Genome-wide analysis of mariner-like transposable elements in rice reveals complex relationships with stowaway miniature inverted repeat transposable elements (MITEs)

Stowaway is a superfamily of miniature inverted repeat transposable elements (MITEs) that is widespread and abundant in plant genomes. Like other MITEs, however, its origin and mode of amplification are poorly understood. Several lines of evidence point to plant mariner-like elements (MLEs) as the autonomous partners of the nonautonomous Stowaway MITEs. To better understand this relationship, we have taken advantage of the nearly complete genome sequences of two rice subspecies to generate the first inventory of virtually all MLEs and Stowaway families coexisting in a single plant species. Thirty-four different MLEs were found to group into three major clades and 25 families. More than 22,000 Stowaway MITEs were identified and classified into 36 families. On the basis of detailed sequence comparisons, MLEs were confirmed to be the best candidate autonomous elements for Stowaway MITEs. Surprisingly, however, sequence similarity between MLE and Stowaway families was restricted to the terminal inverted repeats (TIRs) and, in a few cases, to adjacent subterminal sequences. These data suggest a model whereby most of the Stowaway MITEs in rice were cross-mobilized by MLE transposases encoded by distantly related elements.     

Horizontal versus vertical transmission of parasites in a stochastic spatial model

A number of pathogens may be transmitted from parent to child at or before birth (vertically) or from one individual to another by contact (horizontally). A natural deterministic and non-spatial model, introduced by Lipsitch et al. [Proc. Roy. Soc. London Ser. B 260 (1995) 3211 shows that an epidemic is possible if the vertical transmission or the horizontal transmission is high enough. In contrast, we introduce a stochastic spatial model that shows that, on a particular graph, if the vertical transmission is not high enough, then the infected individuals disappear even for very high horizontal transmission. This illustrates the fact that introducing space may greatly change the qualitative behavior of a model.     

mle-1, a mariner-like transposable element in the nematode Trichostrongylus colubriformis

A mariner-like element termed mle-1 was discovered in the parasitic nematode Trichostrongylus colubriformis. The mle-1 has features which support its assignment as a mariner-like transposable element. Cloned mle-1 was derived from an intron of the tar-1 gene. It comprises 893 bp, includes two 27 bp flanking perfect inverted repeats and is present at approximately 50 copies in the genome. The element contains a coding region which displays homology to transposases, with the greatest amino acid similarity to a Caenorhabditis elegans mariner-like transposase. The coding region contains two 12 bp repeats; these repeats flank an 11 bp segment which accounts for a frameshift in this region. As a candidate transposon, mle-1 provides potential for genetic manipulation of this and related organisms. © 1997 Elsevier Science B.V. All rights reserved.     

Acquisition and loss of modules: the construction set of transposable elements

Phylogenetic analysis of transposable elements (TEs) allows us to define the relationships between the domains or gene(s) that compose them. Moreover, modules of a few amino-acids can be detected within gag, pol, env genes or within the integrase domain of retrotransposons and transposase of DNA elements. The combination of these observations clearly shows that the evolutionary history of TEs is the outcome of the acquisition and loss of modules with differing origins and histories. This raises the question of the origin of TEs: are they derived from viruses? Are they where viruses come from? Do the basic building bricks come from the prokaryotes, and can they be assembled in the eukaryotes? Are the TEs found in prokaryotes the result of the disintegration of complex elements such as retroelements? Do they evolve from the simplest to the more complex, or are they opportunistic sequences evolving by acquiring and/or losing modules which may be either important or superfluous to their fitness (i.e., their ability to transpose). These are some of the questions that are addressed and discussed in the light of the comparative structures of TEs.     

Horizontal and vertical transmission of viruses in the honey bee, Apis mellifera

The most crucial stage in the dynamics of virus infections is the mode of virus transmission. In general, transmission of viruses can occur through two pathways: horizontal and vertical transmission. In horizontal transmission, viruses are transmitted among individuals of the same generation, while vertical transmission occurs from mothers to their offspring. Because of its highly organized social structure and crowded population density, the honey bee colony represents a risky environment for the spread of disease infection. Like other plant and animal viruses, bee viruses use different survival strategies, including utilization of both horizontal and vertical routes, to transmit and maintain levels in a host population. In this review, we explore the current knowledge about the honey bee viruses and transmission routes of bee viruses. In addition, different transmission strategies on the persistence and dynamics of host-pathogen interactions are also discussed.     

PIF- and Pong-like transposable elements: distribution, evolution and relationship with Tourist-like miniature inverted-repeat transposable elements

Miniature inverted-repeat transposable elements (MITEs) are short, nonautonomous DNA elements that are widespread and abundant in plant genomes. Most of the hundreds of thousands of MITEs identified to date have been divided into two major groups on the basis of shared structural and sequence characteristics: Tourist-like and Stowaway-like. Since MITEs have no coding capacity, they must rely on transposases encoded by other elements. Two active transposons, the maize P Instability Factor (PIF) and the rice Pong element, have recently been implicated as sources of transposase for Tourist-like MITEs. Here we report that PIF- and Pong-like elements are widespread, diverse, and abundant in eukaryotes with hundreds of element-associated transposases found in a variety of plant, animal, and fungal genomes. The availability of virtually the entire rice genome sequence facilitated the identification of all the PIF/Pong-like elements in this organism and permitted a comprehensive analysis of their relationship with Tourist-like MITEs. Taken together, our results indicate that PIF and Pong are founding members of a large eukaryotic transposon superfamily and that members of this superfamily are responsible for the origin and amplification of Tourist-like MITEs.     

Microsatellites, transposable elements and the X chromosome

Variability at microsatellite (MS) loci is generally perceived as resulting from an interaction between mutation and genetic drift and, to a lesser extent, selection and recombination. Less investigated has been the reason for MS accumulation in genomes. We present here a simple model that could account for the variation in density of MS loci, assuming that they are created either through replication slippage or in association with transposable elements. Microsatellites then evolve under the forces cited above. We use this framework to revisit two results obtained from high-density genomic maps of the human and mouse genomes built with thousands of CA repeats: MS loci are (1) less variable and (2) less dense on the X chromosome than on autosomes. The first result is most likely explained by differential mutation on the X chromosome and the autosomes. The second result may be explained by differential mutation, provided the distributions of MS loci are still not at equilibrium. Selection, acting either directly on large allele size or indirectly on the transposable elements associated with MS, may explain the same result. The framework developed here is a first step toward more rigorous models, calling for additional data.      

Horizontal and vertical transmission of wild-type and recombinant Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus

Transmission plays a central role in the ecology of baculoviruses and the population dynamics of their hosts. Here, we report on the horizontal and vertical transmission dynamics of wild-type Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus (HaSNPV-WT) and a genetically modified variant (HaSNPV-AaIT) with enhanced speed of action through the expression of an insect-selective scorpion toxin (AaIT). In caged field plots, horizontal transmission of both HaSNPV variants was greatest when inoculated 3rd instar larvae were used as infectors, transmission was intermediate with 2nd instar infectors and lowest with 1st instar infectors. Transmission was greater at a higher density of infectors (1 per plant) than at a lower density (1 per 4 plants); however, the transmission coefficient (number of new infections per initial infector) was lower at the higher density of infectors than at the lower density. HaSNPV-AaIT exhibited a significantly lower rate of transmission than HaSNPV-WT in the field cages. This was also the case in open field experiments. In the laboratory, the vertical transmission of HaSNPV-AaIT from infected females to offspring of 16.7+/-2.1% was significantly lower than that of HaSNPV-WT (30.9+/-2.9%). Likewise, in the field, vertical transmission of HaSNPV-AaIT (8.4+/-1.1%) was significantly lower than that of HaSNPV-WT (12.6+/-2.0%). The results indicate that the recombinant virus will be transmitted at lower rates in H. armigera populations than the wild-type virus. This may potentially affect negatively its long-term efficacy as compared to wild-type virus, but contributing positively to its biosafety.     

Alfalfa transposable elements and variegation

Alfalfa with unstable anthocyanin pigmentation has been independently discovered on six occasions since 1958. Genetic studies showed that each of the six unstable stocks was due to an allele mutable at the basic anthocyanin locus C2 in alfalfa. The alleles are designated c2-m1 through c2-m6. Variegated phenotypes of m1, m2, and m3 are similar and express reversion from the recessive to the dominant state. This reversion produces streaks and sectors of pigment in flower petals and seeds that are otherwise white. Reversion occurs at various times in development and may result in periclinal chimeras. The c2-m4 allele is unique in that it arose during tissue culture, whereas the other mutables were discovered in plant populations. Interestingly, m4 is very stable in planta and only rarely produces a sectored flower, but is very unstable in vitro as measured by about 23% revertant plants regenerated from tissue cultures. Most m4 reversion occurs relatively early in development and results in completely pigmented in vitro revertants, and in large sectors on in planta revertants. Alleles m5 and m6 are phenotypically and genetically similar. Their flowers are basic purple with white streaks thus representing mutation from dominant purple to recessive white. White progeny of m5 and m6 are very stable both in planta and in vitro; reversion of white to purple was never observed. Thus, the loss of function of the dominant allele results in a stable recessive or a deficiency. The absolute stability of m5 white derivatives favors the deficiency model, because transposable element mutations might show reversion. Finally, several mutations are described that reoccur in the mutable populations. It is speculated that they are recent mutations due to transposition of transposable elements.     

Evolution and consequences of transposable elements

Recent studies on transposable elements (TEs) have shed light on the mechanisms that have shaped their evolution. In addition to accumulating nucleotide substitutions over evolutionary time, TEs appear to be especially prone to genetic rearrangements and vertical transmissions across even distantly related species. As a consequence of replicating in host genomes, TEs have a significant mutational effect on their hosts. Although most TE-insertion mutations seem to exert a negative effect on host fitness, a growing body of evidence indicates that some TE-mediated genetic changes have become established features of host species genomes indicating that TEs can contribute significantly to organismic evolution.     

The IS1 elements in Shigella boydii: horizontal transfer,vertical inactivation and target duplication

IS1(SB) and its two variants were identified as the major and minor IS1 elements in Shigella boydii. The nucleotide sequences of IS1(SB), IS1(O157:H7) from Escherichia coli O157:H7 and IS1F from E. coli K12 suggest that these IS1 elements had been horizontally transferred among S. boydii and E. coli O157:H7 and K12. The two IS1(SB) variants and IS1(O157:H7) have transposition activities 7- to 86-fold less than that of IS1(SB), whereas IS1F has little transposition activity. Analysis of the flanking sequences of IS1(SB) and its two variants in S. boydii revealed the nature of regional specificity of the target sites and the sequence dependence of 8 and 9 bp target duplications, for which a model is presented.     

Genome ecosystem and transposable elements species

Transposable elements are known to be “selfish DNA” sequences able to spread and be maintained in all genomes analyzed so far. Their evolution depends on the interaction they have with the other components of the genome, including genes and other transposable elements. These relationships are complex and have often been compared to those of species living and competing in an ecosystem. The aim of this current work is a proposition to fill the conceptual gap existing between genome biology and ecology, assuming that genomic components, such as transposable elements families, can be compared to species interacting in an ecosystem. Using this framework, some of the main models defined in the population genetics of transposable elements can then been reformulated, and some new kinds of realistic relationships, such as symbiosis between different genomic components, can then be modelled and explored.     

Eukaryotic transposable elements and genome evolution

The changes in DNA sequence that have taken place during the evolution of eukaryotic genomes cannot be accounted for simply by base substitutions; some more complex mutations must have taken place as well. Transposable elements can affect gene structure and expression in several ways that suggest that they may have contributed to these evolutionary events.     

Cloning and characterization of mariner-like elements in the soybean aphid, Aphis glycines Matsumura

Soybean aphid, Aphis glycines Matsumura (Hemiptera: Aphididae), is currently the most important insect pest of soybean (Glycine max (L.) Merr.) in the United States and causes significant economic damage worldwide, but little is known about the aphid at the molecular level. Mariner-like transposable elements (MLEs) are ubiquitous within the genomes of arthropods and various other invertebrates. In this study, we report the cloning of MLEs from the soybean aphid genome using degenerate PCR primers designed to amplify conserved regions of mariner transposases. Two of the ten sequenced clones (designated as Agmar1 and Agmar2) contained partial but continuous open reading frames, which shared high levels of homology at the protein level with other mariner transposases from insects and other taxa. Phylogenetic analysis revealed Agmar1 to group within the irritans subfamily of MLEs and Agmar2 within the mellifera subfamily. Southern blot analysis and quantitative PCR analysis indicated a low copy number for Agmar1-like elements within the soybean aphid genome. These results suggest the presence of at least two different putative mariner-like transposases encoded by the soybean aphid genome. Both Agmar1 and Agmar2 could play influential roles in the architecture of the soybean aphid genome. Transposable elements are also thought to potentially mediate resistance in insects through changes in gene amplification and mutations in coding sequences. Finally, Agmar1 and Agmar2 may represent useful genetic tools and provide insights on A. glycines adaptation.     

昆虫的转座子及其功能

转座子是一类散布在基因组中序列重复的DNA片段,它们可以通过特定转座酶在基因组中移动.目前测序的真核生物基因组的结果都显示转座子占基因组中相当大的一部分.目前对于转座子功能的研究主要集中在产生新功能、修饰染色质、保护生殖细胞,以及参与基因组的协同进化上.随着对其功能研究的深入,利用转座子转座能力开发的转基因系统可以改造物种的遗传性状.此外转座子还可以作为一个标尺用以分析物种进化关系.