Global heterochromatic colocalization of transposable elements with minisatellites in the compact genome of the pufferfish Tetraodon nigroviridis

Constitutive Heterochromatin in Eukaryotic Genomes: A Mine of Transposable Elements

Transposable elements (TEs) are abundant components of constitutive heterochromatin of the most diverse evolutionarily distant organisms. TEs enrichment in constitutive heterochromatin was originally described in the model organism Drosophila melanogaster, but it is now considered as a general feature of this peculiar portion of the genomes. The phenomenon of TE enrichment in constitutive heterochromatin has been proposed to be the consequence of a progressive accumulation of transposable elements caused by both reduced recombination and lack of functional genes in constitutive heterochromatin. However, this view does not take into account classical genetics studies and most recent evidence derived by genomic analyses of heterochromatin in Drosophila and other species. In particular, the lack of functional genes does not seem to be any more a general feature of heterochromatin. Sequencing and annotation of Drosophila melanogaster constitutive heterochromatin have shown that this peculiar genomic compartment contains hundreds of transcriptionally active genes, generally larger in size than that of euchromatic ones. Together, these genes occupy a significant fraction of the genomic territory of heterochromatin. Moreover, transposable elements have been suggested to drive the formation of heterochromatin by recruiting HP1 and repressive chromatin marks. In addition, there are several pieces of evidence that transposable elements accumulation in the heterochromatin might be important for centromere and telomere structure. Thus, there may be more complexity to the relationship between transposable elements and constitutive heterochromatin, in that different forces could drive the dynamic of this phenomenon. Among those forces, preferential transposition may be an important factor. In this article, we present an overview of experimental findings showing cases of transposon enrichment into the heterochromatin and their positive evolutionary interactions with an impact to host genomes.

A new view on the scenario of karyotypic stasis in Epinephelidae fish: Cytogenetic, historical, and biogeographic approaches

Epinephelidae (groupers) is an astonishingly diverse group of carnivorous fish widely distributed in reef environments around the world, with growing economic importance. The first chromosomal inferences suggested a conservative scenario for the family. However, to date, this has not been validated using biogeographic and phylogenetic approaches. Thus, to estimate karyotype diversification among groupers, eight species from the Atlantic and Indian oceans were investigated using conventional cytogenetic protocols and fluorescence in situ hybridization of repetitive sequences (rDNA, microsatellites, transposable elements). Despite the remarkable persistence of some symplesiomorphic karyotype patterns, such as all species sharing 2n=48 and most preserve a basal karyotype (2n=48 acrocentrics), the chromosomal diversification in the family revealed an unsuspected evolutionary dynamic, where about 40% of the species escape from the ancestral karyotype pattern. These karyotype changes showed a relation with the historical biogeography, likely as a byproduct of the progressive occupancy of new areas (huge diversity of adaptive and speciation conditions). In this context, oceanic regions harboring more recent clades such as those of the Indo-Pacific, exhibited a higher karyotype diversity. Therefore, the karyotype evolution of Epinephelidae fits well with the expansion and geographic contingencies of its clades, providing a more complex and diverse scenario than previously assumed.

Transposons-Based Clonal Diversity in Trematode Involves Parts of CR1 (LINE) in Eu- and Heterochromatin

Trematode parthenitae have long been believed to form clonal populations, but clonal diversity has been discovered in this asexual stage of the lifecycle. Clonal polymorphism in the model species Himasthla elongata has been previously described, but the source of this phenomenon remains unknown. In this work, we traced cercarial clonal diversity using a simplified amplified fragment length polymorphism (SAFLP) method and characterised the nature of fragments in diverse electrophoretic bands. The repetitive elements were identified in both the primary sequence of the H. elongata genome and in the transcriptome data. Long-interspersed nuclear elements (LINEs) and long terminal repeat retrotransposons (LTRs) were found to represent an overwhelming majority of the genome and the transposon transcripts. Most sequenced fragments from SAFLP pattern contained the reverse transcriptase (RT, ORF2) domains of LINEs, and only a few sequences belonged to ORFs of LTRs and ORF1 of LINEs. A fragment corresponding to a CR1-like (LINE) spacer region was discovered and named CR1-renegade (CR1-rng). In addition to RT-containing CR1 transcripts, we found short CR1-rng transcripts in the redia transcriptome and short contigs in the mobilome. Probes against CR1-RT and CR1-rng presented strikingly different pictures in FISH mapping, despite both being fragments of CR1. In silico data and Southern blotting indicated that CR1-rng is not tandemly organised. CR1 involvement in clonal diversity is discussed.

Mobile Elements in Ray-Finned Fish Genomes

Ray-finned fishes (Actinopterygii) are a very diverse group of vertebrates, encompassing species adapted to live in freshwater and marine environments, from the deep sea to high mountain streams. Genome sequencing offers a genetic resource for investigating the molecular bases of this phenotypic diversity and these adaptations to various habitats. The wide range of genome sizes observed in fishes is due to the role of transposable elements (TEs), which are powerful drivers of species diversity. Analyses performed to date provide evidence that class II DNA transposons are the most abundant component in most fish genomes and that compared to other vertebrate genomes, many TE superfamilies are present in actinopterygians. Moreover, specific TEs have been reported in ray-finned fishes as a possible result of an intricate relationship between TE evolution and the environment. The data summarized here underline the biological interest in Actinopterygii as a model group to investigate the mechanisms responsible for the high biodiversity observed in this taxon.

Integrative genetic map of repetitive DNA in the sole Solea senegalensis genome shows a Rex transposon located in a proto-sex chromosome

Repetitive sequences play an essential role in the structural and functional evolution of the genome, particularly in the sexual chromosomes. The Senegalese sole (Solea senegalensis) is a valuable flatfish in aquaculture albeit few studies have addressed the mapping and characterization of repetitive DNA families. Here we analyzed the Simple Sequence Repeats (SSRs) and Transposable elements (TEs) content from fifty-seven BAC clones (spanning 7.9 Mb) of this species, located in chromosomes by multiple fluorescence in situ hybridization (m-BAC-FISH) technique. The SSR analysis revealed an average density of 675.1 loci per Mb and a high abundance (59.69%) of dinucleotide coverage was observed, being ‘AC’ the most abundant. An SSR-FISH analysis using eleven probes was also carried out and seven of the 11 probes yielded positive signals. ‘AC’ probes were present as large clusters in almost all chromosomes, supporting the bioinformatic analysis. Regarding TEs, DNA transposons (Class II) were the most abundant. In Class I, LINE elements were the most abundant and the hAT family was the most represented in Class II. Rex/Babar subfamily, observed in two BAC clones mapping to chromosome pair 1, showed the longest match. This chromosome pair has been recently reported as a putative sexual proto-chromosome in this species, highlighting the possible role of the Rex element in the evolution of this chromosome. In the Rex1 phylogenetic tree, the Senegalese sole Rex1 retrotransposon could be associated with one of the four major ancient lineages in fish genomes, in which it is included O. latipes.

Chromosomal distribution of the retroelements Rex 1, Rex 3 and Rex 6 in species of the genus Harttia and Hypostomus (Siluriformes: Loricariidae)

ABSTRACT The transposable elements (TE) have been widely applied as physical chromosome markers. However, in Loricariidae there are few physical mapping analyses of these elements. Considering the importance of transposable elements for chromosomal evolution and genome organization, this study conducted the physical chromosome mapping of retroelements (RTEs) Rex1, Rex3 and Rex6 in seven species of the genus Harttia and four species of the genus Hypostomus, aiming to better understand the organization and dynamics of genomes of Loricariidae species. The results showed an intense accumulation of RTEs Rex1, Rex3 and Rex6 and dispersed distribution in heterochromatic and euchromatic regions in the genomes of the species studied here. The presence of retroelements in some chromosomal regions suggests their participation in various chromosomal rearrangements. In addition, the intense accumulation of three retroelements in all species of Harttia and Hypostomus, especially in euchromatic regions, can indicate the participation of these elements in the diversification and evolution of these species through the molecular domestication by genomes of hosts, with these sequences being a co-option for new functions.

Rex Retroelements and Teleost Genomes: An Overview

Repetitive DNA is an intriguing portion of the genome still not completely discovered and shows a high variability in terms of sequence, genomic organization, and evolutionary mode. On the basis of the genomic organization, it includes satellite DNAs, which are organized as long arrays of head-to-tail linked repeats, and transposable elements, which are dispersed throughout the genome. These repeated elements represent a considerable fraction of vertebrate genomes contributing significantly in species evolution. In this review, we focus our attention on Rex1, Rex3 and Rex6, three elements specific of teleost genomes. We report an overview of data available on these retroelements highlighting their significative impact in chromatin and heterochromatin organization, in the differentiation of sex chromosomes, in the formation of supernumerary chromosomes, and in karyotype evolution in teleosts.

Cytogenomic analysis of several repetitive DNA elements in turbot (Scophthalmus maximus)

Repetitive DNA plays a fundamental role in the organization, size and evolution of eukaryotic genomes. The sequencing of the turbot revealed a small and compact genome, as in all flatfish studied to date. The assembly of repetitive regions is still incomplete because it is difficult to correctly identify their position, number and array. The combination of classical cytogenetic techniques along with high quality sequencing is essential to increase the knowledge of the structure and composition of these sequences and, thus, of the structure and function of the whole genome. In this work, the in silico analysis of H1 histone, 5S rDNA, telomeric and Rex repetitive sequences, was compared to their chromosomal mapping by fluorescent in situ hybridization (FISH), providing a more comprehensive picture of these elements in the turbot genome. FISH assays confirmed the location of H1 in LG8; 5S rDNA in LG4 and LG6; telomeric sequences at the end of all chromosomes whereas Rex elements were dispersed along most chromosomes. The discrepancies found between both approaches could be related to the sequencing methodology applied in this species and also to the resolution limitations of the FISH technique. Turbot cytogenomic analyses have proven to add new chromosomal landmarks in the karyotype of this species, representing a powerful tool to investigate targeted genomic sequences or regions in the genetic and physical maps of this species.

Karyotypic Comparison of Hoplias malabaricus (Bloch, 1794) (Characiformes, Erythrinidae) in Central Amazon

Hoplias malabaricus comprises seven karyomorphs (A-G) and evolutionary units have been described in some of them. In this study, the karyotypic composition and genomic organization of individual H. malabaricus from Central Amazon are described and to verify whether they can be classified according to known karyomorphs. Individuals from the Ducke Reserve have 2n = 42 chromosomes, similar to karyomorph A. Individuals from Catalão Lake and Marchantaria Island exhibit 2n = 40 chromosomes, similar to karyomorph C. Regarding the constitutive heterochromatin, individuals from all locations present centromeric/pericentromeric blocks, in addition to some bitelomeric and interstitial markings. The number of chromosomes with nucleolar organizer region, 5S rDNA and 18S rDNA sites varied among the different locations. The Rex 3 element has a compartmentalized distribution at the terminal and centromeric regions of most chromosomes, with subtle differences among populations. Fluorescence in situ hybridization performed with a telomeric probe allowed the detection of these regions only at the terminal ends of the chromosomes. Thus, only the chromosomal macrostructure (karyomorphs A-G) is not sufficient to establish evolutionary units within the H. malabaricus group, considering differences in the genome organization that are found among their populations. Such differences in the genomic organization could be mainly caused by the sedentary habits of this species.

Chromosome mapping of a Tc1-like transposon in species of the catfish Ancistrus

The Tc1 mariner element is widely distributed among organisms and have been already described in different species of fish. The genus Ancistrus (Kner, 1854) has 68 nominal species and is part of an interesting taxonomic and cytogenetic group, as well as presenting a variation of chromosome number, ranging from 2n=34 to 54 chromosomes, and the existence of simple and multiple sex chromosome system and the occurrence of chromosomal polymorphisms involving chromosomes that carry the nucleolus organizer region. In this study, a repetitive element by restriction enzyme, from Ancistrus sp.1 "Flecha" was isolated, which showed similarity with a transposable element Tc1-mariner. Its chromosomal location is distributed in heterochromatic regions and along the chromosomal arms of all specimens covered in this study, confirming the pattern dispersed of this element found in other studies carried out with other species. Thus, this result reinforces the hypothesis that the sequence AnDraI is really a dispersed element isolated. As this isolated sequence showed the same pattern in all species which have different sex chromosomes systems, including in all sex chromosomes, we could know that it is not involved in sex chromosome differentiation.

Transposable elements and early evolution of sex chromosomes in fish

In many organisms, the sex chromosome pair can be recognized due to heteromorphy; the Y and W chromosomes have often lost many genes due to the absence of recombination during meiosis and are frequently heterochromatic. Repetitive sequences are found at a high proportion on such heterochromatic sex chromosomes and the evolution and emergence of sex chromosomes has been connected to the dynamics of repeats and transposable elements. With an amazing plasticity of sex determination mechanisms and numerous instances of independent emergence of novel sex chromosomes, fish represent an excellent lineage to investigate the early stages of sex chromosome differentiation, where sex chromosomes often are homomorphic and not heterochromatic. We have analyzed the composition, distribution, and relative age of TEs from available sex chromosome sequences of seven teleost fish. We observed recent bursts of TEs and simple repeat accumulations around young sex determination loci. More strikingly, we detected transposable element (TE) amplifications not only on the sex determination regions of the Y and W sex chromosomes, but also on the corresponding regions of the X and Z chromosomes. In one species, we also clearly demonstrated that the observed TE-rich sex determination locus originated from a TE-poor genomic region, strengthening the link between TE accumulation and emergence of the sex determination locus. Altogether, our results highlight the role of TEs in the initial steps of differentiation and evolution of sex chromosomes.

Organization and Chromosomal Distribution of Histone Genes and Transposable Rex Elements in the Genome of Astyanax bockmanni (Teleostei, Characiformes)

An important feature of eukaryotic organisms is the number of different repetitive DNA sequences in their genome, a feature not observed in prokaryotes. These sequences are considered to be important components for understanding evolutionary mechanisms and the karyotypic differentiation processes. Thus, we aimed to physically map the histone genes and transposable elements of the Rex family in 6 fish populations of Astyanax bockmanni. FISH results using a histone H1 gene probe showed fluorescent clusters in 2 chromosome pairs in all 6 samples analyzed. In contrast, FISH with a histone H3 probe showed conspicuous blocks in 4 chromosomes in 5 of the 6 populations analyzed. The sixth population revealed 7 chromosomes marked with this probe. Probes for the transposable elements Rex1 and Rex6 showed small sites dispersed on most chromosomes of the 6 populations, and the Rex3 element is located in a big block concentrated in only 1 acrocentric chromosome of 2 populations. As for the other populations, a Rex3 probe showed large blocks in more than 1 chromosome. Fish from Alambari and Campo Novo Stream have Rex3 elements dispersed along most of the chromosomes. Additionally, the conspicuous signals of Rex1, Rex3, and Rex6 were identified in the acrocentric B microchromosome of A. bockmanni found only in individuals of the Alambari River. Thus, we believe that different mechanisms drive the spread of repetitive sequences among the populations analyzed, which appear to be organized differently in the genome of A. bockmanni. The presence of transposable elements in the B chromosome also suggests that these sequences could play a role in the origin and maintenance of the supernumerary element in the genome of this species.

Repetitive sequences: the hidden diversity of heterochromatin in prochilodontid fish

The structure and organization of repetitive elements in fish genomes are still relatively poorly understood, although most of these elements are believed to be located in heterochromatic regions. Repetitive elements are considered essential in evolutionary processes as hotspots for mutations and chromosomal rearrangements, among other functions - thus providing new genomic alternatives and regulatory sites for gene expression. The present study sought to characterize repetitive DNA sequences in the genomes of Semaprochilodus insignis (Jardine & Schomburgk, 1841) and Semaprochilodus taeniurus (Valenciennes, 1817) and identify regions of conserved syntenic blocks in this genome fraction of three species of Prochilodontidae (Semaprochilodus insignis, Semaprochilodus taeniurus, and Prochilodus lineatus (Valenciennes, 1836) by cross-FISH using Cot-1 DNA (renaturation kinetics) probes. We found that the repetitive fractions of the genomes of Semaprochilodus insignis and Semaprochilodus taeniurus have significant amounts of conserved syntenic blocks in hybridization sites, but with low degrees of similarity between them and the genome of Prochilodus lineatus, especially in relation to B chromosomes. The cloning and sequencing of the repetitive genomic elements of Semaprochilodus insignis and Semaprochilodus taeniurus using Cot-1 DNA identified 48 fragments that displayed high similarity with repetitive sequences deposited in public DNA databases and classified as microsatellites, transposons, and retrotransposons. The repetitive fractions of the Semaprochilodus insignis and Semaprochilodus taeniurus genomes exhibited high degrees of conserved syntenic blocks in terms of both the structures and locations of hybridization sites, but a low degree of similarity with the syntenic blocks of the Prochilodus lineatus genome. Future comparative analyses of other prochilodontidae species will be needed to advance our understanding of the organization and evolution of the genomes in this group of fish.

Distribution of the T2-MITE Family Transposons in the Xenopus (Silurana) tropicalis Genome

The T2 family of miniature inverted-repeat transposable elements (T2-MITE) is a prevalent MITE family found in both Xenopus(Silurana) tropicalis and X. laevis. Some subfamilies, particularly T2-A1 and T2-C, may have originated prior to the diversification of the 2 Xenopus lineages and currently include active members in X. tropicalis, whereas another subfamily, T2-E, may have lost its transposition activity even earlier. The distribution of each T2-MITE subfamily in X. tropicalis was investigated and compared to evaluate the evolutionary dynamics of the T2-MITE subfamilies. The subfamilies showed differences in chromosomal distribution, uniformity of insertion density on scaffolds, ratios of upstream to downstream insertions with respect to genes, and their distance from genes. Among these, the T2-C subfamily was interesting because it was frequently inserted upstream and close to genes and because genes with close insertions of this subfamily showed high correlations in spatial expression patterns. This unique distribution and long-lived transposition activity may reflect a mutual relationship evolved between this subfamily and the host.

Structurally Complex Organization of Repetitive DNAs in the Genome of Cobia (Rachycentron canadum)

Repetitive DNAs comprise the largest fraction of the eukaryotic genome. They include microsatellites or simple sequence repeats (SSRs), which play an important role in the chromosome differentiation among fishes. Rachycentron canadum is the only representative of the family Rachycentridae. This species has been focused on several multidisciplinary studies in view of its important potential for marine fish farming. In the present study, distinct classes of repetitive DNAs, with emphasis on SSRs, were mapped in the chromosomes of this species to improve the knowledge of its genome organization. Microsatellites exhibited a diversified distribution, both dispersed in euchromatin and clustered in the heterochromatin. The multilocus location of SSRs strengthened the heterochromatin heterogeneity in this species, as suggested by some previous studies. The colocalization of SSRs with retrotransposons and transposons pointed to a close evolutionary relationship between these repetitive sequences. A number of heterochromatic regions highlighted a greater complex organization than previously supposed, harboring a diversity of repetitive elements. In this sense, there was also evidence of colocalization of active genetic regions and different classes of repetitive DNAs in a common heterochromatic region, which offers a potential opportunity for further researches regarding the interaction of these distinct fractions in fish genomes.

Chromosome mapping of retrotransposable elements Rex1 and Rex3 in Leporinus Spix, 1829 species (Characiformes: Anostomidae) and its relationships among heterochromatic segments and W sex chromosome

The family Anostomidae is an interesting model for studies of repetitive elements, mainly because of the presence of high numbers of heterochromatic segments related to a peculiar system of female heterogamety, which is restricted to a few species of Leporinus genus. Thus, cytogenetic mapping of the retrotransposable elements Rex1, Rex3, and Rex6 was performed in six Leporinus species, to elucidate the genomic organization of this genus. The sequencing of the Rex1 and Rex3 elements detected different base pair compositions in these elements among species, whereas the Rex6 element was not identified in the genomes of these species. FISH analysis using Rex1 detected different distribution patterns, L. elongatus, L. macrocephalus, and L. obtusidens had clusters in the terminal regions, whereas the signals were dispersed throughout all of the chromosomes with some signals in the terminal position in other species. The Rex3 signals were found mainly in the terminal positions in all the chromosomes of all species. The W chromosomes of L. elongatus, L. macrocephalus, and L. obtusidens contained the Rex1 and Rex3 signal in an interstitial position. These results suggest the emergence of different activity levels for these elements during the evolution of the species analyzed. Despite the conserved karyotype macrostructure species Leporinus often discussed, our results show some variation in hybridization patterns, particularly between the species with specific patterns in their sex chromosomes and species without this differentiated system.

Evolutionary dynamics of repetitive DNA in semaprochilodus (characiformes, prochilodontidae): a fish model for sex chromosome differentiation

Distribution of 6 microsatellites and 5 transposable elements on the chromosomes of Semaprochilodus taeniurus and S. insignis, commonly referred to as Jaraqui, was performed using their physical mapping with fluorescence in situ hybridization. In this study, we aim to understand the evolutionary dynamics in genomes of S. taeniurus and S. insignis by comparing the position, abundance and contribution of the repetitive sequences in the origins and differentiation of a ZZ/ZW sex chromosome system in S. taeniurus. Results revealed that distribution patterns of repetitive DNAs along the chromosomes varied considerably. Hybridization signals were observed on several autosomes in both species; however, in S. taeniurus genome, the repetitive sequences were more abundant. In addition, large clusters of known repetitive sequences were detected in sex chromosomes of S. taeniurus. This observation is notable because the accumulation of repetitive DNAs could reflect the degradation of genetic activities and the differentiation of protosex chromosomes, evolving into the heteromorphic ZW pair observed in S. taeniurus.

Transposable elements in fish chromosomes: a study in the marine cobia species

Rachycentron canadum, a unique representative of the Rachycentridae family, has been the subject of considerable biotechnological interest due to its potential use in marine fish farming. This species has undergone extensive research concerning the location of genes and multigene families on its chromosomes. Although most of the genome of some organisms is composed of repeated DNA sequences, aspects of the origin and dispersion of these elements are still largely unknown. The physical mapping of repetitive sequences on the chromosomes of R. canadum proved to be relevant for evolutionary and applied purposes. Therefore, here, we present the mapping by fluorescence in situ hybridization of the transposable element (TE) Tol2, the non-LTR retrotransposons Rex1 and Rex3, together with the 18S and 5S rRNA genes in the chromosome of this species. The Tol2 TE, belonging to the family of hAT transposons, is homogeneously distributed in the euchromatic regions of the chromosomes but with huge colocalization with the 18S rDNA sites. The hybridization signals for Rex1 and Rex3 revealed a semi-arbitrary distribution pattern, presenting differentiated dispersion in euchromatic and heterochromatic regions. Rex1 elements are associated preferentially in heterochromatic regions, while Rex3 shows a scarce distribution in the euchromatic regions of the chromosomes. The colocalization of TEs with 18S and 5S rDNA revealed complex chromosomal regions of repetitive sequences. In addition, the nonpreferential distribution of Rex1 and Rex3 in all heterochromatic regions, as well as the preferential distribution of the Tol2 transposon associated with 18S rDNA sequences, reveals a distinct pattern of organization of TEs in the genome of this species. A heterogeneous chromosomal colonization of TEs may confer different evolutionary rates to the heterochromatic regions of this species.

Evolutionary dynamics of retrotransposable elements Rex1, Rex3 and Rex6 in neotropical cichlid genomes

Background

Transposable elements (TEs) have the potential to produce broad changes in the genomes of their hosts, acting as a type of evolutionary toolbox and generating a collection of new regulatory and coding sequences. Several TE classes have been studied in Neotropical cichlids; however, the information gained from these studies is restricted to the physical chromosome mapping, whereas the genetic diversity of the TEs remains unknown. Therefore, the genomic organization of the non-LTR retrotransposons Rex1, Rex3, and Rex6 in five Amazonian cichlid species was evaluated using physical chromosome mapping and DNA sequencing to provide information about the role of TEs in the evolution of cichlid genomes.

Results

Physical mapping revealed abundant TE clusters dispersed throughout the chromosomes. Furthermore, several species showed conspicuous clusters accumulation in the centromeric and terminal portions of the chromosomes. These TE chromosomal sites are associated with both heterochromatic and euchromatic regions. A higher number of Rex1 clusters were observed among the derived species. The Rex1 and Rex3 nucleotide sequences were more conserved in the basal species than in the derived species; however, this pattern was not observed in Rex6. In addition, it was possible to observe conserved blocks corresponding to the reverse transcriptase fragment of the Rex1 and Rex3 clones and to the endonuclease of Rex6.

Conclusion

Our data showed no congruence between the Bayesian trees generated for Rex1, Rex3 and Rex6 of cichlid species and phylogenetic hypothesis described for the group. Rex1 and Rex3 nucleotide sequences were more conserved in the basal species whereas Rex6 exhibited high substitution rates in both basal and derived species. The distribution of Rex elements in cichlid genomes suggests that such elements are under the action of evolutionary mechanisms that lead to their accumulation in particular chromosome regions, mostly in heterochromatins.

Chromosomal location of retrotransposable REX 1 in the genomes in five Prochilodus (Teleostei: Characiformes

Transposable elements are repetitive DNA sequences comprising a group of segments able to move and carry sequences within the genome. Studies involving comparative genomics have revealed that most vertebrates have different populations of transposable elements with significant differences among species of the same lineage. Few studies have been conducted in fish, the most diverse group of vertebrates, with the objective to locate different types of transposable elements. Therefore, this study proposed to map the retrotransposable element Rex1 applying Fluorescent in situ Hybridization (FISH) in five species of the genus Prochilodus (Prochilodus argenteus, Prochilodus brevis, Prochilodus costatus, Prochilodus lineatus and Prochilodus nigricans). After the application of the Rex1 probe, scattered markings were found throughout the genome of analyzed species, and also the presence of small clusters located in the centromeric and telomeric regions coincident with the heterochromatin distribution pattern. This was the first description of the retrotransposable element Rex1 in Prochilodus genome seeking for a better understanding of the distribution pattern of these retrotransposons in the genome of teleost fish.

Transposable elements as a potential source for understanding the fish genome

Transposable elements are repetitive sequences with the capacity tomove inside of the genome. They constitute the majority of the eukaryotic genomes, and are extensively present in the human genome, representing more than 45% of the genome sequences. The knowledge of the origin and function of these elements in the fish genome is still reduced and fragmented, mainly with regard to its structure and organization in the chromosomes of the representatives of this biological group, with data currently available for very few species that represent the great variety of forms and existing diversity. Comparative analyses ascertain differences in the organization of such elements in the species studied up to the present. They can be part of the heterochromatic regions in some species or be spread throughout the genome in others. The main objective of the present revision is to discuss the aspects of the organization of transposable elements in the fish genome.

A new dispersed element in the genome of the catfish Hisonotus leucofrenatus (Teleostei: Siluriformes: Hypoptopomatinae)

Eight restriction enzymes were used in the prospection and isolation of repetitive sequences in the genome of the catfish Hisonotus leucofrenatus, a siluriform fish species that presents a large heterochromatic block in the W chromosome. In the tested enzymes, only the BamHI enzyme revealed a distinct band of 224 bp G+C value of 37%. In comparative analyses with sequences already available in the GenBank, the BamHI fragment sequence showed similarity with part of a Lepidoptera transposon. Fluorescent in situ hybridization (FISH) revealed that this sequence presents a dispersed pattern in the genome of H. leucofrenatus, forming clusters in some chromosome pairs in the pericentromeric region, which frequently are rich in constitutive heterochromatin. Based on the analysis performed, it can be inferred that the HLBam fragment constitutes a genomically dispersed transposon type element. It can be considered that the findings in this study can contribute to a better understanding of the organization and distribution of transposable elements in the genome of teleost fish.

Assessment of structural variation and molecular mapping of insertion sites of Desmar-like elements in the Hessian fly genome

The Hessian fly (Mayetiola destructor) is an agriculturally important pest of wheat. A mariner element (Desmar1) has been previously identified in the Hessian fly genome. Using Desmar1 as a probe, we isolated individual copies of Desmar-like elements from the Hessian fly genome cloned in bacterial artificial chromosomes (BACs) and studied their structural variability and flanking DNA sequences. The partial Desmar-like copies are relatively more abundant (∼64%) than full length copies (∼36%) in the Hessian fly genome. Most of the full length copies are consistently flanked by an EcoRI restriction site that occurs 32 bp from one end and 66 bp from the other end of the mariner. Using an amplified fragment length polymorphism-PCR (AFLP-PCR) based method, we identified segregating polymorphisms associated with Desmar elements in a F₂ mapping population. We were able to use the segregation data to localize the chromosomal position of three Desmar elements by linkage analysis. As paternal chromosomes are eliminated in the Hessian fly during early embryogenesis, two-thirds of the AFLPs were expected to be polymorphic in the mapping population and this was observed for AFLPs anchored to full length Desmar copies but not to the partial copies. Thus, our data indicate that dead and partial Desmar-like copies are probably associated with less polymorphic regions and may represent mariner graveyards in the Hessian fly genome.

Comparative genomics and molecular dynamics of DNA repeats in eukaryotes

Repeated elements can be widely abundant in eukaryotic genomes, composing more than 50% of the human genome, for example. It is possible to classify repeated sequences into two large families, "tandem repeats" and "dispersed repeats." Each of these two families can be itself divided into subfamilies. Dispersed repeats contain transposons, tRNA genes, and gene paralogues, whereas tandem repeats contain gene tandems, ribosomal DNA repeat arrays, and satellite DNA, itself subdivided into satellites, minisatellites, and microsatellites. Remarkably, the molecular mechanisms that create and propagate dispersed and tandem repeats are specific to each class and usually do not overlap. In the present review, we have chosen in the first section to describe the nature and distribution of dispersed and tandem repeats in eukaryotic genomes in the light of complete (or nearly complete) available genome sequences. In the second part, we focus on the molecular mechanisms responsible for the fast evolution of two specific classes of tandem repeats: minisatellites and microsatellites. Given that a growing number of human neurological disorders involve the expansion of a particular class of microsatellites, called trinucleotide repeats, a large part of the recent experimental work on microsatellites has focused on these particular repeats, and thus we also review the current knowledge in this area. Finally, we propose a unified definition for mini- and microsatellites that takes into account their biological properties and try to point out new directions that should be explored in a near future on our road to understanding the genetics of repeated sequences.

The bandit, a new DNA transposon from a hookworm-possible horizontal genetic transfer between host and parasite

Background

An enhanced understanding of the hookworm genome and its resident mobile genetic elements should facilitate understanding of the genome evolution, genome organization, possibly host-parasite co-evolution and horizontal gene transfer, and from a practical perspective, development of transposon-based transgenesis for hookworms and other parasitic nematodes.

Methodology/Principal Findings

A novel mariner-like element (MLE) was characterized from the genome of the dog hookworm, Ancylostoma caninum, and termed bandit. The consensus sequence of the bandit transposon was 1,285 base pairs (bp) in length. The new transposon was flanked by perfect terminal inverted repeats of 32 nucleotides in length with a common target site duplication TA, and it encoded an open reading frame (ORF) of 342 deduced amino acid residues. Phylogenetic comparisons confirmed that the ORF encoded a mariner-like transposase, which included conserved catalytic domains, and that the bandit transposon belonged to the cecropia subfamily of MLEs. The phylogenetic analysis also indicated that the Hsmar1 transposon from humans was the closest known relative of bandit, and that bandit and Hsmar1 constituted a clade discrete from the Tc1 subfamily of MLEs from the nematode Caenorhabditis elegans. Moreover, homology models based on the crystal structure of Mos1 from Drosophila mauritiana revealed closer identity in active site residues of the catalytic domain including Ser281, Lys289 and Asp293 between bandit and Hsmar1 than between Mos1 and either bandit or Hsmar1. The entire bandit ORF was amplified from genomic DNA and a fragment of the bandit ORF was amplified from RNA, indicating that this transposon is actively transcribed in hookworms.

Conclusions/Significance

A mariner-like transposon termed bandit has colonized the genome of the hookworm A. caninum. Although MLEs exhibit a broad host range, and are identified in other nematodes, the closest phylogenetic relative of bandit is the Hsmar1 element of humans. This surprising finding suggests that bandit was transferred horizontally between hookworm parasites and their mammalian hosts.

Because of its importance to public health, the hookworm parasite has become the focus of increased research over the past decade—research that will ultimately decipher its genetic code. We now report a gene from hookworm chromosomes known as a transposon. Transposons are genes that can move around in the genome and even between genomes of different species. We named the hookworm transposon bandit because hookworms are “thieves” that steal the blood of their hosts, leading to protein deficiency anemia. The bandit transposon is a close relative of a well studied assemblage of transposons, the mariner-like elements, known from the chromosomes of many other organisms. The founding member of this group—the mariner transposon—was isolated originally from a fruit fly; mariner has been harnessed in the laboratory as a valuable gene therapy tool. Likewise, it may be feasible to employ the bandit transposon for genetic manipulation of hookworms and functional genomics to investigate the importance of hookworm genes as new intervention targets. Finally, bandit may have transferred horizontally from primates to hookworm or vice versa in the relatively recent evolutionary history of the hookworm–human host–parasite relationship.

The evolution of transposon repeat-induced point mutation in the genome of Colletotrichum cereale: reconciling sex, recombination and homoplasy in an ''asexual" pathogen

Mobile transposable elements are among the primary drivers of the evolution of eukaryotic genomes. For fungi, repeat-induced point mutation (RIP) silencing minimizes deleterious effects of transposons by mutating multicopy DNA during meiosis. In this study we identify five transposon species from the mitosporic fungus Colletotrichum cereale and report the signature pattern of RIP acting in a lineage-specific manner on 21 of 35 unique transposon copies, providing the first evidence for sexual recombination for this species. Sequence analysis of genomic populations of the retrotransposon Ccret2 showed repeated rounds of RIP mutation acting on different copies of the element. In the RIPped Ccret2 population, there were multiple inferences of incongruence primarily attributed to RIP-induced homoplasy. This study supports the view that the sequence variability of transposon populations in filamentous fungi reflects the activities of evolutionary processes that fall outside of typical phylogenetic or population genetic reconstructions.

Physical chromosome mapping of repetitive DNA sequences in Nile tilapia Oreochromis niloticus: evidences for a differential distribution of repetitive elements in the sex chromosomes

Repetitive DNAs have been extensively applied as physical chromosome markers on comparative studies, identification of chromosome rearrangements and sex chromosomes, chromosome evolution analysis, and applied genetics. Here we report the characterization of repetitive DNA sequences from the Nile tilapia (Oreochromis niloticus) genome by construction and screening of plasmid library enriched with repetitive DNAs, analysis of a BAC-based physical map, and hybridization to chromosomes. The physical mapping of BACs enriched with repetitive sequences and C(o)t-1 DNA (DNA enriched for highly and moderately repetitive DNA sequences) to chromosomes using FISH showed a predominant distribution of repetitive elements in the centromeric and telomeric regions and along the entire length of the largest chromosome pair (X and Y sex chromosomes) of the species. The distribution of repetitive DNAs differed significantly between the p arm of X and Y chromosomes. These findings suggest that repetitive DNAs have had an important role in the differentiation of sex chromosomes.

The dingo non-long terminal repeat retrotransposons from the genome of the hookworm, Ancylostoma caninum

Members of the retrotransposable element (RTE) clade of non-long terminal repeat (LTR) retrotransposon are widely distributed among eukaryote taxa, with representatives known from Caenorhabditis elegans, mammals, mosquitoes, schistosomes, and other taxa. An RTE retrotransposon has not, however, been characterized in detail from a parasitic nematode. Here, we characterize two discrete copies of an RTE-like non-LTR retrotransposon from the genome of the dog hookworm, Ancylostoma caninum. The elements were named dingo-1 and dingo-2. The full-length dingo-1 and dingo-2 elements were 3421 and 3171bp in length, respectively. They exhibited 54% nucleotide sequence identity to one another across their entire length and 40%/58% amino-acid sequence identity/similarity across their open reading frames. dingo-1 and dingo-2 exhibited hallmark structures and sequences of non-LTR retrotransposons of the RTE family including a single open reading frame encoding apurinic-apyrimidinic endonuclease (EN) and reverse transcriptase (RT), in that order. Phylogenetic analyses targeting the RT and the EN domains both confirmed that dingo-1 and dingo-2 were members of the RTE clade and that they were closely related to RTE-1 from C. elegans, to BDDF from Bos taurus and to SR2 from Schistosoma mansoni. Dot blot hybridization indicated that as many as 100-1000 copies of dingo-1 reside within the genome of A. caninum, while detection by RT-PCR of transcripts encoding dingo-like elements suggested that dingo-1 and -2 may be retrotranspositionally active within the genome of A. caninum. The dingo elements are the first retrotransposons to be characterized from a hookworm genome.

Characterization of SR3 reveals abundance of non-LTR retrotransposons of the RTE clade in the genome of the human blood fluke, Schistosoma mansoni

BACKGROUND

It is becoming apparent that perhaps as much as half of the genome of the human blood fluke Schistosoma mansoni is constituted of mobile genetic element-related sequences. Non-long terminal repeat (LTR) retrotransposons, related to the LINE elements of mammals, comprise much of this repetitive component of the schistosome genome. Of more than 12 recognized clades of non-LTR retrotransposons, only members of the CR1, RTE, and R2 clades have been reported from the schistosome genome.

RESULTS

Inspection of the nucleotide sequence of bacterial artificial chromosome number 49_J_14 from chromosome 1 of the genome of Schistosoma mansoni (GenBank AC093105) revealed the likely presence of several RTE-like retrotransposons. Among these, a new non-LTR retrotransposon designated SR3 was identified and is characterized here. Analysis of gene structure and phylogenetic analysis of both the reverse transcriptase and endonuclease domains of the mobile element indicated that SR3 represented a new family of RTE-like non-LTR retrotransposons. Remarkably, two full-length copies of SR3-like elements were present in BAC 49-J-14, and one of 3,211 bp in length appeared to be intact, indicating SR3 to be an active non-LTR retrotransposon. Both were flanked by target site duplications of 10-12 bp. Southern hybridization and bioinformatics analyses indicated the presence of numerous copies (probably >1,000) of SR3 interspersed throughout the genome of S. mansoni. Bioinformatics analyses also revealed SR3 to be transcribed in both larval and adult developmental stages of S. mansoni and to be also present in the genomes of the other major schistosome parasites of humans, Schistosoma haematobium and S. japonicum.

CONCLUSION

Numerous copies of SR3, a novel non-LTR retrotransposon of the RTE clade are present in the genome of S. mansoni. Non-LTR retrotransposons of the RTE clade including SR3 appear to have been remarkably successful in colonizing, and proliferation within the schistosome genome.

Genome evolution and biodiversity in teleost fish

Teleost fish, which roughly make up half of the extant vertebrate species, exhibit an amazing level of biodiversity affecting their morphology, ecology and behaviour as well as many other aspects of their biology. This huge variability makes fish extremely attractive for the study of many biological questions, particularly of those related to evolution. New insights gained from different teleost species and sequencing projects have recently revealed several peculiar features of fish genomes that might have played a role in fish evolution and speciation. There is now substantial evidence that a round of tetraploidization/rediploidization has taken place during the early evolution of the ray-finned fish lineage, and that hundreds of duplicate pairs generated by this event have been maintained over hundreds of millions of years of evolution. Differential loss or subfunction partitioning of such gene duplicates might have been involved in the generation of fish variability. In contrast to mammalian genomes, teleost genomes also contain multiple families of active transposable elements, which might have played a role in speciation by affecting hybrid sterility and viability. Finally, the amazing diversity of sex determination systems and the plasticity of sex chromosomes observed in teleost might have been involved in both pre- and postmating reproductive isolation. Comparison of data generated by current and future genome projects as well as complementary studies in other species will allow one to approach the molecular and evolutionary mechanisms underlying genome diversity in fish, and will certainly significantly contribute to our understanding of gene evolution and function in humans and other vertebrates.