenetic relationships were reconstructed under maximum likelihood in IQ-TREE 2 (Minh et al., 2020), with the best substitution model selected based on AIC scores (flags --m and --merit). Branch supports were estimated by applying 1,000 replicates of ultrafast bootstrap.

Results

Search for canonical Galileo copies

Sequences of Galileo were masked in all analyzed genomes (^{Table S1}), except for D. ercepeae and D. nannoptera - which belong to the melanogaster and nannoptera groups, respectively. Assemblies showed satisfactory levels of completeness, with the majority having more than 90% of single-copy orthologous genes (S). The exception was eight species, with S percentages ranging from 70% to 90% (see ^{Table S4}). In the second round of searches, conducted using local BLASTn with TPases as queries, 37 species yielded positive hits after the filtering process (^{Table S1}). The positive results in the BLASTn search were limited to species within the Drosophila and Lordiphosa genera (Drosophilinae subfamily, Drosophilini tribe). All identified TPase sequences exhibited mutations, including stop codons, coding frame shifts, or both.

Phylogenetic analysis and abundance of Galileo sequences

The final sizes of nucleotide and amino acid alignments were 1,035 bp and 345 amino acids, respectively. The best amino acid substitution model was JTT+G4+F, based on the Akaike Information Criterion (AIC). Every copy of Galileo found in the genomes was placed in the same clade as its query. Major clades exhibited strong node support (PP > 0.95), with exceptions mainly observed among intraspecific sequences.

The query Dana\Galileo recovered three clades: the first two (yellow, ^{Figure S1}) containing sequences found in genomes of the melanogaster group (in which D. ananassae is phylogenetically placed); and the third (orange clade, ^{Figure S1}) containing sequences found in species of the montium group, along with Lordiphosa collinella and L. stackelbergi (pink sequences, ^{Figure S1}). Dwil\Galileo clustered homologous sequences found in the willistoni group (light pink sequences, ^{Figure S1}), along with its sister saltans group (blue sequences, ^{Figure S1}). On the other hand, the sequences of Galileo found by Dvir\Galileo (green clade, ^{Figure S1}) in species of the virilis group formed a sister clade (PP = 1.0) to those of the willistoni and saltans groups. Finally, Dper\Galileo recovered Galileo from species belonging to the obscura group (red clade, ^{Figure S1}), and Dmoj\Galileo retrieved sequences in D. mojavensis (purple clade, ^{Figure S1}). The abundance of Galileo sequences in these species, as assessed by the coverage analysis in RepeatProfiler, showed that the TPase region had lower coverage than that of TIRs in all cases (Figures 1 and ^S2-S7).

Figure 1 -
Coverage graphs for six queries of Galileo against its corresponding species: (A) Dana\Galileo in Drosophila ananassae; (B) Dbuz\Galileo in D. buzzatii; (C) Dmoj\Galileo in D. mojavensis; (D) Dper\Galileo in D. persimilis; (E) Dvir\Galileo in D. virilis; and (F) Dwil\Galileo in D. willistoni. Colors correspond to the coverage scale on the right side of each graph. Axis X corresponds to base pairs positions.

Inference of HTT events

Two major incongruences were found between host species (Figure 2A) and Galileo phylogenies. The first is the similarity of elements found in Lordiphosa collinella and Lordiphosa stackelbergi with species of the montium group (Figure 2B). The second incongruence (Figure 2C) is the clade formed by virilis (Drosophila subgenus) and willistoni plus saltans groups (Sophophora subgenus). No signals of HTT events were detected (p-value > 0.05) between the species of the virilis group and the willistoni and saltans groups (Figure 2D). However, HTT was detected (p-value < 0.05) between L. collinella and L. stackelbergi and species of the montium group. Signals were also detected between the melanogaster and montium groups, both belonging to the Sophophora subgenus (Figure 2E). Estimates of divergence times (^{Table S5}) span from ~679 thousand years ago (D. auraria x L. stackelbergi) to ~6 million years ago (D. carrolli × D. watanabei).

Figure 2 -
(A) Ultrametric tree showing the phylogenetic relationships between species harboring nearly complete transposases, assessed through maximum likelihood. Ultrafast bootstrap (UFboot) not shown, as for all nodes UFboot = 100. (B and C) Majority-rule consensus tree showing the phylogenetic relationships between sequences of Galileo, (B) found in genomes of the montium group of Drosophila and species of the Lordiphosa genus, and (C) found in genomes of the saltans, virilis and willistoni groups of Drosophila; numbers next to each node reflect its posterior probability support. (D and E) Results of the horizontal transposon transfer (HTT) analysis in vhica, between (D) saltans, virilis and willistoni groups of Drosophila; and (E) Lordiphosa genus and melanogaster and montium groups of Drosophila. (D and E) Red squares represent statistically significant (P < 0.05) pairwise comparisons between sequences of Galileo, indicating a HTT event. Phylogenetic relationships between host genomes are shown by ultrametric trees drawn on the external sides of each graph.

Discussion

The 163 genomes analyzed in this study provided a broader sampling across Drosophilidae when compared to previous studies (Marzo et al., 2008; Acurio, 2015), including many different taxonomic levels. We were able to search for Galileo in the genomes of the two subfamilies - Drosophilinae and, for the first time, Steganinae. Furthermore, our sampling included two tribes of the first (Colocasiomyini and Drosophilini) and two tribes of the latter (Gitonini and Steganini). Indeed, the Drosophila genus is a paraphyletic lineage due to the offshoot of several genera within its phylogenetic tree (Suvorov et al., 2022); e.g., the Lordiphosa genus is placed within the Sophophora subgenus as a sister lineage to the Neotropical clade, which includes the saltans and willistoni groups (Figure 2D).

Galileo is fragmentally widespread in Drosophilidae

The majority of Galileo sequences recovered in our study consisted of fragments. Indeed, high levels of structural dynamism in Galileo have been described both within and between genomes, as TIRs presented variable sizes (see review in Marzo et al., 2008). Therefore, our results suggest that the canonical Galileo is widespread and abundant in the genomes of Drosophilidae, although its copies are potentially defective. Given the lack of coding for a transposase, these copies would be incapable of autonomous transposition, remaining as relics - as in the case of Miniature Inverted-repeat Transposable Elements (MITEs).

The hypothesis of classifying these fragmented copies as MITEs of Galileo in D. mojavensis was considered by Marzo et al. (2013a), but was discarded by those authors because the sequences were longer and had a lower copy number compared to typical MITEs. However, our analysis of normalized coverage suggested the opposite; highly amplified short segments of Galileo TIRs were detected (Figures 1 and ^S2-S7), consistent with the size of MITEs. In D. virilis, for example, the TPase segment of Dvir\Galileo had a low coverage (~10X) while its TIRs had a coverage of < 200X (Figure 1E). Although strong evidence was found, further characterization is still needed to assist in the classification of these short canonical sequences as MITEs.

Interestingly, Galileo seems to be highly amplified in Neotropical species. Among the 15 species with the highest copy number (Figure 3; ^{Table S1}), eight are endemic to the Neotropical region: D. mojavensis, D. sturtevanti, D. willistoni, D. paulistorum, D. navojoa, and D. buzzatii, D. tropicalis, and D. montana (listed from the highest to the lowest copy number). In fact, the heterogeneity found across the Neotropical region provides innumerous distinct environments, challenging the survival of species (Miranda et al., 2022). Such environments also impact genomes, as expanding into new areas may relieve the epigenetic silencing or control of TEs, leading to their mobilization and amplification (Gregory, 2001; Rebollo et al., 2010; Antoniolli et al., 2023). For instance, D. willistoni - which harbors an exceptional diversity of Galileo (Gonçalves et al., 2014) - is distributed throughout the Neotropical region, and TEs differentially populate its genomes (Bertocchi et al., 2022).

Figure 3 -
Figure 3 - Number of sequences (X axis) masked as Galileo elements by RepeatMasker for the top 15 species (Y axis) with the highest number of sequences. Species highlighted in bold are endemic to the Neotropical region.

Signals of HTT in the Sophophora subgenus

The overall congruence between the phylogeny of Galileo and that of its host genomes, in terms of clustering species of the same group into the same clade (^{Figure S1}), may be explained by vertical transmission (Acurio, 2015). However, the observed incongruence involving copies found in Lordiphosa and species of the montium group (Figure 2B) was confirmed as horizontal transfer (HTT) event (Figure 2E). The Lordiphosa genus is actually a sister lineage to the willistoni group, and its MRCA with the montium group diverged around 40 million years ago (Mya) (Suvorov et al., 2022). In this case, the oldest HTT event between them (L. stacklbergi × D. punjabiensis) is estimated to have occurred at around 2.2 Mya; much more recent than their MRCA.

Other cases of HTT involved the melanogaster and montium groups, whose MRCA diverged around 20 Mya (Suvorov et al., 2022); also much older than the oldest HTT detected between them (around 6 Mya for D. carrolli × D. watanabei). The species involved with HTT events occur in sympatry, mainly in the Palearctic region of Asia (TaxoDros v1.04) - which permits a niche overlap. Addittionaly, Galileo exhibits a patchy distribution both in the Lordiphosa genus and the melanogaster and montium groups (^{Table S1}); in this case, the TE is present in some species but absent in another closely related one(s).

Furthermore, a specific THAP binding site for the Galileo transposase was identified at the 3’ end TIRs (Marzo et al., 2013b). The sequences of Galileo found in these species involved in HTT cases presented highly conserved and amplified 3’ TIRs (Figures 1 and ^S2-S7), providing further support for the plausibility of such HTT events. Nonetheless, the successful establishment of a TE in new genomes is highly dependent on its transposition rate (Le Rouzic and Capy, 2005), as it must avoid being lost in the population due to genetic drift (Blumenstiel, 2019). While L. stackelbergi presented a low number of sequences (49 sequences), L. collinella harbors more than 680 sequences (^{Table S1}), similar to D. buzzatii (604 sequences), in which Galileo was first described. Many other cases of low copy number were also detected (^{Table S1}), and the smallest include D. ambigua (10), D. punjabiensis (37). and D. watanabei (58). The process of stochastic loss of an element may explain both its patchy distribution and low copy number (Blumenstiel, 2019), as observed in mariner-like elements in Drosophila (Lohe et al., 1995) and Rex elements in the ray-finned fish Characidium (Pucci et al., 2018).

Lineage sorting explains the similarity between the saltans, virilis and willistoni groups

Marzo et al. (2008) described a high similarity between the copies found in the genomes of D. virilis and D. willistoni. Interestingly, the first belongs to the Drosophila subgenus, while the latter belongs to the Sophophora subgenus - their MRCA diverged around 49.9 Mya (Suvorov et al., 2022). Acurio (2015) later confirmed this close relationship, identifying it along with the guarani and tripunctata groups (Drosophila subgenus). Our results further corroborate both studies by expanding the sample size to include D. littoralis and D. novamexicana (virilis group).

Interestingly, Galileo sequences found in each of these two groups clustered into sister clades that corresponded to their host species, with the addition of sequences from the saltans group in the latter. This clade (virilis + saltans + willistoni) was the first to split in the evolution of Galileo - also congruent with Marzo et al. (2008). These authors also proposed two explanations for the incongruence between the phylogenies of Galileo and its host genomes: lineage sorting with ancestral HTT (Acurio, 2015); or horizontal transfer itself. As no signal of HTT was detected between or within these three species groups (Figure 2A), lineage sorting is a plausible explanation (Cummings, 1994). In this case, the transposon is vertically transmitted, but its copies coalesce prior to the split between the host species (Tenaillon et al., 2010) or are differentially lost along the branches of the species tree (Marzo et al., 2008).

Conclusions

The evolutionary history of Galileo in Drosophilidae is marked mostly by vertical and possibly ancient horizontal transmissions, as identified by Acurio (2015), with stochastic loss through genetic drift occurring while species diverged. In addition, its high fragmentation level is compatible with the characteristics of MITEs, although a thorough characterization is still needed to confirm this. Galileo found favorable conditions for its amplification in the heterogeneous Neotropical region, with an astounding copy number detected in Drosophilidae species inhabiting this area. Finally, considering the potential of Galileo to induce chromosomal rearrangements and their evolutionary implications, the HTT described between Lordiphosa and the montium group, and between the latter and the melanogaster group, these results raise an intriguing question (Alfredo Ruiz, personal communication): could evolution be infectious?

Acknowledgements

The authors thank Dr. Arnaud Le Rouzic and Dr. Gabriel L. Wallau for technical assistance with the vhica analysis and Dr. Alfredo Ruiz for inspiring comments in early stages of this study. This study was supported by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), under scholarship No. 141319/2020-8, and research productivity grant No. 312781/2018-0.

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Supplementary material

The following online material is available for this article:

Figure S1 - Phylogenetic relationships between sequences of Galileo found across genomes of Drosophilidae, reconstructed through Bayesian Inference.

Figure S2 - Normalized coverage graphs for Dana\Galileo used for searching transposase sequences across genomes of Drosophilidae.

Figure S3 - Normalized coverage graphs for Dbuz\Galileo used for searching transposase sequences across genomes of Drosophilidae.

Figure S4 - Normalized coverage graphs for Dmoj\Galileo used for searching transposase sequences across genomes of Drosophilidae.

Figure S5 - Normalized coverage graphs for Dper\Galileo used for searching transposase sequences across genomes of Drosophilidae.

Figure S6 - Normalized coverage graphs for Dvir\Galileo used for searching transposase sequences across genomes of Drosophilidae.

Figure S7 - Normalized coverage graphs for Dwil\Galileo used for searching transposase sequences across genomes of Drosophilidae.

Table S1 - List and taxonomy of Drosophilidae species included in this study, including positive results from BLASTn searches of the Galileo transposase sequences and accession numbers to the genome assembly and short-read sequencing data on NCBI.

Table S2 - List of genes used to normalize the results of profile and abundance of Galileo across the analyzed genomes in this study.

Table S3 - List of genes used for Codon Usage Bias (CUB) comparisons in the analysis of horizontal transposon transfer (HTT) in vhica R package.

Table S4 - Statistics of assembly completeness for each analyzed genome.

Table S5 - Statistically significant results of pairwise comparisons of horizontal transposon transfer performed with vhica at HTT-DB.

Edited by

Associate Editor:

Loreta Brandão de Freitas

Publication Dates

• Publication in this collection
  29 Mar 2024
• Date of issue
  2023

History

• Received
  08 May 2023
• Accepted
  30 Jan 2024