Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence

Analysis of phenotypes altered by temperature stress and hipermutability in Drosophila willistoni

Drosophila willistoni (Sturtevant, 1916) is a species of the willistoni group of Drosophila having wide distribution from the South of USA (Florida) and Mexico to the North of Argentina. It has been subject of many evolutionary studies within the group, due to its considerable ability to successfully occupy a wide range of environments and also because of its great genetic variability expressed by different markers. The D. willistoni 17A2 strain was collected in 1991 in the state of Rio Grande do Sul, Brazil (30°05'S, 51°39'W), and has been maintained since then at the Drosophila laboratory of UFRGS. Different to the other D. willistoni strains maintained in the laboratory, the 17A2 strain spontaneously produced mutant males white-like (white eyes) and sepia-like (brown eyes) in stocks held at 17°C. In order to discover if this strain is potentially hypermutable, we submitted it to temperature stress tests. Eighteen isofemale strains were used in our tests and, after the first generation, all the individuals produced in each strain were maintained at 29°C. Different phenotype alterations were observed in subsequent generations, similar to mutations already well characterized in D. melanogaster (white, sepia, blistered and curly). In addition, an uncommon phenotype alteration with an apparent fusion of the antennae was observed, but only in the isofemale line nº 31. This last alteration has not been previously described as a mutation in the D. melanogaster species. Our results indicate that the D. willistoni 17A2 strain is a candidate for hypermutability, which presents considerable cryptic genetic variability. Different factors may be operating for the formation of this effect, such as the mobilization of transposable elements, effect of inbreeding and alteration of the heat-shock proteins functions.

Genome size and genome evolution in diploid Triticeae species

One of the intriguing issues concerning the dynamics of plant genomes is the occurrence of intraspecific variation in nuclear DNA amount. The aim of this work was to assess the ranges of intraspecific, interspecific, and intergeneric variation in nuclear DNA content of diploid species of the tribe Triticeae (Poaceae) and to examine the relation between life form or habitat and genome size. Altogether, 438 plants representing 272 lines that belong to 22 species were analyzed. Nuclear DNA content was estimated by flow cytometry. Very small intraspecific variation in DNA amount was found between lines of Triticeae diploid species collected from different habitats or between different morphs. In contrast to the constancy in nuclear DNA amount at the intraspecific level, there are significant differences in genome size between the various diploid species. Within the genus Aegilops, the 1C DNA amount ranged from 4.84 pg in A. caudata to 7.52 pg in A. sharonensis; among genera, the 1C DNA amount ranged from 4.18 pg in Heteranthelium piliferum to 9.45 pg in Secale montanum. No evidence was found for a smaller genome size in annual, self-pollinating species relative to perennial, cross-pollinating ones. Diploids that grow in the southern part of the group's distribution have larger genomes than those growing in other parts of the distribution. The contrast between the low variation at the intraspecific level and the high variation at the interspecific one suggests that changes in genome size originated in close temporal proximity to the speciation event, i.e., before, during, or immediately after it. The possible effects of sudden changes in genome size on speciation processes are discussed.

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.

Cassandra retrotransposons carry independently transcribed 5S RNA

We report a group of TRIMs (terminal-repeat retrotransposons in miniature), which are small nonautonomous retrotransposons. These elements, named Cassandra, universally carry conserved 5S RNA sequences and associated RNA polymerase (pol) III promoters and terminators in their long terminal repeats (LTRs). They were found in all vascular plants investigated. Uniquely for LTR retrotransposons, Cassandra produces noncapped, polyadenylated transcripts from the 5S pol III promoter. Capped, read-through transcripts containing Cassandra sequences can also be detected in RNA and in EST databases. The predicted Cassandra RNA 5S secondary structures resemble those for cellular 5S rRNA, with high information content specifically in the pol III promoter region. Genic integration sites are common for Cassandra, an unusual feature for abundant retrotransposons. The 5S in each LTR produces a tandem 5S arrangement with an inter-5S spacing resembling that of cellular 5S. The distribution of 5S genes is very variable in flowering plants and may be partially explained by Cassandra activity. Cassandra thus appears both to have adapted a ubiquitous cellular gene for ribosomal RNA for use as a promoter and to parasitize an as-yet-unidentified group of retrotransposons for the proteins needed in its lifecycle.

A phylogenetic analysis of indel dynamics in the cotton genus

Genome size evolution is a dynamic process involving counterbalancing mechanisms whose actions vary across lineages and over time. Whereas the primary mechanism of expansion, transposable element (TE) amplification, has been widely documented, the evolutionary dynamics of genome contraction have been less thoroughly explored. To evaluate the relative impact and evolutionary stability of the mechanisms that affect genome size, we conducted a phylogenetic analysis of indel rates for 2 genomic regions in 4 Gossypium genomes: the 2 coresident genomes (A(T) and D(T)) of tetraploid cotton and its model diploid progenitors, Gossypium arboreum (A) and Gossypium raimondii (D). We determined the rates of sequence gain or loss along each branch, partitioned by mechanism, and how these changed during species divergence. In general, there has been a propensity toward growth of the diploid genomes and contraction in the polyploid. Most of the size difference between the diploid species occurred prior to polyploid divergence and was largely attributable to TE amplification in the A/A(T) genome. After separating from the true parents of the polyploid genomes, both diploid genomes experienced slower sequence gain than in the ancestor, due to fewer TE insertions in the A genome and a combination of increased deletions and decreased TE insertions in the D genome. Both genomes of the polyploid displayed increased rates of deletion and decreased rates of insertion, leading to a rate of near stasis in D(T) and overall contraction in A(T) resulting in polyploid genome contraction. As expected, TE insertions contributed significantly to the genome size differences; however, intrastrand homologous recombination, although rare, had the most significant impact on the rate of deletion. Small indel data for the diploids suggest the possibility of a bias as the smaller genomes add less or delete more sequence through small indels than do the larger genomes, whereas data for the polyploid suggest increased sequence turnover in general (both as small deletions and small insertions). Illegitimate recombination, although not demonstrated to be a dominant mechanism of genome size change, was biased in the polyploid toward deletions, which may provide a partial explanation of polyploid genomic downsizing.

Retroelement insertional polymorphisms, diversity and phylogeography within diploid, D-genome Aegilops tauschii (Triticeae, Poaceae) sub-taxa in Iran

BACKGROUND AND AIMS

The diploid goat grass Aegilops tauschii (2n = 2x = 14) is native to the Middle East and is the D-genome donor to hexaploid bread wheat. The aim of this study was to measure the diversity of different subspecies and varieties of wild Ae. tauschii collected across the major areas where it grows in Iran and to examine patterns of diversity related to the taxa and geography.

METHODS

Inter-retroelement amplified polymorphism (IRAP) markers were used to analyse the biodiversity of DNA from 57 accessions of Ae. tauschii from northern and central Iran, and two hexaploid wheats. Key Results Eight IRAP primer combinations amplified a total of 171 distinct DNA fragments between 180 and 3200 bp long from the accessions, of which 169 were polymorphic. On average, about eight fragments were amplified with each primer combination, with more bands being amplified from accessions from the north-west of the country than from other accessions.

CONCLUSIONS

The IRAP markers showed high levels of genetic diversity. Analysis of all accessions together did not allow the allocation of individuals to taxa based on morphology, but showed a tendency to put accessions from the north-west apart from others regions. It is speculated that this could be due to different activity of retroelements in the different regions. Within the two taxa with most accessions, there was a range of IRAP genotypes that could be correlated closely with geographical origin. This supports suggestions that the centre of origin of the species is towards the south-east of the Caspian Sea. IRAP is an appropriate marker system to evaluate genetic diversity and evolutionary relationships within the taxa, but it is too variable to define the taxa themselves, where more slowly evolving morphological, DNA sequence or chromosomal makers may be more appropriate.

Isolation and characterization of genomic retrotransposon sequences from octoploid strawberry (Fragaria x ananassa Duch.)

Strawberry (Fragaria spp.) is a kind of herbaceous perennial plant that propagates vegetatively. The conserved domains of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy groups of LTR retrotransposons were amplified from the cultivated strawberry (Fragaria x ananassa Duch.). Sequence analysis of clones demonstrated that 5 of 19 Ty1-copia group unique sequences and 2 of 10 Ty3-gypsy unique sequences in F. x ananassa genome possessed either stop codon or frameshift. Ty1-copia group sequences are highly heterogeneous (divergence ranged from 1 to 69.8%), but the Ty3-gypsy group sequences are less (divergence ranged from 1 to 10%). Southern dot blot hybridization result suggested that both of the LTR retrotransposons are present in the genome of cultivated strawberry with high copy number (Ty1-copia group 2,875 Ty3-gypsy group 348). RT-PCR amplification from total RNA, which was extracted from leaves of micropropagated strawberry plants, did not yield either of the RT fragments. This is the first report on the presence of RT sequences of Ty1-copia and Ty3-gypsy group retrotransposons in F. x ananassa genome.

Evidence of multiple horizontal transfers of the long terminal repeat retrotransposon RIRE1 within the genus Oryza

Horizontal gene transfer, defined as the transmission of genetic material between reproductively isolated species, has been considered for a long time to be a rare phenomenon. Most well-documented cases of horizontal gene transfer have been described in prokaryotes or in animals and they often involve transposable elements. The most abundant class of transposable elements in plant genomes are the long terminal repeat (LTR) retrotransposons. Because of their propensity to increase their copy number while active, LTR retrotransposons can have a significant impact on genomics changes during evolution. In a previous study, we showed that in the wild rice species Oryza australiensis, 60% of the genome is composed of only three families of LTR retrotransposons named RIRE1, Wallabi and Kangourou. In the present study, using both in silico and experimental approaches, we show that one of these three families, RIRE1, has been transferred horizontally between O. australiensis and seven other reproductively isolated Oryza species. This constitutes a new case of horizontal transfer in plants.

Characterization and comparative analysis of sequence-specific amplified polymorphisms based on two subfamilies of IRRE retrotransposons in Iris missouriensis (Iridaceae)

DNA markers based on transposable-element polymorphisms are potentially useful alternatives to anonymous fragment-length polymorphisms (AFLPs). We developed the retrotransposon sequence-specific amplified polymorphism (retrotransposon SSAP) technique for the angiosperm Iris missouriensis (Iridaceae) in order to evaluate its use in generating population-genetic markers. Our cloning strategy identified two groups of long-terminal repeat retrotransposons of the IRRE family. Primers homologous to conserved regions of these elements generated repeatable and polymorphic markers. In comparison, the AFLP protocol failed to produce useful markers in our hands in this species. To investigate the distribution and evolutionary tempo of the two retrotransposons, we developed a phylogeny of representative species of subgenus Limniris based on chloroplast sequence. Sequences of both groups of retrotransposons were widespread in Limniris, but we also found evidence of substantial sequence and copy-number evolution since the divergence of I. missouriensis from other Limniris species. We corroborated these results with quantitative real-time PCR estimates of relative copy number. Importantly, the geographic structure of retrotransposon SSAP was strikingly different for the two groups of retrotransposons, indicating that different mutational dynamics and/or selective pressures govern their distribution. Although these primers should be useful for population-genetic studies of Iris missouriensis and other Limniris species, our findings reinforce the need for caution in evaluating transposable-element markers used to analyze the relatedness of populations or cultivars, as very different conclusions may be reached depending on the sequence amplified.

CORRELATED EVOLUTION OF GENOME SIZE AND CELL VOLUME IN DIATOMS (BACILLARIOPHYCEAE)(1)

A correlation between genome size and cell volume has been observed across diverse assemblages of eukaryotes. We examined this relationship in diatoms (Bacillariophyceae), a phylum in which cell volume is of critical ecological and biogeochemical importance. In addition to testing whether there is a predictive relationship across extant species, we tested whether evolutionary divergences in genome size were correlated with evolutionary divergences in cell size (using independent contrasts). We estimated total DNA content for 16 diatom species using a flow cytometer and estimated cell volumes using critical dimensions with scaling equations. Our independent contrast analyses indicated a significant correlated evolution between genome size and cell volume. We then explored the evolutionary and ecological implications of this evolutionary relationship. Diatom cell volume is an important component of the global carbon cycle; therefore, understanding the mechanisms that drive diatom genome evolution has both evolutionary and ecological importance.

Epigenetic control of plant stress response

Living organisms have the clearly defined strategies of stress response. These strategies are predefined by a genetic make-up of the organism and depend on a complex regulatory network of molecular interactions. Although in most cases, the plant response to stress based on the mechanisms of tolerance, resistance, and avoidance has clearly defined metabolic pathways, the ability to acclimate/adapt after a single generation exposure previously observed in several studies (Boyko A et al. [2007]: Nucleic Acids Res 35:1714-1725; Boyko and Kovalchuk, unpublished data), represents an interesting phenomenon that cannot be explained by Mendelian genetics. The latest findings in the field of epigenetics and the process of a reversible control over gene expression and inheritance lead to believe that organisms, especially plants, may have a flexible short-term strategy of the response to stress. Indeed, the organisms that can modify gene expression reversibly have an advantage in evolutionary terms, since they can avoid unnecessary excessive rearrangements and population diversification. This review covers various epigenetic processes involved in plant stress response. We focus on the mechanisms of DNA methylation and histone modifications responsible for the protection of somatic cells and inheritance of stress memories.

Assessment of genetic and epigenetic stability in long-term in vitro shoot culture of pea (Pisum sativum L.)

In vitro clonal propagation of plants should generate identical copies of the selected genotype. However, associated stress might result in a breakdown of control mechanisms and consequent instability of the genome. We have used several molecular methods to assess the genetic stability of long-term propagated (24 years) multiple shoot in vitro culture of pea (Pisum sativum L.). We focused on assessing the stability of repetitive sequences, such as simple sequence repeats (SSR) and retrotransposons, both comprising a large part of genome. No differences were found when seedlings (Co-2004) or original seed (Co-1982) controls and long-term or newly established in vitro (one subculture cycle) samples were investigated by the SSR, inter-repeats (ISSR) or inter-retrotransposon amplified polymorphism (IRAP) method. However, the more global amplified fragment length polymorphism (AFLP) and particularly the methylation sensitive MSAP methods detected 11 and 18% polymorphism among samples, respectively. Interestingly, investigation of the global cytosine methylation status by HPCE measurement revealed no statistically significant differences. Some evidence of retrotransposon re-arrangement was observed by sequence-specific amplification polymorphism. This occurred mostly in the abundant Ty3-gypsy type Cyclop element and to a smaller extent in the Ogre element. Alternatively, no polymorphism was detected among the PDR-1 element of the Ty1-copia type retrotransposon. Based on these results, multiple shoot culture of pea maintained over a long period may be considered as a true to type multiplication method of the original genotype.

IRAP and REMAP for retrotransposon-based genotyping and fingerprinting

Retrotransposons can be used as markers because their integration creates new joints between genomic DNA and their conserved ends. To detect polymorphisms for retrotransposon insertion, marker systems generally rely on PCR amplification between these ends and some component of flanking genomic DNA. We have developed two methods, retrotransposon-microsatellite amplified polymorphism (REMAP) analysis and inter-retrotransposon amplified polymorphism (IRAP) analysis, that require neither restriction enzyme digestion nor ligation to generate the marker bands. The IRAP products are generated from two nearby retrotransposons using outward-facing primers. In REMAP, amplification between retrotransposons proximal to simple sequence repeats (microsatellites) produces the marker bands. Here, we describe protocols for the IRAP and REMAP techniques, including methods for PCR amplification with a single primer or with two primers and for agarose gel electrophoresis of the product using optimal electrophoresis buffers and conditions. This protocol can be completed in 1-2 d.

Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza

Long terminal repeat (LTR) retrotransposons constitute a significant portion of most eukaryote genomes and can dramatically change genome size and organization. Although LTR retrotransposon content variation is well documented, the dynamics of genomic flux caused by their activity are poorly understood on an evolutionary time scale. This is primarily because of the lack of an experimental system composed of closely related species whose divergence times are within the limits of the ability to detect ancestrally related retrotransposons. The genus Oryza, with 24 species, ten genome types, different ploidy levels and over threefold genome size variation, constitutes an ideal experimental system to explore genus-level transposon dynamics. Here we present data on the discovery and characterization of an LTR retrotransposon family named RWG in the genus Oryza. Comparative analysis of transposon content (approximately 20 to 27,000 copies) and transpositional history of this family across the genus revealed a broad spectrum of independent and lineage-specific changes that have implications for the evolution of genome size and organization. In particular, we provide evidence that the basal GG genome of Oryza (O. granulata) has expanded by nearly 25% by a burst of the RWG lineage Gran3 subsequent to speciation. Finally we describe the recent evolutionary origin of Dasheng, a large retrotransposon derivative of the RWG family, specifically found in the A, B and C genome lineages of Oryza.

Ty1-copiaretrotransposon-based SSAP marker development and its potential in the genetic study of cucurbits

Three long terminal repeat (LTR) sequences of Ty1-copia retrotransposons were identified in cucumber ( Cucumis sativus L.) and named Tcs 1, Tcs 2, and Tcs 3. A sequence-specific amplification polymorphism (SSAP) marker system based on these LTR sequences displayed a higher level of polymorphism than AFLPs in cucumber. This marker system could also detect loci in other Cucumis species for genetic diversity analysis. The three Tcs LTRs existed within the exons of genes because of the effective amplification band patterns from the cDNA templates. The potential usefulness of the SSAP marker system in studies of the evolution of genes or genomes was verified after exploring loci changes in first and second generations of a synthetic allotetraploid in Cucumis. This study is the first report of the development of a retrotransposon-based marker system and the SSAP technique in cucurbits.

Direct determination of the effects of genotype and extreme temperature on the transposition of roo in long-term mutation accumulation lines of Drosophila melanogaster

Transposable elements (TEs) are mobile repetitive DNA sequences that constitute a structurally dynamic component of genomes. In order to understand the dynamics of TEs it is necessary to have information about the control of transposition and its dependence of environmental factors. After a great deal of previous work on transposition conducted on long-term mutation accumulation (MA) lines of Drosophila melanogaster started in 1987, only roo out of 16 families was found active in this genotype. Here we test the effect of the modification of the genetic background by introducing a Cy chromosome, and the effect of extreme temperature (28 degrees C) on the transposition rate of roo. Thermal stress did not affect the transposition rate, whereas the presence of a Cy chromosome in heterozygosis lowered it. There was an excess of insertions in the X chromosome, with respect to autosomes, and in the proximal and distal regions of chromosome arms that can be interpreted as target site preference. One of the control lines became highly unstable with mean insertion and excision rates of 3.0 x 10(-3) and 8.5 x 10(-4), respectively. Instability arose spontaneously during generations of mutation accumulation, and can be attributed to "de novo" mutation. Transposition in the unstable line could be directly studied on the progeny of individual males and females, from where we deduced that transposition occurs mainly, if not exclusively, in males, with a rate of 1.125 insertions per gamete. In situ hybridization with an LTR probe showed that most excisions (12 out of 14) were precise. Our data show the prominent role of genotype in transposition control and can explain rapid turnovers in the genome without increasing the number of copies.

Differential impact of retrotransposon populations on the genome of allotetraploid tobacco (Nicotiana tabacum)

LTR-retrotransposons contribute substantially to the structural diversity of plant genomes. Recent models of genome evolution suggest that retrotransposon amplification is offset by removal of retrotransposon sequences, leading to a turnover of retrotransposon populations. While bursts of amplification have been documented, it is not known whether removal of retrotransposon sequences occurs continuously, or is triggered by specific stimuli over short evolutionary periods. In this work, we have characterized the evolutionary dynamics of four populations of copia-type retrotransposons in allotetraploid tobacco (Nicotiana tabacum) and its two diploid progenitors Nicotiana sylvestris and Nicotiana tomentosiformis. We have used SSAP (Sequence-Specific Amplification Polymorphism) to evaluate the contribution retrotransposons have made to the diversity of tobacco and its diploid progenitor species, to quantify the contribution each diploid progenitor has made to tobacco's retrotransposon populations, and to estimate losses or amplifications of retrotransposon sequences subsequent to tobacco's formation. Our results show that the tobacco genome derives from a turnover of retrotransposon sequences with removals concomitant with new insertions. We have detected unique behaviour specific to each retrotransposon population, with differences likely reflecting distinct evolutionary histories and activities of particular elements. Our results indicate that the retrotransposon content of a given plant species is strongly influenced by the host evolutionary history, with periods of rapid turnover of retrotransposon sequences stimulated by allopolyploidy.

Comparative cross-species alternative splicing in plants

Alternative splicing (AS) can add significantly to genome complexity. Plants are thought to exhibit less AS than animals. An algorithm, based on expressed sequence tag (EST) pairs gapped alignment, was developed that takes advantage of the relatively small intron and exon size in plants and directly compares pairs of ESTs to search for AS. EST pairs gapped alignment was first evaluated in Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and tomato (Solanum lycopersicum) for which annotated genome sequence is available and was shown to accurately predict splicing events. The method was then applied to 11 plant species that include 17 cultivars for which enough ESTs are available. The results show a large, 3.7-fold difference in AS rates between plant species with Arabidopsis and rice in the lower range and lettuce (Lactuca sativa) and sorghum (Sorghum bicolor) in the upper range. Hence, compared to higher animals, plants show a much greater degree of variety in their AS rates and in some plant species the rates of animal and plant AS are comparable although the distribution of AS types may differ. In eudicots but not monocots, a correlation between genome size and AS rates was detected, implying that in eudicots the mechanisms that lead to larger genomes are a driving force for the evolution of AS.

Random distribution pattern and non-adaptivity of genome size in a highly variable population of Festuca pallens

BACKGROUND AND AIMS

The spatial and statistical distribution of genome sizes and the adaptivity of genome size to some types of habitat, vegetation or microclimatic conditions were investigated in a tetraploid population of Festuca pallens. The population was previously documented to vary highly in genome size and is assumed as a model for the study of the initial stages of genome size differentiation.

METHODS

Using DAPI flow cytometry, samples were measured repeatedly with diploid Festuca pallens as the internal standard. Altogether 172 plants from 57 plots (2.25 m(2)), distributed in contrasting habitats over the whole locality in South Moravia, Czech Republic, were sampled. The differences in DNA content were confirmed by the double peaks of simultaneously measured samples.

KEY RESULTS

At maximum, a 1.115-fold difference in genome size was observed. The statistical distribution of genome sizes was found to be continuous and best fits the extreme (Gumbel) distribution with rare occurrences of extremely large genomes (positive-skewed), as it is similar for the log-normal distribution of the whole Angiosperms. Even plants from the same plot frequently varied considerably in genome size and the spatial distribution of genome sizes was generally random and unautocorrelated (P > 0.05). The observed spatial pattern and the overall lack of correlations of genome size with recognized vegetation types or microclimatic conditions indicate the absence of ecological adaptivity of genome size in the studied population.

CONCLUSIONS

These experimental data on intraspecific genome size variability in Festuca pallens argue for the absence of natural selection and the selective non-significance of genome size in the initial stages of genome size differentiation, and corroborate the current hypothetical model of genome size evolution in Angiosperms (Bennetzen et al., 2005, Annals of Botany 95: 127-132).

Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families

Although copia retrotransposons are major components of all plant genomes, the evolutionary relationships between individual copia families and between elements from different plant species are only poorly studied. We used 20 copia families from the large-genome plants barley and wheat to identify 46 families of homologous copia elements from rice and 22 from Arabidopsis, two plant species with much smaller genomes. In total, 599 copia elements were analyzed. Phylogenetic analysis showed that copia elements from the four species can be classified into six ancient lineages that existed before the divergence of monocots and dicots. The six lineages show a surprising degree of conservation in sequence organization and other characteristics across species. Additionally, the phylogenetic data suggest at least one case of horizontal gene transfer between the Arabidopsis and rice lineages. Insertion time estimates for 522 high-copy elements showed that retrotransposons from rice were active at different times in waves of activity lasting 0.5-2 million years, depending on the family, whereas elements from wheat and barley had longer periods of activity. We estimated that half of the rice copia elements are truncated or otherwise rearranged after approximately 790,000 yr, which is almost twice the half-life of Arabidopsis elements. In contrast, wheat and barley copia elements appear to have a massively longer half-life, beyond our ability to estimate from the available data. These findings suggest that genome size can be explained by the specific rate of DNA removal from the genome and the length of active periods of retrotransposon families.

Microcolinearity and genome evolution in the AdhA region of diploid and polyploid cotton (Gossypium)

Genome sizes vary by several orders of magnitude, driven by mechanisms such as illegitimate recombination and transposable element proliferation. Prior analysis of the CesA region in two cotton genomes that diverged 5-10 million years ago (Ma), and acquired a twofold difference in genome size, revealed extensive local conservation of genic and intergenic regions, with no evidence of the global genome size difference. The present study extends the comparison to include BAC sequences surrounding the gene encoding alcohol dehydrogenase A (AdhA) from four cotton genomes: the two co-resident genomes (A(T) and D(T)) of the allotetraploid, Gossypium hirsutum, as well as the model diploid progenitors, Gossypium arboreum (A) and Gossypium raimondii (D). In contrast to earlier work, evolution in the AdhA region reflects, in a microcosm, the overall difference in genome size, with a nearly twofold difference in aligned sequence length. Most size differences may be attributed to differential accumulation of retroelements during divergence of the genome diploids from their common ancestor, but in addition there has been a biased accumulation of small deletions, such that those in the smaller D genome are on average twice as large as those in the larger A genome. The data also provide evidence for the global phenomenon of 'genomic downsizing' in polyploids shortly after formation. This in part reflects a higher frequency of small deletions post-polyploidization, and increased illegitimate recombination. In conjunction with previous work, the data here confirm the conclusion that genome size evolution reflects many forces that collectively operate heterogeneously among genomic regions.

Patterns of thermal adaptation of Bacillus simplex to the microclimatically contrasting slopes of 'Evolution Canyons' I and II, Israel

Identification of selective forces that drive evolution and speciation of bacteria in natural habitats is a central issue in bacterial ecology and evolution. Exploring the adaptive evolution of Bacillus simplex at 'Evolution Canyons' I and II, Israel, we report here on the impact of high heat stress on the speciation progress of individual evolutionary lineages. These canyons represent similar ecological replicates, separated by 40 km, in which the orientation of the sun yields a strong sun-exposed and hot 'African' south-facing slope (SFS) versus a rather cooler and mesic-lush 'European' north-facing slope (NFS) within a distance of only 50-100 m at the bottom and 400 m at the top. Among 131 strains studied, in Luria-Bertani broth, 'African' strains grow better than 'European' strains at a stressful high temperature (43.25 degrees C). The results suggest that adaptation to the hotter and more stressful SFS is continuously ongoing. The patterns of heat adaptation override the phylogenetic history of individual lineages. A positive correlation of growth rates at 43.25 degrees C and 20 degrees C, more markedly among 'African' strains, reflects probably the broader temperature range on the SFS. Summarizing, the hot temperature stress on the 'African' slope is a major environmental force driving the twin evolutionary processes of adaptation and speciation of B. simplex at 'Evolution Canyon'. Finally, we discuss the data in light of current controversies on species concepts.

Life without GAG: The BARE-2 retrotransposon as a parasite's parasite

A large proportion of the plant LTR (Long Terminal Repeat) retrotransposons are partly or completely unable to synthesize their own machinery for transposition. However, most of these inactive or non-autonomous elements are likely able to retrotranspose, based on their insertional polymorphism. Therefore, they must be parasitic on one or more active partners. Here, we describe the parasitism of the chimeric BARE-2 element on the active BARE-1 (Barley RetroElement-2 and -1 respectively). These two elements are present in the Triticeae and related species, and are together polymorphic among closely related accessions. BARE-2 elements are unable to synthesize their own GAG protein, and harbor a specific ATG deletion in the gag ORF. However, BARE-2 sequences are conserved with BARE-1 in the PBS (Primer Binding Site), PSI (Packaging SIgnal) and DIS (DImerization Signal) domains. As these motifs have been shown to allow parasitism among the lentiviruses, we conclude that BARE-2 is probably a partial parasite of the BARE-1 element because the machinery of the latter can complement the defective GAG of the former. This example emphasizes that we must characterize the parasitic network of LTR retrotransposons and its implication for integration of autonomous, inactive, and non-autonomous elements in order to understand current and past host genome evolution.

Transposable elements are enriched within or in close proximity to xenobiotic-metabolizing cytochrome P450 genes

Background

Transposons, i.e. transposable elements (TEs), are the major internal spontaneous mutation agents for the variability of eukaryotic genomes. To address the general issue of whether transposons mediate genomic changes in environment-adaptation genes, we scanned two alleles per each of the six xenobiotic-metabolizing Helicoverpa zea cytochrome P450 loci, including CYP6B8, CYP6B27, CYP321A1, CYP321A2, CYP9A12v3 and CYP9A14, for the presence of transposon insertions by genome walking and sequence analysis. We also scanned thirteen Drosophila melanogaster P450s genes for TE insertions by in silico mapping and literature search.

Results

Twelve novel transposons, including LINEs (long interspersed nuclear elements), SINEs (short interspersed nuclear elements), MITEs (miniature inverted-repeat transposable elements), one full-length transib-like transposon, and one full-length Tcl-like DNA transpson, are identified from the alleles of the six H. zea P450 genes. The twelve transposons are inserted into the 5'flanking region, 3'flanking region, exon, or intron of the six environment-adaptation P450 genes. In D. melanogaster, seven out of the eight Drosophila P450s (CYP4E2, CYP6A2, CYP6A8, CYP6A9, CYP6G1, CYP6W1, CYP12A4, CYP12D1) implicated in insecticide resistance are associated with a variety of transposons. By contrast, all the five Drosophila P450s (CYP302A1, CYP306A1, CYP307A1, CYP314A1 and CYP315A1) involved in ecdysone biosynthesis and developmental regulation are free of TE insertions.

Conclusion

These results indicate that TEs are selectively retained within or in close proximity to xenobiotic-metabolizing P450 genes.

Radiation of the Tnt1 retrotransposon superfamily in three Solanaceae genera

BACKGROUND

Tnt1 was the first active plant retrotransposon identified in tobacco after nitrate reductase gene disruption. The Tnt1 superfamily comprises elements from Nicotiana (Tnt1 and Tto1) and Lycopersicon (Retrolyc1 and Tlc1) species. The study presented here was conducted to characterise Tnt1-related sequences in 20 wild species of Solanum and five cultivars of Solanum tuberosum.

RESULTS

Tnt1-related sequences were amplified from total genomic DNA using a PCR-based approach. Purified fragments were cloned and sequenced, and clustering analysis revealed three groups that differ in their U3 region. Using a network approach with a total of 453 non-redundant sequences isolated from Solanum (197), Nicotiana (140) and Lycopersicon (116) species, it is demonstrated that the Tnt1 superfamily can be treated as a population to resolve previous phylogenetic multifurcations. The resulting RNAseH network revealed that sequences group according to the Solanaceae genus, supporting a strong association with the host genome, whereas tracing the U3 region sequence association characterises the modular evolutionary pattern within the Tnt1 superfamily. Within each genus, and irrespective of species, nearly 20% of Tnt1 sequences analysed are identical, indicative of being part of an active copy. The network approach enabled the identification of putative "master" sequences and provided evidence that within a genus these master sequences are associated with distinct U3 regions.

CONCLUSION

The results presented here support the hypothesis that the Tnt1 superfamily was present early in the evolution of Solanaceae. The evidence also suggests that the RNAseH region of Tnt1 became fixed at the host genus level whereas, within each genus, propagation was ensured by the diversification of the U3 region. Different selection pressures seemed to have acted on the U3 and RNAseH modules of ancestral Tnt1 elements, probably due to the distinct functions of these regions in the retrotransposon life cycle, resulting in both co evolution and adaptation of the element population with its host.

SINEs of progress: Mobile element applications to molecular ecology

Mobile elements represent a unique and under-utilized set of tools for molecular ecologists. They are essentially homoplasy-free characters with the ability to be genotyped in a simple and efficient manner. Interpretation of the data generated using mobile elements can be simple compared to other genetic markers. They exist in a wide variety of taxa and are useful over a wide selection of temporal ranges within those taxa. Furthermore, their mode of evolution instills them with another advantage over other types of multilocus genotype data: the ability to determine loci applicable to a range of time spans in the history of a taxon. In this review, I discuss the application of mobile element markers, especially short interspersed elements (SINEs), to phylogenetic and population data, with an emphasis on potential applications to molecular ecology.

Identification of Active Transposon dTok , a Member of the hAT Family, in Rice

Recent completion of the sequencing of the rice genome has revealed that it contains >40% repetitive sequences, most of which are related to inactive transposable elements. During the molecular analysis of the floral organ number 1/multiple pistil 2 (fon1/mp2) mutant, we identified an active transposable element dTok0 that was inserted at the kinase domain of FON1, a homolog of CLAVATA1. Insertion of the element into FON1 generated an 8 bp duplication of its target sites, which is one of the major characteristics of the hAT family of transposons. The dTok0 element was actively transposed out of the FON1 gene, leaving 5-8 bp footprints. Reinsertion into a new location was observed at a low frequency. Analysis of the genome sequence showed that the rice cultivar 'Nipponbare' contains 25 copies of dTok elements; similar numbers were present in all the Oryza species examined. Because dTok0 does not encode a transposase, enzyme activity should be provided in trans. We identified a putative autonomous transposon, Tok1 that contains an intact open reading frame of the Ac-like transposase.

Molecular-genetic biodiversity in a natural population of the yeast Saccharomyces cerevisiae from "Evolution Canyon": microsatellite polymorphism, ploidy and controversial sexual status

The yeast S. cerevisiae is a central model organism in eukaryotic cell studies and a major component in many food and biotechnological industrial processes. However, the wide knowledge regarding genetics and molecular biology of S. cerevisiae is based on an extremely narrow range of strains. Studies of natural populations of S. cerevisiae, not associated with human activities or industrial fermentation environments, are very few. We isolated a panel of S. cerevisiae strains from a natural microsite, "Evolution Canyon" at Mount Carmel, Israel, and studied their genomic biodiversity. Analysis of 19 microsatellite loci revealed high allelic diversity and variation in ploidy level across the panel, from diploids to tetraploids, confirmed by flow cytometry. No significant differences were found in the level of microsatellite variation between strains derived from the major localities or microniches, whereas strains of different ploidy showed low similarity in allele content. Maximum genetic diversity was observed among diploids and minimum among triploids. Phylogenetic analysis revealed clonal, rather than sexual, structure of the triploid and tetraploid subpopulations. Viability tests in tetrad analysis also suggest that clonal reproduction may predominate in the polyploid subpopulations.

Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice

Retrotransposons are the main components of eukaryotic genomes, representing up to 80% of some large plant genomes. These mobile elements transpose via a "copy and paste" mechanism, thus increasing their copy number while active. Their accumulation is now accepted as the main factor of genome size increase in higher eukaryotes, besides polyploidy. However, the dynamics of this process are poorly understood. In this study, we show that Oryza australiensis, a wild relative of the Asian cultivated rice O. sativa, has undergone recent bursts of three LTR-retrotransposon families. This genome has accumulated more than 90,000 retrotransposon copies during the last three million years, leading to a rapid twofold increase of its size. In addition, phenetic analyses of these retrotransposons clearly confirm that the genomic bursts occurred posterior to the radiation of the species. This provides direct evidence of retrotransposon-mediated variation of genome size within a plant genus.

Mapped Ds/T-DNA launch pads for functional genomics in barley

A system for targeted gene tagging and local saturation mutagenesis based on maize transposable elements (Ac/Ds) was developed in barley (Hordeum vulgare L.). We generated large numbers of transgenic barley lines carrying a single copy of the non-autonomous maize Ds element at defined positions in the genome. Independent Ds lines were either generated by activating Ds elements in existing single-copy lines after crossing with AcTPase-expressing plants or by Agrobacterium-mediated transformation. Genomic DNA flanking Ds and T-DNA insertion sites from over 200 independent lines was isolated and sequenced, and was used for a sequence based mapping strategy in a barley reference population. More than 100 independent Ds insertion sites were mapped and can be used as launch pads for future targeted tagging of genes in the vicinity of the insertion sites. Sequence analysis of Ds and T-DNA flanking regions revealed a sevenfold preference of both mutagens for insertion into non-redundant, gene-containing regions of the barley genome. However, whilst transposed Ds elements preferentially inserted adjacent to regions with a high number of predicted and experimentally validated matrix attachment regions (nuclear MARs), this was not the case for T-DNA integration sites. These findings and an observed high transposition frequency from mapped launch pads demonstrate the future potential of gene tagging for functional genomics and gene discovery in barley.

Intraspecific DNA content variability in Festuca pallens on different geographical scales and ploidy levels

BACKGROUND AND AIMS

Intraspecific genome size variability of Festuca pallens occurring on relict rocky steppes in Central Europe was studied on two ploidy levels and three geographical scales: (1) local scale of 24 populations, (2) landscape scale of three transects in river canyons or hill systems, and (3) global scale of 160 samples covering the whole distribution area.

METHODS

DAPI flow cytometry of homogeneously cultivated samples (>or=1 year), measured randomly with two internal standards, Lycopersicon esculentum and Pisum sativum. Differences in DNA content were confirmed (1) by the double peaks of simultaneously measured samples, (2) based on measurements carried out in different seasons, and (3) by additional measurements with propidium iodide.

KEY RESULTS

On a global scale, the relative DNA content ranged between 1.170-fold in diploids and 1.164-fold in tetraploids. A maximum difference of 1.088-fold between the mean relative DNA content of nearby populations was found. In 16 of 24 populations significant variability was shown (P<0.001, 1.121-fold as maximum). For both ploidy levels, the relative genome size had the same range and geographical pattern, correlated with geographical coordinates (P<0.01). Diploids with larger genomes occur on relict habitats (P<0.01), and in areas of periglacial steppes (20,000 years ago; P<0.02). In tetraploids, the relative DNA content differs among the three previously recognized geographical types (Alpine, Pannonian and Scabrifolia, P<0.001). Tetraploids have a relative DNA content smaller than twice that of the diploids (P<0.001). An influence of microhabitat on DNA content variation was not confirmed.

CONCLUSIONS

Genome size variability occurs over all spatial scales: intrapopulation, landscape and global. Correlation between geographical coordinates and palaeovegetation type, concomitant with diploids and tetraploids, and no influence of microhabitat were found. Genome size decreases in tetraploids. Lower CVs, and thus higher accuracy, resolution and reproducibility, favour DAPI measurements for the study of intraspecific genome size variability.

Direct determination of the influence of extreme temperature on transposition and structural mutation rates of Drosophila melanogaster mobile elements

Two sets of mutation accumulation lines, one reared at 28 degrees C and the other at 24 degrees C, were compared for their transposition and rearrangement rates of eleven transposable element families. The changes affecting mobile elements were analysed by the Southern technique and in situ hybridization. No differences were found between treated and control lines. The role of the host genotype in transposition control and the significance of structural mutations in transposable element dynamics are discussed.

Diversity and evolution of Ty1-copia and Ty3-gypsy retroelements in the non-photosynthetic flowering plants Orobanche and Phelipanche (Orobanchaceae)

We present the first study on the diversity and evolution of Ty1-copia and Ty3-gypsy retroelements in a group of non-photosynthetic flowering plants. To this end partial sequences of the reverse transcriptase (rt) gene were obtained from 20 clones for each retroelement type from seven and six accessions of Orobanche and Phelipanche (Orobanchaceae), respectively. Overall sequence similarity is higher in Ty3-gypsy elements than in Ty1-copia elements in agreement with the results from other angiosperm groups. Higher sequence diversity and stronger phylogenetic structure, especially of Ty1-copia sequences, in Orobanche species compared to Phelipanche species support the previously suggested hypothesis (based on karyological and cytological data) that genomes of Orobanche species are more dynamic than those of Phelipanche species. No evidence was found for intraspecific differences of retroelement diversity nor for differences between pest taxa and their putative wild relatives, e.g., O. crenata and O. owerini. The occurrence of a few sequences from Phelipanche species in clades otherwise comprising sequences from Orobanche species might be due to horizontal gene transfer, but the alternative of vertical transmission cannot be rejected unambiguously.

Quantification of the retrotransposon BARE-1 reveals the dynamic nature of the barley genome

We used quantitative real-time PCR analysis to measure the copy number of the BARE-1 retrotransposon in 5 cultivars of barley (Hordeum vulgare), as well as in samples from its wild relative, Hordeum spontaneum. Two sets of PCR primers were used to amplify regions within the long terminal repeat (LTR) and the reverse transcriptase (RT) gene of BARE-1 (GenBank accession Z17327). The LTR primers detected an average of 2.148 x 105 +/- 0.012 x 105 copies per haploid genome among barley samples, whereas the RT primers detected an average of 1.588 x 104 +/- 0.085 x 104 copies. The average ratio of LTR:RT was estimated to be 13.5:1. This finding indicates that more than 7% of the barley genome is occupied by BARE-1 elements in the form of solo LTRs and another 2.6% of the genome is occupied by the full-length element. Taken together, BARE-1 sequences represent approximately 9.6% of the barley genome among the barley plants used in this study. For the above estimation, a genome size of 5.44 x 103 Mb for H. vulgare and 5.39 x 103 Mb for H. spontaneum were assumed. Our study on quantification results of the BARE-1 for a small group of barley cultivars showed that there are significant differences among cultivars in terms of BARE-1 copy number, providing further evidence that BARE-1 is active and has a major role in shaping the barley genome as a result of breeding and selection. Quantification results also showed that most of the elements (> 90%) are present as truncated copies (solo LTRs). These results show that there is a high level of recombination leading to the formation of truncated elements and a subsequent DNA loss from the genome. Taken together, our study provides a glimpse into a dynamic micro-evolutionary process that is the by-product of genome reshuffling and directional selection in barley breeding programs.

Retand: a novel family of gypsy-like retrotransposons harboring an amplified tandem repeat

In this paper we describe a pair of novel Ty3/gypsy retrotransposons isolated from the dioecious plant Silene latifolia, consisting of a non-autonomous element Retand-1 (3.7 kb) and its autonomous partner Retand-2 (11.1 kb). These two elements have highly similar long terminal repeat (LTR) sequences but differ in the presence of the typical retroelement coding regions (gag-pol genes), most of which are missing in Retand-1. Moreover, Retand-2 contains two additional open reading frames in antisense orientation localized between the pol gene and right LTR. Retand transcripts were detected in all organs tested (leaves, flower buds and roots) which, together with the high sequence similarity of LTRs in individual elements, indicates their recent transpositional activity. The autonomous elements are similarly abundant (2,700 copies) as non-autonomous ones (2,100 copies) in S. latifolia genome. Retand elements are also present in other Silene species, mostly in subtelomeric heterochromatin regions of all chromosomes. The only exception is the subtelomere of the short arm of the Y chromosome in S. latifolia which is known to lack the terminal heterochromatin. An interesting feature of the Retand elements is the presence of a tandem repeat sequence, which is more amplified in the non-autonomous Retand-1.

Mobilized retrotransposon Tos17 of rice by alien DNA introgression transposes into genes and causes structural and methylation alterations of a flanking genomic region

Tos17 is a copia-like endogenous retrotransposon of rice, which can be activated by various stresses such as tissue culture and alien DNA introgression. To confirm element mobilization by introgression and to study possible structural and epigenetic effects of Tos17 insertion on its target sequences, we isolated all flanking regions of Tos17 in an introgressed rice line (Tong35) that contains minute amount of genomic DNA from wild rice (Zizania latifolia). It was found that there has been apparent but limited mobilization of Tos17 in this introgression line, as being reflected by increased but stable copy number of the element in progeny of the line. Three of the five activated copies of the element have transposed into genes. Based on sequence analysis and Southern blot hybridization with several double-enzyme digests, no structural change in Tos17 could be inferred in the introgression line. Cytosine methylation status at all seven CCGG sites within Tos17 was also identical between the introgression line and its rice parent (Matsumae)-all sites being heavily methylated. In contrast, changes in structure and cytosine methylation patterns were detected in one of the three low-copy genomic regions that flank newly transposed Tos17, and all changes are stably inherited through selfed generations.

Ecological–genetic feedback in DNA repair in wild barley, Hordeum spontaneum

Regulation of genetic variation in natural populations is a problem of primary importance to evolutionary biology. In the reported study, the repair efficiency of double strand DNA breaks was compared in six wild barley accessions from Israeli natural populations of H. spontaneum: three from mesic populations (one from Maalot and two from Mount Meron, Upper Galilee) and three from xeric populations (one from Wadi Quilt in the Judean Desert and two from Sede Boqer, in the northern Negev Desert). Pulsed field gel electrophoresis was used to score double-strand breaks of DNA (DSBs) caused by methyl methanesulphonate (MMS) treatment. All six accessions were also tested for heat tolerance: four of these, three xeric and one mesic (from Maalot population), were scored as heat tolerant whereas both accessions from Mount Meron population displayed heat sensitivity. MMS caused a significant increase in the level of DSBs relative to the control in all accessions. The major questions were whether and how the efficiency of DNA repair after mutagenic treatment is affected by the environmental conditions and accession's adaptation to these conditions. Differences were found among the accessions in the repair pattern. Plants of two out of the four heat tolerant accessions did not manage to repair DNA neither at 25 degrees Celsius nor at 37 degrees Celsius. The remaining two heat tolerant accessions significantly repaired the breaks at 37 degrees Celsius, but not at 25 degrees Celsius. By contrast, plants of the two heat susceptible accessions significantly lowered the level of DSBs at 25 degrees Celsius but not at 37 degrees Celsius. Therefore, the accessions that proved capable to repair the induced damages in DNA at one of the two temperatures displayed a pattern that may imply the existence of a negative feedback mechanism in regulation of genetic variation. Such a dependence of DNA integrity on environment and genotype may serve an important factor for maintaining relatively high level of mutability without increasing the genetic load.

On The Necessity to Study Natural Bacterial Populations-The Model of Bacillus Simplex From "Evolution Canyons" I and II, Israel

How do bacteria evolve and speciate in natural environments? How does bacterial evolution relate to bacterial systematics? Exploring these answers is essential because bacteria profoundly impact life in general and, in particular, that of humans. Much insight into bacterial microevolution has come from theoretical and computational studies and from multigenerational laboratory systems ("Experimental Evolution"). These studies, however, do not take into account the diversity of modes of how bacteria can evolve under the complexity of the real world, i.e., nature. We argue, therefore, that for a comprehensive understanding of bacterial microevolution, it is essential to study natural populations. We underline our argument by introducing theBacillus simplexmodel from "Evolution Canyon", Israel. This metapopulation splits into different evolutionary lineages that have adapted to the microclimatically different slopes of "Evolution Canyon". It was shown that temperature stress is a major environmental factor driving theB. simplexadaptation and speciation progress. Therefore, this model population has proven highly suitable to study bacterial microevolution in natural habitats. Finally, we discuss theB. simplexintrapopulation divergence of lineages in light of current controversies on bacterial species concepts and taxon identification.

Retrotransposons: Metaparasites and Agents of Genome Evolution

Transposable elements comprise the bulk of higher plant genomes. The majority of these elements are the Class I LTR retrotransposons, which transpose via an RNA intermediate in a "Copy-and-Paste" mechanism. Because retrotransposons use cellular resources and their own enzymes to replicate independently of the genome as a whole, and have thereby become in many cases more predominant than the cellular genes, they have been considered "selfish DNA" and nuclear parasites. They are thought to share many features of the internal life cycle of retroviruses such as HIV (lentiviruses). However, whereas at least some of the retroviruses arriving in an organism during an infection must be functional in order for the infection to proceed, some LTR retrotransposon families appear to completely lack active members even though they remain mobile. Furthermore, the process of retrotransposition is inherently error-prone and mutagenic, giving rise to "pseudospecies," or clusters of imperfect copies. The non-autonomous retrotransposons are able to cis- and trans-parasitize host retrotransposons to gain mobility, much as do defective interfering particles of RNA viruses. Hence, a complex dynamic is set up, whereby the impact of retrotransposons on genomes can be under selection on the organismal level; the impact of non-autonomous retrotransposons on autonomous ones can likewise be under selection if there is selection on the autonomous elements themselves. We are exploring the retrotransposon life cycle and the causes and possible consequences of non-autonomy at each stage regarding genome evolution.

"Evolution Canyon": A Microcosm of Life's Evolution Focusing on Adaptation and Speciation

Local microcosmic natural laboratories, dubbed "Evolution Canyon" (EC) models, reinforce studies of regional and global macrocosmic ecological theaters across life and unravelevolution in action.The EC model laboratories permit genomic, proteomic, and phenomic studies highlighting speciation and adaptation at a microscale. Critical transplant experiment tests can evaluate interslope differential fitness. Novel techniques of genetic mapping, sequence nucleotide polymorphisms (SNPs), and wide genome coding and noncoding expressions can unravel evolutionary dynamics. Finally, fundamental problems such as stress effects on nonrandom mutations, lateral transfers, splicing variations, sex, and social evolutions, and adaptive strategies of prokaryotes and eukaryotes are testable. We are studying four "Evolution Canyons" (EC I-IV) in the Carmel, Galilee, Negev, and Golan mountains. We've identified 2,500 species in EC I (Carmel) from bacteria to mammals in an area of 7,000 m. Higher terrestrial species richness was found on the more stressful tropical "African" slope (AS). Aquatic species richness was higher on the milder, temperate "European" slope (ES). In soil fungi we found interslope local and regional adaptive divergence in sex, melanism, and conidia. In nine out of 14 (64%) model organisms across life we identified largely higher genetic polymorphisms on the more stressful "African" slope. In some model species we found higher mutation rates, gene conversion, recombination, DNA repair, and larger genome size as well as interslope divergent micro-satellites, molecular polymorphisms, retrotransposons, and wide-genome gene expression on the more stressful AS. Remarkably, interslope incipient sympatric speciation was found across life. The "Evolution Canyon" model represents the Israeli ecological equivalent of the Galapagos Islands. Micro-climatic selection overrides drift and drives both interslope adaptive radiation and incipient sympatric speciation. The EC model could potentially highlight many mysteries of evolutionary biology.

TRIM retrotransposons occur in apple and are polymorphic between varieties but not sports

Retrotransposon markers have been demonstrated to be powerful tools for investigating linkage, evolution and genetics diversity in plants. In the present study, we identified and cloned three full-size TRIM (terminal-repeat retrotransposon in miniature) group retrotransposon elements from apple (Malus domestica) cv. 'Antonovka', the first from the Rosaceae. To investigate their utility as markers, we designed primers to match the long terminal repeats (LTRs) of the apple TRIM sequences. We found that PCR reactions with even a single primer produced multiple bands, suggesting that the copy number of these TRIM elements is relatively high, and that they may be locally clustered or nested in the genome. Furthermore, the apple TRIM primers employed in IRAP (inter-retrotransposon amplified polymorphism) or REMAP (retrotransposon-microsatellite amplified polymorphism) analyses produced unique, reproducible profiles for 12 standard apple cultivars. On the other hand, all seven of the sport mutations in this study were identical to their mother cultivar. Genetic similarity values calculated from the IRAP/REMAP analyses or the STMS (sequence tagged microsatellite sites) analysis were generally comparable. PAUP cluster analysis based on IRAP and REMAP markers in apple and Japanese quince generated an NJ tree that is in good accordance with both a tree based on SMTS markers and the origin of the studied samples. Our results demonstrate that, although they do not encode the proteins necessary to carry out a life cycle and are thereby non-autonomous, TRIMs are at least as polymorphic in their insertion patterns as conventional complete retrotransposons.

GENOMEMASKER package for designing unique genomic PCR primers

BACKGROUND

The design of oligonucleotides and PCR primers for studying large genomes is complicated by the redundancy of sequences. The eukaryotic genomes are particularly difficult to study due to abundant repeats. The speed of most existing primer evaluation programs is not sufficient for large-scale experiments.

RESULTS

In order to improve the efficiency and success rate of automatic primer/oligo design, we created a novel method which allows rapid masking of repeats in large sequence files, for example in eukaryotic genomes. It also allows the detection of all alternative binding sites of PCR primers and the prediction of PCR products. The new method was implemented in a collection of efficient programs, the GENOMEMASKER package. The performance of the programs was compared to other similar programs. We also modified the PRIMER3 program, to be able to design primers from lowercase-masked sequences.

CONCLUSION

The GENOMEMASKER package is able to mask the entire human genome for non-unique primers within 6 hours and find locations of all binding sites for 10,000 designed primer pairs within 10 minutes. Additionally, it predicts all alternative PCR products from large genomes for given primer pairs.

Oligonucleotide microarray analysis of strain- and gender-associated gene expression in the human blood fluke, Schistosoma japonicum

Schistosomiasis is a chronic and debilitating disease caused by blood flukes (digenetic trematodes) of the genus Schistosoma. Schistosomiasis japonica, a zoonosis caused by Schistosoma japonicum, is endemic to the Philippines and China. We utilised a 22,575 feature custom oligonucleotide DNA microarray designed from public domain databases of schistosome-expressed sequence tags to explore differential gene expression between the Philippine (SJP) and Chinese (SJC) strains of S. japonicum, and between male and female S. japonicum. We found that 593, 664 and 426 probes were differentially expressed between the two geographical strains when we compared mix sexed adults, male worms and female worms. Additionally, the study revealed that 1163 male- and 1016 female-associated probes were differentially expressed in SJP whereas 1047 male- and 897 female-associated probes were differentially expressed in SJC. The study greatly expands previously published data of strain and gender-associated differential expression in S. japonicum. Further, these new data provide a stepping stone for understanding the complexities of the biology, sexual differentiation, maturation, and development of human schistosomes, signaling new approaches for identifying novel intervention and diagnostic targets against schistosomiasis.

Development of an efficient retrotransposon-based fingerprinting method for rapid pea variety identification

Fast and efficient DNA fingerprinting of crop cultivars and individuals is frequently used in both theoretical population genetics and in practical breeding. Numerous DNA marker technologies exist and the ratio of speed, cost and accuracy are of importance. Therefore even in species where highly accurate and polymorphic marker systems are available, such as microsatellite SSR (simple sequence repeats), also alternative methods may be of interest. Thanks to their high abundance and ubiquity, temporary mobile retrotransposable elements come into recent focus. Their properties, such as genome wide distribution and well-defined origin of individual insertions by descent, predetermine them for use as molecular markers. In this study, several Ty3-gypsy type retrotransposons have been developed and adopted for the inter-retrotransposon amplified polymorphism (IRAP) method, which is suitable for fast and efficient pea cultivar fingerprinting. The method can easily distinguish even between genetically closely related pea cultivars and provide high polymorphic information content (PIC) in a single PCR analysis.

Genome complexity and repetitive DNA in metazoans from extreme marine environments

As genomics converges with ecology and evolution to identify the fundamental linkages between genome structure and function, genome and transcriptome complexity will need to be measured in organisms from more diverse habitats, most often in the absence of complete sequence data. Here, we describe the complexity of ten genomes measured by a novel, high-throughput fluorescence-based kinetic hybridization assay. We applied the Shannon information index, H, and a related, fluorescence-adjusted index, H(f), as unique metrics of the hybridization kinetics to complement the conventional rate constant, k. A strong, positive relationship was present between H(f), and the repetitive DNA content of five eukaryotic genomes previously determined by Cot kinetic analyses (Onchorynchus keta, Ilyanassa obsoleta, Bos taurus, Limulus polyphemus, Saccharyomyces cerevisiae). This relationship was used to characterize the complexity of previously unstudied genomic samples in five metazoan taxa from three marine environments, including deep-sea hydrothermal vents (Alvinella pompejana), the temperate subtidal (Streblospio benedicti), and Antarctic coastal bays (Sterechinus neumayeri, Odontaster validus, Tritonia antarctica). Contrary to the predictions of nucleotypic theory, Antarctic invertebrates consistently had the lowest quantities of repetitive DNA in conjunction with low metabolic rates and highly protracted rates of cell division and larval development. Conversely, hydrothermal vent species with rapid cell division and growth do not have significantly different genome sizes or particularly low amounts of repetitive DNA as compared to non-vent, deep-sea taxa. Furthermore, there appears to be a positive correlation between the temperature at which the most abundant repetitive sequence classes anneal and habitat thermal stability. Thus, our study reveals a potential shift in repetitive sequence representation between these extreme environments that may be related to genome function in species living at these different thermal regimes.

Adaptation and incipient sympatric speciation of Bacillus simplex under microclimatic contrast at "Evolution Canyons" I and II, Israel

The microevolutionary dynamics of prokaryotes in natural habitats, such as soil, is poorly understood in contrast to our increasing knowledge on their immense diversity. We performed microevolutionary analyses on 945 soil isolates of Bacillus simplex from "Evolution Canyons" I (Carmel, Israel) and II (Galilee, Israel). These canyons represent similar ecological replicates, separated by 40 km, with highly contrasting interslope abiotic and biotic conditions in each (within a distance of only 100-400 m). Strains representing genetic groups were identical in their 16S sequences, suggesting high genetic similarity and monophyletic origin. Parallel and nested phylogenetic structures correlated with ecological contrasts rather than geographical distance. Additionally, slope-specific populations differed substantially in their diversity. The levels of DNA repair (determined by UV sensitivity) and spontaneous mutation rate (resistance to rifampicin) relate to ecological stress and phylogeny. Altogether, the results suggest adaptive radiation at a microscale. We discuss the observed adaptive population structures in the context of incipient sympatric speciation in soil bacteria. We conclude that, despite different biology, prokaryotes, like sexually reproducing eukaryotes, may consist of true species and parallel ecological speciation in eukaryotes.