Interpopulation variation of transposable elements of the hAT superfamily in Drosophila willistoni (Diptera: Drosophilidae): in-situ approach

Abstract

Transposable elements are abundant and dynamic part of the genome, influencing organisms in different ways through their presence or mobilization, or by acting directly on pre- and post-transcriptional regulatory regions. We compared and evaluated the presence, structure, and copy number of three hAT superfamily transposons (hobo, BuT2, and mar) in five strains of Drosophila willistoni species. These D. willistoni strains are of different geographical origins, sampled across the north-south occurrence of this species. We used sequenced clones of the hAT elements in fluorescence in-situ hybridizations in the polytene chromosomes of three strains of D. willistoni. We also analyzed the structural characteristics and number of copies of these hAT elements in the 10 currently available sequenced genomes of the willistoni group. We found that hobo, BuT2, and mar were widely distributed in D. willistoni polytene chromosomes and sequenced genomes of the willistoni group, except for mar, which is restricted to the subgroup willistoni. Furthermore, the elements hobo, BuT2, and mar have different evolutionary histories. The transposon differences among D. willistoni strains, such as variation in the number, structure, and chromosomal distribution of hAT transposons, could reflect the genomic and chromosomal plasticity of D. willistoni species in adapting to highly variable environments.

Keywords:
Transposable elements; Drosophila willistoni; hAT superfamily; polytene chromosomes

Introduction

Transposable elements (TEs) constitute part of the repetitive fraction of the genome and can move within and between host genomes. TEs are thought to be present in virtually all genomes and are best studied in the genus Drosophila (Diptera: Drosophilidae) (Wicker et al., 2007). TEs are considered generators of evolutionary novelty, as they can interact with host genomes in a variety of ways, although they were previously characterized as junk DNA. They can be found close to regulatory regions over- or under-expressing genes, as constituents of heterochromatin, and may increase the propensity to chromosomal variations, among other possible roles such as an inducer of cancers (Cáceres et al., 2001; Catania et al., 2004; Bertocchi et al., 2018)

The proposed life cycle of TEs can be summarized as: insertion by Horizontal Transposon Transfer (HTT) or reactivation in the host genome; increase in copy number (proliferation) and dispersal in the host population; and, over time, accumulation of mutations (diversification) (Wallau et al., 2012). Sexual reproduction eventually allows TEs to be distributed in most individuals of a population and/or species. At any stage of the cycle, a TE can be lost by the genome or, to a lesser extent, undergo HTT and restart the cycle (Schaack et al., 2010; Wallau et al., 2012). HTT has been shown to perpetuate TEs in host genomes, and HTT events are increasingly identified in the most varied groups of eukaryotes (Wells and Feschotte, 2020).

As classified by Wicker et al. (2007), TEs are divided hierarchically, first into two classes according to the transposition mechanism: class I via intermediary RNA (retrotransposons) and class II via intermediary DNA (transposons). Class II elements, termed transposons, use the enzyme transposase for mobilization; they are subdivided into two subclasses according to the number of DNA strands that are cleaved in the transposition process. Subclass 1 elements cleave the two strands of DNA by a “cut-and-paste” mechanism, and subclass 2 elements cleave only one of the strands, which has other transposition mechanisms. TEs are then classified into orders, superfamilies, families, and subfamilies according to their structural characteristics and conservation of nucleotide and amino-acid sequences.

TEs may also be classified according to their autonomy for mobilization. TEs can be autonomous, that is, possess the entire enzymatic structure needed to carry out their own mobilization; or non-autonomous, when they need the enzymatic machinery of other autonomous TE copies to mobilize. An example of Class II non-autonomous elements are termed miniature inverted-repeat transposable elements (MITEs) (González and Petrov, 2009). MITEs are cross-mobilized by autonomous elements, as they generally conserve the recognition sequences for transposases, the TIRs. They can also be found in high copy numbers in genomes (Deprá et al., 2012; Loreto et al., 2018).

The hAT superfamily is present in animals, plants, and fungi. It is subdivided into three families: Ac, buster, and tip (Arensburger et al., 2011; Zhang et al., 2013; Rossato et al., 2014). Elements of the hAT superfamily have an 8 bp target site duplication (TSD) and short Terminal Inverted Repeats (TIRs) between 10-25 bp and 2.5-5 kb in size (Feschotte and Pritham, 2007). The elements hobo, BuT2, and mar belong to the Ac, tip, and buster families respectively (Deprá et al., 2012; Rossato et al., 2014). The canonical hobo (HFL1) was initially described in Drosophila melanogaster and consisted of 2959 bp length, encoding a 1.9-kb transposase gene, and 12 bp of TIRs (Calvi et al., 1991). Hobo was originally described to be limited to the melanogaster subgroup (Ortiz and Loreto, 2008; reviewed in Loreto et al., 2018). BuT2 is 2775 bp long and encodes a 643 aa transposase and 12 bp of TIRs (Rossato et al., 2014). BuT2 was initially described in Drosophila buzzatii, in regions of inversion breakpoints, which indicates a recent mobilization, although it is only sparsely present in the genome of this species (Cáceres et al., 2001; Casals et al., 2006). The canonical mar-MITE element was originally identified in D. willistoni and has 610 bp and 11 bp of TIRs. Mar is restricted to the willistoni subgroup, and until now partially complete copies have been found only in Drosophila tropicalis, with approximately 2600 bp (Holyoake and Kidwell, 2003; Deprá et al., 2012).

Dobzhansky (1950) described the first polytene photomap of D. willistoni, this map was further redrawn in Valente and Araújo, 1985, Regner et al., 1996, Bhutkar et al., 2008, and Rohde and Valente, 2012. The chromosome complement of D. willistoni consists of two pairs of metacentric chromosomes (IIL, IIR, XL, and XR arms), an acrocentric pair (III arm), and a Y submetacentric chromosome (Dobzhansky and Powell, 1975; Santos-Colares et al., 2003). D. willistoni is notable for having multiple chromosomal inversions in every natural population examined (review by Rohde and Valente, 2012).

The first sequenced genome of D. willistoni was that of strain Gd-H4-1, the result of several generations of sister-brother crosses to obtain a strain without segregating inversions, i.e., a monokaryotypic strain (Drosophila 12 Genomes Consortium et al., 2007). Strain Gd-H4-1 lacks the high degree of polymorphism and variability found in natural populations of this widely distributed tropical species (review by Zanini et al., 2015). Two additional strains of D. willistoni were recently sequenced by Kim et al. (2021), who found considerable differences between these strains in the number of repetitive sequences such as transposons and microsatellite elements.

Our research group has been studying several aspects of the chromosomal plasticity of D. willistoni (Valente and Araújo, 1985; Valente et al., 1993; Valente et al., 2003; Rohde and Valente, 2012; Garcia et al., 2015). The goal of the present study was to contribute to understanding the high degree of variability of D. willistoni over its wide geographical distribution. In view of the significant environmental differences encountered by this species, the chromosomal variations characteristic for D. willistoni strains, and the differences found in the number of repetitive fractions in different strains, we compared and characterized the organization and distribution of three transposable elements of the hAT superfamily in different D. willistoni strains. Studies such as this can clarify how different habitats are capable of promoting evolutionary changes in TEs and hosts.

Material and Methods

Fly stocks and chromosomal preparations

Three strains of D. willistoni were used in this study (^{Table S1}). These strains have been maintained in the laboratory by mass crosses and cultivated in cornmeal culture medium (Marques et al., 1966) under controlled temperature (20 ± 1 °C). The polytene chromosome preparations were obtained with third-instar larval salivary glands, squashed, and fixed in 2:1:2 ethanol-lactic acid-acetic acid, v/v.

Probe preparation and fluorescence in-situ hybridization (FISH)

TE clones were used as a template for the PCR labeling probe for FISH: BuT2 in D. willistoni (GenBank accession number KF669641.1) obtained from Rossato et al. (2014)⁠; mar_trop: sequence of the mar element of D. tropicalis (GenBank accession number JQ654772.1) (obtained from Deprá et al., 2012)⁠; and hobo in D. willistoni (submitted GenBank accession number OK032551, this study). For this last, genomic DNA from strain Gd-H4-1 was used to amplify the hobo transposon. The primers used were hobo CN 991 (5′-ACCGTCGACATGTGGAC-3′) and hobo CN 1598 (5′-GGATGGCAATAGGAAGC- 3′) (Deprá et al., 2009). The amplified sample was visualized on 0.8% agarose gel. The bands were purified using the GFX Purification Kit (GE Healthcare) and cloned using the TOPO-TA cloning vector (Invitrogen, Carlsbad, CA, USA). Cloned PCR products were sequenced using the universal primers M13 (forward and reverse) at Macrogen (Korea).

The TE probes BuT2, mar_trop, and hobo were marked directly by PCR, using Biotin-16-dUTP (Jena Bioscience). Slide preparations, hybridizations, and washes were performed according to Deprá et al. (2010), with minor modifications. FISH experiments were established in 77% of the stringency. The signal was detected using streptavidin-Cy3 and the chromosomes were counterstained with Fluoroshield with DAPI. The slides were analyzed using the epifluorescence microscope ZEISS Axiophot (Zeiss, Germany). The images were captured using Zeiss ZEN (blue edition) software. The final editing of the images used Adobe Photoshop CS6. The hybridization signals were quantified by visual inspections and using the ImageJ software (Schneider et al., 2012). The following premises were applied to measurements of the hybridization signals: area less than 9.99 µm² as non-hybridization borderline, and an area larger than 10 µm² for each hybridization on the five chromosome arms (XR, XL, IIR, IIL, and III). In the chromocenter, we considered the presence or absence of a hybridization signal.

Genome searches

Searches for homologous sequences to BuT2, hobo, and mar were carried out in the genomes of the species of the willistoni group available in NCBI and Kim et al. (2021), last accessed in January 2021. Versions of the assemblies, species, and strains used in this study are available in ^{Table S2}.

The queries used were: mar sequence from D. tropicalis (GenBank accession number JQ654772.1), BuT2 (GenBank accession number KF669641.1), and hobo (GenBank accession number OK032551) from D. willistoni available in NCBI. BLASTn searches were performed on the Galaxy platform, using default parameters (Afgan et al., 2016). The sequences with an E-value lower than e^-10 were extracted for each genome.

Sequence analysis

The sequence alignments were performed using MAFFT (Katoh and Standley, 2013), with default parameter values. AliView (Larsson, 2014) was used for sequence editing and visualization. Mar sequences are very variable in copy number, length, and structure, and therefore the alignment for phylogenetic reconstruction of the mar copies was submitted to two refinement steps: 1) copies with 100% of the identity in each genome were filtered by the CD-HIT Suite (Huang et al., 2010); and subsequently, 2) the alignment was manually inspected to exclude small and/or very degenerate sequences. All mar sequences after refinement (MITEs, relics, complete and partially complete) were used in phylogenetic reconstruction, except: Dwil_Gd_scf2_3; Dins_ctg2309_5, Dins_ctg424, Dins_ctg1175, Dins_ctg1948; Dtro_ctg108_3, Dtro_ctg108_4, Dtro_ctg838, Dtro_ctg804, Dtro_ctg19. All sequences of hobo and BuT2 retrieved were used in the phylogenetic trees.

The phylogenetic trees were inferred by Bayesian Analysis in MrBayes 3.2.6. implemented in the CIPRES gateway (Miller et al., 2010; Ronquist et al., 2012). The evolutionary models GTR+G (hobo), HKY+G (BuT2), and JC+I (mar) were indicated by MrModeltest2 (Nylander, 2004). The analysis was run for at least 10,000,000 generations, sampling trees every 1,000 generations, with 25% of the initial results as burn-in. MEGAX (Kumar et al., 2018) was used to measure the divergence of the sequences by p-distance and Neighbor-Joining phylogenetic reconstruction for the mar sequences (data not shown).

Also, we performed a phylogenetic reconstruction of the D. willistoni hobo in the hAT superfamily, using the Maximum Likelihood method and Le-Gascuel model (LG) (Le and Gascuel, 2008) by MEGA X (Kumar et al., 2018), with the transposase database based on Arensburger et al. (2011) and Rossato et al. (2014). The transposase sequences were aligned by MUSCLE, implemented in MEGA X.

Results

FISH of the BuT2, hobo, and mar elements in polytene chromosomes of D. willistoni strains

For the FISH experiments, we used polytene chromosomes from the three strains of D. willistoni from different geographic locations. The strains were: D. willistoni-Gd-H4-1, an inbred lineage; D. willistoni-WIP-4, descended from a natural population maintained in the laboratory for approximately 60 years and considered by us a standard karyotype for the species; and a natural population, D. willistoni-SG12.00, collected in the 2000s in Montevideo (Figure 1 and ^{Table S1}). Clear differences were detected in the number and distribution of signals along the chromosomal arms of these strains (Figure 2A-I).

Figure 1 -
Geographical origins of the Drosophila willistoni strains analyzed in silico and in situ, and information about hAT TE copies. Lines indicate the approximate geographical distributions of the three subspecies of Drosophila willistoni (Mardiros et al., 2016). The numbers of TE copies in polytene chromosomes were measured by ImageJ software (Schneider et al., 2012) and visually. The ordinal number represents stronger signals, and increasing from + to +++ indicate the relative strength of intensity of signals on chromosome arms, as detected visually on polytene chromosome arms. In the table: - indicates absence of information; c and nc indicate presence and absence of signals on the chromocenter, respectively; w indicates weak signals; +,++ and +++, increasing from + to +++ indicate the relative strength of intensity of signals detected visually on polytene chromosomes by FISH.

Figure 2 -
FISH in polytene chromosomes of Drosophila willistoni strains: (A-C) D. willistoni-Gd-H4-1; (D-F) D. willistoni-WIP-4; and (G-I) D. willistoni-SG12.00. The probes used are indicated in the lower right corner and the strains in the lower left corner of the images. Chromosomes were counterstained with DAPI (blue) and transposable element probes were labeled with Cy3 (red). Scale bar=10 µm.

The three probes used were derived from clones of TEs BuT2, hobo, and mar, and were termed BuT2, hobo, and mar_trop, respectively. FISH experiments with the BuT2 probe revealed differences among the strains in the distribution and number of signals. In D. willistoni-Gd-H4-1, visually many strong signals were detected along all chromosomes and the chromocenter (Figure 2B), while in D. willistoni-WIP-4 visually strong signals were observed on the IIR and IIL chromosome arms (Figure 2E). In D. willistoni-SG12.00, only two stronger signals of BuT2 hybridization signals were visible on the IIR and IIL arms (Figure 2H), and some signals were detected also in the chromocenter. We noted a pattern in the production of signals according to the geographic origin of the strains; the northernmost strain (from above the Equator; Figure 1) had more signals and more intense signals than the other, more southern strains (Figure 1).

With the hobo probe, the pattern was almost the opposite of that seen for BuT2: the strain from the extreme southern part of the distribution (D. willistoni-SG12.00 - Figure 1) showed many stronger signals on all chromosome arms, mainly in the euchromatin and chromocenter (Figure 2G). D. willistoni-Gd-H4-1 and D. willistoni-WIP-4 showed one stronger signal on the IIR arm, and we also observed more signals with less intensity in the D. willistoni -Gd-H4-1 (Figure 2A, D).

Concerning the mar_trop probe, D. willistoni-WIP-4 showed many stronger signals in all chromosome arms and the chromocenter (Figure 2F). Although the ImageJ software estimated around the same number of mar copies in the strains D. willistoni-Gd-H4-1 and D. willistoni-SG12.00 (Figure 1), differences between the two strains were apparent (Figure 2C and 2I), mainly concerning the intensity and distribution of the signals along the chromosomal complement. D. willistoni-Gd-H4-1 showed stronger signals along the five chromosome arms and the chromocenter, while D. willistoni-SG12.00 showed signals on the chromocenter and on the arms near the chromocenter, with no signals observed on the III chromosome.

Transposons in-silico search in Drosophila willistoni group genomes

hobo search

The cloned fragment of the element hobo from D. willistoni-Gd-H4-1 contained 439 bp and was 74.7% identical to that of the D. melanogaster canonical hobo (Calvi et al., 1991). D. willistoni-hobo alignments were mainly between nucleotide positions 991 and 1428 of the canonical hobo element. The BLASTn search showed that the D. willistoni-hobo fragment presented 93% identical to the hobo element of the Mediterranean fruit fly Ceratitis capitata (Diptera: Tephritidae) (Cc-HRE-GenBank access number U51454.1) (Handler and Gomez, 1996). To establish the relationship between the D. willistoni-hobo and Cc-HRE (C. capitata) putative transposase and the hAT superfamily elements, we assembled the transposase sequences described by Arensburger et al. (2011) and Rossato et al. (2014). A phylogenetic reconstruction of the hAT superfamily showed that D. willistoni-hobo and Cc-HRE (C. capitata-hobo) were grouped with Ac family elements (^{Figure S1}). These formed a clade with Howilli2 (D. willistoni), Cc-HRE (Ceratitis capitata), Homo1 (D. mojavensis), canonical hobo (D. melanogaster), Hermes (Musca domestica; Diptera: Muscidae), Homer (Bactrocera tryoni; Diptera: Tephritidae), Hoana1 (Drosophila ananassae), Hoana8 (D. ananassae), Hermit (Lucilia cuprina; Diptera: Calliphoridae), and Hoana3 (D. ananassae).

Using the hobo sequence obtained here (cloned element from D. willistoni strain Gd-H4-1), we performed BLASTn against the 10 sequenced genomes belonging to seven species of the willistoni group (^{Table S3}). Sequences homologous to the hobo fragment from D. willistoni were identified in the seven species of the willistoni group: D. willistoni (three strains), D. paulistorum (two strains), D. equinoxialis, D. tropicalis, D. insularis, D. sucinea, and D. nebulosa (Figure 3 and Figure 4A). In a search for complete copies of hobo in these genomes, we recovered homologous sequences and added 3000 bp from the hobo on each end. However, no complete copies were identified (codifying transposase and TIRs at the ends). A schematic representation of these sequences is shown in Figure 4A.

Figure 3 -
Information on species and evolutionary relationships of sequenced genomes of the willistoni group. Schematic evolutionary relationships among species of the willistoni group are based on Finet et al., (2021). (-) Absence; (+) presence; State = Structural characteristics of TE; CP = Complete or Partially complete copies; DR = Degenerate or Relic copies; MITE = miniature inverted-repeat transposable elements.

Figure 4 -
Schematic representation of reconstructed hobo, BuT2, and mar copies in the willistoni group. (A) hobo: all sequences are represented; (B) BuT2: all sequences are represented and transposase is formed by 5 exons, indicated by descending ordinal numbers; (C) mar: mar-MITE and degenerate sequences in D. willistoni-Gd-H4-1, D. willistoni-L17, D. willistoni-00, D. paulistorum-L06, D. paulistorum-L12, and D. equinoxialis were grouped. Regions of terminal inverted repeats shown inside black block, transposase coding region inside red line, and probes used in FISH experiments inside pink block. Only indels and deletions of nucleotides with more than 10 bp are represented.

With respect to the willistoni subgroup, in the genomes of D. willistoni-Gd-H4-1, D. willistoni-L17, D. willistoni-00, D. paulistorum-L06, and D. paulistorum-L12 we identified the most complete copies of hobo (≈2850 bp), with small additions in the region of the transposase, 12 bp TIRs conserved and identical to the canonical hobo and TSDs (Figure 3, Figure 4A and ^{Table S3}). In the genomes of D. willistoni-Gd-H4-1, D. paulistorum-L06, and D. paulistorum-L12 we also observed smaller hobo-like fragments without TIRs at both ends (Figure 4A).

The hobo-like sequences retrieved from the D. equinoxialis, D. tropicalis, and D. insularis genomes are smaller fragments (Figure 3), conserved mainly in the 520 to 1720 bp region of canonical hobo transposase, without TIRs or conserved TSDs (Figure 4A and ^{Table S3}).

In the bocainensis subgroup, complete sequences of D. sucinea and D. nebulosa were not identified (Figure 3). Copy Dsuc_ctg141 in D. sucinea and copies Dneb_ctg3 and Dneb_ctg46 in D. nebulosa had identical canonical TIRs (Figure 4A and ^{Table S4}). In both species, TSDs were not present or were variable.

In order to address the average divergence of the hobo sequences found within and between species/strains, we evaluated the p-distance (^{Table S4}). The intragenomic divergences in D. willistoni strains were 3.91% in D. willistoni-L17, 13.64% in D. willistoni-00, and 13.88% in D. willistoni-Gd-H4-1. Intragenomic divergence of 4.1% was observed in D. paulistorum-L12 and 7.98% in D. paulistorum-L6. The values of interspecies divergence ranged from 3.74% between D. paulistorum-L12 and D. willistoni-L17 to 13.05% between D. tropicalis and D. willistoni-Gd-H4-1. Figure 5 shows the Bayesian tree obtained for all hobo copies from the willistoni species group identified in this study. The phylogeny showed low resolution in several nodes, groupings with sequences of different species and subgroups, and some polytomies. One group was formed by D. willistoni strains, D. paulistorum strains, D. nebulosa, and D. sucinea copies. The recurrent grouping between sequences of D. nebulosa and D. sucinea was also evidenced. The relationships among the willistoni group species together with the branch lengths indicate that these sequences are very similar, likely with recent mobilization.

Figure 5 -
Phylogenetic relationships of hobo copies in the willistoni group. Unrooted Bayesian tree (GTR+G) based on nucleotide sequences. Node supports are shown by posterior probability. Drosophila melanogaster hobo canonical sequence is shown in black; the hobo_clone was used in the FISH experiments. Different strains and species are indicated in different colors, as shown in the legend. Further information on hobo sequences is available in ^{Table S3}.

BuT2 search

Sequences homologous to the element BuT2 were detected in the 10 genomes of the willistoni group analyzed; however, no complete TE copies were identified (Figure 4B). In the subgroup willistoni, partially complete copies of BuT2 were identified in D. willistoni strains. However, in the bocainensis subgroup (D. sucinea and D. nebulosa), only one short partial BuT2 fragment (764 bp) without TIRs was identified in both species (Figure 3).

In D. willistoni, two homologous BuT2 sequences were identified in the sequenced strains. The most complete sequences, i.e., in D. willistoni-Gd-H4-1 with 2742 bp (Dwil_scf2_2), D. willistoni-L17 with 2695 bp (Dwil_ctg8), and D. willistoni-00 with 2737 bp (Dwil_ctg1698), were 91% identical to the BuT2 element including 12 bp TIRs (Figure 4B and ^{Table S5}). Furthermore, the Dwil_scf2_2, Dwil_ctg8, and Dwil_ctg1698 sequences of BuT2 in D. willistoni were flanked by 8 bp TSDs. In these three D. willistoni strains, the TSDs were conserved, with one mismatch in D. willistoni-Gd-H4-1 (^{Table S5}). The other copies of D. willistoni-Gd-H4-1 (Dwil_scf2), D. willistoni-L17 (Dwil_ctg326), and D. willistoni-00 (Dwil_ctg675) were incomplete: without the TE initial region, with a size of 837-1032 bp, TIRs conserved in the TE 3’ region, and with large deletions in the exon regions 1, 2 and 4 of transposase (Figure 4B).

BuT2 copies in D. paulistorum-L06, D. paulistorum-L12, D. equinoxialis, and D. tropicalis genomes were defective, with deletions in the five exons of BuT2 transposase (Figure 3, Figure 4B, and ^{Table S5}). The 12 bp TIRs were conserved in D. paulistorum-L06, D. paulistorum-L12, and D. tropicalis copies (Figure 3 and ^{Table S5}). The D. insularis genome with one BuT2 copy lacked the 263 bp 5’ end of TE (Figure 4B).

The BuT2 intragenomic divergence in the different D. willistoni strains ranged from 9.11% in D. willistoni-Gd-H4-1 and D. willistoni-00 to 10.29% in D. willistoni-L17. An intragenomic divergence of 13.91% was observed in D. paulistorum-L06, and 17.99% in D. paulistorum-L12. Interspecies divergence values ranged from 0.13% between D. nebulosa and D. sucinea to 53.13% between D. sucinea and D. paulistorum-L06. ^{Table S6} shows the average divergence of the BuT2 sequences found within and between the species and strains. All copies of BuT2 retrieved in the sequenced genomes of the willistoni group were used to construct a phylogeny (Figure 6). Species of the bocainensis and willistoni subgroups formed two clusters with well-established relationships. The clade of the willistoni subgroup showed different groupings with high probability, with copies of D. willistoni strains, D. paulistorum strains, and all sequences of D. tropicalis. Two groups formed by copies of D. willistoni strains showed short branch lengths, which indicates that copies of different strains are very similar.

Figure 6 -
Phylogenetic relationships of the BuT2 copies in the willistoni group. Unrooted Bayesian tree (HKY+G) based on nucleotide sequences. Node supports are shown by posterior probability. Drosophila buzzatti BuT2 canonical sequence is shown in black; the BuT2_clone was used in the FISH experiments. Different strains and species are indicated in different colors, as shown in the legend. Further information about BuT2 sequences is available in ^{Table S5}.

mar search

We started the search for homologous sequences to the mar element in the willistoni group genomes by using the query clone_8 from D. tropicalis (JQ654772.1), also used in the FISH experiments. Mar homologous sequences recovered in the genomes were aligned using the full-length mar reconstructed by Deprá et al. (2012) in order to obtain putative full copies.

We recovered mar-like sequences in D. willistoni-Gd-H4-1, D. willistoni-L17, D. willistoni-00, D. paulistorum-L06, D. paulistorum-L12, D. equinoxialis, D. tropicalis, and D. insularis genomes (Figure 3). The exact number of copies in D. willistoni, D. paulistorum, and D. equinoxialis strains was difficult to determine because the genome contains some small fragmented copies that were not captured in the searches. Also, the copy number is variable among the species. In the bocainensis subgroup (D. sucinea and D. nebulosa) no mar-like sequences were identified (Figure 4C).

Mar full-length copies or putatively active were recovered only from the D. tropicalis genome. Partially complete copies were observed in D. willistoni-Gd-H4-1 (7 copies), D. willistoni-L17 (5 copies), and D. willistoni-00 (6 copies); degenerate and mar MITE copies were identified also in these strains (Figure 3 and Figure 4C). In D. tropicalis, we found the most complete sequence (Dtro_ctg748), with 2760 bp but with small gaps, the largest with a 39 bp base at position 2170-2207 in the reconstructed mar (^{Table S7}). In the genome of D. insularis we recovered only a few copies of mar relics (Figure 3 and Figure 4C) and no full-length or MITE. In D. insularis, 6 mar sequences (Dins_ctg2309_2, Dins_ctg2309_3, Dins_ctg2309_4, Dins_ctg2309_6, Dins_ctg2309_7, and Dins_ctg2309_8) were flanked by the BEL-LTR retrotransposon and the Transib1 transposon (identified by Censor).

Mar-MITEs, similarly to canonical mar sequences, were retrieved in D. willistoni-Gd-H4-1, D. willistoni-L17, D. willistoni-00, D. equinoxialis, and D. paulistorum-L12 (Figure 4C). The most degenerate copies were found in D. paulistorum-L06 and D. paulistorum-L12; in these strains, even the largest sequences had many small deletions.

For the mar divergence analysis, we used the conserved mar region in genomes of the willistoni subgroup. The intragenomic divergence in the different D. willistoni strains varied by around 10.33% in D. willistoni-Gd-H4-1, 12.83% in D. willistoni-00, and 10.4% in D. willistoni-L17 (^{Table S8}). We found an intragenomic divergence of 8.99% in D. paulistorum-L06 and 24.51% in D. paulistorum-L12. Interspecies divergence ranged from ~17% between the D. equinoxialis and D. willistoni strains to 43.29% between D. insularis and D. equinoxialis (^{Table S8}).

We reconstructed the phylogenetic relationships between mar sequences using different methods (for more details see the Material and Methods section) (Figure 7A, 7B, and ^{Figure S2}). Figure 7A shows a phylogenetic tree constructed with partially complete sequences obtained from the willistoni group genomes, except the degenerate sequences Dtro_ctg838, Dtro_ctg804, and Dins_ctg1175. In Figure 7B, the phylogenetic relationships were generated employing the same sequences from Figure 7A and the representative copies of mar MITEs. Degenerate copies were manually selected according to the blocks of the alignments in the genomes of D. willistoni (3 strains), D. paulistorum (2 strains), and D. equinoxialis. In the two phylogenetic reconstructions (Figure 7A and 7B), the potentially complete sequences of D. tropicalis were positioned basally in the phylogeny, followed by the partially completed sequences of D. willistoni, and degenerate sequences of D. equinoxialis (Box I - Fig 7B). Mar MITEs and other degenerate sequences (relic sequences) formed a larger cluster composed of a small clade containing two other partially complete sequences of D. willistoni (Box II - Fig 7B), and a large clade including the other sequences (Box III - Fig 7B). In box III, sequences from one species usually appeared interspersed among the other species, possibly reflecting a low divergence between some, as well as low posterior probability values. For example, in D. insularis there was a clear clustering of the degenerate sequences in one of the well-supported branches; however, some of these sequences are related to MITEs from D. equinoxialis, although with low support value (0.57). When analyzing all the sequences recovered in the genomes, it was not possible to clearly identify the relationships established, mainly between MITE and degenerate sequences, probably because of the low sequence divergence (^{Figure S2}).

Figure 7 -
Phylogenetic relationships of the mar copies in the willistoni subgroup. A: Bayesian tree of partially complete mar copies in the sequenced genomes of D. willistoni strains, D. equinoxialis, D. tropicalis, and D. insularis. Very degenerate copies of D. tropicalis and D. insularis were excluded from this analysis. B: Bayesian tree of mar partially complete, MITEs and relic copies in the sequenced genomes of the willistoni subgroup. This tree shows partially complete and relic copies used in A, and representative copies of mar MITES and degenerate copies in the D. willistoni strains, D. paulistorum strains, and D. equinoxialis genomes. AF518731_mar is the canonical mar-MITE of D. willistoni; mar_trop was used in the FISH experiments. Three different clades are indicated in boxes I, II, and III. Different strains and species are indicated in different colors, as shown in the legend. Degenerate sequences and MITEs are indicated by asterisks. Further information about mar sequences is available in ^{Table S7}.

Discussion

Drosophila willistoni was the first species in the willistoni group to be described, by Samuel Williston in 1896 (Dobzhansky and Powell, 1975). Dobzhansky (1950) described the karyotype of the species, and only in 2007 was the first genome sequenced, by the Drosophila 12 Genomes Consortium et al. (2007). Currently, there are more than 100 Drosophila genomes available (Kim et al., 2021). This allows us to carry out more robust analyses to improve knowledge of the mechanisms involved in the evolution of species, transposons, and host genomes. The availability in our laboratory of strains of different geographical origins and which also have their genome sequenced, allows studies such as this one that are important to deepen the knowledge about the differences in the content and distribution of TE in the same species. Here, we conducted a detailed in-silico search to analyze hobo, BuT2, and mar transposons in available genomes of the willistoni group (Kim et al., 2021). In addition, we analyzed the copy number and spatial distribution of these hAT transposons on polytene chromosomes of some D. willistoni strains. Further, D. willistoni-Gd-H4-1, D. willistoni-WIP-4, and D. willistoni-SG12.00 were used for in-situ analyses; D. willistoni-L17 and D. willistoni-00 were used for in-silico analysis; and D. willistoni-Gd-H4-1 was used for both in-situ and in-silico analyses. The available genomes were from the D. willistoni species subgroup, represented by D. willistoni, D. paulistorum, D. equinoxialis, D. tropicais, and D. insularis; and the bocainensis subgroup, represented by D. nebulosa and D. sucinea.

Our results showed that the same TEs (hobo, BuT2, and mar) varied widely in the copy number and structure of copies, even among the different Drosophila strains. Regarding the same TEs (Figure 3 and Figure 4A-C), the number of hybridization signals on the polytene chromosomes varied in the different populations: D. willistoni-Gd-H4-1, D. willistoni-WIP-4, and D. willistoni-SG12.00 (Figure 2A-I). Furthermore, in the strains D. willistoni-L17, D. willistoni-00, and D. willistoni-Gd-H4-1, we identified variations in the number and structure of copies of the same TEs (Figure 3 and Figure 4A-C). This suggests that different populations of D. willistoni have undergone changes in the TE content or different selective pressures on TE in that host genome. Differences between insertion sites of the same TE in D. willistoni strains have been previously observed. Regner et al. (1996) identified by in-situ hybridization, in D. willistoni-17A2 strain 10 insertion sites of the P element coinciding with the breakpoints of inversions, but in D. willistoni-WIP-11A observed only hybridization signals on heterochromatin (Regner et al., 1996). Using Southern blot hybridization, Sassi et al. (2005) found differences in the number of TE copies of the P element, also among D. willistoni populations. In D. mojavensis, Palazzo et al. (2014) also found variability in the distribution and number of copies of the Bari element in different subspecies.

We observed different copy numbers for the elements of the hAT superfamily in the different D. willistoni strains of different subspecies, both in-situ and in-silico. A similar situation was reported in D. willistoni-L17, from an unknown locality in Uruguay, which proved to have many more repetitive fractions, mainly retrotransposons, than D. willistoni-00 from Santa Maria de Ostuna, Nicaragua (Kim et al., 2021). The differences observed between the in-situ analysis strains, particularly for the mar transposon (Figure 1 and Figure 2C, 2F and 2I), may be related to the chromosomal/genomic characteristics of the different populations of the species. D. willistoni can be subdivided into three subspecies: D. w. willistoni, D. w. winge, and D. w. quechua (Ayala and Tracey, 1973; Mardiros et al., 2016), that have different geographic distributions. As shown in Figure 1, D. willistoni has a predominantly neotropical distribution, from Mexico and south Florida to the southernmost part of South America and from the Pacific to the Atlantic oceans (Spassky et al., 1971; Zanini et al., 2015). The strains used in the in-situ and in-silico analyses represent populations arranged along the geographic distribution of the different subspecies (Figure 1): D. willistoni-Gd-H4-1 (Guadeloupe Island - willistoni subspecies), D. willistoni-WIP-4 (Bahia, Brazil - winge subspecies), and D. willistoni-SG12.00 (Montevideo, Uruguay - winge subspecies), used in in-situ and in-silico analyses; and D. willistoni-L17 (Uruguay - winge subspecies) and D. willistoni-00 (Santa Maria de Ostuna, Nicaragua - willistoni subspecies) used only in in-silico analyses.

The differences in copy numbers of the elements of the hAT superfamily analyzed here may be related to the chromosomal and genomic plasticity required to allow D. willistoni to occupy different habitats within its geographic distribution. The chromosomal and genomic plasticity of D. willistoni has been demonstrated in the large number of rearrangements previously found in different populations (Dobzhansky, 1957; Valente and Araújo, 1985; Regner and Valente, 1993; Rohde et al., 2006; Bhutkar et al., 2008; Rohde and Valente, 2012). A characteristic common to all D. willistoni populations is paracentric inversions on the five chromosomal arms, although the location and amount of inversions vary among populations - Review in Rohde and Valente (2012). Rohde and Valente (2012) identified and cataloged 50 different rearrangements in 30 populations of polymorphic chromosomes of D. willistoni that segregate at different frequencies, with a clear latitudinal cline, from North to South America, along the species’ distribution.

Additional evidence to support this hypothesis comes from the records of reproductive isolation between strains: populations found in Central America, North America, and northern Caribbean islands are reproductively isolated from South American and southern Caribbean island strains (Figure 1) (Mardiros et al., 2016). Partial reproductive isolation between populations influences gene exchange and consequently influences the differences of transposable elements in different populations.

For D. willistoni-Gd-H4-1 (the only one for which we have on our Drosophila Laboratory and whole sequenced genome) we obtained different estimates of copy numbers using different approaches (in-situ and in-silico). Our results showed that with the hobo element the different approaches were in accordance with the presence of low copy numbers (one by in-situ and three by in-silico). For the BuT2 and mar elements, we observed discrepancies between the analyses (Figure 1 and 2). In hobo, we found stronger signals (identified by the ImageJ software) and some weaker ones could be seen in the FISH picture (Figure 2A). Also, three hobo copies were detected in the sequenced genome, only one of which was complete (Figure 4A). However, in both BuT2 and mar, the number of sequences differed between the two approaches; the largest difference was observed in mar, copy number estimated by FISH was higher (by visual analysis) than the number retrieved in the sequenced genome (Figures 1, 2, and 4). The discrepancy between the number of copies found using FISH and in-silico may be related to two factors: limitations of each approach and intrinsic characteristics of the BuT2 and mar TEs that make it difficult to identify an absolute number of copies. In the case of BuT2 and mar, elements are considered MITEs, and share structural characteristics such as small nonautonomous elements, present in high and variable copy numbers, conservation of TIRs, and rich in AT region (Bureau and Wessler, 1992; Jiang et al., 2004; Feschotte et al., 2005). Regarding the sequenced genomes, although large amounts of DNA data are available, many genomes are not fully known because of the difficulty in assembling the repetitive fraction, sequences obtained with NGS platforms are short and simply do not span long repetitive sequences, and numerous copies of reads can be nearly identical, leading to the tendency to group them into single and collapsed contigs (Mascher and Stein, 2014; De Bustos et al., 2016). This type of difference has been observed in other studies using different techniques; for instance, in D. simulans, with the hAT hosimary element, the number of copies estimated by in-silico and Southern blot was higher than estimated by FISH (Deprá et al., 2010). Maside et al. (2005) also reported differences between different techniques (PCR amplification and in-situ hybridization) of the S-element in D. melanogaster, noting that the amplification method can be more biased toward high-frequency elements than the in-situ method, which uses to identify the insertion sites.

We also investigated the presence and structure of copies of the hobo, BuT2, and mar elements in the sequenced genomes of the willistoni species group. In our analysis, the hAT transposase phylogenetic tree revealed three major clusters of related sequences (^{Figure S1}), as previously referred to as the Buster family, Tip family, and Ac family by Rossato et al. (2014). The D. willistoni-hobo putative transposase fell within the Ac family, as did the other hAT from Drosophila, except for the elements mar (Buster family) and BuT2 (Tip family) (Deprá et al., 2012; Rossato et al., 2014). The hobo element TSD consensus sequence (5`-nTnnnnAn-3`) also indicates that D. willistoni-hobo is an Ac element (Arensburger et al., 2011; Rossato et al., 2014). The cluster formed by D. willistoni-hobo is composed of elements previously described in fly species from different genera: Drosophila willistoni (Howilli2); D. melanogaster (canonical hobo), D. ananassae (Hoana1, Hoana3, and Hoana8), and D. mojavensis (Homo1), as well as Ceratitis capitata (Cc-HRE), Bactrocera tryoni (Homer), Musca domestica (Hermes), and Lucilia cuprina (Hermit) (Handler and Gomez, 1996; Ortiz and Loreto, 2009).

Hobo-like elements identified in the willistoni group genomes are closely related to the canonical hobo (D. melanogaster), as conserved and identical TIRs in D. willistoni (three sequenced strains), D. paulistorum (two sequenced strains), D. sucinea, and D. nebulosa genomes (Figure 4A-C) (Calvi et al., 1991). However, there was little divergence between the sequences of species in the willistoni group, including D. sucinea and D. nebulosa belonging to the bocainensis subgroup. Furthermore, as seen in the phylogenetic tree, the hobo copies do not cluster similarly to the phylogeny of the species in the willistoni group, so HTT events cannot be ruled out. Moreover, sequences close to hobo, called hobo-brothers elements, showed incongruities with the TE and host Drosophila species phylogenies, suggesting possible cases of horizontal transfer (Bernardo and Loreto, 2013). The presence of hobo-like sequences was previously identified only in some strains of D. willistoni collected in Brazil, including D. willistoni-WIP-4, but were absent in the Amazon strain and in other species of the willistoni group, by Southern and Dot blot hybridization (Loreto et al., 1997). In the melanogaster subgroup, hobo elements were found in three forms: canonical (complete or deleted, lacking the central part of the sequence), relic (having TIRs and conserved subterminal sequences or defective in one TIR), and elements such as MITEs (review by Loreto et al., 2018). We also identified sequences in canonical and relic form in willistoni group genomes, except in D. equinoxialis, D. tropicalis, and D. insularis, since in these genomes we found only degenerate copies (Figure 3).

BuT2 and mar were characterized as MITE sequences in D. willistoni genomes (Holyoake and Kidwell, 2003; Deprá et al., 2012; Rossato et al., 2014). The BuT2 MITE elements identified in the D. willistoni-Gd-H4-1 genome have conserved TIRs but also the unusually low copy number (24 copies) that is common in MITE elements (Rossato et al., 2014). Our in-silico searches were not able to recover BuT2 MITE sequences in genomes of the willistoni species group (Figure 3 and Figure 4B). We also identified more BuT2 hybridization signals in chromosomes of D. willistoni-Gd-H4-1 than in the sequenced genome of D. willistoni-Gd-H4-1 (Figure 1, Figure 2B and Figure 4B). The likely reason for the differences observed between the in-silico and in-situ approaches is that our searches retrieved only full-length and relic BuT2 copies (Figure 3 and Figure 4B). We identified only BuT2-like degenerate sequences in the bocainensis subgroup, and one fragment each in D. sucinea and D. nebulosa (Figure 3 and Figure 4B). We found high rates of divergence between the sequences of species from the willistoni subgroup and the bocainensis subgroup, reaching 53.13% between D. sucinea and D. paulistorum-L06. This agrees with the phylogenetic tree, which showed the sequences of the bocainensis subgroup grouping separately from the willistoni subgroup (^{Table S6} and Figure 5). These sequences of the bocainensis subgroup are degenerate copies and have high divergence rates, which may be due either to a stochastic loss of element BuT2 in the genomes of the bocainensis subgroup, or to retrieval of sequences homologous to other BuT elements such as BuT1 in our searches (Cáceres et al., 2001; Wallau et al., 2012). Furthermore, the phylogenetic tree (Figure 5) has BuT2 copies of the willistoni subgroup with a distribution similar to the evolution of the species in the group, and were probably vertically transmitted during the evolution of these species (Rossato et al., 2014; Zanini et al., 2018; Finet et al., 2021). Our results agree with the findings by Rossato et al. (2014), who hypothesized that BuT2 was inserted in the ancestor of the neotropical willistoni/saltans groups and that MITEs expanded in the willistoni group.

BuT2 showed more signals of hybridization in D. willistoni-Gd-H4-1 and D. willistoni-WIP4 (Figure 2B, E), whereas only two hybridization signals were identified in D. willistoni-SG12.00 (Figure 2H). Assuming that the many hybridization signals in the D. willistoni-Gd-H4-1 chromosome are of the BuT2 MITE sequences described by Rossato et al. (2014), we hypothesized that the BuT2 MITE sequences proliferated in D. willistoni-Gd-H4-1 and D. willistoni-WIP4 but not in D. willistoni-SG12.00. The presence of BuT2 MITE sequences in the willistoni group is not completely clear, and further studies with several other strains are necessary. Interestingly, BuT2 is associated with inversion breakpoints in D. buzzatii chromosomes (Cáceres et al., 2001).

When the mar elements were characterized, the only genome of the willistoni group sequenced was D. willistoni-Gd-H4-1 (Drosophila 12 Genomes Consortium et al., 2007; Deprá et al., 2012). We found mar elements only in species of the willistoni subgroup (Figure 3 and Figure 4C), reinforcing the idea that this element invaded the genomes after the separation of the willistoni and bocainensis subgroups, as proposed by Deprá et al. (2012), and considering that the D. willistoni subgroup diverged approximately 7.3 Mya (review by Zanini et al., 2018).

Mar elements were one of the first MITE families discovered in the D. willistoni genome (Holyoake and Kidwell, 2003). The origin of the different MITE families is unclear; one hypothesis is that MITEs originate from deletions of autonomous copies (Deprá et al., 2012; Fattash et al., 2013). Only in D. tropicalis, a low number of copies and one potentially complete copy (Dtrop_ctg748) were identified (Figure 3 and Figure 4). This sequence is likely ancestral, as apparent from the phylogenetic reconstruction (Figure 7A and 7B). However, in the genomes of D. willistoni (three sequenced strains), D. paulistorum (two sequenced strains) and D. equinoxialis (Figure 3 and Figure 4), we observed expansion of mar sequences, possibly originating from deletion of the TE transposase region (Figure 7A and 7B). MITES can be considered genomic superparasites because they conserve the transposase recognition regions for mobilization and are usually found in high copy numbers (Fattash et al., 2013).

TEs in host genomes tend to survive by horizontal transmission to other hosts. When a TE inserts into a new host it tends to proliferation within a genome and within a population, accumulation of mutations, loss of element by inactivation, diversification within host, and element persistence within host (Schaack et al., 2010). In D. paulistorum-L06 we found a large number of relic or degenerate copies (Figure 3 and Figure 4), but did not identify MITEs. One hypothesis is that this genome possibly did not undergo expansion of MITEs, but rather of complete copies that mutated over time. Additionally, the lower diversity of the mar sequences observed in D. paulistorum-L06 (8.99%) compared to the sequences found in D. paulistorum-L12 (24.51%) may be a function of the different geographical origins of the strains. D. paulistorum-L12 is Andean-Brazilian, from within the large geographic region of origin (Brazil, Ecuador, Peru, Colombia, and Venezuela) (Zanini et al., 2018). D. paulistorum-L06 from San Salvador (El Salvador) has been maintained in the laboratory since 1955 (Kim et al., 2021) (Figure 3), explaining the lower diversity of mar in this genome. The genome of D. insularis retained a low copy number, highly related but relic or degenerate (Figure 3, Figure 4, Figure 7A and 7B).

The dynamics of the TE and host genome coevolution are complex. In this study we showed the evolutionary history of the elements hobo, BuT2, and mar in the sequenced genomes of the willistoni group, as well as the distribution and estimated number of copies in the polytene chromosomes in three strains of D. willistoni from different geographic locations. We also compared different approaches (in-situ and in-silico) in examining the genome of D. willistoni-Gd-H4-1. The genome can be viewed as an ecosystem inhabited by diverse communities of TEs that seek to proliferate through interactions with each other TEs and with the genome as a whole and other component of the cell (Venner et al., 2009; Bourque et al., 2018). Evolutionary forces such as natural selection and genetic drift can also shape the distribution and accumulation of TEs in host genomes (Kidwell, 2002; Chénais et al., 2012; Bourque et al., 2018; Moschetti et al., 2020). For example, mobilization in the host genome or colonization of new genomes is necessary to avoid loss by genetic drift, and potentially deleterious inserts will not remain in the population for many generations (Le Rouzic and Capy, 2006; Venner et al., 2009; Bourque et al., 2018). Through a genomic and cytogenetic approach, we reported that different populations (strains) of one species, D. willistoni, maintain and share the same transposon differently. Our data also showed that the genetic plasticity enabled by transposable elements can help species such as D. willistoni to occupy very different environments over its wide geographic distribution.

Acknowledgements

We thank Dr. Thales R. O. de Freitas for the use of his laboratory for the FISH experiments. We also wish to thank the reviewers for their important comments. This study was supported by research grants and fellowships from CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior), CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico), and FAPERGS (Fundação de Amparo à pesquisa do Estado do Rio Grande do Sul).

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Supplementary material

The following online material is available for this article:

Table S1 - Information for the Drosophila willistoni strains used in the FISH experiments.

Table S2 - Information on genomes of the willistoni group used in this study.

Table S3 - Hobo sequences identified in the willistoni group genomes.

Table S4 - Nucleotide divergence percentages of hobo sequences.

Table S5 - BuT2 sequences identified in the willistoni group genomes.

Table S6 - Nucleotide divergence percentages of BuT2 sequences.

Table S7 - Mar sequences identified in the willistoni group genomes.

Table S8 - Nucleotide divergence percentages of mar sequences.

Figure S1 - Phylogenetic relationships of the hAT superfamily.

Figure S2 - Neighbor-Joining tree of mar sequences.

Publication Dates

• Publication in this collection
  16 Mar 2022
• Date of issue
  2022

History

• Received
  10 Sept 2021
• Accepted
  31 Jan 2022