Mobile elements and the genesis of microsatellites in dipterans

Mutation protocols share with sexual reproduction the physiological role of producing genetic variation within 'constraints that deconstrain'

Because the universe of possible DNA sequences is inconceivably vast, organisms have evolved mechanisms for exploring DNA sequence space while substantially reducing the hazard that would otherwise accrue to any process of random, accidental mutation. One such mechanism is meiotic recombination. Although sexual reproduction imposes a seemingly paradoxical 50% cost to fitness, sex evidently prevails because this cost is outweighed by the advantage of equipping offspring with genetic variation to accommodate environmental vicissitudes. The potential adaptive utility of additional mechanisms for producing genetic variation has long been obscured by a presumption that the vast majority of mutations are deleterious. Perhaps surprisingly, the probability for adaptive variation can be increased by several mechanisms that generate mutations abundantly. Such mechanisms, here called 'mutation protocols', implement implicit 'constraints that deconstrain'. Like meiotic recombination, they produce genetic variation in forms that minimize potential for harm while providing a reasonably high probability for benefit. One example is replication slippage of simple sequence repeats (SSRs); this process yields abundant, reversible mutations, typically with small quantitative effect on phenotype. This enables SSRs to function as adjustable 'tuning knobs'. There exists a clear pathway for SSRs to be shaped through indirect selection favouring their implicit tuning-knob protocol. Several other molecular mechanisms comprise probable components of additional mutation protocols. Biologists might plausibly regard such mechanisms of mutation not primarily as sources of deleterious genetic mistakes but also as potentially adaptive processes for 'exploring' DNA sequence space.

Enriched tandemly repeats in chromosomal fusion points of Rineloricaria latirostris (Boulenger, 1900) (Siluriformes: Loricariidae)

Cytogenetic data showed the enrichment of repetitive DNAs in chromosomal rearrangement points between closely related species in armored catfishes. Still, few studies integrated cytogenetic and genomic data aiming to identify their prone-to-break DNA sites. Here, we aimed to obtain the repetitive fraction in Rineloricaria latirostris to recognize the microsatellite and homopolymers flanking the regions previously described as chromosomal fusion points. The results indicated that repetitive DNAs in R. latirostris are predominantly DNA transposons, and considering the microsatellite and homopolymers, A/T-rich expansions were the most abundant. The in situ localization demonstrated the A/T-rich repetitive sequences are scattered on the chromosomes, while A/G-rich microsatellites units were accumulated in some regions. The DNA transposon hAT, the 5S rDNA, and 45S rDNA (previously identified in Robertsonian fusion points in R. latirostris) are clusterized with some microsatellites, especially (CA)n, (GA)n, and poly-A, which also are enriched in regions of chromosomal fusions. Our findings demonstrated that repetitive sequences such as rDNAs, hAT transposon, and microsatellite units flank probable evolutionary breakpoint regions in R. latirostris. However, due to the sequence unit homologies in different chromosomal sites, these repeat DNAs only may have facilitated chromosome fusion events in R. latirostris rather than work as a double-strand breakpoint site.

Transposable Elements: Major Players in Shaping Genomic and Evolutionary Patterns

Transposable elements (TEs) are ubiquitous genetic elements, able to jump from one location of the genome to another, in all organisms. For this reason, on the one hand, TEs can induce deleterious mutations, causing dysfunction, disease and even lethality in individuals. On the other hand, TEs can increase genetic variability, making populations better equipped to respond adaptively to environmental change. To counteract the deleterious effects of TEs, organisms have evolved strategies to avoid their activation. However, their mobilization does occur. Usually, TEs are maintained silent through several mechanisms, but they can be reactivated during certain developmental windows. Moreover, TEs can become de-repressed because of drastic changes in the external environment. Here, we describe the ‘double life’ of TEs, being both ‘parasites’ and ‘symbionts’ of the genome. We also argue that the transposition of TEs contributes to two important evolutionary processes: the temporal dynamic of evolution and the induction of genetic variability. Finally, we discuss how the interplay between two TE-dependent phenomena, insertional mutagenesis and epigenetic plasticity, plays a role in the process of evolution.

Eusociality in snapping shrimps is associated with larger genomes and an accumulation of transposable elements

Despite progress uncovering the genomic underpinnings of sociality, much less is known about how social living affects the genome. In different insect lineages, for example, eusocial species show both positive and negative associations between genome size and structure, highlighting the dynamic nature of the genome. Here, we explore the relationship between sociality and genome architecture in Synalpheus snapping shrimps that exhibit multiple origins of eusociality and extreme interspecific variation in genome size. Our goal is to determine whether eusociality leads to an accumulation of repetitive elements and an increase in genome size, presumably due to reduced effective population sizes resulting from a reproductive division of labor, or whether an initial accumulation of repetitive elements leads to larger genomes and independently promotes the evolution of eusociality through adaptive evolution. Using phylogenetically informed analyses, we find that eusocial species have larger genomes with more transposable elements (TEs) and microsatellite repeats than noneusocial species. Interestingly, different TE subclasses contribute to the accumulation in different species. Phylogenetic path analysis testing alternative causal relationships between sociality and genome architecture is most consistent with the hypothesis that TEs modulate the relationship between sociality and genome architecture. Although eusociality appears to influence TE accumulation, ancestral state reconstruction suggests moderate TE abundances in ancestral species could have fueled the initial transitions to eusociality. Ultimately, we highlight a complex and dynamic relationship between genome and social evolution, demonstrating that sociality can influence the evolution of the genome, likely through changes in demography related to patterns of reproductive skew.

Distribution of Merlin in eukaryotes and first report of DNA transposons in kinetoplastid protists

DNA transposons are defined as repeated DNA sequences that can move within the host genome through the action of transposases. The transposon superfamily Merlin was originally found mainly in animal genomes. Here, we describe a global distribution of the Merlin in animals, fungi, plants and protists, reporting for the first time their presence in Rhodophyceae, Metamonada, Discoba and Alveolata. We identified a great variety of potentially active Merlin families, some containing highly imperfect terminal inverted repeats and internal tandem repeats. Merlin-related sequences with no evidence of mobilization capacity were also observed and may be products of domestication. The evolutionary trees support that Merlin is likely an ancient superfamily, with early events of diversification and secondary losses, although repeated re-invasions probably occurred in some groups, which would explain its diversity and discontinuous distribution. We cannot rule out the possibility that the Merlin superfamily is the product of multiple horizontal transfers of related prokaryotic insertion sequences. Moreover, this is the first account of a DNA transposon in kinetoplastid flagellates, with conserved Merlin transposase identified in Bodo saltans and Perkinsela sp., whereas it is absent in trypanosomatids. Based on the level of conservation of the transposase and overlaps of putative open reading frames with Merlin, we propose that in protists it may serve as a raw material for gene emergence.

Population-Based Cytogenetic Banding Analysis and Phylogenetic Relationships of the Neotropical Fungus-Farming Ant Trachymyrmex holmgreni Wheeler, 1925

Trachymyrmex is one of the most species-rich genera within fungus-farming ants and presents intraspecific cytogenetic polymorphisms as well as possible cryptic species. This ant genus is currently paraphyletic. Therefore, to unravel systematic and taxonomic misunderstandings, it is necessary to incorporate new information. We aimed to cytogenetically and genetically examine Trachymyrmex holmgreni populations from southern and northern Brazil to identify intraspecific chromosomal variations that support incipient speciation and reveal the species' position in a molecular phylogeny. Our cytogenetic approach did not show population variation in the mapping of both 18S rDNA and the TTAGG(6) motif, presenting instead a pattern characteristic of correlated species. However, the clustered pattern of the microsatellite GA(15) showed significant differences among populations: a well-defined block in each homologue, distinctly irregular signs between homologues, and blocks in 2 pairs of homologues. Our phylogenetic reconstruction yielded unexpected results, grouping representatives of 3 former morphological groups into 1 clade, namely T. urichii, T. papulatus, and T. holmgreni. Previously, it was suggested that northern and southern populations of T. holmgreni may be undergoing incipient speciation, but we can only indicate that the southernmost population differs prominently from the others in its distribution pattern of the microsatellite GA(15). Our study also supports the uniformity of karyotypes and repetitive DNA from both telomeric sequences and ribosomal DNA in Trachymyrmex studied here. In addition, we clarify some phylogenetic uncertainties within the genus and suggest further relevant systematic changes. Finally, additional studies utilizing other probes and additional populations may allow the detection of hidden genetic variation.

Comparative Genomics Analysis Reveals High Levels of Differential Retrotransposition among Primates from the Hominidae and the Cercopithecidae Families

Mobile elements (MEs), making ∼50% of primate genomes, are known to be responsible for generating inter- and intra-species genomic variations and play important roles in genome evolution and gene function. Using a bioinformatics comparative genomics approach, we performed analyses of species-specific MEs (SS-MEs) in eight primate genomes from the families of Hominidae and Cercopithecidae, focusing on retrotransposons. We identified a total of 230,855 SS-MEs, with which we performed normalization based on evolutionary distances, and we also analyzed the most recent SS-MEs in these genomes. Comparative analysis of SS-MEs reveals striking differences in ME transposition among these primate genomes. Interesting highlights of our results include: 1) the baboon genome has the highest number of SS-MEs with a strong bias for SINEs, while the crab-eating macaque genome has a sustained extremely low transposition for all ME classes, suggesting the existence of a genome-wide mechanism suppressing ME transposition; 2) while SS-SINEs represent the dominant class in general, the orangutan genome stands out by having SS-LINEs as the dominant class; 3) the human genome stands out among the eight genomes by having the largest number of recent highly active ME subfamilies, suggesting a greater impact of ME transposition on its recent evolution; and 4) at least 33% of the SS-MEs locate to genic regions, including protein coding regions, presenting significant potentials for impacting gene function. Our study, as the first of its kind, demonstrates that mobile elements evolve quite differently among these primates, suggesting differential ME transposition as an important mechanism in primate evolution.

Role of microsatellites in genetic analysis of Bombyx mori silkworm: a review

In the genome of Bombyx mori Linnaeus (1758), the microsatellites, or simple sequence repeats (SSR), feature among their particular characteristics a high adenine and thymine (A/T) content, low number of repeats, low frequency, and a grouping in "families" with similar flanking regions. Such characteristics may be the result of a complex interaction between factors that limit the size and dispersion of SSR loci—such as their high association with transposons—and mean that microsatellites within this taxon suitable as molecular markers are relatively rare. The determination of genetic profiles in populations and cell lines has not been affected owing to the high level of polymorphism, nor has the analysis of diversity, structure and genetic relationships. However, the scarcity of suitable microsatellites has restricted their application in genetic mapping, limiting them to preliminary identification of gene location of genes or quantitative trait loci (QTLs) related to thermotolerance, resistance to viruses, pigmentation patterns, body development and the weight of the cocoon, the cortex, the pupa and the filament. The review confirms that, as markers, microsatellites are versatile and perform well. They could thus be useful both to advance research in emerging countries with few resources seeking to promote sericulture in their territories, and to advance in the genetic and molecular knowledge of characteristics of productive and biological interest, given the latest technological developments in terms of the sequencing, identification, isolation and genotyping of SSR loci.

High-throughput sequencing and graph-based cluster analysis facilitate microsatellite development from a highly complex genome

Despite recent advances in high-throughput sequencing, difficulties are often encountered when developing microsatellites for species with large and complex genomes. This probably reflects the close association in many species of microsatellites with cryptic repetitive elements. We therefore developed a novel approach for isolating polymorphic microsatellites from the club-legged grasshopper (Gomphocerus sibiricus), an emerging quantitative genetic and behavioral model system. Whole genome shotgun Illumina MiSeq sequencing was used to generate over three million 300 bp paired-end reads, of which 67.75% were grouped into 40,548 clusters within RepeatExplorer. Annotations of the top 468 clusters, which represent 60.5% of the reads, revealed homology to satellite DNA and a variety of transposable elements. Evaluating 96 primer pairs in eight wild-caught individuals, we found that primers mined from singleton reads were six times more likely to amplify a single polymorphic microsatellite locus than primers mined from clusters. Our study provides experimental evidence in support of the notion that microsatellites associated with repetitive elements are less likely to successfully amplify. It also reveals how advances in high-throughput sequencing and graph-based repetitive DNA analysis can be leveraged to isolate polymorphic microsatellites from complex genomes.

Helitrons, the Eukaryotic Rolling-circle Transposable Elements

Helitrons, the eukaryotic rolling-circle transposable elements, are widespread but most prevalent among plant and animal genomes. Recent studies have identified three additional coding and structural variants of Helitrons called Helentrons, Proto-Helentron, and Helitron2. Helitrons and Helentrons make up a substantial fraction of many genomes where nonautonomous elements frequently outnumber the putative autonomous partner. This includes the previously ambiguously classified DINE-1-like repeats, which are highly abundant in Drosophila and many other animal genomes. The purpose of this review is to summarize what we have learned about Helitrons in the decade since their discovery. First, we describe the history of autonomous Helitrons, and their variants. Second, we explain the common coding features and difference in structure of canonical Helitrons versus the endonuclease-encoding Helentrons. Third, we review how Helitrons and Helentrons are classified and discuss why the system used for other transposable element families is not applicable. We also touch upon how genome-wide identification of candidate Helitrons is carried out and how to validate candidate Helitrons. We then shift our focus to a model of transposition and the report of an excision event. We discuss the different proposed models for the mechanism of gene capture. Finally, we will talk about where Helitrons are found, including discussions of vertical versus horizontal transfer, the propensity of Helitrons and Helentrons to capture and shuffle genes and how they impact the genome. We will end the review with a summary of open questions concerning the biology of this intriguing group of transposable elements.

Microsatellites in Pursuit of Microbial Genome Evolution

Microsatellites or short sequence repeats are widespread genetic markers which are hypermutable 1-6 bp long short nucleotide motifs. Significantly, their applications in genetics are extensive due to their ceaseless mutational degree, widespread length variations and hypermutability skills. These features make them useful in determining the driving forces of evolution by using powerful molecular techniques. Consequently, revealing important questions, for example, what is the significance of these abundant sequences in DNA, what are their roles in genomic evolution? The answers of these important questions are hidden in the ways these short motifs contributed in altering the microbial genomes since the origin of life. Even though their size ranges from 1 -to- 6 bases, these repeats are becoming one of the most popular genetic probes in determining their associations and phylogenetic relationships in closely related genomes. Currently, they have been widely used in molecular genetics, biotechnology and evolutionary biology. However, due to limited knowledge; there is a significant gap in research and lack of information concerning hypermutational mechanisms. These mechanisms play a key role in microsatellite loci point mutations and phase variations. This review will extend the understandings of impacts and contributions of microsatellite in genomic evolution and their universal applications in microbiology.

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.

Homopolymer tract organization in the human malarial parasite Plasmodium falciparum and related Apicomplexan parasites

BACKGROUND

Homopolymeric tracts, particularly poly dA.dT, are enriched within the intergenic sequences of eukaryotic genomes where they appear to act as intrinsic regulators of nucleosome positioning. A previous study of the incomplete genome of the human malarial parasite Plasmodium falciparum reports a higher than expected enrichment of poly dA.dT tracts, far above that anticipated even in this highly AT rich genome. Here we report an analysis of the relative frequency, length and spatial arrangement of homopolymer tracts for the complete P. falciparum genome, extending this analysis to twelve additional genomes of Apicomplexan parasites important to human and animal health. In addition, using nucleosome-positioning data available for P. falciparum, we explore the correlation of poly dA.dT tracts with nucleosome-positioning data over key expression landmarks within intergenic regions.

RESULTS

We describe three apparent lineage-specific patterns of homopolymeric tract organization within the intergenic regions of these Apicomplexan parasites. Moreover, a striking pattern of enrichment of overly long poly dA.dT tracts in the intergenic regions of Plasmodium spp. uniquely extends into protein coding sequences. There is a conserved spatial arrangement of poly dA.dT immediately flanking open reading frames and over predicted core promoter sites. These key landmarks are all relatively depleted in nucleosomes in P. falciparum, as would be expected for poly dA.dT acting as nucleosome exclusion sequences.

CONCLUSIONS

Previous comparative studies of homopolymer tract organization emphasize evolutionary diversity; this is the first report of such an analysis within a single phylum. Our data provide insights into the evolution of homopolymeric tracts and the selective pressures at play in their maintenance and expansion.

DINE-1, the highest copy number repeats in Drosophila melanogaster are non-autonomous endonuclease-encoding rolling-circle transposable elements (Helentrons)

Background

The Drosophila INterspersed Elements-1 (DINE-1/INE1) transposable elements (TEs) are the most abundant component of the Drosophila melanogaster genome and have been associated with functional gene duplications. DINE-1 TEs do not encode any proteins (non-autonomous) thus are moved by autonomous partners. The identity of the autonomous partners has been a mystery. They have been allied to Helitrons (rolling-circle transposons), MITEs (DNA transposons), and non-LTR retrotransposons by different authors.

Results

We report multiple lines of bioinformatic evidence that illustrate the relationship of DINE-1 like TEs to endonuclease-encoding rolling-circle TEs (Helentrons). The structural features of Helentrons are described, which resemble the organization of the non-autonomous partners, but differ significantly from canonical Helitrons. In addition to the presence of an endonuclease domain fused to the Rep/Helicase protein, Helentrons have distinct structural features. Evidence is presented that illustrates that Helentrons are widely distributed in invertebrate, fish, and fungal genomes. We describe an intermediate family from the Phytophthora infestans genome that phylogenetically groups with Helentrons but that displays Helitron structure. In addition, evidence is presented that Helentrons can capture gene fragments in a pattern reminiscent of canonical Helitrons.

Conclusions

We illustrate the relationship of DINE-1 and related TE families to autonomous partners, the Helentrons. These findings will allow their proper classification and enable a more accurate understanding of the contribution of rolling-circle transposition to the birth of new genes, gene networks, and genome composition.

Microsatellite organization in the grasshopper Abracris flavolineata (Orthoptera: Acrididae) revealed by FISH mapping: remarkable spreading in the A and B chromosomes

With the aim of acquiring deeper knowledge about repetitive DNAs chromosomal organization in grasshoppers, we used fluorescent in situ hybridization (FISH) to map the distribution of 16 microsatellite repeats, including mono-, di-, tri- and tetra-nucleotides, in the chromosomes of the species Abracris flavolineata (Acrididae), which harbors B chromosome. FISH revealed two main patterns: (i) exclusively scattered signals, and (ii) scattered and specific signals, forming evident blocks. The enrichment was observed in both euchromatic and heterochromatic areas and only the motif (C)30 was absent in heterochromatin. The A and B chromosomes were enriched with all the elements that were mapped, being observed in the B chromosome more distinctive blocks for (GA)15 and (GAG)10. For A complement distinctive blocks were noticed for (A)30, (CA)15, (CG)15, (GA)15, (CAC)10, (CAA)10, (CGG)10, (GAA)10, (GAC)10 and (GATA)8. These results revealed an intense spreading of microsatellites in the A. flavolineata genome that was independent of the A+T or G+C enrichment in the repeats. The data indicate that the microsatellites compose the B chromosome and could be involved in the evolution of this element in this species, although no specific relationship with any A chromosome was observed to discuss about its origin. The systematic analysis presented here contributes to the knowledge of repetitive DNA chromosomal organization among grasshoppers including the B chromosomes.

Tetris is a foldback transposon that provided the building blocks for an emerging satellite DNA of Drosophila virilis

Transposable elements (TEs) and satellite DNAs (satDNAs) are abundant components of most eukaryotic genomes studied so far and their impact on evolution has been the focus of several studies. A number of studies linked TEs with satDNAs, but the nature of their evolutionary relationships remains unclear. During in silico analyses of the Drosophila virilis assembled genome, we found a novel DNA transposon we named Tetris based on its modular structure and diversity of rearranged forms. We aimed to characterize Tetris and investigate its role in generating satDNAs. Data mining and sequence analysis showed that Tetris is apparently nonautonomous, with a structure similar to foldback elements, and present in D. virilis and D. americana. Herein, we show that Tetris shares the final portions of its terminal inverted repeats (TIRs) with DAIBAM, a previously described miniature inverted transposable element implicated in the generation of chromosome inversions. Both elements are likely to be mobilized by the same autonomous TE. Tetris TIRs contain approximately 220-bp internal tandem repeats that we have named TIR-220. We also found TIR-220 repeats making up longer (kb-size) satDNA-like arrays. Using bioinformatic, phylogenetic and cytogenomic tools, we demonstrated that Tetris has contributed to shaping the genomes of D. virilis and D. americana, providing internal tandem repeats that served as building blocks for the amplification of satDNA arrays. The β-heterochromatic genomic environment seemed to have favored such amplification. Our results imply for the first time a role for foldback elements in generating satDNAs.

Genome-wide DNA polymorphisms in two cultivars of mei (Prunus mume sieb. et zucc.)

Background

Mei (Prunus mume Sieb. et Zucc.) is a famous ornamental plant and fruit crop grown in East Asian countries. Limited genetic resources, especially molecular markers, have hindered the progress of mei breeding projects. Here, we performed low-depth whole-genome sequencing of Prunus mume ‘Fenban’ and Prunus mume ‘Kouzi Yudie’ to identify high-quality polymorphic markers between the two cultivars on a large scale.

Results

A total of 1464.1 Mb and 1422.1 Mb of ‘Fenban’ and ‘Kouzi Yudie’ sequencing data were uniquely mapped to the mei reference genome with about 6-fold coverage, respectively. We detected a large number of putative polymorphic markers from the 196.9 Mb of sequencing data shared by the two cultivars, which together contained 200,627 SNPs, 4,900 InDels, and 7,063 SSRs. Among these markers, 38,773 SNPs, 174 InDels, and 418 SSRs were distributed in the 22.4 Mb CDS region, and 63.0% of these marker-containing CDS sequences were assigned to GO terms. Subsequently, 670 selected SNPs were validated using an Agilent’s SureSelect solution phase hybridization assay. A subset of 599 SNPs was used to assess the genetic similarity of a panel of mei germplasm samples and a plum (P. salicina) cultivar, producing a set of informative diversity data. We also analyzed the frequency and distribution of detected InDels and SSRs in mei genome and validated their usefulness as DNA markers. These markers were successfully amplified in the cultivars and in their segregating progeny.

Conclusions

A large set of high-quality polymorphic SNPs, InDels, and SSRs were identified in parallel between ‘Fenban’ and ‘Kouzi Yudie’ using low-depth whole-genome sequencing. The study presents extensive data on these polymorphic markers, which can be useful for constructing high-resolution genetic maps, performing genome-wide association studies, and designing genomic selection strategies in mei.

Transposable elements and their potential role in complex lung disorder

Transposable elements (TEs) are a class of mobile genetic elements (MGEs) that were long regarded as junk DNA, which make up approximately 45% of the genome. Although most of these elements are rendered inactive by mutations and other gene silencing mechanisms, TEs such as long interspersed nuclear elements (LINEs) are still active and translocate within the genome. During transposition, they may create lesions in the genome, thereby acting as epigenetic modifiers. Approximately 65 disease-causing LINE insertion events have been reported thus far; however, any possible role of TEs in complex disorders is not well established. Chronic obstructive pulmonary disease (COPD) is one such complex disease that is primarily caused by cigarette smoking. Although the exact molecular mechanism underlying COPD remains unclear, oxidative stress is thought to be the main factor in the pathogenesis of COPD. In this review, we explore the potential role of oxidative stress in epigenetic activation of TEs such as LINEs and the subsequent cascade of molecular damage. Recent advancements in sequencing and computation have eased the identification of mobile elements. Therefore, a comparative study on the activity of these elements and markers for genome instability would give more insight on the relationship between MGEs and complex disorder such as COPD.

Non-LTR retrotransposons and microsatellites: Partners in genomic variation

The human genome is laden with both non-LTR (long-terminal repeat) retrotransposons and microsatellite repeats. Both types of sequences are able to, either actively or passively, mutagenize the genomes of human individuals and are therefore poised to dynamically alter the human genomic landscape across generations. Non-LTR retrotransposons, such as L1 and Alu, are a major source of new microsatellites, which are born both concurrently and subsequently to L1 and Alu integration into the genome. Likewise, the mutation dynamics of microsatellite repeats have a direct impact on the fitness of their non-LTR retrotransposon parent owing to microsatellite expansion and contraction. This review explores the interactions and dynamics between non-LTR retrotransposons and microsatellites in the context of genomic variation and evolution.

Revisiting an important component of plant genomes: microsatellites

Microsatellites are some of the most highly variable repetitive DNA tracts in genomes. Few studies focus on whether the characteristic instability of microsatellites is linked to phenotypic effects in plants. We summarise recent data to investigate how microsatellite variations affect gene expression and hence phenotype. We discuss how the basic characteristics of microsatellites may contribute to phenotypic effects. In summary, microsatellites in plants are universal and highly mutable, they coexist and coevolve with transposable elements, and are under selective pressure. The number of motif nucleotides, the type of motif and transposon activity all contribute to the nonrandom generation and decay of microsatellites, and to conservation and distribution biases. Although microsatellites are generated by accident, they mature through responses to environmental change before final decay. This process is mediated by organism adjustment mechanisms, which maintain a balance between birth versus death and growth versus decay in microsatellites. Close relationships also exist between the physical structure, variation and functionality of microsatellites: in most plant species, sequences containing microsatellites are associated with catalytic activity and binding functions, are expressed in the membrane and organelles, and participate in the developmental and metabolic processes. Microsatellites contribute to genome structure and functional plasticity, and may be considered to promote species evolution in plants in response to environmental changes. In conclusion, the generation, loss, functionality and evolution of microsatellites can be related to plant gene expression and functional alterations. The effect of microsatellites on phenotypic variation may be as significant in plants as it is in animals.

Genome-wide characterization and linkage mapping of simple sequence repeats in mei (Prunus mume Sieb. et Zucc.)

Because of its popularity as an ornamental plant in East Asia, mei (Prunus mume Sieb. et Zucc.) has received increasing attention in genetic and genomic research with the recent shotgun sequencing of its genome. Here, we performed the genome-wide characterization of simple sequence repeats (SSRs) in the mei genome and detected a total of 188,149 SSRs occurring at a frequency of 794 SSR/Mb. Mononucleotide repeats were the most common type of SSR in genomic regions, followed by di- and tetranucleotide repeats. Most of the SSRs in coding sequences (CDS) were composed of tri- or hexanucleotide repeat motifs, but mononucleotide repeats were always the most common in intergenic regions. Genome-wide comparison of SSR patterns among the mei, strawberry (Fragaria vesca), and apple (Malus×domestica) genomes showed mei to have the highest density of SSRs, slightly higher than that of strawberry (608 SSR/Mb) and almost twice as high as that of apple (398 SSR/Mb). Mononucleotide repeats were the dominant SSR motifs in the three Rosaceae species. Using 144 SSR markers, we constructed a 670 cM-long linkage map of mei delimited into eight linkage groups (LGs), with an average marker distance of 5 cM. Seventy one scaffolds covering about 27.9% of the assembled mei genome were anchored to the genetic map, depending on which the macro-colinearity between the mei genome and Prunus T×E reference map was identified. The framework map of mei constructed provides a first step into subsequent high-resolution genetic mapping and marker-assisted selection for this ornamental species.

Expansion of microsatellites on evolutionary young Y chromosome

Sex chromosomes are an ideal system to study processes connected with suppressed recombination. We found evidence of microsatellite expansion, on the relatively young Y chromosome of the dioecious plant sorrel (Rumex acetosa, XY1Y2 system), but no such expansion on the more ancient Y chromosomes of liverwort (Marchantia polymorpha) and human. The most expanding motifs were AC and AAC, which also showed periodicity of array length, indicating the importance of beginnings and ends of arrays. Our data indicate that abundance of microsatellites in genomes depends on the inherent expansion potential of specific motifs, which could be related to their stability and ability to adopt unusual DNA conformations. We also found that the abundance of microsatellites is higher in the neighborhood of transposable elements (TEs) suggesting that microsatellites are probably targets for TE insertions. This evidence suggests that microsatellite expansion is an early event shaping the Y chromosome where this process is not opposed by recombination, while accumulation of TEs and chromosome shrinkage predominate later.

Tandem repeat-containing MITEs in the clam Donax trunculus

Two distinct classes of repetitive sequences, interspersed mobile elements and satellite DNAs, shape eukaryotic genomes and drive their evolution. Short arrays of tandem repeats can also be present within nonautonomous miniature inverted repeat transposable elements (MITEs). In the clam Donax trunculus, we characterized a composite, high copy number MITE, named DTC84. It is composed of a central region built of up to five core repeats linked to a microsatellite segment at one array end and flanked by sequences holding short inverted repeats. The modular composition and the conserved putative target site duplication sequence AA at the element termini are equivalent to the composition of several elements found in the cupped oyster Crassostrea virginica and in some insects. A unique feature of D. trunculus element is ordered array of core repeat variants, distinctive by diagnostic changes. Position of variants in the array is fixed, regardless of alterations in the core repeat copy number. Each repeat harbors a palindrome near the junction with the following unit, being a potential hotspot responsible for array length variations. As a consequence, variations in number of tandem repeats and variations in flanking sequences make every sequenced element unique. Core repeats may be thus considered as individual units within the MITE, with flanking sequences representing a "cassette" for internal repeats. Our results demonstrate that onset and spread of tandem repeats can be more intimately linked to processes of transposition than previously thought and suggest that genomes are shaped by interplays within a complex network of repetitive sequences.

Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species

Microsatellites are ubiquitous in Eukaryotic genomes. A more complete understanding of their origin and spread can be gained from a comparison of their distribution within a phylogenetic context. Although information for model species is accumulating rapidly, it is insufficient due to a lack of species depth, thus intragroup variation is necessarily ignored. As such, apparent differences between groups may be overinflated and generalizations cannot be inferred until an analysis of the variation that exists within groups has been conducted. In this study, we examined microsatellite coverage and motif patterns from 454 shotgun sequences of 154 Eukaryote species from eight distantly related phyla (Cnidaria, Arthropoda, Onychophora, Bryozoa, Mollusca, Echinodermata, Chordata and Streptophyta) to test if a consistent phylogenetic pattern emerges from the microsatellite composition of these species. It is clear from our results that data from model species provide incomplete information regarding the existing microsatellite variability within the Eukaryotes. A very strong heterogeneity of microsatellite composition was found within most phyla, classes and even orders. Autocorrelation analyses indicated that while microsatellite contents of species within clades more recent than 200 Mya tend to be similar, the autocorrelation breaks down and becomes negative or non-significant with increasing divergence time. Therefore, the age of the taxon seems to be a primary factor in degrading the phylogenetic pattern present among related groups. The most recent classes or orders of Chordates still retain the pattern of their common ancestor. However, within older groups, such as classes of Arthropods, the phylogenetic pattern has been scrambled by the long independent evolution of the lineages.

Long microsatellites and unusually high levels of genetic diversity in the Orthoptera

Much remains to be learned about the mutational processes governing the evolution of microsatellite repeat regions and the associated levels of genetic diversity observed at microsatellite markers across populations or species. An extensive survey of microsatellite variation in 210 insect species from six major orders revealed that within Orthopterans, which are characterized by giant genomes, levels of genetic diversity were ~20% higher and microsatellite repeat arrays were longer than in any other group. Because of the mutation dependence on repeat length, this result suggests a higher microsatellite loci mutation rate in the Orthoptera. We deem it plausible that differences among insect orders, either in mismatch repair systems or in abundance of transposable element-derived microsatellites, can shape the size distribution of both genomes and microsatellite repeat regions. Our findings emphasise that observed levels of genetic diversity can greatly vary across species (orders at least) because of molecular differences in the mechanisms that determine microsatellite size, and are therefore critical to conservation and population genetics studies, where microsatellite repeat variability is primarily interpreted in terms of population demography and history.

A matter of life or death: how microsatellites emerge in and vanish from the human genome

Microsatellites--tandem repeats of short DNA motifs--are abundant in the human genome and have high mutation rates. While microsatellite instability is implicated in numerous genetic diseases, the molecular processes involved in their emergence and disappearance are still not well understood. Microsatellites are hypothesized to follow a life cycle, wherein they are born and expand into adulthood, until their degradation and death. Here we identified microsatellite births/deaths in human, chimpanzee, and orangutan genomes, using macaque and marmoset as outgroups. We inferred mutations causing births/deaths based on parsimony, and investigated local genomic environments affecting them. We also studied birth/death patterns within transposable elements (Alus and L1s), coding regions, and disease-associated loci. We observed that substitutions were the predominant cause for births of short microsatellites, while insertions and deletions were important for births of longer microsatellites. Substitutions were the cause for deaths of microsatellites of virtually all lengths. AT-rich L1 sequences exhibited elevated frequency of births/deaths over their entire length, while GC-rich Alus only in their 3' poly(A) tails and middle A-stretches, with differences depending on transposable element integration timing. Births/deaths were strongly selected against in coding regions. Births/deaths occurred in genomic regions with high substitution rates, protomicrosatellite content, and L1 density, but low GC content and Alu density. The majority of the 17 disease-associated microsatellites examined are evolutionarily ancient (were acquired by the common ancestor of simians). Our genome-wide investigation of microsatellite life cycle has fundamental applications for predicting the susceptibility of birth/death of microsatellites, including many disease-causing loci.

Rise of the machines--recommendations for ecologists when using next generation sequencing for microsatellite development

Next generation sequencing is revolutionizing molecular ecology by simplifying the development of molecular genetic markers, including microsatellites. Here, we summarize the results of the large-scale development of microsatellites for 54 nonmodel species using next generation sequencing and show that there are clear differences amongst plants, invertebrates and vertebrates for the number and proportion of motif types recovered that are able to be utilized as markers. We highlight that the heterogeneity within each group is very large. Despite this variation, we provide an indication of what number of sequences and consequent proportion of a 454 run are required for the development of 40 designable, unique microsatellite loci for a typical molecular ecological study. Finally, to address the challenges of choosing loci from the vast array of microsatellite loci typically available from partial genome runs (average for this study, 2341 loci), we provide a microsatellite development flowchart as a procedural guide for application once the results of a partial genome run are obtained.

A novel class of miniature inverted repeat transposable elements (MITEs) that contain hitchhiking (GTCY)(n) microsatellites

The movement of miniature inverted repeat transposable elements (MITEs) modifies genome structure and function. We describe the microsatellite-associated interspersed nuclear element 2 (MINE-2), that integrates at consensus WTTTT target sites, creates dinucleotide TT target site duplications (TSDs), and forms predicted MITE-like secondary structures; a 5' subterminal inverted repeat (SIR; AGGGTTCCGTAG) that is partially complementary to a 5' inverted repeat (IR; ACGAAGCCCT) and 3'-SIRs (TTACGGAACCCT). A (GTCY)(n) microsatellite is hitchhiking downstream of conserved 5'MINE-2 secondary structures, causing flanking sequence similarity amongst mobile microsatellite loci. Transfection of insect cell lines indicates that MITE-like secondary structures are sufficient to mediate genome integration, and provides insight into the transposition mechanism used by MINE-2s.

Mining non-model genomic libraries for microsatellites: BAC versus EST libraries and the generation of allelic richness

BACKGROUND

Simple sequence repeats (SSRs) are tandemly repeated sequence motifs common in genomic nucleotide sequence that often harbor significant variation in repeat number. Frequently used as molecular markers, SSRs are increasingly identified via in silico approaches. Two common classes of genomic resources that can be mined are bacterial artificial chromosome (BAC) libraries and expressed sequence tag (EST) libraries.

RESULTS

288 SSR loci were screened in the rapidly radiating Hawaiian swordtail cricket genus Laupala. SSRs were more densely distributed and contained longer repeat structures in BAC library-derived sequence than in EST library-derived sequence, although neither repeat density nor length was exceptionally elevated despite the relatively large genome size of Laupala. A non-random distribution favoring AT-rich SSRs was observed. Allelic diversity of SSRs was positively correlated with repeat length and was generally higher in AT-rich repeat motifs.

CONCLUSION

The first large-scale survey of Orthopteran SSR allelic diversity is presented. Selection contributes more strongly to the size and density distributions of SSR loci derived from EST library sequence than from BAC library sequence, although all SSRs likely are subject to similar physical and structural constraints, such as slippage of DNA replication machinery, that may generate increased allelic diversity in AT-rich sequence motifs. Although in silico approaches work well for SSR locus identification in both EST and BAC libraries, BAC library sequence and AT-rich repeat motifs are generally superior SSR development resources for most applications.

Generation of microsatellite repeat families by RTE retrotransposons in lepidopteran genomes

Background

Developing lepidopteran microsatellite DNA markers can be problematical, as markers often exhibit multiple banding patterns and high frequencies of non-amplifying "null" alleles. Previous studies identified sequences flanking simple sequence repeat (SSR) units that are shared among many lepidopteran species and can be grouped into microsatellite-associated DNA families. These families are thought to be associated with unequal crossing-over during DNA recombination or with transposable elements (TEs).

Results

We identified full-length lepidopteran non-LTR retrotransposable elements of the RTE clade in Heliconius melpomene and Bombyx mori. These retroelements possess a single open reading frame encoding the Exonuclease/Endonuclease/Phosphatase and the Reverse Transcriptase/nLTR domains, a 5' UTR (untranslated region), and an extremely short 3' UTR that regularly consists of SSR units. Phylogenetic analysis supported previous suggestions of horizontal transfer among unrelated groups of organisms, but the diversity of lepidopteran RTE elements appears due to ancient divergence of ancestral elements rather than introgression by horizontal transfer. Similarity searches of lepidopteran genomic sequences in GenBank identified partial RTE elements, usually consisting of the 3' terminal region, in 29 species. Furthermore, we identified the C-terminal end of the Reverse Transcriptase/nLTR domain and the associated 3' UTR in over 190 microsatellite markers from 22 lepidopteran species, accounting for 10% of the lepidopteran microsatellites in GenBank. Occasional retrotransposition of autonomous elements, frequent retrotransposition of 3' partial elements, and DNA replication slippage during retrotransposition offers a mechanistic explanation for the association of SSRs with RTE elements in lepidopteran genomes.

Conclusions

Non-LTR retrotransposable elements of the RTE clade therefore join a diverse group of TEs as progenitors of SSR units in various organisms. When microsatellites are isolated using standard SSR enrichment protocols and primers designed at complementary repeated regions, amplification from multiple genomic sites can cause scoring difficulties that compromise their utility as markers. Screening against RTE elements in the isolation procedure provides one strategy for minimizing this problem.

Comparative genomic analysis reveals species-dependent complexities that explain difficulties with microsatellite marker development in molluscs

Reliable population DNA molecular markers are difficult to develop for molluscs, the reasons for which are largely unknown. Identical protocols for microsatellite marker development were implemented in three gastropods. Success rates were lower for Gibbula cineraria compared to Littorina littorea and L. saxatilis. Comparative genomic analysis of 47.2 kb of microsatellite containing sequences (MCS) revealed a high incidence of cryptic repetitive DNA in their flanking regions. The majority of these were novel, and could be grouped into DNA families based upon sequence similarities. Significant inter-specific variation in abundance of cryptic repetitive DNA and DNA families was observed. Repbase scans show that a large proportion of cryptic repetitive DNA was identified as transposable elements (TEs). We argue that a large number of TEs and their transpositional activity may be linked to differential rates of DNA multiplication and recombination. This is likely to be an important factor explaining inter-specific variation in genome stability and hence microsatellite marker development success rates. Gastropods also differed significantly in the type of TEs classes (autonomous vs non-autonomous) observed. We propose that dissimilar transpositional mechanisms differentiate the TE classes in terms of their propensity for transposition, fixation and/or silencing. Consequently, the phylogenetic conservation of non-autonomous TEs, such as CvA, suggests that dispersal of these elements may have behaved as microsatellite-inducing elements. Results seem to indicate that, compared to autonomous, non-autonomous TEs maybe have a more active role in genome rearrangement processes. The implications of the findings for genomic rearrangement, stability and marker development are discussed.

A helitron-like transposon superfamily from lepidoptera disrupts (GAAA)(n) microsatellites and is responsible for flanking sequence similarity within a microsatellite family

Transposable elements (TEs) are mobile DNA regions that alter host genome structure and gene expression. A novel 588 bp non-autonomous high copy number TE in the Ostrinia nubilalis genome has features in common with miniature inverted-repeat transposable elements (MITEs): high A + T content (62.3%), lack of internal protein coding sequence, and secondary structure consisting of subterminal inverted repeats (SIRs). The O. nubilalis TE has inserted at (GAAA)(n) microsatellite loci, and was named the microsatellite-associated interspersed nuclear element (MINE-1). Non-autonomous MINE-1 superfamily members also were identified downstream of (GAAA)(n) microsatellites within Bombyx mori and Pectinophora gossypiella genomes. Of 316 (GAAA)(n) microsatellites from the B. mori whole genome sequence, 201 (63.6%) have associated autonomous or non-autonomous MINE-1 elements. Autonomous B. mori MINE-1s a encode a helicase and endonuclease domain RepHel-like protein (BMHELp1) indicating their classification as Helitron-like transposons and were renamed Helitron1_BM. Transposition of MINE-1 members in Lepidoptera has resulted in the disruption of (GAAA)(n) microsatellite loci, has impacted the application of microsatellite-based genetic markers, and suggests genome sequence that flanks TT/AA dinucleotides may be required for target site recognition by RepHel endonuclease domains.

Evolutionary conserved lineage of Angela-family retrotransposons as a genome-wide microsatellite repeat dispersal agent

A detailed examination of 45 pea (Pisum sativum L.) simple sequence repeat (SSR) loci revealed that 21 of them included homologous sequences corresponding to the long terminal repeat (LTR) of a novel retrotransposon. Further investigation, including full-length sequencing, led to its classification as an RLC-Angela-family-FJ434420 element. The LTR contained a variable region ranging from a simple TC repeat (TC)(11) to more complex repeats of TC/CA, (TC)(12-30), (CA)(18-22) and was up to 146 bp in length. These elements are the most abundant Ty1/copia retrotransposons identified in the pea genome and also occur in other legume species. It is interesting that analysis of 63 LTR-derived sequences originating from 30 legume species showed high phylogenetic conservation in their sequence, including the position of the variable SSR region. This extraordinary conservancy led us to the proposition of a new lineage, named MARTIANS, within the Angela family. Similar LTR structures and partial sequence similarities were detected in more distant members of this Angela family, the barley BARE-1 and rice RIRE-1 elements. Comparison of the LTR sequences from pea and Medicago truncatula elements indicated that microsatellites arise through the expansion of a pre-existing repeat motif. Thus, the presence of an SSR region within the LTR seems to be a typical feature of this MARTIANS lineage, and the evidence gathered from a wide range of species suggests that these elements may facilitate amplification and genome-wide dispersal of associated SSR sequences. The implications of this finding regarding the evolution of SSRs within the genome, as well as their utilization as molecular markers, are discussed.

Isolation and characterization of microsatellite markers from the Mediterranean fruit fly, Ceratitis capitata: cross-species amplification in other Tephritidae species reveals a varying degree of transferability

The Mediterranean fruit fly, Ceratitis capitata, is a pest of major economic importance and has become a model for the development of SIT control programs for insect pests. Significant information has been accumulated on classical and population genetics of this species during the past 2 decades. However, the availability of molecular markers is limited. Here, we present the isolation and characterization of 159 microsatellite clones and the development of 108 polymorphic microsatellite markers for this insect pest. Mapping by in situ hybridization to polytene chromosomes of 21 microsatellite clones enriched the cytogenetic map that was previously constructed by our group. The enriched map provides a large number of STSs for future genome mapping projects. Cross-species amplification of these microsatellite loci in 12 Tephritidae species and sequence analysis of several amplification products indicated a varying degree of transferability and their possible usefulness as molecular and genetic markers in these species where genetic and molecular tools are limited.

Repetitive genome elements in a European corn borer, Ostrinia nubilalis, bacterial artificial chromosome library were indicated by bacterial artificial chromosome end sequencing and development of sequence tag site markers: implications for lepidopteran genomic research

The European corn borer, Ostrinia nubilalis, is a serious pest of food, fiber, and biofuel crops in Europe, North America, and Asia and a model system for insect olfaction and speciation. A bacterial artificial chromosome library constructed for O. nubilalis contains 36 864 clones with an estimated average insert size of >or=120 kb and genome coverage of 8.8-fold. Screening OnB1 clones comprising approximately 2.76 genome equivalents determined the physical position of 24 sequence tag site markers, including markers linked to ecologically important and Bacillus thuringiensis toxin resistance traits. OnB1 bacterial artificial chromosome end sequence reads (GenBank dbGSS accessions ET217010 to ET217273) showed homology to annotated genes or expressed sequence tags and identified repetitive genome elements, O. nubilalis miniature subterminal inverted repeat transposable elements (OnMITE01 and OnMITE02), and ezi-like long interspersed nuclear elements. Mobility of OnMITE01 was demonstrated by the presence or absence in O. nubilalis of introns at two different loci. A (GTCT)n tetranucleotide repeat at the 5' ends of OnMITE01 and OnMITE02 are evidence for transposon-mediated movement of lepidopteran microsatellite loci. The number of repetitive elements in lepidopteran genomes will affect genome assembly and marker development. Single-locus sequence tag site markers described here have downstream application for integration within linkage maps and comparative genomic studies.

Exon-primed intron-crossing (EPIC) PCR markers of Helicoverpa armigera (Lepidoptera: Noctuidae)

Applying microsatellite DNA markers in population genetic studies of the pest moth Helicoverpa armigera is subject to numerous technical problems, such as the high frequency of null alleles, occurrence of size homoplasy, presence of multiple copies of flanking sequence in the genome and the lack of PCR amplification robustness between populations. To overcome these difficulties, we developed exon-primed intron-crossing (EPIC) nuclear DNA markers for H. armigera based on ribosomal protein (Rp) and the Dopa Decarboxylase (DDC) genes and sequenced alleles showing length polymorphisms. Allele length polymorphisms were usually from random indels (insertions or deletions) within introns, although variation of short dinucleotide DNA repeat units was also detected. Mapping crosses demonstrated Mendelian inheritance patterns for these EPIC markers and the absence of both null alleles and allele 'dropouts'. Three examples of allele size homoplasies due to indels were detected in EPIC markers RpL3, RpS6 and DDC, while sequencing of multiple individuals across 11 randomly selected alleles did not detect indel size homoplasies. The robustness of the EPIC-PCR markers was demonstrated by PCR amplification in the related species, H. zea, H. assulta and H. punctigera.

Evolution of a complex minisatellite DNA sequence

Minisatellites are tandem repeats of short DNA units widely distributed in genomes. However, the information on their dynamics in a phylogenetic context is very limited. Here we have studied the organization of the MsH43 locus in several species of primates and from these data we have reconstructed the evolutionary history of this complex minisatellite. Overall, with the exception of gibbon, MsH43 has an organization that is asymmetric, since the distribution of repeats is distinct between the 5' and 3' halves, and heterogeneous since there are many different repeats, some of them characteristic of each species. Inspection of the MsH43 arrays showed the existence of many duplications and deletions, suggesting the implication of slippage processes in the generation of polymorphism. Concerning the evolutionary history of this minisatellite, we propose that the birth of MsH43 may be situated before the divergence of Old World Monkeys since we found the existence of some MsH43 repeat motifs in prosimians and New World Monkeys. The analysis of MsH43 in apes revealed the existence of an evolutionary breakpoint in the pathway that originated African great apes and humans. Remarkably, human MsH43 is more homologous to orang-utan than to the corresponding sequence in gorilla and chimpanzee. This finding does not comply with the evolutionary paradigm that continuous alterations occur during the course of genome evolution. To adjust our results to the standard phylogeny of primates, we propose the existence of a wandering allele that was maintained almost unaltered during the period that extends between orang-utan and humans.

Transcriptome Analysis of ESTs from a Chaetognath Reveals a Deep-Branching Clade of Retrovirus-Like Retrotransposons

Chaetognaths constitute a small marine phylum exhibiting several characteristic which are highly unusual in animal genomes, including two classes of both rRNA and protein ribosomal genes. As in this phylum presence of retrovirus-like elements has never been documented, analysis of a published expressed sequence tag (EST) collection of the chaetognath Spadella cephaloptera has been made. Twelve sequences representing transcript sections of reverse transcriptase domain of active retrotransposons were isolated from~11,000 ESTs. Five of them are originated from Gypsy retrovirus-like elements, whereas the other are transcripts from a Bel-Pao LTR-retrotransposon, a Penelope-like element and LINE retrotransposons. Moreover, a part of a putative integrase has also been found. Phylogenetic analyses suggest a deep-branching clade of the retrovirus-like elements, which is in agreement with the probably Cambrian origin of the phylum. Moreover, retrotransposons have not been found in telomeric-like transcripts which are probably constituted by both vertebrate and arthropod canonical repeats.

Abundant and species-specific DINE-1 transposable elements in 12 Drosophila genomes

Evidence is presented that DINE-1 is a highly abundant miniature inverted-repeat transposable element (MITE) family present in all 12 Drosophila species with whole-genome sequence available.

Background

Miniature inverted-repeat transposable elements (MITEs) are non-autonomous DNA-mediated transposable elements (TEs) derived from autonomous TEs. Unlike in many plants or animals, MITEs and other types of DNA-mediated TEs were previously thought to be either rare or absent in Drosophila. Most other TE families in Drosophila exist at low or intermediate copy number (around < 100 per genome).

Results

We present evidence here that the dispersed repeat Drosophila interspersed element 1 (DINE-1; also named INE-1 and DNAREP1) is a highly abundant DNA-mediated TE containing inverted repeats found in all 12 sequenced Drosophila genomes. All DINE-1s share a similar sequence structure, but are more homogeneous within species than they are among species. The inferred phylogenetic relationship of the DINE-1 consensus sequence from each species is generally consistent with the known species phylogeny, suggesting vertical transmission as the major mechanism for DINE-1 propagation. Exceptions observed in D. willistoni and D. ananassae could be due to either horizontal transfer or reactivation of ancestral copies. Our analysis of pairwise percentage identity of DINE-1 copies within species suggests that the transpositional activity of DINE-1 is extremely dynamic, with some lineages showing evidence for recent transpositional bursts and other lineages appearing to have silenced their DINE-1s for long periods of time. We also find that all species have many DINE-1 insertions in introns and adjacent to protein-coding genes. Finally, we discuss our results in light of a recent proposal that DINE-1s belong to the Helitron family of TEs.

Conclusion

We find that all 12 Drosophila species with whole-genome sequence contain the high copy element DINE-1. Although all DINE-1s share a similar structure, species-specific variation in the distribution of average pairwise divergence suggests that DINE-1 has gone through multiple independent cycles of activation and suppression. DINE-1 also has had a significant impact on gene structure evolution.

The LTR retrotransposon micropia in the cardini group of Drosophila (Diptera: Drosophilidae): a possible case of horizontal transfer

The presence of the micropia retroelement from the Ty1-copia family of LTR retroelements was investigated in three species of the Drosophila cardini group. Southern blot analysis suggested the existence of at least four micropia copies in the genomes of D. cardinoides, D. neocardini and D. polymorpha populations. The high sequence similarity between dhMiF2 and Dm11 clones (micropia retroelements isolated from D. hydei and D. melanogaster, respectively) with micropia sequences amplified from D. cardini group genome supports the hypothesis that this retroelement plays an active role in horizontal transfer events between D. hydei and the D. cardini group.

Evolution of genes and genomes on the Drosophila phylogeny

Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

Global patterns of sequence evolution in Drosophila

Background

Sequencing of the genomes of several Drosophila allows for the first precise analyses of how global sequence patterns change among multiple, closely related animal species. A basic question is whether there are characteristic features that differentiate chromosomes within a species or between different species.

Results

We explored the euchromatin of the chromosomes of seven Drosophila species to establish their global patterns of DNA sequence diversity. Between species, differences in the types and amounts of simple sequence repeats were found. Within each species, the autosomes have almost identical oligonucleotide profiles. However, X chromosomes and autosomes have, in all species, a qualitatively different composition. The X chromosomes are less complex than the autosomes, containing both a higher amount of simple DNA sequences and, in several cases, chromosome-specific repetitive sequences. Moreover, we show that the right arm of the X chromosome of Drosophila pseudoobscura, which evolved from an autosome 10 – 18 millions of years ago, has a composition which is identical to that of the original, left arm of the X chromosome.

Conclusion

The consistent differences among species, differences among X chromosomes and autosomes and the convergent evolution of X and neo-X chromosomes demonstrate that strong forces are acting on drosophilid genomes to generate peculiar chromosomal landscapes. We discuss the relationships of the patterns observed with differential recombination and mutation rates and with the process of dosage compensation.

[Microsatellites or the eukaryotic genome: life cycle concept and neutrality issues]

Microsatellite markers have a great discriminating power. Widely exploited in many disciplines such as forensic science, medical genetics, conservation biology and molecular ecology, they are also used in human population genetics to illuminate our origins. However, strikingly, their fundamental evolutionary mechanisms remain obscure, because of the difficulty of disentangling the complex and numerous factors involved. After a brief summary of their basic characteristics, the concept of life cycle size-dependant is explored. The major mechanisms known to explain the four different phases of their life (conception, birth, growing and senescence/renaissance) are discussed. Emerging questions about their neutrality are also investigated, pointing out a real need to improve our understanding of their mutational dynamics.