In a prior study 17, we used the inferred phylogenetic reconstruction of Ty3/Gypsy and Retroviridae LTR retroelements based on both gag and polpolyproteins as the criterion to create phylogenetically informative HMM profiles 18. Figure 1A shows a radial version of this tree, which clearly supports the usually accepted monophyly of the Ty3/Gypsy and Retroviridae groups and all their assumed lineages (clades, genera and classes) 56789101112131419202122232425. This view of the origin of Retroviridae indicates that these retroviruses had a common origin, e.g. a Ty3/Gypsy LTR retrotransposon (for more information in this topic, see 11 and references therein). Interestingly, inferred gag-pol tree suggests a putative Retroviridae root in the Ty3/Gypsy evolutionary history, which according to this new analysis, is close to Micropia/Mdg3 clade 14 and other Ty3/Gypsy lineages described in bilateria genomes. This perspective suggests that the first Retroviridae ancestor emerged before or during the split between protostomes and deuterostomes together with several Ty3/Gypsy lineages, which apparently have distant counterparts (Athila and Tat clades 1920) in the genomes of plants. Taking into account that the Retroviridae are true viruses capable of escaping their hosts, this scenario might also be traced back to an ancient horizontal transference from protostomes to vertebrates and the colonization of the vertebrate genomes by these viral agents from that point on. However these two alternatives, whilst equally exciting perspectives, should be re-evaluated based on the separate analysis of gag and pol polyproteins. The phylogenetic analysis of the pol polyprotein (Figure 1B) is consistent with gag-pol tree, due to the grouping of the taxa into clusters. In fact, the bootstrap robustness of the different clades and genera reported by gag-pol tree comes from the strong pol phylogenetic signal. This means that the pol signal is the essential analytical substrate responsible for the current view on the evolutionary history and taxonomy of Ty3/Gypsy and Retroviridae LTR retroelements. However, the pol signal does not support the Retroviridae root suggested by the gag-pol tree, and does not reveal a well-supported alternative link between the Ty3/Gypsy and Retroviridae groups. Pol tree is consistent with gag-pol tree in to delineate a scenario of emergence for vertebrate retroviruses preceding the protostomes-deuterostomes split. However, the root suggested by pol tree falls close to errantiviruses the canonical Ty3/Gypsy retroviruses of flies 262728. Indirectly, this indicates that whatever the relationship between Micropia/Mgd3 clade and the Retroviridae, the relationship depends on the gag polyprotein. Consistent with this, the independent phylogenetic analysis of the gag polyprotein (Figure 1C) groups the Retroviridae class II with Micropia/Mdg3 clade and other Ty3/Gypsy lineages described in bilateria genomes. The gag phylogeny also reveals how the Ty3/Gypsy origin of vertebrate retroviruses is anything but straightforward. This tree also clusters gammaretroviruses (class I) with the Athila/Tat clades of plants, and suggests proximity between the Retroviridae class III and errantiviruses, and other Ty3/Gypsy lineages. In other words, the gag signal fails to support the monophyly of the two Ty3/Gypsy or Retroviridae groups and suggests an alternative scenario. That is, based on gag and depending on the class, it follows that the Retroviridae code for different gags, each having one or more distant counterparts among Ty3/Gypsy LTR retroelements.

Phylogenetic analyses performed based on gag are rarely reported, due to the fast rate of evolution of this polyprotein. However, the alignment from which we inferred the gag tree was manually constructed and its accuracy tested by comparative analyses. We contrasted all gag sequences with each other using the NCBI BLAST search 29 available at GyDB. Comparisons revealed that gag sequences belonging to a Ty3/Gypsy or Retroviridae clade, genus or class are usually more similar to their lineage counterparts than to other gag sequences (data not shown). This analysis also revealed a core of similarity that is common to all Ty3/Gypsy and Retroviridae gags. This core spans the CA-NC region and its most conserved traits appear to be the MHR at CA 30, and the zinc finger Cys-X2-Cys-X4-His-X4-Cys (CCHC) array at NC 31. Evaluation of this core shows that the Retroviridae code for 3 different types of gag, each exhibiting a particular amino acidic architecture phenotype that depends on the class differentiation. While the 2 Retroviridae classes I and II appear to be related according to BLAST analyses (data not shown), they present greater divergence based on several phenotypic features preserved depending on the class (Figure 2A and 2B). Class III is extremely dissimilar to classes I and II based on gag, but preserves several features at the C-terminus that might be distantly related or equivalent to those of class I (Figure 2A and 2C). The most prominent, but obviously not unique, difference between the 3 classes is the variability in the number of CCHC arrays at NC. Class I NCs usually show one CCHC array, class II NCs exhibit two, and class III gags have no CCHC arrays at their C-terminus. BLAST analyses also revealed how the Ty3/Gypsy lineages related to classes I and II by gag tree, display greater similarity to different Retroviridae taxa belonging to these 2 classes than to other Ty3/Gypsy lineages. As an example, Tables 1 and 2 summarize the top similarity hits obtained from 4 comparisons conducted using 2 Micropia/Mdg3 and 2 Tatgag sequences as queries. All BLAST analyses were supported by additional sequence comparisons between the different gag queries and the collection of HMM profiles, available at GyDB via the HMM server (data not show). Additionally, we provide qualitative evidence of this relationship through alignment comparisons. Figure 3 shows a multiple alignment revealing domain similarity between gammaretroviruses (i.e. class I) and the Athila and Tat clades of plants. Figure 4A demonstrates that Micropia/Mdg3 clade and other bilateria Ty3/Gypsy lineages, such as the Mag clade, code for gags following similar CA-NC architecture to class II lentiviral gags. Gag relationship similarities between class III and other Ty3/Gypsy or Retroviridae lineages are not supported by BLAST analyses. However, Figure 4B shows a multiple alignment between spumaretroviruses and errantiviruses, which according to the qualitative domain similarity merits further attention.

Comparative analyses confirm phenotypic features in the gag polyprotein that distantly relate each Retroviridae class with one or more of the Ty3/Gypsy lineages evaluated. The similarity spans the CA-NC core and the most prominent feature in common is the variability in the number of CCHC arrays per NC. With very few exceptions, the Athila/Tat elements of plants usually code for NCs exhibiting one CCHC array, Micropia/Mdg3 and Mag elements code for NCs usually exhibiting 2 arrays (except Mag elements of C.elegans), and errantiviral gags have not CCHC arrays at their C-terminus. This indicates that the number of CCHC arrays per NC is evolutionarily preserved depending on the Ty3/Gypsy lineage and the Retroviridae class, and that this phenotype is an excellent indicator of taxonomy and evolution. For simplicity's sake, we do not discuss all Ty3/Gypsy cases. We discuss but one example, the most interesting instance of using this indicator – the chromodomain-containing Ty3/Gypsy LTR retrotransposons 14 called chromoviruses 13. Chromoviruses are the most ancient branch of Ty3/Gypsy LTR retroelements as they have been described in the genomes of plants, fungi and vertebrates (for a more extensive information about chromoviruses, see 233233). It noteworthy that all Ty3/Gypsy LTR retroelements of plants can be divided in 2 major branches – chromoviruses and Athila/Tat – and that chromoviruses appear to be the only branch of Ty3/Gypsy LTR retroelements capable of colonizing the genomes of fungi. A prior study 30 reported that this branch of Ty3/Gypsy LTR retroelements displays similarity (we confirm) to gammaretroviruses based on CA-NC. However, we have also found how that chromoviruses show similarities to class II in addition to a number of Ty3/Gypsy lineages (for this reason chromoviruses fall at an intermediate position in the gag phylogeny). With rare exceptions, NCs coded by chromoviruses usually bear one CCHC array (data not shown). In contrast, the different Ty3/Gypsy lineages described in bilateria organisms show greater variability in the number of CCHC arrays at NC thantheir Ty3/Gypsy counterparts of plants and fungi (i.e. chromoviruses and the Athila/Tat branch). Gag evidence thus relates class I to the most likely CA-NC phenotype of Ty3/Gypsy ancestors predating the split between plants and the ophistokonts (fungi and animals) and classes II and III with other CA-NC phenotypes, more frequently observed among the Ty3/Gypsy LTR retroelements of protostomes and deuterostomes.

Through phylogenetic analyses, we have shown that the pol signal is primarily responsible for the branching of Ty3/Gypsy and Retroviridae LTR retroelements in 2 monophyletic groups. That is the usual evolutionary perspective based on the RT and other pol polyprotein domains. We have also shown that gag signal discloses an alternative scenario wherein each Retroviridae class can be related to one or more Ty3/Gypsy lineages. An in-depth examination of gag diversity through comparative analyses has revealed the phenotypic variations involved in this differential similarity. Gag evidence is thus well supported. An interesting question is whether this evidence should be considered a convergence due to the fast rate of evolution of the gag polyprotein, or if it is due to an ancient divergence. Certainly, the most robust components of the pol polyprotein – the RT, RNAse H and INT – usually support the traditional perspective originally delineated by RT analyses 12. However, the strong signal from these 3 proteins disguises the particular perspective provided by another pol protein domain – the PR. Non-redundant studies focusing on Ty3/Gypsy and Retroviridae PRs are rarely reported as this enzyme presents identical analytical difficulty to gag due to its fast rate of evolution. Despite this it is well known that LTR retroelement PRs in general are aspartic peptidases belonging to clan AA (following MEROPS Database classification 34). Within clan AA, Retroviridae PRs are divided into 2 protein families, retropepsins (family A2) and spumaretropepsins (family A9). Family A2 groups all PRs coded by classes I and II and family A9 collects the PRs coded by spumaretroviruses (class III). Such a classification keeps going because retropepsins and spumaretropepsins are strongly dissimilar each other and do not group on a single branch in any analysis (data not shown). On the other hand, Ty3/Gypsy PRs are extremely variable and little is known about them. MEROPS Database at least classifies many Ty3/Gypsy examples within family A2 because these PRs display great similarity to retropepsins. However, not all Ty3/Gypsy PR are similar to retropepsins as not all Retroviridae PRs are retropepsins. Because no study evaluates the relationships between Ty3/Gypsy and Retroviridae PRs, we investigated this topic, taking into consideration the differentiation of the 2 groups of LTR retroelements into lineages. It is worth remembering that while gag and pol signals are in disagreement over the taxonomical groups, they do support the differentiation into clades, genera and classes of Ty3/Gypsy and Retroviridae LTR retroelements.

Prior research performed using structure-based alignments and structural comparisons based on HIV-1 PR and other retropepsins, have revealed how LTR retroelement PRs dimerize in their active form (for a more extensive review in this topic, see 35 and references therein). Each lobe of the PR dimer carries a structural feature called the flap, which is a β-hairpin loop that covers the active site and has 2 flexible alternating forms, closed and semi-open (see Figure 5). We have extensively studied not only Ty3/Gypsy and Retroviridae PRs but also other clan AA PRs (data not shown). Interestingly, the Retroviridae differentiation into classes reveals 3 PR isoforms each preserving a particular flap motif. Class II PRs usually harbor a sequence GIGG amino acid motif (Figure 5A), which at the tertiary structure level constitute the flap in HIV-1 PR and other class II PRs (see 35 and references therein). In contrast class I PRs were found to preserve a GATG variant of this motif (Figure 5B), and within class III spumaretroviral PRs preserve a TIHG variant of the same sequence motif (Figure 5C). Ty3/Gypsy LTR retroelements also code for a variety of isoforms, which evolutionarily preserve a particular flap motif state depending on the lineage, in the same manner as classes I, II and III. A number of these states are very similar but not identical to that preserved by class I. Multiple alignment of gammaretroviruses (class I) and several Ty3/Gypsy lineages based on PR is shown in Figure 6A. In its consensus form, this variant delineates a GANG motif recognizable by the predominance of an alanine (or a hydrophobic residue) and an aspartate/asparagine/threonine at the second and third positions of the motif, respectively. The GANG variant is widespread among the PRs coded by Ty3/Gypsy LTR retroelements of plants, fungi and animals. This variant also predominates in the PRs coded by caulimoviruses of plants and Ty1/Copia LTR retroelements, and two datasets of prokaryotic PRs related to clan AA (data not shown). Therefore, GANG variant appears to be the most likely ancestral state of the flap of the PRs coded by Ty3/Gypsy ancestors predating the split between plants and the ophistokonts. Consistent with gag evidence, GIGG and TIHG PR variants exhibited by classes II and III PRs are rarely observed among Ty3/Gypsy LTR retroelements of plants and fungi. In plants, only Tat clade elements code for PRs presenting a poorly preserved flap motif, which might be discretely related to the GIGG variant (data not shown). As Athila clade elements (the sibling of Tat clade in plants) code for GANG PRs, we may assume that the PR flap motif transits from one state to another. Among the Ty3/Gypsy lineages of fungi, only TF1-2 clade code for GIGG PRs, which is a variant more frequently observed among Ty3/Gypsy LTR retroelements of protostomes. In contrast, the GIGG variant carried by the PRs coded by Micropia/Mdg3 clade and other Ty3/Gypsy lineages is almost identical to that of Retroviridae class II (Figure 6B). The TIHG variant is absent from the Ty3/Gypsy PRs of plants. In fungi, only a putative chromoviral lineage called Ty3 clade (see 17 and references therein) code for PRs harboring a highly diverged motif that in its consensus form can be distantly related to the TIHG variant (data not shown). In contrast, a number of Ty3/Gypsy errantiviruses code for PRs carrying a TIHG motif identical to that of class III spumaretroviruses (Figure 6C). Finally, investigating other sequences not considered in this study, we also found that Gmr-1 clade 3637 a Ty3/Gypsy lineage recently described in deuterostomes also code for TIHG PRs (data not shown). The PR scenario thus reveals consistency with gag in suggesting that Retroviridae class I is most likely related to the phenotype of Ty3/Gypsy ancestors predating the spilt between plants and the ophistokonts. In contrast, classes II and IIIshould be more properly related to Ty3/Gypsy lineages whose ancestors probably emerged before or during the transition of bilateria organisms into protostomes and deuterostomes.

As already shown, gag polyprotein and the PR depict a new scenario as an alternative to the traditional monophyletic insight (2 groups of LTR retroelements) suggested by prior RT, RNAse H and INT analyses. Onto understand the two opposing scenarios, we performed phylogenetic analyses based on the RT, RNAse H and INT and found consistency with the traditional perspective of 2 separate LTR retroelement groups using the RT and RNAse H (131415). Analysis of the INT revealed different perspectives depending on the NJ or parsimony method used in the analysis (see Methods). While the NJ method supports the 2 LTR retroelement groups, the parsimony method splits the Retroviridae into 2 branches not supported by bootstrap (data not shown). This is because our model of INT alignment covers the 3 subdomains described in the amino acidic architecture of a conventional INT domain. The traditional core used for inferring INT phylogenies is common to all INTs in general, and includes 2 of these sub-domains; the conserved zinc finger "HHCC" binding motif 38 at the N-terminus, and the central sub-domain containing the conserved D-D-E trait 3940. The C-terminal sub-domain of all INTs is usually dismissed from analysis because it is less preserved than the other 2 sub-domains. In Ty3/Gypsy and RetroviridaeINTs, it is definite that this sub-domain is a small trait called GPY/F module, which was probably recruited modularly during evolution 14. The module name refers to the strongly preserved GPY/F amino acid motif 14, which will be referred to as the canonical motif throughout the rest of this paper. Indeed, the GPY/F module appears to be responsible of the signal discrepancy in phylogenetic analyses (INT parsimony tree performed without this module is in agreement with the NJ analysis, data not shown). From that point, we investigated the GPY/F module in relation to the 3 Retroviridae classes. The module, seen from this viewpoint, shows a number of protein isoforms based on GPY/F motif polymorphisms. With rare exceptions, the modules of class I INTs usually preserve the canonical motif, while the modules of classes II and III exhibit other variants (Figure 7A). Here, classes II and III do not make an intrinsic phenotypic distinction, each genus exhibiting a particular variant of the motif within these 2 classes. The modules coded by Ty3/Gypsy LTR retroelements delineate similar perspective. As shown in Figure 7B, while the canonical motif is practically predominant in the modules of Ty3/Gypsy elements of plants and fungi, the modules of bilateria Ty3/Gypsy LTR retroelements are rich in motif polymorphisms (canonical motif included). This indicates that Ty3/Gypsy LTR retroelements described in bilateria organisms exhibit greater GPY/F motif variability than their Ty3/Gypsy counterparts of plants and fungi, and strongly suggests a number of transitions from the canonical motif toward other states during evolution. This scenario is not completely consistent with gag and PR perspectives; for instance, while Micropia/Mdg3 modules preserve the canonical motif, the different Retroviridae genera belonging to class II exhibit different motif polymorphisms. Nevertheless, the GPY/F module relates the Retroviridae class I with Ty3/Gypsy LTR retroelements of plants and fungi through the common preservation of the canonical motif, while classes II and III can be related with bilateria Ty3/Gypsy LTR retroelements by an increase of the motif variability. In fact, the whole module of class I INTs appears to be more similar to those preserved by the INTs of chromoviruses (Figure 8A) and Athila and Tat clades (Figure 8B) than to those of classes II and III. Alignment between classes I and II reveals a dramatic loss of sequence information by class II during evolution (Figure 8C). The module carried by spumaretroviral INTs is similar to that of class I, but they greatly differ in the motif (Figure 8D). That is, spumaretroviral modules lost the GPY/F motif, substituting it with a highly diverged KT/SP motif. Again, this outlines an intriguing parallelism between spumaretroviruses and Ty3/Gypsy errantiviruses because the modules of these 2 LTR retroelement lineages are qualitatively similar (Figure 8D). Moreover, Ty3/Gypsy errantiviruses also lost their GPY/F motif during evolution. Therefore, whatever the INT function involving the GPY/F module coded by the Retroviridae class I, this class appears to be a molecular fossil preserving GPY/F module phenotypes that were predominant among Ty3/Gypsy ancestors, predating the split between plants fungi and animals. In contrast, Retroviridae classes II and III maintain a number of module isoforms more recently emerged during evolution.

Phylogenetic analysis inferred based on all concatenated gag and pol products coded by Ty3/Gypsy and Retroviridae LTR retroelements shows the robustness of their phylogenetic signal regarding the clustering of OTUs 56789101112131419202122232425. We used the parsimony method to infer this phylogeny, but the clustering of OTUs is independent of the method of phylogenetic reconstruction used (see Methods). The gag-pol analysis also divides Ty3/Gypsy and Retroviridae LTR retroelements into 2 separate branches, as suggested by original approaches in this topic 1241. We do not disagree this classification for 2 reasons; first, the strong phylogenetic signal of RT, RNAseH, and INT cannot be dismissed;and second, the Retroviridae (except gammaretroviruses) can be distinguished from Ty3/Gypsy LTR retroelements by features such as the presence of accessory genes. Nevertheless, thecurrent Ty3/Gypsy and Retroviridae classification only exposes the modern evolutionary history of these 2 groups of retroelements (we have shown how their ancient history is not straightforward). Due to the wide distribution of Ty3/Gypsy elements in eukaryotes, the usual means of transference of a canonical Ty3/Gypsy LTR retrotransposon is probably vertical. However, the viral nature of a true Ty3/Gypsy or Retroviridae exogenous retrovirus resides in its capability of horizontal transference from one host to another via infection. Moreover, the incidence of mechanisms such as gene recruitment, genome rearrangement, recombination and chimerism in LTR retroelement evolution, presents difficulties in identifying the true natural history of Ty3/Gypsy and Retroviridae LTR retroelements. This suggests that the most realistic (not yet proposed) model for describing Ty3/Gypsy and Retroviridae evolution alternates gradual and modular evolution, and combines vertical and horizontal means of transference.

The traditional argument supporting the Ty3/Gypsy origins of vertebrate retroviruses is shown by their similarity in sequence and genome structure 41. The question is, however, what genetic material is more informative for exploring the relationships between these two (and other) groupsof LTR retroelements, highl y variable traits such as gag and PR or strongly preserved substrates such as the RT, RNAseH and INT? Certainly, RT, RNAseH and INT are an excellent means of classifying Ty3/Gypsy and Retroviridae LTR retroelements into lineages. However, phylogenetic analyses based on RT, RNAseH and INT are not exact enough to resolve the ancient evolutionary history of these 2 groups. This is because the inferred phylogeny based on these proteins does not necessarily coincide with the true natural history of the full-length retroelement genome. Here, the advantage of using the gag-pol alignment to infer the phylogeny is the increase in statistical power of the analysis, allowing the opportunity to correct the single gene tree discrepancies. This analytical strategy is useful but has limitations for which solutions remain elusive; the inferred tree can accumulate systematic errors due to the use of concatenated information. We have shown how gag-pol tree suggests a Ty3/Gypsy root in the origins of vertebrate retroviruses that is close to the Micropia/Mdg3 clade. However, evaluation of gag and pol polyproteins separately yields discordant information. Here, while pol phylogeny supports the traditional perspective (2 retroelement groups), gag phylogeny describes a new scenario that appears to be informative with respect to the ancient patterns of diversity of Ty3/Gypsy and Retroviridae LTR retroelements. Certainly, the phylogenetic signal of the gag polyprotein has several limitations due to its fast evolution. To overcome these limitations we investigated other protein domains and used different methodologies to evaluate the significance of the new scenario. The most important feature here is that, for first time in the scientific literature, we have carried out a non-redundant study of three independent proteins that have rarely been attempted before because their difficulty.

Our investigation conclusively reveals that the taxonomical differentiation into the 3 Retroviridae classes I, II and III discloses 3 different gag and PR products, and that each product has one or more distant Ty3/Gypsy counterparts. The analysis of the GPY/F module reveals partial consistency and how the similarity of class I to Ty3/Gypsy LTR retroelements of plant and fungi, is significant. Our results thus support an ancient scenario of polyphyly involving the 3 Retroviridae classes and different Ty3/Gypsy lineages. Here, we stress that the identification of the Retroviridae classes is not a conclusion but an assumption based on previous studies 678910. Notwithstanding, we cannot argue for the existence of a direct ancestor between each class and any particular Ty3/Gypsy lineage. Classes I and II are sufficiently similar to corroborate their accepted evolutionary relationship, and it can also be assumed that Ty3/Gypsy and Retroviridae phylogeny is incomplete (sequencing projects are continuously disclosing new lineages). Despite this, the similarity of each class by simple convergence to different Ty3/Gypsy lineages based on 3 independent protein products is an implausible parsimonious explanation. Moreover, while class III spumaretroviruses are dissimilar to classes I and II, our results reveal that they in turn display an intriguing domain similarity to errantiviruses that ought to be followed up. Hence we think that the class differentiation probably unravels certain aspects of vertebrate retroviruses related to their ancient Ty3/Gypsy origins. Instead of a single root to this new scenario, we show how an ancient evolutionary network between the 2 groups can exist, with its most interesting aspect being its polyphyly. (The Ty3/Gypsy lineages related to each class does not constitute a monophyletic branch in any phylogeny). Therefore, our approach strongly suggest that class I is a molecular fossil that emerged quite soon in Ty3/Gypsy evolution, while classes II and III emerged later, together with the ancestors of Ty3/Gypsy LTR retroelements described in protostomes.

The evolutionary network identified by classes I, II, III is inconsistent with the idea of a unique Retroviridae ancestor. It follows that various scenarios may either support or disprove such a network. Assuming this network exists, the most likely scenario relates Ty3/Gypsy elements of plants and fungi with the Retroviridae class I. This scenario assumes the existence of a distant evolutionary relationship between the lineages or an ancient horizontal transfer of chromoviruses from fungi (or plants) to vertebrates. Indeed, chromoviruses are the most ancient lineage of Ty3/Gypsy LTR retrotransposons. They are rich in genetic variability, and are also present in the genome of many vertebrates 233233. In both cases, the most likely explanation for the relationship between class I and Athila/Tat retroviruses and retrotransposons of plants is that chromoviruses and class I are related, an argument suggested by a previous study 30. Nevertheless, chromoviruses of vertebrate organisms are usually more similar to their chromoviral counterparts of fungi than to those of plants. Therefore the chromoviral scenario does not explain why class I and Athila/Tat elements of plants are similar each other based on gag. On the other hand, chromoviruses have not yet been described in protostomes, echinoderms and urochordates; furthermore it remains unclear whether chromoviruses were inexorably driven to extinction in these organisms or were horizontally transmitted from plants/fungi to vertebrates. Consequently, the chromoviral scenario does not clarify why classes II and III and the Ty3/Gypsy lineages of protostomes share sequence similarities and phenotypic features rarely found among the Ty3/Gypsy lineages of plants and fungi. With this in mind, a new theoretical principle is posited here for debate and further research. The simplest hypothesis is that classes I, II and III probably evolved from at least 3 Ty3/Gypsy ancestors and emerged at different evolutionary times prior to the split between protostomes and deuterostomes (the three kings hypothesis). Several points involved in the background of this hypothesis should be emphasized. First, we include the words "at least" to acknowledge the three classes but do not dismiss the possibility of more Ty3/Gypsy ancestors in the evolutionary history of the Retroviridae. Second, "different times of emergence" suggests, but does not necessarily mean, independent origins. Class II may in fact be directly related to class I, but the emergence of class II seems more recent and in parallel with the emergence of the ancestorsof several Ty3/Gypsy lineages, such as the Micropia/Mdg3 clade (or others). Class III spumaretroviruses delineate identical perspective with Ty3/Gypsy errantiviruses. Third, we use the term "polyphyletic" because the Ty3/Gypsy lineages related to each class do not constitute a monophyletic branch in any phylogeny. Moreover, viral evolution is always a polyphyletic challenge involving ecological parameters such as host populations, environment, vectors, mechanisms of transmissions, etc.

We have described how the different gags, PRs and GPY/F modules evaluated show a variability that is preserved, depending on the Ty3/Gypsy lineage and Retroviridae class (or genus). While class I can be related to Ty3/Gypsy elements of plants and fungi, classes II and III preserve phenotypic features typically observed among Ty3/Gypsy elements of protostomes. That is the evolutionary perspective provided by the protein product of 3 independent coding regions. We have discussed this evidence but have not yet interpreted why the diversity and phylogeny of Ty3/Gypsy and Retroviridae LTR retroelements are so different regarding the different gag or pol substrates. In general, the action of viruses and mobile genetic elements is important in host evolution 16424344454647 because they are vectors of evolution and potential inducers of diseases and genetic disorders, such as chromosome rearrangements and inversions 48. However, if the action of viruses and mobile genetic elements might somehow influence the host evolution, it is reasonable that host evolution could also constrain the evolution of these genetic agents. We thus speculate with the possibility of selective influences imposed on Retroviridae genes such as the rt, rnase h and int (and other regions) to optimize essential functions, such as retrotranscription and integration (according to the complexity of the new genome environment provided by vertebrate organisms). This probably involves gradual evolution but also a number of molecular mechanisms, such as gene recruitment and recombination to generate variability and new effective genetic combinations. Here, it is important to keep in mind that except gammaretroviruses and other exceptions, the Retroviridae usually incorporate accessory genes, usually needed to adjust diverse aspects of their replication and infectivity (these features appear to be specific of retroviruses infecting vertebrate organisms). On the other hand, a prior study 15 supports a putative chimeric origin of the Retroviridae RNAse H domain and the modular acquisition of the GPY/F module by Ty3/Gypsy and Retroviridae INTs 14. Moreover, D-type betaretroviruses probably are viral hybrids between a B-type betaretrovirus and a C-type gammaretrovirus 51749. Finally, a number of studies reveal how recombination is a mechanism frequently embraced by HIV evolution to generate variability. Two studies reveal for instance how recombination of M subtypes, has resulted in the generation of multiple circulating recombinant forms consisting of mosaic HIV-1 lineages 5051.

Regarding coding regions such as gag, pr and gpy/f module, we think that these traits reveal features and aspects involving different evolutionary strategies, but which are intrinsic and taxonomically related with ancient events of retroelement speciation and divergence. This argument finds an important evolutionary marker in the variability in the number of CCHC arrays at NC and the different PR and GPY/F module isoforms. Indeed, the CCHC array at NC is involved in virion assembly, RNA packaging, reverse transcription and integration processes 52. On the other hand, the flap lies over the PR active site and conveys specificity to the enzyme by carrying important substrate-binding functions (for more information in this topic, see 355354). Finally, while the GPY/F module is now under investigation, the C-terminal end of the INT appears to be important in the integration of the retroelement into the host genome 5556. The variability of these three regions probably reveals different evolutionary strategies of speciation and divergence, which can be assumed older than previously supposed, since it does not only occur in the Retroviridae group, but also in all Ty3/Gypsy LTR retroelements of plants, fungi and animals. Here, the three kings hypothesis and its testing (in one sense or another) does not affect the evidence we have presented. That is, class I, II and III taxonomically code for 3 gag, PR and GPY/F products that have one or more distant counterparts among Ty3/Gypsy LTR retroelements. However, the most interesting aspect of the gag-PR-GPY/F variability is that it appears to be constrained by the bio-distribution of Ty3/Gypsy LTR retroelements. In turn, the diversity patterns of the Retroviridae based on these regions appear to be recurrent into the evolutionary performance of Ty3/Gypsy LTR retroelements, the most interesting aspect of which is that they seem polyphyletic. Therefore the evolutionary network between Ty3/Gypsy and Retroviridae LTR retroelements is informative regarding an ancestral history, which is in some respects similar to those models of evolution indistinctly described by population genetics and quasi-species theory (for more details see 57). This means that further analysis of the evolutionary network we disclose in this study challenges the involvement of different parameters such as bio-distribution, host's populations, environment, vectors and mechanisms of transmissions, etc. With this aim, our hypothesis makes possible a first evaluation of this new scenario we present in a forthcoming manuscript (submitted for publication). In this approach, we use the number of CCHC arrays at NC and the different PR and GPY/F module isoforms as evolutionary markers to trace the network. This is by superimposing not only Ty3/Gypsy and Retroviridae LTR retroelements, but also other LTR retroelement groups over their host bio-distribution.

This work is part of the GyDB Project 17 an ongoing database launched with the aim of phylogenetically analyzing and classifying mobile genetic elements based on their diversity and evolutionary profile. In the first iteration, we consider the Ty3/Gypsy and Retroviridae LTR retroelements of eukaryotes. We have investigated 120 non-redundant full-length Ty3/Gypsy and Retroviridae genomes collected from NCBI 58. An extended version of the gag-pol tree evaluated summarizing names, taxonomy, hosts, and Genbank accessions of all retroelement taxa used to perform this analysis, is available online as the Additional file 1 accompanying this paper. By clicking the name of each OTU in this tree, the user can browse the GyDB and locate a file providing information of the OTU selected, including a link to the Genbank accession of the requested element at NCBI. The gag-pol tree can also be found online in the Section Phylogenies at GyDB 59.

In general, all Ty3/Gypsy and Retroviridae LTR retroelements have 2 polyproteins in common – gag and pol. Gag is composed of 3 domains -MA, CA and NC -, pol is usually carrier of 4 domains – PR, RT, RNAse H and INT. Note however that PR can be coded separately or in frame with gag and other protein domains. We have used and analyzed a gag-pol multiple alignment ~1700 residues in size, constructed based on the concatenation of the CA, NC, PR, RT, RNAseH and INT cores. The gag-pol alignment is freely accessible within the GyDB collection deposited at Biotechvana Bioinformatics 60. The alignment is available in 6 formats at the following URL 61. We have also analyzed the gag and pol polyproteins by separate dividing the gag-pol alignment into 2 independent alignments CA-NC and PR-RT-RNAseH-INT, to perform phylogenetic or comparative analyses.

Alignments were compared using GENEDOC editor 62 in shaded mode and the following groups of amino acid similarity: [T,S small nucleophile amino acids] [K,R,H basic amino acids], [D,E,N,Q acidic amino acid and relative amides], and [L,I,V,M,A,G,P,F,Y,W hydrophobic amino acids]. Similarities between gag sequences were correlated using different gag queries to the CORES database available via the NCBI BLAST search 29 at GyDB, using BLASTp search mode. BLAST databases available at GyDB are non-redundant, small and include only Ty3/Gypsy and Retroviridae or related sequences, allowing flexible comparisons between both distantly and closely related sequences with homologous known functions.

Comparative analyses based on sequence logos involved CheckAlign 1.0 63 in Shannon's algorithm mode 64 and correction factor. Sequence logomethodology was originally introduced by Schneider et al. 6566 to display consensus sequences for DNA and protein alignments. Later, Schneider dismissed the term "consensus" 67, arguing that a logo provides more information than the consensus sequence of a protein or DNA alignment. While this can be controversial because there are many manners to obtain or describe a consensus sequence, logos methodology being one of them, we are in agreement with the proposition of the original author in the use of the term "sequence logo" suggested in his website 68. We employ the term "sequence logo" to describe the resultant output reported by this analysis, and then refer to the protein information underlying the content shape of the logos constructed, based on our alignments as "amino acidic architecture". This term may be useful to describe with a single word – consensus, core and amino acid patterns. CheckAlign directly builds the logo from an ungapped alignment using the conventional methodology 6566. Here, the maximum uncertainty by position in a protein alignment is log₂ 20 = 4.3. In the case of gapped alignments, CheckAlign automatically builds the logo, taking the gap as another amino acid species. Here, the tool considers the maximum uncertainty by position to be log₂ 21 = 4.4 for protein alignments (for more details about CheckAlign see 63).

The 3D structure of the HIV-1 PR 69 was modeled using SWISS-PDBViewer 3.7 SP5 70, and PDB file 1A30 as input. The PDB file was downloaded from RCSB Protein Data Bank 71.

Phylogenetic reconstructions of Ty3/Gypsy and Retroviridae LTR retroelements inferred from gag-pol, pol and gag alignments employed the PHYLIP 3.6 package 72. We first generated 100 bootstrap replicates of each alignment using SEQBOOT. Second, we used the protein sequence parsimony method of Felsenstein, based on the approaches of Eck and Dayhoff 73 and Fitch 74 to perform the analyses. Here, the bootstrap file was used as an input to PROTPARS and the input randomized using the following parameters, random number seed = 5 and number of times to jumble = 5. Third, CONSENSE was used to obtain a MRC tree 75 using the tree file generated by PROTPARS as an input. As the MRC tree usually consists of all clusters that occur >50% of the time, we took consensus values >55 as a bootstrap reference. Bootstrap values were used to scale the trees.

We also tested the NJ method 76 using different models of distances implemented in PROTDIST. Here, it is important to keep in mind that the overall efficiency of the different methods of phylogenetic reconstruction in building the true tree vary with substitution rate, transition-transversion ratio, and sequence divergence 7778. With the particular material we studied, parsimony and NJ trees support the clustering of OTUs into clades and genera in gag-pol and pol analyses, and they are consistent in not supporting the monophyly of each group in gag analyses. However, parsimony phylogenies proved more consistent with comparative analyses than NJ trees when inferring phylogenies including or evaluating the gag and/or PR proteins. Parsimony analyses also reported better bootstrapping and were more consistent with the three Retroviridae classes than NJ analyses (NJ trees only support classes I and II).