Bmmar1: a basal lineage of the mariner family of transposable elements in the silkworm moth, Bombyx mori

Exploring horizontal transfer of mariner transposable elements among ants and aphids

Aphids and ants are mutualistic species with a close space-time relationship, which may facilitate the occurrence of horizontal transfer events between these insect groups. Myrmar-like mariner elements were previously isolated from two ant (Myrmica ruginodis and Tapinoma ibericum) and two aphid species (Aphis fabae and Aphis hederae). The aim of this work is to determine the presence of Myrmar-like mariner elements in new ant and aphid species, as well as to analyze the likelihood of horizontal transfer events between these taxa. To accomplish this, the Myrmar-like element has been isolated from five aphid species and six ant species. Among these new analyzed species, full-length Myrmar-like mariner elements with very high sequence similarity have been isolated from the aphids Aphis nerii, Aphis spiraecola, Brachycaudus cardui, and Rhopalosiphum maidis as well as from the ants Lasius grandis and Lasius niger, even though aphids and ants belong to two insect orders (Hemiptera and Hymenoptera) that have evolved independently for at least 300 million-years. Both Lasius species establish frequent mutualistic relationships with multiple aphid species, including A. nerii, A. spiraecola, and B. cardui. The study of the putative protein encoded by them and the phylogenetic analysis suggests that they could be active transposons shared by aphids and ants through horizontal transfer events. Additionally, mariner elements with internal deletion were found in several aphids and one ant species, showing a high degree of sequence similarity among them. The characteristics of these elements with internal deletion suggest a complex origin involving various evolutionary processes, possibly including also horizontal transfer events. Myrmar-like elements have also been isolated from the other ant species, although without similarity with the aphid mariner sequences. Myrmar-like elements are also present in phylogenetically distant insect species, as well as in one crustacean species. The phylogenetic study carried out with all Myrmar-like elements suggests the probable occurrence of horizontal transfer events.

Dynamics of nuclear matrix attachment regions during 5th instar posterior silk gland development in Bombyx mori

Background

Chromatin architecture is critical for gene expression during development. Matrix attachment regions (MARs) control and regulate chromatin dynamics. The position of MARs in the genome determines the expression of genes in the organism. In this study, we set out to elucidate how MARs temporally regulate the expression of the fibroin heavy chain (FIBH) gene during development. We addressed this by identifying MARs and studying their distribution and differentiation, in the posterior silk glands of Bombyx mori during 5th instar development.

Results

Of the MARs identified on three different days, 7.15% MARs were common to all 3 days, whereas, 1.41, 19.27 and 52.47% MARs were unique to day 1, day 5, and day 7, respectively highlighting the dynamic nature of the matrix associated DNA. The average chromatin loop length based on the chromosome wise distribution of MARs and the distances between these MAR regions decreased from day 1 (253.91 kb) to day 5 (73.54 kb) to day 7 (39.19 kb). Further significant changes in the MARs in the vicinity of the FIBH gene were found during different days of 5^th instar development which implied their role in the regulation and expression of the FIBH gene.

Conclusions

The presence of MARs in the flanking regions of genes found to exhibit differential expression during 5^th instar development indicates their possible role in the regulation of their expression. This reiterates the importance of MARs in the genomic functioning as regulators of the molecular mechanisms in the nucleus. This is the first study that takes into account the tissue specific genome-wide MAR association and the potential role of these MARs in developmentally regulated gene expression. The current study lays a foundation to understand the genome wide regulation of chromatin during development.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08446-3.

Aphids and Ants, Mutualistic Species, Share a Mariner Element with an Unusual Location on Aphid Chromosomes

Aphids (Hemiptera, Aphididae) are small phytophagous insects. The aim of this study was to determine if the mariner elements found in the ant genomes are also present in Aphis fabae and Aphis hederae genomes and the possible existence of horizontal transfer events. Aphids maintain a relationship of mutualism with the ants. The close contact between these insects could favour horizontal transfer events of transposable elements. Myrmar mariner element isolated from Myrmica ruginodis and Tapinoma ibericum ants have also been found in the two Aphis species: A. fabae and A. hederae (Afabmar-Mr and Ahedmar-Mr elements). Besides, Afabmar-Mr could be an active transposon. Myrmar-like elements are also present in other insect species as well as in one Crustacean species. The phylogenetic study carried out with all Myrmar-like elements suggests the existence of horizontal transfer. Most aphids have 2n = 8 with a XX-X0 sex determination system. Their complicated life cycle is mostly parthenogenetic with sexual individuals only in autumn. The production of X0 males, originated by XX females which produce only spermatozoa with one X chromosome, must necessarily occur through specialized cytogenetic and molecular mechanisms which are not entirely known. In both aphid species, the mariner elements are located on all chromosomes, including the X chromosomes. However, on the two X chromosomes, no positive signals are detected in their small DAPI-negative telomere regions. The rDNA sites are located, as in the majority of Aphids species, on one of the telomere regions of each X chromosome. The hybridization patterns obtained by double FISH demonstrate that Afabmar-Mr and Ahedmar-Mr elements do not hybridize at the rDNA sites of their host species. Possible causes for the absence of these transposons in the rDNA genes are discussed, probably related with the X chromosome biology.

Insights on mauritiana-like Elements Diversity in Mayetiola destructor and M. hordei (Diptera: Cecidomyiidae)

Mariner-like elements (MLEs) are class II transposons belonging to the Tc1-mariner family, that have successfully invaded many insect genomes. In the current study, the availability of the Hessian fly Mayetiola destructor genome has enabled us to perform in silico analysis of MLEs using as query the previously described mariner element (Desmar1) belonging to mauritiana subfamily. Eighteen mauritiana-like elements were detected and were clustered into three main groups named Desmar1-like, MauCons1 and MauCons2. Subsequently, in vitro analysis was carried out to investigate mauritiana-like elements in M. destructor as well as in Mayetiola hordei using primers designed from TIRs of the previously identified MLEs. PCR amplifications were successful and a total of 12 and 17 mauritiana-like elements were discovered in M. destructor and M. hordei, respectively. Sequence analyses of mauritiana-like elements obtained in silico and in vitro have showed that MauCons1 and MauCons2 elements share low similarity with Desmar1 ranging from 50% to 55% suggesting different groups under mauritiana subfamily have invaded the genomes of M. destructor and M. hordei. These groups are likely inherited by vertical transmission that subsequently underwent different evolutionary histories. This work describes new mauritiana-like elements in M. destructor that are distinct from the previouslydiscovered Desmar1 and provides the first evidence of MLEs belonging to mauritiana subfamily in M. hordei.

Diversity and Evolution of pogo and Tc1/mariner Transposons in the Apoidea Genomes

Bees (Apoidea), the largest and most crucial radiation of pollinators, play a vital role in the ecosystem balance. Transposons are widely distributed in nature and are important drivers of species diversity. However, transposons are rarely reported in important pollinators such as bees. Here, we surveyed 37 bee genomesin Apoidea, annotated the pogo and Tc1/mariner transposons in the genome of each species, and performed a phylogenetic analysis and determined their overall distribution. The pogo and Tc1/mariner families showed high diversity and low abundance in the 37 species, and their proportion was significantly higher in solitary bees than in social bees. DD34D/mariner was found to be distributed in almost all species and was found in Apis mellifera, Apis mellifera carnica, Apis mellifera caucasia, and Apis mellifera mellifera, and Euglossa dilemma may still be active. Using horizontal transfer analysis, we found that DD29-30D/Tigger may have experienced horizontal transfer (HT) events. The current study displayed the evolution profiles (including diversity, activity, and abundance) of the pogo and Tc1/mariner transposons across 37 species of Apoidea. Our data revealed their contributions to the genomic variations across these species and facilitated in understanding of the genome evolution of this lineage.

Divergent evolution profiles of DD37D and DD39D families of Tc1/mariner transposons in eukaryotes

DNA transposons play a significant role in shaping the size and structure of eukaryotic genomes. The Tc1/mariner transposons are the most diverse and widely distributed superfamily of DNA transposons and the structure and distribution of several Tc1/mariner families, such as DD35E/TR, DD36E/IC, DD37E/TRT, and DD41D/VS, have been well studied. Nonetheless, a greater understanding of the structure and diversity of Tc1/mariner transposons will provide insight into the evolutionary history of eukaryotic genomes. Here, we conducted further analysis of DD37D/maT and DD39D (named Guest, GT), which were identified by the specific catalytic domains DD37D and DD39D. Most transposons of the maT family have a total length of approximately 1.3 kb and harbor a single open reading frame encoding a ~ 346 amino acid (range 302-398 aa) transposase protein, flanked by short terminal inverted repeats (TIRs) (13-48 base pairs, bp). In contrast, GTs transposons were longer (2.0-5.8 kb), encoded a transposase protein of ~400 aa (range 140-592 aa), and were flanked by short TIRs (19-41 bp). Several conserved motifs, including two helix-turn-helix (HTH) motifs, a GRPR (GRKR) motif, a nuclear localization sequence, and a DDD domain, were also identified in maT and GT transposases. Phylogenetic analyses of the DDD domain showed that the maT and GT families each belong to a monophyletic clade and appear to be closely related to DD41D/VS and DD34D/mariner. In addition, maTs are mainly distributed in invertebrates (144 species), whereas GTs are mainly distributed in land plants through a small number of GTs are present in Chromista and animals. Sequence identity and phylogenetic analysis revealed that horizontal transfer (HT) events of maT and GT might occur between kingdoms and phyla of eukaryotes; however, pairwise distance comparisons between host genes and transposons indicated that HT events involving maTs might be less frequent between invertebrate species and HT events involving GTs may be less frequent between land plant species. Overall, the DD37D/maT and DD39D/GT families display significantly different distribution and tend to be identified in more ancient evolutionary families. The discovery of intact transposases, perfect TIRs, and target site duplications (TSD) of maTs and GTs illustrates that the DD37D/maT and DD39D/GT families may be active. Together, these findings improve our understanding of the diversity of Tc1/mariner transposons and their impact on eukaryotic genome evolution.

Traveler, a New DD35E Family of Tc1/Mariner Transposons, Invaded Vertebrates Very Recently

The discovery of new members of the Tc1/mariner superfamily of transposons is expected based on the increasing availability of genome sequencing data. Here, we identified a new DD35E family termed Traveler (TR). Phylogenetic analyses of its DDE domain and full-length transposase showed that, although TR formed a monophyletic clade, it exhibited the highest sequence identity and closest phylogenetic relationship with DD34E/Tc1. This family displayed a very restricted taxonomic distribution in the animal kingdom and was only detected in ray-finned fish, anura, and squamata, including 91 vertebrate species. The structural organization of TRs was highly conserved across different classes of animals. Most intact TR transposons had a length of ∼1.5 kb (range 1,072-2,191 bp) and harbored a single open reading frame encoding a transposase of ∼340 aa (range 304-350 aa) flanked by two short-terminal inverted repeats (13-68 bp). Several conserved motifs, including two helix-turn-helix motifs, a GRPR motif, a nuclear localization sequence, and a DDE domain, were also identified in TR transposases. This study also demonstrated the presence of horizontal transfer events of TRs in vertebrates, whereas the average sequence identities and the evolutionary dynamics of TR elements across species and clusters strongly indicated that the TR family invaded the vertebrate lineage very recently and that some of these elements may be currently active, combining the intact TR copies in multiple lineages of vertebrates. These data will contribute to the understanding of the evolutionary history of Tc1/mariner transposons and that of their hosts.

Semaphorin-1a-like gene plays an important role in the embryonic development of silkworm, Bombyx mori

Fuyin-lethal red egg (Fuyin-lre) is a red egg mutant discovered from the germplasm resource Fuyin of Bombyx mori. The embryo of Fuyin-lre stops developing at the late stage of gastrulation due to chromosome structural variation. In this work, precise mutation sites at both ends of the mutated region were determined, and two inserted sequences with lengths of 1232 bp and 1845 bp were obtained at both ends of the mutation region. Interestingly, a bmmar1 transposon was detected in the inserted 1845 bp sequence. Bmmar1 possesses features of the Tcl/mariner superfamily of transposable elements (TEs), which belongs to class II TEs that use a DNA-mediated "cut and paste" mechanism to transpose. This finding suggests that Fuyin-lre mutation might be related to the "cut and paste" action of bmmar1. The mutation resulted in the deletion of 9 genes in the mutation region, of which the red egg gene re (BMSK0002766) did not affect embryonic development of B. mori, and the BMSK0002765 gene was unexpressed during the early stage of embryonic development. The RNA interference results of the remaining 7 genes suggest that the semaphorin-1a-like gene (BMSK0002764) had a major contribution to the embryonic lethality of Fuyin-lre.

Complex Evolutionary History of Mboumar, a Mariner Element Widely Represented in Ant Genomes

Mboumar-9 is an active mariner-transposable element previously isolated in the ant Messor bouvieri. In this work, a mariner-like element, Mboumar, isolated from 22 species of ants, is analyzed. These species belong to nine different subfamilies, including Leptanillinae, the most primitive ant subfamily, and Myrmicinae and Formicidae, the most derived ones. Consequently, Mboumar-like elements seem to be well-represented in ant genomes. The phylogenetic tree drawn for mariner elements is highly inconsistent with the phylogeny of host ants, with almost identical elements found in clearly distant species and, on the contrary, more variable elements in closely related species. The inconsistency between the two phylogenetic trees indicates that these transposable elements have evolved independently from the speciation events of the ants that host them. Besides, we found closer genetic relationships among elements than among their host ants. We also found potential coding copies with an uninterrupted open reading frame of 345 aa in 11 species. The putative transposase codified by them showed a high sequence identity with the active Mboumar-9 transposase. The results of selection tests suggest the intervention of purifying selection in the evolution of these elements. Overall, our study suggests a complex evolutionary history of the Mboumar-like mariner in ants, with important participation of horizontal transfer events. We also suggest that the evolutionary dynamics of Mboumar-like elements can be influenced by the genetic system of their host ants, which are eusocial insects with a haplodiploid genetic system.

An Analysis of IS630/Tc1/mariner Transposons in the Genome of a Pacific Oyster, Crassostrea gigas

Transposable elements represent the DNA fragments capable of increasing their copy number and moving within the genome. Class II mobile elements represents the DNA transposons, which transpose via excision and the subsequent reinsertion at random genomic loci. The increase of their copy number occurs only when the transposition event is coupled with the replication. IS630/Tc1/mariner DNA transposon superfamily is one of the largest and widely distributed among the Class II elements. In this work, we provide a detailed analysis of IS630/Tc1/mariner DNA transposons from the Pacific oyster, Crassostrea gigas. IS630/Tc1/mariner transposons represented in the genome of the Pacific oyster belong to four families, Tc1 (DD34E), mariner (DD34D), pogo (DDxD), and rosa (DD41D). More than a half of IS630/Tc1/mariner elements from C. gigas belong to Tc1 family. Furthermore, Mariner-31_CGi element was shown to represent a new and previously unknown family with DD37E signature. We also discovered the full-size transcripts of eight elements from Tc1, mariner, and pogo families, three of which can, presumably, retain their transposition activity.

Genome-wide identification and evolution of TC1/Mariner in the silkworm (Bombyx mori) genome

TC1/Mariner transposons belong to class II transposable elements (TEs) that use DNA-mediated "cut and paste" mechanism to transpose, and they have been identified in almost all organisms. Although silkworm (Bombyx mori) has a large amount of TC1/Mariner elements, the genome wide information of this superfamily in the silkworm is unknown. In this study, we have identified 2670 TC1/Mariner (Bmmar) elements in the silkworm genome. All the TEs were classified into 22 families by means of fgclust, a tool of repetitive sequence classification, seven of which was first reported in this study. Phylogenetic and structure analyses based on the catalytic domain (DDxD/E) of transposase sequences indicated that all members of TC1/Mariner were grouped into five subgroups: Mariner, Tc1, maT, DD40D and DD41D/E. Of these five subgroups, maT rather than Mariner possessed most members of TC1/Mariner (51.23%) in the silkworm genome. In particular, phylogenetic analysis and structure analysis revealed that Bmmar15 (DD40D) formed a new basal subgroup of TC1/Mariner element in insects, which was referred to as bmori. Furthermore, we concluded that DD40D appeared to intermediate between mariner and Tc1. Finally, we estimated the insertion time for each copy of TC1/Mariner in the silkworm and found that most of members were dramatically amplified during a period from 0 to 1 mya. Moreover, the detailed functional data analysis showed that Bmmar1, Bmmar6 and Bmmar9 had EST evidence and intact transposases. These implied that TC1/Mariner might have potential transpositional activity. In conclusion, this study provides some new insights into the landscape, origin and evolution of TC1/Mariner in the insect genomes.

Transposable elements in the Anopheles funestus transcriptome

Transposable elements (TEs) are present in most of the eukaryotic genomes and their impact on genome evolution is increasingly recognized. Although there is extensive information on the TEs present in several eukaryotic genomes, less is known about the expression of these elements at the transcriptome level. Here we present a detailed analysis regarding the expression of TEs in Anopheles funestus, the second most important vector of human malaria in Africa. Several transcriptionally active TE families belonging both to Class I and II were identified and characterized. Interestingly, we have identified a full-length putative active element (including the presence of full length TIRs in the genomic sequence) belonging to the hAT superfamily, which presents active members in other insect genomes. This work contributes to a comprehensive understanding of the landscape of transposable elements in A. funestus transcriptome. Our results reveal that TEs are abundant and diverse in the mosquito and that most of the TE families found in the genome are represented in the mosquito transcriptome, a fact that could indicate activity of these elements.The vast diversity of TEs expressed in A. funestus suggests that there is ongoing amplification of several families in this organism.

Transposition of the bamboo Mariner-like element Ppmar1 in yeast

The moso bamboo genome contains the two structurally intact and thus potentially functional mariner-like elements Ppmar1 and Ppmar2. Both elements contain perfect terminal inverted repeats (TIRs) and a full-length intact transposase gene. Here we investigated whether Ppmar1 is functional in yeast (Saccharomyces cerevisiae). We have designed a two-component system consisting of a transposase expression cassette and a non-autonomous transposon on two separate plasmids. We demonstrate that the Ppmar1 transposase Pptpase1 catalyses excision of the non-autonomous Ppmar1NA element from the plasmid and reintegration at TA dinucleotide sequences in the yeast chromosomes. In addition, we generated 14 hyperactive Ppmar1 transposase variants by systematic single amino acid substitutions. The most active transposase variant, S171A, induces 10-fold more frequent Ppmar1NA excisions in yeast than the wild type transposase. The Ppmar1 transposon is a promising tool for insertion mutagenesis in moso bamboo and may be used in other plants as an alternative to the established transposon tagging systems.

Transposition burst of mariner-like elements in the sequenced genome of Rhodnius prolixus

Transposable elements (TEs) are widespread in insect's genomes. However, there are wide differences in the proportion of the total DNA content occupied by these repetitive sequences in different species. We have analyzed the TEs present in R. prolixus (vector of the Chagas disease) and showed that 3.0% of this genome is occupied by Class II TEs, belonging mainly to the Tc1-mariner superfamily (1.65%) and MITEs (1.84%). Interestingly, most of this genomic content is due to the expansion of two subfamilies belonging to: irritans himar, a well characterized subfamily of mariners, and prolixus1, one of the two novel subfamilies here described. The high amount of sequences in these subfamilies suggests that bursts of transposition occurred during the life cycle of this family. In an attempt to characterize these elements, we performed an in silico analysis of the sequences corresponding to the DDD/E domain of the transposase gene. We performed an evolutionary analysis including network and Bayesian coalescent-based methods in order to infer the dynamics of the amplification, as well as to estimate the time of the bursts identified in these subfamilies. Given our data, we hypothesized that the TE expansions occurred around the time of speciation of R. prolixus around 1.4 mya. This suggestion lays on the "Transposon Model" of TE evolution, in which the members of a TE population that are replicative active are present at multiple loci in the genome, but their replicative potential varies, and of the "Life Cycle Model" that states that when present-day TEs have been involved in amplification bursts, they share an ancestral copy that dates back to this initial amplification.

Evolutionary history of the Azteca-like mariner transposons and their host ants

Three different complete mariner elements were found in the genome of the ant Tapinoma nigerrimum. One (Tnigmar-Mr) was interrupted by a 900-bp insertion that corresponded to an incomplete member of a fourth mariner element, called Azteca. In this work, we isolate and characterize full-length Tnigmar-Az elements in T. nigerrimum. The purpose of this study is to clarify the evolutionary history of Azteca elements and their hosts as well as the possible existence of horizontal transfer processes. For this, Azteca-like elements were also retrieved from the available sequences of various ant genomes, representing four different ant subfamilies: Dolichoderinae, Formicinae, Myrmicinae, and Ponerinae. The tree topology resulting for the Azteca-like elements bore very little resemblance to that of their respective hosts. The pervasive presence of Azteca-like elements in all ant genomes, together with the observation that extant copies are usually younger than the genomes that host them, could be explained either by lineage sorting or by recent horizontal transfer of active elements. However, the finding of closer genetic relationships between elements than between the ants that host them is consistent with the latter scenario. This is clearly observed in Sinvmar-Az, Tnigmar-Az, Acepmar-Az, and Cflomar-Az elements, suggesting the existence of horizontal transfer processes. On the contrary, some elements displayed more divergence than did the hosts harboring them. This may reflect either further horizontal transfer events or random lineage sorting.

Genomic landscape and evolutionary dynamics of mariner transposable elements within the Drosophila genus

BACKGROUND

The mariner family of transposable elements is one of the most widespread in the Metazoa. It is subdivided into several subfamilies that do not mirror the phylogeny of these species, suggesting an ancient diversification. Previous hybridization and PCR studies allowed a partial survey of mariner diversity in the Metazoa. In this work, we used a comparative genomics approach to access the genus-wide diversity and evolution of mariner transposable elements in twenty Drosophila sequenced genomes.

RESULTS

We identified 36 different mariner lineages belonging to six distinct subfamilies, including a subfamily not described previously. Wide variation in lineage abundance and copy number were observed among species and among mariner lineages, suggesting continuous turn-over. Most mariner lineages are inactive and contain a high proportion of damaged copies. We showed that, in addition to substitutions that rapidly inactivate copies, internal deletion is a major mechanism contributing to element decay and the generation of non-autonomous sublineages. Hence, 23% of copies correspond to several Miniature Inverted-repeat Transposable Elements (MITE) sublineages, the first ever described in Drosophila for mariner. In the most successful MITEs, internal deletion is often associated with internal rearrangement, which sheds light on the process of MITE origin. The estimation of the transposition rates over time revealed that all lineages followed a similar progression consisting of a rapid amplification burst followed by a rapid decrease in transposition. We detected some instances of multiple or ongoing transposition bursts. Different amplification times were observed for mariner lineages shared by different species, a finding best explained by either horizontal transmission or a reactivation process. Different lineages within one species have also amplified at different times, corresponding to successive invasions. Finally, we detected a preference for insertion into short TA-rich regions, which appears to be specific to some subfamilies.

CONCLUSIONS

This analysis is the first comprehensive survey of this family of transposable elements at a genus scale. It provides precise measures of the different evolutionary processes that were hypothesized previously for this family based on PCR data analysis. mariner lineages were observed at almost all "life cycle" stages: recent amplification, subsequent decay and potential (re)-invasion or invasion of genomes.

A novel cluster of mariner-like elements belonging to mellifera subfamily from spiders and insects: implications of recent horizontal transfer on the South-West Islands of Japan

Mariner-like elements (MLEs) have been isolated from various eukaryotic genomes and they are divided into 15 subfamilies, including main five subfamilies: mauritiana, cecropia, mellifera/capitata, irritans, and elegans/briggsae. In the present study, MLEs belonging to mellifera subfamily were isolated from various spiders and insects (Hymenoptera and Lepidoptera) inhabiting the South-West Islands of Japan and neighboring regions. MLEs isolated from 15 different species formed a distinct novel cluster in mellifera subfamily. MLEs obtained from three different species [i.e., the bee Amegilla senahai subflavescens (Amsmar1), the wasp Campsomeris sp. (Casmar1), and the swallowtail butterfly Pachliopta aristolochiae (Paamar1)] contained an intact open reading frame that encoded a putative transposase. These transposases exhibited high similarity of 97.9% among themselves. In case of Casmar1, the presence of an intact ORF was found in high frequencies (i.e., 11 out of 12 clones). In addition, these transposases also showed the presence of a terminal inverted repeat-binding motif, DD(34)D and two highly conserved amino acid motifs, (W/L)(I/L)PHQL and YSP(D/N)L(A/S)P. These two motifs differed from previously known motifs, WVPHEL and YSPDLAP. MLEs isolated from these three different species may have been inserted into their genomes by horizontal transfer. Furthermore, the presence of an intact ORF suggests that they are still active in habitats along these isolated islands.

Trematode Himasthla elongata mariner element (Hemar): structure and applications

We cloned and analyzed Hemar1-the full-length mariner of Himasthla elongata. Hemar1 amount and distribution in the genome is typical for the transposable elements. Hemar1 closest relatives found in databases are the mariner-like element (MLE) of Girardia tigrina with 88% similarity in the most conserved transposase domain and Cemar1 of Caenorhabditis elegans with the most similar inverted terminal repeats. Hydra's (Cnidaria) MLE are the next in similarity to Hemar1. We checked whether sequences similar to Hemar1 exist in intermediate and definitive hosts of the parasitic trematode and did not find obvious similarity. This fact, together with the data of Hemar1 evolutionary position, argues against recent MLE-mediated horizontal transfer in this parasite-host model. Our results demonstrate that H. elongata generates genomic variability in asexual parthenogenetic generations within the snail. Transposon insertional display based on full-length sequence showed that Hemar1 could be located in the regions involved in generating clonal diversity in rediae and cercariae, that is, trematode parthenitae.

The ant genomes have been invaded by several types of mariner transposable elements

To date, only three types of full-length mariner elements have been described in ants, each one in a different genus of the Myrmicinae subfamily: Sinvmar was isolated from various Solenopsis species, Myrmar from Myrmica ruginodis, and Mboumar from Messor bouvieri. In this study, we report the coexistence of three mariner elements (Tnigmar-Si, Tnigmar-Mr, and Tnigmar-Mb) in the genome of a single species, Tapinoma nigerrimum (subfamily Dolichoderinae). Molecular evolutionary analyses of the nucleotide sequence data revealed a general agreement between the evolutionary history of most the elements and the ant species that harbour them, and suggest that they are at the vertical inactivation stage of the so-called Mariner Life Cycle. In contrast, significantly reduced levels of synonymous divergence between Mboumar and Tnigmar-Mb and between Myrmar and Botmar (a mariner element isolated from Bombus terrestris), relative to those observed between their hosts, suggest that these elements arrived to the species that host them by horizontal transfer, long after the species' split. The horizontal transfer events for the two pairs of elements could be roughly dated within the last 2 million years and about 14 million years, respectively. As would be expected under this scenario, the coding sequences of the youngest elements, Tnigmar-Mb and Mboumar, are intact and, thus, potentially functional. Each mariner element has a different chromosomal distribution pattern according to their stage within the Mariner Life Cycle. Finally, a new defective transposable element (Azteca) has also been found inserted into the Tnigmar-Mr sequences showing that the ant genomes have been invaded by at least four different types of mariner elements.

Molecular characterization of mariner-like elements in emerald ash borer, Agrilus planipennis (Coleoptera, Polyphaga)

Emerald ash borer (EAB, Agrilus planipennis), an exotic invasive pest, has killed millions of ash trees (Fraxinus spp.) in North America and continues to threaten the very survival of the entire Fraxinus genus. Despite its high-impact status, to date very little knowledge exists for this devastating insect pest at the molecular level. Mariner-like elements (MLEs) are transposable elements, which are ubiquitous in occurrence in insects and other invertebrates. Because of their low specificity and broad host range, they can be used for epitope-tagging, gene mapping, and in vitro mutagenesis. The majority of the known MLEs are inactive due to in-frame shifts and stop codons within the open reading frame (ORF). We report on the cloning and characterization of two MLEs in A. planipennis genome (Apmar1 and Apmar2). Southern analysis indicated a very high copy number for Apmar1 and a moderate copy number for Apmar2. Phylogenetic analysis revealed that both elements belong to the irritans subfamily. Based on the high copy number for Apmar1, the full-length sequence was obtained using degenerate primers designed to the inverted terminal repeat (ITR) sequences of irritans MLEs. The recovered nucleotide sequence for Apmar1 consisted of 1,292 bases with perfect ITRs, and an ORF of 1,050 bases encoding a putative transposase of 349 amino acids. The deduced amino acid sequence of Apmar1 contained the conserved regions of mariner transposases including WVPHEL and YSPDLAP, and the D,D(34)D motif. Both Apmar1 and Apmar2 could represent useful genetic tools and provide insights on EAB adaptation.

Amplified fragment length polymorphism mapping of quantitative trait loci for economically important traits in the silkworm, Bombyx mori

Cocoon related characteristics are economically important traits in the silkworm, Bombyx mori L. (Lepidoptera: Bombycidae). In this study a genetic linkage map was developed that identified QTL controlling the cocoon weight, cocoon shell weight, and cocoon shell percentage using 161 amplified fragment length polymorphism (AFLP) markers. Twenty PstI/TaqI primer combinations were employed to genotype 78 F(2) progenies derived from a cross between P107 Japanese inbred line and Khorasan Lemon Iranian native strain. Among polymorphic markers, 159 AFLP markers were assigned to 24 linkage groups at the LOD threshold of 2.5 that varied in length from 4 to 299 cM. The total length of the linkage map was 2747 cM, giving an average marker resolution of 19.31 cM. A total of 21 AFLP markers were identified that were distributed over the ten linkage groups linked to the three studied traits using the composite interval mapping method. The explained variation rate by QTL controlling cocoon weight, cocoon shell weight, and cocoon shell percentage ranged from 0.02% to 64.85%, 0.2% to 49.11%, and 0.04% to 84.20%, respectively. These QTL controlled by different actions as well as under dominance, additive, partial dominance, dominance, and over dominance.

Mariner transposons as genetic tools in vertebrate cells

Transposable elements (TEs) are being investigated as potential molecular tools in genetic engineering, for use in procedures such as transgenesis and insertional mutagenesis. Naturally active and reconstructed active TEs are both being studied to develop non-viral delivery vehicles. To date, the active elements being used include three Mariner-Like Elements (MLEs). We review below the studies that have investigated the ability of these MLEs to insert a transgene in vertebrate cells.

Genome-wide screening and characterization of transposable elements and their distribution analysis in the silkworm, Bombyx mori

To elucidate the contribution of transposable elements (TEs) to the silkworm genome structure and evolution, we have conducted genome-wide analysis of TEs using the newly released genome assembly. The TEs made up 35% of the genome and contributed greatly to the genome size. Non-long terminal repeat retrotransposons (non-LTRs) and short interspersed nuclear elements (SINEs) were the predominant TE classes. From characterization of the TE distribution in the genome, it was revealed that non-LTRs, especially R1 clade elements, are frequently inserted into GC-rich regions. The GC content of non-LTRs themselves was over 40%, which indicate their contribution to the GC content of the insertion region. TEs accumulated in regions with low gene density, and there were relatively strong positive correlations between TE density and chromosomal recombination rate. We also characterized the clade distribution of the non-LTRs. The silkworm non-LTRs represented 10 of the 16 previously defined clades, which had the most variety than that reported for other genomes. Two partial CRE clade elements were found, which is one of the most ancient lineages of non-LTRs, and have been only found in Trypanosoma and fungi before. This analysis suggests that Bombyx genome is influenced by numerous amounts and variety of TEs.

Mariner-like elements in Rhynchosciara americana (Sciaridae) genome: molecular and cytological aspects

Two mariner-like elements, Ramar1 and Ramar2, are described in the genome of Rhynchosciara americana, whose nucleotide consensus sequences were derived from multiple defective copies containing deletions, frame shifts and stop codons. Ramar1 contains several conserved amino acid blocks which were identified, including a specific D,D(34)D signature motif. Ramar2 is a defective mariner-like element, which contains a deletion overlapping in most of the internal region of the transposase ORF while its extremities remain intact. Predicted transposase sequences demonstrated that Ramar1 and Ramar2 phylogenetically present high identity to mariner-like elements of mauritiana subfamily. Southern blot analysis indicated that Ramar1 is widely represented in the genome of Rhynchosciara americana. In situ hybridizations showed Ramar1 localized in several chromosome regions, mainly in pericentromeric heterochromatin and their boundaries, while Ramar2 appeared as a single band in chromosome A.

Characterization of EamaT1, a member of maT family of transposable elements from the earthworm Eisenia andrei (Annelida, Oligochaeta)

The maT family is a unique clade within the Tc1-mariner superfamily, and their distribution is to date known as being limited to invertebrates. A novel transposon named EamaT1 is described from the genome of the earthworm Eisenia andrei. The full sized EamaT1 was obtained by degenerate and inverse PCR-based amplification. Sequence analysis of multiple copies of the EamaT1, which consisted of 0.9 and 1.4 kb elements, showed that the consensual EamaT1 with inverted terminal repeats (ITRs) of 69 bp was 1,422 bp long and flanked by a duplicated TA dinucleotide. The EamaT1 is present in approximately 120-250 copies per diploid genome but undergoes an inactivation process as a result of accumulating multiple mutations and is nonfunctional. The open reading frame (ORF) of the EamaT1 consensus encoding 356 amino acid sequences of transposase contained a DD37D signature and a conserved paired-like DNA binding motif for the transposition mechanism. The result of ITRs comparison confirmed their consensus terminal sequences (5'-CAGGGTG-3') and AT-rich region on the internal bases for ITRs-transposase interaction.

Molecular characterization and phylogenetic position of a new mariner-like element in the coastal crab, Pachygrapsus marmoratus

Mariner-like elements (MLEs) are class-II transposable elements that move within the genome of their hosts by means of a DNA-mediated "cut and paste" mechanism. MLEs have been identified in several organisms, from most of the phyla. Nevertheless, only a few of the sequences characterized contain an intact open reading frame. Investigation of the genome of a coastal crab, Pachygrapsus marmoratus, has identified nine Pacmmar elements, two of which have an open reading frame encoding a putatively functional transposase. Nucleic acid analyses and comparison with the previous data showed that the GC contents of MLEs derived from coastal organisms such as P. marmoratus are significantly higher than those of terrestrial MLEs and significantly lower than those of hydrothermal ones. Furthermore, molecular phylogeny analyses have shown that Pacmmar elements constitute a new lineage of the irritans subfamily within the mariner family.

The N-terminus of Himar1 mariner transposase mediates multiple activities during transposition

Mariner family transposons are perhaps the most widespread transposable elements of eukaryotes. While we are beginning to understand the precise mechanism of transposition of these elements, the structure of their transposases are still poorly understood. We undertook an extensive mutagenesis of the N-terminal third of the transposase of the Himar1 mariner transposon to begin the process of determining the structure and evolution of mariner transposases. N and C-terminal deletion analyses localized the DNA binding domain of Himar1 transposase to the first 115 amino acids. Alanine scanning of 23 selected sites within this region uncovered mutations that not only affected DNA binding but DNA cleavage as well. The behavior of other mutations strongly suggested that the N-terminus is also involved in multimerization of the transposase on a single inverted terminal repeat and in paired ends complex formation which brings together the two ends of the transposon. Finally, two hyperactive mutations at conserved sites suggest that mariner transposases are under a pattern of stabilizing selection in nature with regard to how efficiently they mediate transposition, resulting in a population of "average" transposons.

Species sympatry and horizontal transfers of Mariner transposons in marine crustacean genomes

Mariner-like elements (MLEs) have been widely detected in terrestrial species. The first complete MLE isolated from a marine invertebrate was detected in the genome of the hydrothermal crab Bythograea thermydron by Halaimia-Toumi et al. [Halaimia-Toumi, N., Casse, N., Demattei, M.V., Renault, S., Pradier, E., Bigot, Y., Laulier, M., 2004. The GC-rich transposon Bytmar1 from the deep-sea hydrothermal crab, Bythograea thermydron, may encode three transposase isoforms from a single ORF. J. Mol. Evol. 59, 747-760] and called Bytmar1. Here, we report the isolation of three new Bytmar1 relatives from the genomes of one hydrothermal amphipod Ventiella sulfuris (Vensmar1) and two coastal crustacea, Maia brachydactila (Maibmar1) and Cancer pagurus (Canpmar1). Like Bytmar1, these MLEs have an unusually high GC content, a high CpG ratio, and a low TpA ratio. Their consensus sequence encodes a transposase that is preceded by an N-flag, as in Bytmar1, which could be a marine feature. Only one of the 19 clones obtained, Vensmar1.3, encoded for a full-length transposase. The phylogenetic analyses revealed that all these Bytmar1-related elements can be differentiated into two clusters, corresponding to the coastal or hydrothermal origin of their hosts. They also confirmed that the irritans sub-family comprises at least four lineages that seem to depend on the taxonomical position and habitat of their hosts. Finally, we observed that elements coding for two potentially complete transposases exhibiting 99.5% similarity, Bytmar1.11 and Vensmar1.3, were present in the genome of two distantly related hydrothermal crustacea, one Amphipod and one Decapod. The hypothesis of horizontal transfers is discussed in the light of the sequence similarities observed.

Detection of a mariner-like element and a miniature inverted-repeat transposable element (MITE) associated with the heterochromatin from ants of the genus Messor and their possible involvement for satellite DNA evolution

The satellite DNA of ants Messor bouvieri, M. barbarus and M. structor, studied in a previous paper, is organized as tandemly repeated 79-bp monomers in the three species showing high sequence similarity. In the present paper, a mariner-like element (Mboumar) and a new MITE (miniature inverted-repeat transposable element) called IRE-130, inserted into satellite DNA from M. bouvieri, are analyzed. The study of Mboumar element, of its transcription and the putative transposase that it would encode, suggests that it could be an active element. Mboumar elements inserted into IRE-130 elements have also been detected. It is the first time, to our knowledge, that a MITE has been described in Hymenoptera and it is also the first time that a mariner-like element inserted into a MITE has been detected. A mariner-like element, inserted into satellite DNA from M. structor and in M. barbarus, also has been found. The results seem to indicate that transposition events have participated in the satellite DNA mobilization and evolution.

Gambol and Tc1 are two distinct families of DD34E transposons: analysis of the Anopheles gambiae genome expands the diversity of the IS630-Tc1-mariner superfamily

Tc1 is a family of DNA transposons found in diverse organisms including vertebrates, invertebrates and fungi. Tc1 belongs to the IS630-Tc1-mariner superfamily, which is characterized by common 'TA' target site and conserved D(Asp)DE(Glu) or DDD catalytic triad. All functional Tc1-like transposons contain a transposase with a DD34E catalytic triad. We conducted a systematic analysis of DD34E transposons in the African malaria mosquito, Anopheles gambiae, using a reiterative and exhaustive search program. In addition to previously described Tc1-like elements, we uncovered 26 new DD34E transposons including a novel family that we named gambol. Designation of family status to gambol is based on phylogenetic analyses of transposase sequences that showed gambol and Tc1 transposons as distinct clades that were separated by mariner and other families of the IS630-Tc1-mariner superfamily. The distinction between Tc1 and gambol is also consistent with the unique TIRs in gambol elements and the presence of a 'W[I/L/V]DEDC' signature near their N-termini. This signature is predicted as part of the 'RED' domain, a component of the 'PAI' and 'RED' DNA binding domains in Tc1 and possibly mariner. Although gambol appears to be related to a few DD34E transposons from cyanobacteria and fungi, no gambol has been reported in any other insects or animals thus far. Several gambol and Tc1 elements have intact ORFs and different genomic copies with high sequence identity, which suggests that they may have been recently active.

Molecular Analysis of Divergence in Tachinid Uzi (Exorista Sorbillans) Populations in India

Exorista sorbillans is a tachinid endoparasitoid of silkworm, Bombyx mori, and is globally known as uzi. It causes economic injury to the cocoon crop in silkworm cultivating areas of India, except those above 400 m above mean sea level (AMSL) in the foothills of the Himalayas (Darjeeling). It is reported that the sericulture tract of south India became infected with this pest only since 1980 through an accidental transportation of cocoons from West Bengal. To ascertain whether the genome of this parasitoid is differentiating into discrete gene pools in contrasting geo-climatic conditions, molecular profiling of four populations (Es (Annatapur), Es(Ramanagaram), Es (Channapatna) and Es(Kodathi) from south India and Es(Murshidabad) from Murshidabad, West Bengal was undertaken with 13 ISSR, 3 RAPD and six non-random primers designed from various repeat sequences of B. mori . MANOVA indicated significance for the Roy's largest root estimate (55.4; F =18.47; p = 0.002) for the variability contributed by the replication. Further, hierarchical clustering done on the basis of Euclidean distance matrix and Nei's unbiased Phylip clustering put Es(Murshidabad) at the maximum distance from those of south India and 29 markers could also be identified which significantly differentiateEs(Murshidabad) from others. However, Nei's statistics for gene diversity in sub-populations reveal considerably high gene-flow (3.44 and 2.51) among the populations around Bangalore. The gene-flow between Es(Murshidabad) and other population is lowest but cannot be ignored. The comparison of endosymbiont specific 16SrRNA and fts Z gene (partial) sequences through clustalW (gcgMSF) revealed a closer relationship of Es(Murshidabad) with Es(Annatapur) and Es (Ramanagaram) and is not congruent with the relationships discussed above. The significance of this maiden study with a tachinid fly-pest is discussed in the context of understanding the diversification of Uzi fly-pest and also establishing this pest as a relevant biological material for studying microevolution in future.

Diverse DNA transposons in rotifers of the class Bdelloidea

We surveyed the diversity, structural organization, and patterns of evolution of DNA transposons in rotifers of the class Bdelloidea, a group of basal triploblast animals that appears to have evolved for millions of years without sexual reproduction. Representatives of five superfamilies were identified: ITm (IS630/Tc/mariner), hAT, piggyBac, helitron, and foldback. Except for mariners, no fully intact copies were found. Mariners, both intact and decayed, are present in high copy number, and those described here may be grouped in several closely related lineages. Comparisons across lineages show strong evidence of purifying selection, whereas there is little or no evidence of such selection within lineages. This pattern could have resulted from repeated horizontal transfers from an exogenous source, followed by limited intragenomic proliferation, or, less plausibly, from within-host formation of new lineages under host- or element-based selection for function, in either case followed by eventual inactivation and decay. Unexpectedly, the flanking sequences surrounding the majority of mariners are very similar, indicating either insertion specificity or proliferation as part of larger DNA segments. Members of all superfamilies are present near chromosome ends, associated with the apparently domesticated retroelement Athena, in large clusters composed of diverse DNA transposons, often inserted into each other, whereas the examined gene-rich regions are nearly transposon-free.

Retrotransposable elements on the W chromosome of the silkworm, Bombyx mori

The sex chromosomes of the silkworm, Bombyxmori, are designated ZW(XY) for females and ZZ(XX) for males. The W chromosome of B. mori does not recombine with the Z chromosome and autosomes and no genes for morphological characters have been mapped to the W chromosome as yet. Furthermore, femaleness is determined by the presence of a single W chromosome, regardless of the number of autosomes or Z chromosomes. To understand these interesting features of the W chromosome, it is necessary to analyze the W chromosome at the molecular biology level. Initially to isolate DNA sequences specific for the W chromosome as randomly amplified polymorphic DNA (RAPD) markers, we compared the genomic DNAs between males and females by PCR with arbitrary 10-mer primers. To the present, we have identified 12 W-specific RAPD markers, and with the exception of one RAPD marker, all of the deduced amino acid sequences of these W-specific RAPD markers show similarity to previously reported amino acid sequences of retrotransposable elements from various organisms. After constructing a genomic DNA lambda phage library of B. mori we obtained two lambda phage clones, one containing the W-Kabuki RAPD sequence and one containing the W-Samurai RAPD sequence and found that these DNA sequences comprised nested structures of many retrotransposable elements. To further analyze the W chromosome, we obtained 14 W-specific bacterial artificial chromosome (BAC) clones from three BAC libraries and subjected these clones to shotgun sequencing. The resulting assembly of sequences did not produce a single contiguous sequence due to the presence of many retrotransposable elements. Therefore, we coupled PCR with shotgun sequencing. Through these analyses, we found that many long terminal repeat (LTR) and non-LTR retrotransposons, retroposons, DNA transposons and their derivatives, have accumulated on the W chromosome as strata. These results strongly indicate that retrotransposable elements are the main structural component of the W chromosome.

Classification and nomenclature of retrotransposable elements

The classification and nomenclature of retrotransposable elements is reviewed. A comparison is made between the initial classification summarized in Capy et al. (1997b), and the more recent proposal based on the classification of the viruses (Hull, 2001). Several problems, mainly relating to the position of elements belonging to the DIRS-like or Bel-like groups, are discussed. The first classification is now out of date, and must be revisited to take account of the discovery of new elements, however the second cannot be extended to the DNA elements. There is therefore, clear evidence of the need to adopt a general and a common classification.

Characterization of multiple lineages of Tc1-like elements within the genome of the amphibian Xenopus tropicalis

We have used genomic sequencing data extracted from the first assembly of the Xenopus tropicalis genome combined with a degenerated PCR approach to identify multiple lineages of Tc1 related transposable elements. Full-length elements were isolated in each lineage and were characterized. Most of them exhibit the typical characteristics of Tc1-like elements (TLEs). An open reading frame (ORF) encoding a 340-350 aa transposase containing a [D, D(34)E] signature was found as well as conserved inverted terminal repeats (ITRs) at each extremities. These ITRs could vary in length, depending on the TLE lineage. These new TLEs were named Eagle, Froggy, Jumpy, Maya, Xeminos, XtTXr and XtTXz. Phylogenetic analyses indicate that their closest relatives are present in the genomes of actinopterygian and amphibian. Interestingly, Maya and Xeminos share remarkable characteristics. Maya contains a [D,D(36)E] motif but is not related to any described TLE so far. Xeminos is the first vertebrate TLE strongly related to an invertebrate lineage. Finally, we have identified for most of these TLEs, copies containing an intact transposase ORF suggesting that these elements may still be active.

The GC-rich transposon Bytmar1 from the deep-sea hydrothermal crab, Bythograea thermydron, may encode three transposase isoforms from a single ORF

Mariner-like elements (MLEs) are classII transposons with highly conserved sequence properties and are widespread in the genome of animal species living in continental environments. We describe here the first full-length MLE found in the genome of a marine crustacean species, the deep-sea hydrothermal crab Bythograea thermydron (Crustacea), named Bytmar1. A comparison of its sequence features with those of the MLEs contained in the genomes of continental species reveals several distinctive characteristics. First, Bytmar1 elements contains an ORF that may encode three transposase isoforms 349, 379, and 398 amino acids (aa) in long. The two biggest proteins are due to the presence of a 30- and 49-aa flag, respectively, at the N-terminal end of the 349-aa cardinal MLE transposase. Their GC contents are also significantly higher than those found in continental MLEs. This feature is mainly due to codon usage in the transposase ORF and directly interferes with the curvature propensities of the Bytmar1 nucleic acid sequence. Such an elevated GC content may interfere with the ability of Bytmar 1 to form an excision complex and, in consequence, with its efficiency to transpose. Finally, the origin of these characteristics and their possible consequences on transposition efficiency are discussed.

The Caenorhabditis briggsae genome contains active CbmaT1 and Tcb1 transposons

The maT clade of transposons is a group of transposable elements intermediate in sequence and predicted protein structure to mariner and Tc transposons, with a distribution thus far limited to a few invertebrate species. We present evidence, based on searches of publicly available databases, that the nematode Caenorhabditis briggsae has several maT-like transposons, which we have designated as CbmaT elements, dispersed throughout its genome. We also describe two additional transposon sequences that probably share their evolutionary history with the CbmaT transposons. One resembles a fold back variant of a CbmaT element, with long (380-bp) inverted terminal repeats (ITRs) that show a high degree (71%) of identity to CbmaT1. The other, which shares only the 26-bp ITR sequences with one of the CbmaT variants, is present in eight nearly identical copies, but does not have a transposase gene and may therefore be cross mobilised by a CbmaT transposase. Using PCR-based mobility assays, we show that CbmaT1 transposons are capable of excising from the C. briggsae genome. CbmaT1 excised approximately 500 times less frequently than Tcb1 in the reference strain AF16, but both CbmaT1 and Tcb1 excised at extremely high frequencies in the HK105 strain. The HK105 strain also exhibited a high frequency of spontaneous induction of unc-22 mutants, suggesting that it may be a mutator strain of C. briggsae.

A potentially functional mariner transposable element in the protist Trichomonas vaginalis

Mariner transposable elements encoding a D,D34D motif-bearing transposase are characterized by their pervasiveness among, and exclusivity to, animal phyla. To date, several hundred sequences have been obtained from taxa ranging from cnidarians to humans, only two of which are known to be functional. Related transposons have been identified in plants and fungi, but their absence among protists is noticeable. Here, we identify and characterize Tvmar1, the first representative of the mariner family to be found in a species of protist, the human parasite Trichomonas vaginalis. This is the first D,D34D element to be found outside the animal kingdom, and its inclusion in the mariner family is supported by both structural and phylogenetic analyses. Remarkably, Tvmar1 has all the hallmarks of a functional element and has recently expanded to several hundred copies in the genome of T. vaginalis. Our results show that a new potentially active mariner has been found that belongs to a distinct mariner lineage and has successfully invaded a nonanimal, single-celled organism. The considerable genetic distance between Tvmar1 and other mariners may have valuable implications for the design of new, high-efficiency vectors to be used in transfection studies in protists.

Identification of mariner elements from house flies (Musca domestica) and German cockroaches (Blattella germanica)

Full-length mariner elements were isolated and sequenced from house flies (Musca domestica) and German cockroaches (Blattella germanica). The amino acid sequence of the house fly mariner element (accession number: AF373028) showed 99.5% identity with Mos1 and peach elements, whereas the German cockroach mariner element (accession number: AF355143) showed 98.8% and 99.8% identity, respectively. Sequence analysis revealed that the mariner elements in house flies and German cockroaches differed from the active Mos1 mariner element by seven and 15 nucleotides, respectively. Four essential nucleotide substitutions at positions 64, 154, 305, and 1203, which have been proposed to contribute to the loss of activity of the inactive elements, were detected in the German cockroach mariner element. In contrast, although the mariner element in house flies contained substitutions at positions 64, 154, and 305, it retained T at position 1203, identical to active mariner elements. Mariner is present in approximately eight copies in the German cockroach genome.

Molecular diversity and phylogenetic analysis of mariner-like transposons in the genome of the silkworm Bombyx mori

Genome-wide screening of mariner-like elements (MLEs) in the silkworm Bombyx mori has revealed the presence of five different types of MLEs (Bmmar1, Bmmar2, Bmmar3, Bmmar4 and Bmmar5). We isolated and characterized sixty copies of the MLEs representing the five Bmmar types. Their nucleotide sequences, nucleotide compositions, deduced transposase sequences, codon preferences, and the copy numbers showed extensive variations. Phylogenetic analysis of the sequences revealed that Bmmar1, Bmmar2, and Bmmar3 have been in the B. mori genome for a long time, while Bmmar4 is probably a recent invader of the genome. Because of the long-term association of Bmmar1 and Bmmar2 with the genome, highly mutated miniature Bmmar1 and Bmmar2 are widespread in the genome, and the footprints of these elements are also present in different silkworm genes. However, miniature copies of Bmmar4 were not detected. This recently acquired element has very few mutations. None of the characterized copies had functional transposase open reading frames. They essentially exist as fossils in the genome.

Identification of two mariner-like elements in the genome of the mosquito Ochlerotatus atropalpus

Two distinct mariner-like elements, Atmar-1 and Atmar-2, were isolated from the genome of the mosquito Ochlerotatus atropalpus. Full-sized Atmar-1 elements, obtained by screening a genomic library, have a 1293-bp consensus sequence with 27-bp inverted terminal repeats and a 1047-bp open reading frame (ORF) encoding the transposase. The Atmar-2 elements were amplified by polymerase chain reaction from genomic DNA and contain the central part of the transposase ORF. Individual clones of both mariner elements contain deletions, frameshifts, and stop codons. The Atmar-1 elements are present in 370-1200 copies, while the Atmar-2 elements are present in approximately 100-300 copies per haploid genome. One of the Atmar-1 elements, Atmar-1.33, could be mobilized, suggesting the presence of functional Atmar-1 elements elsewhere in the genome. Phylogenetic analysis demonstrated that Atmar-1 elements belong to the irritans subfamily and Atmar-2 elements to the cecropia subfamily of mariner elements.

The 62-kb upstream region of Bombyx mori fibroin heavy chain gene is clustered of repetitive elements and candidate matrix association regions

We sequenced an 80 kb DNA region containing the complete sequence of the silkworm Bombyx mori fibroin gene and its flanking, especially the upstream, regions (-62 kb). About 30% of the 62 kb upstream region is composed of repetitive elements including short interspersed elements Bm1, long interspersed elements L1Bm and mariner-like elements Bmmar1 which are widespread over the silkworm genome. This 62 kb region is also enriched of commonly considered matrix association region (MAR) motifs. A total of 25 individual MAR recognition signatures (MRSs) were identified, with 24 at the upstream and one at the downstream region. Combining two newly developed MAR prediction programs (MAR-finder and Chrclass), ten candidate MARs were predicted, with five containing MRS and seven related to the repetitive elements. The wide distribution of nested repetitive elements, candidate MARs, DNase I hypersensitive sites and other potential regulatory factors recognition sites indicates this region is probably a unique huge cis-acting element contributing to the regulation of the spatial and temporal specificity and efficiency of fibroin gene expression.

Neutral evolution of ten types of mariner transposons in the genomes of Caenorhabditis elegans and Caenorhabditis briggsae

Ten types of mariner transposable elements (232 individual sequences) are present in the completed genomic DNA sequence of Caenorhabditis elegans and the partial sequence of Caenorhabditis briggsae. We analyze these replicated instances of mariner evolution and find that elements of a type have evolved within their genomes under no selection on their transposase genes. Seven of the ten reconstructed ancestral mariners carry defective transposase genes. Selection has acted during the divergence of some ancestral elements. The neutrally-evolving mariners are used to analyze the pattern of molecular evolution in Caenorhabditis. There is a significant mutational bias against transversions and significant variation in rates of change across sites. Deletions accumulate at a rate of 0.034 events/bp per substitution/site, with an average size of 166 bp (173 gaps observed). Deletions appear to obliterate preexisting deletions over time, creating larger gaps. Insertions accumulate at a rate of 0.019 events/bp per substitution/site, with an average size of 151 bp (61 events). Although the rate of deletion is lower than most estimates in other species, the large size of deletions causes rapid elimination of neutral DNA: a mariner's "half-life" (the time by which half an element's sequence should have been deleted) is approximately 0.1 subsitutions/site. This high rate of DNA deletion may explain the compact nature of the nematode genome.

A comparative phylogenetic analysis of full-length mariner elements isolated from the Indian tasar silkmoth, Antheraea mylitta (Lepidoptera: saturniidae)

Mariner like elements (MLEs) are widely distributed type II transposons with an open reading frame (ORF) for transposase. We studied comparative phylogenetic evolution and inverted terminal repeat (ITR) conservation of MLEs from Indian saturniid silkmoth, Antheraea mylitta with other full length MLEs submitted in the database. Full length elements from A. mylitta were inactive with multiple mutations. Many conserved amino acid blocks were identified after aligning transposase sequences. Mariner signature sequence, DD(34)D was almost inva ri able although a few new class of elements had different signatures. A. mylitta MLEs (Anmmar) get phylogene ti cally classified under cecropia subfamily and cluster closely with the elements from other Bombycoidea superfamily members implying vertical transmission from a common ancestor. ITR analysis showed a conserved sequence of AGGT(2-8N)ATAAGT for forward repeat and AGGT(2-8N)ATGAAAT for reverse repeat. These results and additional work may help us to understand the dynamics of MLE distribution in A. mylitta and construction of appropriate vectors for mariner mediated transgenics.

Bmmar6, a second mori subfamily mariner transposon from the silkworm moth Bombyx mori

A second member of the divergent mori subfamily of mariner transposons, Bmmar6, is described from the silkworm moth Bombyx mori genome. A confident consensus sequence for Bmmar6 was obtained from a single genomic copy, 17 EST sequences, and the direct sequencing of a 'family' sequence from an amplification of all full-length genomic copies. Bmmar6 is most similar to Bmmar1 in the mori subfamily, which now also includes several fly and nematode transposons. These might be viewed as a discrete family of transposons within the IS630-Tc1-mariner superfamily with a distinctive D,D37D catalytic motif, and another small divergent D,D41D clade is recognized as their sister group of transposons.

Molecular evolutionary analyses of mariners and other transposable elements in fire ants (Hymenoptera: Formicidae)

Screens of a library of genomic DNA made during a recent study of the fire ant Solenopsis invicta revealed the presence of three distinct types of transposable elements (TEs). Two of the recovered sequences showed a high similarity to long-terminal repeat (LTR) retrotransposons, while the third showed a high homology to mariner elements. To investigate the distribution and relationships of mariners in related ants, we PCR-amplified these elements from additional Solenopsis species. Phylogenetic analyses showed that they form a single group within the mauritiana subfamily that is part of a larger clade derived from hymenopteran species. We also present partial sequence data for the two LTR-retrotransposons and describe their phylogenetic affinities.