Plant transposable elements: where genetics meets genomics

Analysis of the chromatin binding affinity of retrotransposases reveals novel roles in diploid and tetraploid cotton

LTR-retrotransposable elements are major components of diploid (Gossypium arboreum) and tetraploid (Gossypium hirsutum) cotton genomes that have undergone dramatic increases in copy number during the course of evolution. However, little is known about the biological functions of LTR-retrotransposable elements in cotton. Here, we show that a copia-like LTR-retrotransposable element has maintained considerable activity in both G. arboreum and G. hirsutum. We identified two functional domains of the retrotransposon and analyzed their expression levels in various cotton tissues, including leaves, ovules, and germinating seeds. ChIP-qPCR (chromatin immunoprecipitation followed by quantitative PCR), using a copia-specific antibody, established that copia-like proteins primarily bind to the first exons of several protein-coding genes in cotton cells. This finding suggests that retrotransposons play a novel, important role in regulating the transcriptional activities of protein-coding genes with various biological activities.

Repetitive DNA in the Architecture, Repatterning, and Diversification of the Genome of Aegilops speltoides Tausch (Poaceae, Triticeae)

The genome's adaptability to environmental changes, especially during rapid climatic fluctuations, underlies the existence and evolution of species. In the wild, genetic and epigenetic genomic changes are accompanied by significant alterations in the complex nuclear repetitive DNA fraction. Current intraspecific polymorphism of repetitive DNA is closely related to ongoing chromosomal rearrangements, which typically result from erroneous DNA repair and recombination. In this study, we addressed tandem repeat patterns and interaction/reshuffling both in pollen mother cell (PMC) development and somatogenesis in the wild diploid cereal Aegilops speltoides, with a focus on genome repatterning and stabilization. Individual contrasting genotypes were investigated using the fluorescent in situ hybridization (FISH) approach by applying correlative fluorescence and electron microscopy. Species-specific Spelt1 and tribe-specific Spelt52 tandem repeats were used as the markers for monitoring somatic and meiotic chromosomal interactions and dynamics in somatic interphase nuclei. We found that, the number of tandem repeat clusters in nuclei is usually lower than the number on chromosomes due to the associations of clusters of the same type in common blocks. In addition, tightly associated Spelt1-Spelt52 clusters were revealed in different genotypes. The frequencies of nonhomologous/ectopic associations between tandem repeat clusters were revealed in a genotype-/population-specific manner. An increase in the number of tandem repeat clusters in the genome causes an increase in the frequencies of their associations. The distal/terminal regions of homologous chromosomes are separated in nuclear space, and nonhomologous chromosomes are often involved in somatic recombination as seen by frequently formed interchromosomal chromatin bridges. In both microgametogenesis and somatogenesis, inter- and intrachromosomal associations are likely to lead to DNA breaks during chromosome disjunction in the anaphase stage. Uncondensed/improperly packed DNA fibers, mainly in heterochromatic regions, were revealed in both the meiotic and somatic prophases that might be a result of broken associations. Altogether, the data obtained showed that intraorganismal dynamics of repetitive DNA under the conditions of natural out-crossing and artificial intraspecific hybridization mirrors the structural plasticity of the Ae. speltoides genome, which is interlinked with genetic diversity through the species distribution area in contrasting ecogeographical environments in and around the Fertile Crescent.

LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes

The accumulation and removal of transposable elements (TEs) is a major driver of genome size evolution in eukaryotes. In plants, long terminal repeat (LTR) retrotransposons (LTR-RTs) represent the majority of TEs and form most of the nuclear DNA in large genomes. Unequal recombination (UR) between LTRs leads to removal of intervening sequence and formation of solo-LTRs. UR is a major mechanism of LTR-RT removal in many angiosperms, but our understanding of LTR-RT-associated recombination within the large, LTR-RT-rich genomes of conifers is quite limited. We employ a novel read-based methodology to estimate the relative rates of LTR-RT-associated UR within the genomes of four conifer and seven angiosperm species. We found the lowest rates of UR in the largest genomes studied, conifers and the angiosperm maize. Recombination may also resolve as gene conversion, which does not remove sequence, so we analyzed LTR-RT-associated gene conversion events (GCEs) in Norway spruce and six angiosperms. Opposite the trend for UR, we found the highest rates of GCEs in Norway spruce and maize. Unlike previous work in angiosperms, we found no evidence that rates of UR correlate with retroelement structural features in the conifers, suggesting that another process is suppressing UR in these species. Recent results from diverse eukaryotes indicate that heterochromatin affects the resolution of recombination, by favoring gene conversion over crossing-over, similar to our observation of opposed rates of UR and GCEs. Control of LTR-RT proliferation via formation of heterochromatin would be a likely step toward large genomes in eukaryotes carrying high LTR-RT content.

Transposable Elements in the Organization and Diversification of the Genome of Aegilops speltoides Tausch (Poaceae, Triticeae)

Repetitive DNA-specifically, transposable elements (TEs)-is a prevailing genomic fraction in cereals that underlies extensive genome reshuffling and intraspecific diversification in the wild. Although large amounts of data have been accumulated, the effect of TEs on the genome architecture and functioning is not fully understood. Here, plant genome organization was addressed by means of cloning and sequencing TE fragments of different types, which compose the largest portion of the Aegilops speltoides genome. Individual genotypes were analyzed cytogenetically using the cloned TE fragments as the DNA probes for fluorescence in situ hybridization (FISH). The obtained TE sequences of the Ty1-copia, Ty3-gypsy, LINE, and CACTA superfamilies showed the relatedness of the Ae. speltoides genome to the Triticeae tribe and similarities to evolutionarily distant species. A significant number of clones consisted of intercalated fragments of TEs of various types, in which Fatima (Ty3-gypsy) sequences predominated. At the chromosomal level, different TE clones demonstrated sequence-specific patterning, emphasizing the effect of the TE fraction on the Ae. speltoides genome architecture and intraspecific diversification. Altogether, the obtained data highlight the current species-specific organization and patterning of the mobile element fraction and point to ancient evolutionary events in the genome of Ae. speltoides.

Impact of transposable elements on genome structure and evolution in bread wheat

BACKGROUND

Transposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution. The most recent assembly of hexaploid bread wheat recovered the highly repetitive TE space in an almost complete chromosomal context and enabled a detailed view into the dynamics of TEs in the A, B, and D subgenomes.

RESULTS

The overall TE content is very similar between the A, B, and D subgenomes, although we find no evidence for bursts of TE amplification after the polyploidization events. Despite the near-complete turnover of TEs since the subgenome lineages diverged from a common ancestor, 76% of TE families are still present in similar proportions in each subgenome. Moreover, spacing between syntenic genes is also conserved, even though syntenic TEs have been replaced by new insertions over time, suggesting that distances between genes, but not sequences, are under evolutionary constraints. The TE composition of the immediate gene vicinity differs from the core intergenic regions. We find the same TE families to be enriched or depleted near genes in all three subgenomes. Evaluations at the subfamily level of timed long terminal repeat-retrotransposon insertions highlight the independent evolution of the diploid A, B, and D lineages before polyploidization and cases of concerted proliferation in the AB tetraploid.

CONCLUSIONS

Even though the intergenic space is changed by the TE turnover, an unexpected preservation is observed between the A, B, and D subgenomes for features like TE family proportions, gene spacing, and TE enrichment near genes.

Substantial Epigenetic Variation Causing Flower Color Chimerism in the Ornamental Tree Prunus mume Revealed by Single Base Resolution Methylome Detection and Transcriptome Sequencing

Epigenetic changes caused by methylcytosine modification participate in gene regulation and transposable element (TE) repression, resulting in phenotypic variation. Although the effects of DNA methylation and TE repression on flower, fruit, seed coat, and leaf pigmentation have been investigated, little is known about the relationship between methylation and flower color chimerism. In this study, we used a comparative methylomic⁻transcriptomic approach to explore the molecular mechanism responsible for chimeric flowers in Prunus mume "Danban Tiaozhi". High-performance liquid chromatography-electrospray ionization mass spectrometry revealed that the variation in white (WT) and red (RT) petal tissues in this species is directly due to the accumulation of anthocyanins, i.e., cyanidin 3,5-O-diglucoside, cyanidin 3-O-glucoside, and peonidin 3-O-glucoside. We next mapped the first-ever generated methylomes of P. mume, and found that 11.29⁻14.83% of the genomic cytosine sites were methylated. We also determined that gene expression was negatively correlated with methylcytosine level in general, and uncovered significant epigenetic variation between WT and RT. Furthermore, we detected differentially methylated regions (DMRs) and DMR-related genes between WT and RT, and concluded that many of these genes, including differentially expressed genes (DEGs) and transcription factor genes, are critical participants in the anthocyanin regulatory pathway. Importantly, some of the associated DEGs harbored TE insertions that were also modified by methylcytosine. The above evidence suggest that flower color chimerism in P. mume is induced by the DNA methylation of critical genes and TEs.

Transposable Elements Contribute to the Adaptation of Arabidopsis thaliana

Transposable elements (TEs) are mobile genetic elements with very high mutation rates that play important roles in shaping genome architecture and regulating phenotypic variation. However, the extent to which TEs influence the adaptation of organisms in their natural habitats is largely unknown. Here, we scanned 201 representative resequenced genomes from the model plant Arabidopsis thaliana and identified 2,311 polymorphic TEs from noncentromeric regions. We found expansion and contraction of different types of TEs in different A. thaliana populations. More importantly, we identified two TE insertions that are likely candidates to play a role in adaptive evolution. Our results highlight the importance of variations in TEs for the adaptation of plants in general in the context of rapid global climate change.

Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes

Maize is an important crop with a high level of genome diversity and heterosis. The genome sequence of a typical female line, B73, was previously released. Here, we report a de novo genome assembly of a corresponding male representative line, Mo17. More than 96.4% of the 2,183 Mb assembled genome can be accounted for by 362 scaffolds in ten pseudochromosomes with 38,620 annotated protein-coding genes. Comparative analysis revealed large gene-order and gene structural variations: approximately 10% of the annotated genes were mutually nonsyntenic, and more than 20% of the predicted genes had either large-effect mutations or large structural variations, which might cause considerable protein divergence between the two inbred lines. Our study provides a high-quality reference-genome sequence of an important maize germplasm, and the intraspecific gene order and gene structural variations identified should have implications for heterosis and genome evolution.

Next generation sequencing reveals packaging of host RNAs by brome mosaic virus

Although RNA viruses evolved the mechanisms of specific encapsidation, miss-packaging of cellular RNAs has been reported in such RNA virus systems as flock house virus or cucumber necrosis virus. To find out if brome mosaic virus (BMV), a tripartite RNA virus, can package cellular RNAs, BMV was propagated in barley and in Nicotiana benthamiana hosts, purified by cesium chloride (CsCl) gradient ultracentrifugation followed by nuclease treatment to remove any contaminating cellular (host) RNAs. The extracted virion RNA was then sequenced by using next-generation sequencing (NGS RNA-Seq) with the Illumina protocol. Bioinformatic analysis revealed the content of host RNAs ranging from 0.07% for BMV extracted from barley to 0.10% for the virus extracted from N. benthamiana. The viruses from two sources appeared to co-encapsidate different patterns of host-RNAs, including ribosomal RNAs (rRNAs), messenger RNAs (mRNAs) but also mitochondrial and plastid RNAs and, interestingly, transposable elements, both transposons and retrotransposons. Our data reveal that BMV virions can carry host RNAs, having a potential to mediate horizontal gene transfer (HGT) in plants.

Characterization of leaf transcriptome, development and utilization of unigenes-derived microsatellite markers in sugarcane (Saccharum sp. hybrid)

Sugarcane (Saccharum species hybrid) is the major source of sugar (> 80% sugar) in the world and is cultivated in more than 115 countries. It has recently gained attention as a source of biofuel (ethanol). Due to genomic complexity, the development of new genomic resources is imperative in understanding the gene regulation and function, and to fine tune the genetic improvement of sugarcane. In this study, a cDNA library was constructed from mature leaves so as to develop ESTs resources which were further compared with nucleotide and protein databases to explore the functional identity of sugarcane genes. The non-redundant ESTs (unigenes) were categorized into 18 metabolic functions. The major categories were bioenergetics and photosynthesis (4%), cell metabolism (5%), development related protein (3%), membrane-related, mobile genetic elements (5%), signal transduction (2%), DNA (1%), RNA (1%) and protein (2%) metabolism, other metabolic processes (3%), transcription factors (1%), transport (4%) and proteins related to stress/defense (4%). From 540 unique ESTs, 212 simple sequence repeats were identified, of which 206 were from 463 singlets and six were mined from 77 contig sequences. A total of 540 unique EST sequences were used for SSR search of which 97 (17.9%) contained specified SSR motifs, generating 212 unique SSRs. The genes characterized in this study and the EST-derived microsatellite markers identified from the cDNA library will enrich genomic resources for association- and linkage-mapping studies in sugarcane.

The pomegranate (Punica granatum L.) genome provides insights into fruit quality and ovule developmental biology

Pomegranate (Punica granatum L.) has an ancient cultivation history and has become an emerging profitable fruit crop due to its attractive features such as the bright red appearance and the high abundance of medicinally valuable ellagitannin-based compounds in its peel and aril. However, the limited genomic resources have restricted further elucidation of genetics and evolution of these interesting traits. Here, we report a 274-Mb high-quality draft pomegranate genome sequence, which covers approximately 81.5% of the estimated 336-Mb genome, consists of 2177 scaffolds with an N50 size of 1.7 Mb and contains 30 903 genes. Phylogenomic analysis supported that pomegranate belongs to the Lythraceae family rather than the monogeneric Punicaceae family, and comparative analyses showed that pomegranate and Eucalyptus grandis share the paleotetraploidy event. Integrated genomic and transcriptomic analyses provided insights into the molecular mechanisms underlying the biosynthesis of ellagitannin-based compounds, the colour formation in both peels and arils during pomegranate fruit development, and the unique ovule development processes that are characteristic of pomegranate. This genome sequence provides an important resource to expand our understanding of some unique biological processes and to facilitate both comparative biology studies and crop breeding.

In silico Phylogenetic Analysis of hAT Transposable Elements in Plants

Transposable elements of the hAT family exhibit a cross-kingdom distribution. The plant hAT transposons are proposed to play a critical role in plant adaptive evolution and DNA damage repair. The sequencing of an increasing number of plant genomes has facilitated the discovery of a plethora of hAT elements. This enabled us to perform an in-depth phylogenetic analysis of consensus hAT sequences in the fully-sequenced genomes of 11 plant species that represent diverse taxonomic divisions. Four putative nucleotide sequences were detected in cottonwood that were similar to the corresponding animal hAT elements, which are possibly sequence artifacts. Phylogenetic trees were constructed based both on the known and putative hAT sequences, by employing two different methods of phylogenetic inference. On the basis of the reconstructed phylogeny, plant hAT elements have rather evolved through kingdom-specific vertical gene transfer and gene amplifications within eudicotyledons, monocotyledons, and chlorophytes. Furthermore, the plant hAT sequences were searched for conserved DNA and amino acid sequence features. In this way, diagnostic sequence patterns were detected which allowed us to assign functional annotations to the plant hAT sequences.

Identification of transposons near predicted lncRNA and mRNA pools of Prunus mume using an integrative transposable element database constructed from Rosaceae plant genomes

This study focused on the construction of a database of transposable elements (TEs) from Rosaceae plants, the third most economically important plant family in temperate regions, and its transcriptomics applications. The evolutionary effects of TEs on gene regulation have been explored, and TE insertions can be the molecular bases of changes in gene structure and function. However, a specific Rosaceae plant TE database (RPTEdb) is lacking. The genomes of several Rosaceae plants have been sequenced, providing the opportunity to mine TE data at a whole-genome level. Therefore, we constructed the RPTEdb, a collective and comprehensive database of 19,596 annotated TEs in the genomes of Rosaceae plants using previously described identification and annotation methods and published genome sequences. The user-friendly web-based database provides access to research tools through hyperlinks, including Browse, TE tree, tools, JBrowse, and search sections, and through the inputting of sequences on the main webpage. Next, we performed one advanced application in which TEs near predicted long non-coding RNA (lncRNA) and mRNA domains within white and red petal-tissue transcriptomes of Prunus mume 'Fuban Tiaozhi' were identified, revealing 16 TEs that overlapped or were near 16 differentially expressed lncRNA domains, and 54 TEs that overlapped or were near 54 differentially expressed mRNA domains, and the TEs' possible functions were also discussed. We believe that the RPTEdb will contribute to the understanding of TE roles in the structural, functional and evolutionary dynamics of Rosaceae plant genomes.

Landscape of Transposable Elements Focusing on the B Chromosome of the Cichlid Fish Astatotilapia latifasciata

B chromosomes (Bs) are supernumerary elements found in many taxonomic groups. Most B chromosomes are rich in heterochromatin and composed of abundant repetitive sequences, especially transposable elements (TEs). B origin is generally linked to the A-chromosome complement (A). The first report of a B chromosome in African cichlids was in Astatotilapia latifasciata, which can harbor 0, 1, or 2 Bs Classical cytogenetic studies found high a TE content on this B chromosome. In this study, we aimed to understand TE composition and expression in the A. latifasciata genome and its relation to the B chromosome. We used bioinformatics analysis to explore the genomic organization of TEs and their composition on the B chromosome. The bioinformatics findings were validated by fluorescent in situ hybridization (FISH) and real-time PCR (qPCR). A. latifasciata has a TE content similar to that of other cichlid fishes and several expanded elements on its B chromosome. With RNA sequencing data (RNA-seq), we showed that all major TE classes are transcribed in the brain, muscle, and male and female gonads. An evaluation of TE transcription levels between B- and B+ individuals showed that few elements are differentially expressed between these groups and that the expanded B elements are not highly transcribed. Putative silencing mechanisms may act on the B chromosome of A. latifasciata to prevent the adverse consequences of repeat transcription and mobilization in the genome.

The Role of Transposable Elements in Speciation

Understanding the phenotypic and molecular mechanisms that contribute to genetic diversity between and within species is fundamental in studying the evolution of species. In particular, identifying the interspecific differences that lead to the reduction or even cessation of gene flow between nascent species is one of the main goals of speciation genetic research. Transposable elements (TEs) are DNA sequences with the ability to move within genomes. TEs are ubiquitous throughout eukaryotic genomes and have been shown to alter regulatory networks, gene expression, and to rearrange genomes as a result of their transposition. However, no systematic effort has evaluated the role of TEs in speciation. We compiled the evidence for TEs as potential causes of reproductive isolation across a diversity of taxa. We find that TEs are often associated with hybrid defects that might preclude the fusion between species, but that the involvement of TEs in other barriers to gene flow different from postzygotic isolation is still relatively unknown. Finally, we list a series of guides and research avenues to disentangle the effects of TEs on the origin of new species.

Complex signatures of genomic variation of two non-model marine species in a homogeneous environment

BACKGROUND

Genomic tools are increasingly being used on non-model organisms to provide insights into population structure and variability, including signals of selection. However, most studies are carried out in regions with distinct environmental gradients or across large geographical areas, in which local adaptation is expected to occur. Therefore, the focus of this study is to characterize genomic variation and selective signals over short geographic areas within a largely homogeneous region. To assess adaptive signals between microhabitats within the rocky shore, we compared genomic variation between the Cape urchin (Parechinus angulosus), which is a low to mid-shore species, and the Granular limpet (Scutellastra granularis), a high shore specialist.

RESULTS

Using pooled restriction site associated DNA (RAD) sequencing, we described patterns of genomic variation and identified outlier loci in both species. We found relatively low numbers of outlier SNPs within each species, and identified outlier genes associated with different selective pressures than those previously identified in studies conducted over larger environmental gradients. The number of population-specific outlier loci differed between species, likely owing to differential selective pressures within the intertidal environment. Interestingly, the outlier loci were highly differentiated within the two northernmost populations for both species, suggesting that unique evolutionary forces are acting on marine invertebrates within this region.

CONCLUSIONS

Our study provides a background for comparative genomic studies focused on non-model species, as well as a baseline for the adaptive potential of marine invertebrates along the South African west coast. We also discuss the caveats associated with Pool-seq and potential biases of sequencing coverage on downstream genomic metrics. The findings provide evidence of species-specific selective pressures within a homogeneous environment, and suggest that selective forces acting on small scales are just as crucial to acknowledge as those acting on larger scales. As a whole, our findings imply that future population genomic studies should expand from focusing on model organisms and/or studying heterogeneous regions to better understand the evolutionary processes shaping current and future biodiversity patterns, particularly when used in a comparative phylogeographic context.

A transposition-active Phyllostachys edulis long terminal repeat (LTR) retrotransposon

Due to infrequent sexual reproduction, moso bamboo breeding by hybridization is extremely technically difficult. Insertional mutagenesis based on endogenous active transposons may thus serve as an alternative method to create new germplasm of moso bamboo. In the present study, using LTR-STRUC, a full-length intact long terminal repeat (LTR) retrotransposon was identified in the moso bamboo genome and was named PHRE2 (Phyllostachys edulis retrotransposon 2). The 5' and 3' LTR sequences of PHRE2 were highly (98.39%) similar. PHRE2 contains all domains necessary for transposition such as gag, pr, rt, rh, and int. The coding frames of these essential domains were complete and had no apparent mutations. In addition, PHRE2 possessed a prime binding site (PBS), a polypurine tract (PPT), and two typical sequences of LTR retrotransposons. A genome-wide scan showed that the moso bamboo genome has only one full-length sequence of PHYRE2. After its transfer to Arabidopsis thaliana, an increase in PHRE2 copy number occurred in the T₃ plants compared to in the T₂ plants. After moso bamboo seedlings were grown in tissue culture or treated by irradiation or plant hormones, the copy number of PHRE2 significantly increased. These findings indicate that PHRE2 has the capacity for transposition, which can be induced by environmental conditions.

Massive Loss of DNA Methylation in Nitrogen-, but Not in Phosphorus-Deficient Zea mays Roots Is Poorly Correlated With Gene Expression Differences

DNA methylation in plants plays a role in transposon silencing, genome stability and gene expression regulation. Environmental factors alter the methylation pattern of DNA and recently nutrient stresses, such as phosphate starvation, were shown to alter DNA methylation. Furthermore, DNA methylation had been frequently addressed in plants with notably small genomes that are poor in transposons. Here, we compare part of the DNA methylome of nitrogen- and phosphorus-deficient maize roots by reduced representation sequencing and analyze their relationship with gene expression under prolonged stresses. Tremendous DNA methylation loss was encountered in maize under nitrogen-deficiency, but much less with phosphorus-deficiency. This occurred only in the symmetrical cytosine context, predominantly in CG context, but also in the CHG context. In contrast to other plants, differential methylation in the more flexible CHH context was essentially absent. In both deficiency conditions a similar number of differentially expressed genes were found and differentially methylated regions (DMRs) were predominantly identified in transposable elements (TEs). A minor fraction of such DMRs was associated with altered gene expression of nearby genes. Interestingly, although these TEs were mostly hypomethylated, they were associated with both up- or down regulated gene expression. Our results suggest a different methylome regulation in maize compared to rice and Arabidopsis upon nutrient deficiencies and point to highly nutrient- and species-specific dynamics of genomic DNA methylation. Description of Significance: DNA methylation suppresses transposons in plant genomes, but was also associated with other genome protective functions and gene expression regulation. Recently it was shown that DNA methylation dynamically responds to several abiotic and biotic environmental factors, but to a large instance, DNA methylation is also heritable. DNA methylation changes have also been reported under phosphorus starvation in rice and Arabidopsis, but its relation with other nutrients and its importance for individual gene expression remains unclear. Here, DNA methylation changes upon the deficiency of two major essential nutrients, nitrogen and phosphorus, were studied in parallel with gene expression responses in maize roots. We show context, nutrient- and species-specific patterns in the methylome, as well as its relation with the nutrient-deficiency transcriptome. While cases of differentially methylated regions in the vicinity of differentially expressed genes were apparent, both positive and negative roles on the gene expression were identified, irrespective of the context.

FAR1-RELATED SEQUENCE (FRS) and FRS-RELATED FACTOR (FRF) Family Proteins in Arabidopsis Growth and Development

Transposable elements make important contributions to adaptation and evolution of their host genomes. The well-characterized transposase-derived transcription factor FAR-RED ELONGATED HYPOCOTYLS3 (FHY3) and its homologue FAR-RED IMPAIRED RESPONSE1 (FAR1) have crucial functions in plant growth and development. In addition, FHY3 and FAR1 are the founding members of the FRS (FAR1-RELATED SEQUENCE) and FRF (FRS-RELATED FACTOR) families, which are conserved among land plants. Although the coding sequences of many putative FRS and FRF orthologs have been found in various clades of angiosperms, their physiological functions remain elusive. Here, we summarize recent progress toward characterizing the molecular mechanisms of FHY3 and FAR1, as well as other FRS-FRF family proteins, examining their roles in regulating plant growth and development. This review also suggests future directions for further functional characterization of other FRS-FRF family proteins in plants.

Transposon-Derived Non-coding RNAs and Their Function in Plants

Transposable elements (TEs) are often regarded as harmful genomic factors and indeed they are strongly suppressed by the epigenetic silencing mechanisms. On the other hand, the mobilization of TEs brings about variability of genome and transcriptome which are essential in the survival and evolution of the host species. The vast majority of such controlling TEs influence the neighboring genes in cis by either promoting or repressing the transcriptional activities. Although TEs are highly repetitive in the genomes and transcribed in specific stress conditions or developmental stages, the trans-acting regulatory roles of TE-derived RNAs have been rarely studied. It was only recently that TEs were investigated for their regulatory roles as a form of RNA. Particularly in plants, TEs are ample source of small RNAs such as small interfering (si) RNAs and micro (mi) RNAs. Those TE-derived small RNAs have potentials to affect non-TE transcripts by sequence complementarity, thereby generating novel gene regulatory networks including stress resistance and hybridization barrier. Apart from the small RNAs, a number of long non-coding RNAs (lncRNAs) are originated from TEs in plants. For example, a retrotransposon-derived lncRNA expressed in rice root acts as a decoy RNA or miRNA target mimic which negatively controls miRNA171. The post-transcriptional suppression of miRNA171 in roots ensures the stabilization of the target transcripts encoding SCARECROW-LIKE transcription factors, the key regulators of root development. In this review article, the recent discoveries of the regulatory roles of TE-derived RNAs in plants will be highlighted.

Convergent adaptive evolution in marginal environments: unloading transposable elements as a common strategy among mangrove genomes

Several clades of mangrove trees independently invade the interface between land and sea at the margin of woody plant distribution. As phenotypic convergence among mangroves is common, the possibility of convergent adaptation in their genomes is quite intriguing. To study this molecular convergence, we sequenced multiple mangrove genomes. In this study, we focused on the evolution of transposable elements (TEs) in relation to the genome size evolution. TEs, generally considered genomic parasites, are the most common components of woody plant genomes. Analyzing the long terminal repeat-retrotransposon (LTR-RT) type of TE, we estimated their death rates by counting solo-LTRs and truncated elements. We found that all lineages of mangroves massively and convergently reduce TE loads in comparison to their nonmangrove relatives; as a consequence, genome size reduction happens independently in all six mangrove lineages; TE load reduction in mangroves can be attributed to the paucity of young elements; the rarity of young LTR-RTs is a consequence of fewer births rather than access death. In conclusion, mangrove genomes employ a convergent strategy of TE load reduction by suppressing element origination in their independent adaptation to a new environment.

The Aegilops tauschii genome reveals multiple impacts of transposons

Wheat is an important global crop with an extremely large and complex genome that contains more transposable elements (TEs) than any other known crop species. Here, we generated a chromosome-scale, high-quality reference genome of Aegilops tauschii, the donor of the wheat D genome, in which 92.5% sequences have been anchored to chromosomes. Using this assembly, we accurately characterized genic loci, gene expression, pseudogenes, methylation, recombination ratios, microRNAs and especially TEs on chromosomes. In addition to the discovery of a wave of very recent gene duplications, we detected that TEs occurred in about half of the genes, and found that such genes are expressed at lower levels than those without TEs, presumably because of their elevated methylation levels. We mapped all wheat molecular markers and constructed a high-resolution integrated genetic map corresponding to genome sequences, thereby placing previously detected agronomically important genes/quantitative trait loci (QTLs) on the Ae. tauschii genome for the first time.

Tracking the genome-wide outcomes of a transposable element burst over decades of amplification

Rice (Oryza sativa) has a unique combination of attributes that made it an ideal host to track the natural behavior of very active transposable elements (TEs) over generations. In this study, we have exploited its small genome and propagation by self or sibling pollination to identify and characterize two strain pairs, EG4/HEG4 and A119/A123, undergoing bursts of the nonautonomous miniature inverted repeat transposable element mPing. Comparative sequence analyses of these strains have advanced our understanding of (i) factors that contribute to sustaining a TE burst for decades, (ii) features that distinguish a natural TE burst from bursts in cell culture or mutant backgrounds, and (iii) the extent to which TEs can rapidly diversify the genome of an inbred organism.

To understand the success strategies of transposable elements (TEs) that attain high copy numbers, we analyzed two pairs of rice (Oryza sativa) strains, EG4/HEG4 and A119/A123, undergoing decades of rapid amplification (bursts) of the class 2 autonomous Ping element and the nonautonomous miniature inverted repeat transposable element (MITE) mPing. Comparative analyses of whole-genome sequences of the two strain pairs validated that each pair has been maintained for decades as inbreds since divergence from their respective last common ancestor. Strains EG4 and HEG4 differ by fewer than 160 SNPs and a total of 264 new mPing insertions. Similarly, strains A119 and A123 exhibited about half as many SNPs (277) as new mPing insertions (518). Examination of all other potentially active TEs in these genomes revealed only a single new insertion out of ∼40,000 loci surveyed. The virtual absence of any new TE insertions in these strains outside the mPing bursts demonstrates that the Ping/mPing family gradually attains high copy numbers by maintaining activity and evading host detection for dozens of generations. Evasion is possible because host recognition of mPing sequences appears to have no impact on initiation or maintenance of the burst. Ping is actively transcribed, and both Ping and mPing can transpose despite methylation of terminal sequences. This finding suggests that an important feature of MITE success is that host recognition does not lead to the silencing of the source of transposase.

Computational identification of harmful mutation regions to the activity of transposable elements

Background

Transposable elements (TEs) are interspersed DNA sequences that can move or copy to new positions within a genome. TEs are believed to promote speciation and their activities play a significant role in human disease. In the human genome, the 22 AluY and 6 AluS TE subfamilies have been the most recently active, and their transposition has been implicated in many inherited human diseases and in various forms of cancer. Therefore, understanding their transposition activity is very important and identifying the factors that affect their transpositional activity is of great interest. Recently, there has been some work done to quantify the activity levels of active Alu TEs based on variation in the sequence. Given this activity data, an analysis of TE activity based on the position of mutations is conducted.

Results

A method/simulation is created to computationally predict so-called harmful mutation regions in the consensus sequence of a TE; that is, mutations that occur in these regions decrease the transpositional activity dramatically. The methods are applied to the most active subfamily, AluY, to identify the harmful regions, and seven harmful regions are identified within the AluY consensus with q-values less than 0.05. A supplementary simulation also shows that the identified harmful regions covering the AluYa5 RNA functional regions are not occurring by chance. This method is then applied to two additional TE families: the Alu family and the L1 family, to computationally detect the harmful regions in these elements.

Conclusions

We use a computational method to identify a set of harmful mutation regions. Mutations within the identified harmful regions decrease the transpositional activity of active elements. The correlation between the mutations within these regions and the transpositional activity of TEs are shown to be statistically significant. Verifications are presented using the activity of AluY elements and the secondary structure of the AluYa5 RNA, providing evidence that the method is successfully identifying harmful mutation regions.

Transposable elements generate population-specific insertional patterns and allelic variation in genes of wild emmer wheat (Triticum turgidum ssp. dicoccoides)

BACKGROUND

Natural populations of the tetraploid wild emmer wheat (genome AABB) were previously shown to demonstrate eco-geographically structured genetic and epigenetic diversity. Transposable elements (TEs) might make up a significant part of the genetic and epigenetic variation between individuals and populations because they comprise over 80% of the wild emmer wheat genome. In this study, we performed detailed analyses to assess the dynamics of transposable elements in 50 accessions of wild emmer wheat collected from 5 geographically isolated sites. The analyses included: the copy number variation of TEs among accessions in the five populations, population-unique insertional patterns, and the impact of population-unique/specific TE insertions on structure and expression of genes.

RESULTS

We assessed the copy numbers of 12 TE families using real-time quantitative PCR, and found significant copy number variation (CNV) in the 50 wild emmer wheat accessions, in a population-specific manner. In some cases, the CNV difference reached up to 6-fold. However, the CNV was TE-specific, namely some TE families showed higher copy numbers in one or more populations, and other TE families showed lower copy numbers in the same population(s). Furthermore, we assessed the insertional patterns of 6 TE families using transposon display (TD), and observed significant population-specific insertional patterns. The polymorphism levels of TE-insertional patterns reached 92% among all wild emmer wheat accessions, in some cases. In addition, we observed population-specific/unique TE insertions, some of which were located within or close to protein-coding genes, creating allelic variations in a population-specific manner. We also showed that those genes are differentially expressed in wild emmer wheat.

CONCLUSIONS

For the first time, this study shows that TEs proliferate in wild emmer wheat in a population-specific manner, creating new alleles of genes, which contribute to the divergent evolution of homeologous genes from the A and B subgenomes.

TGTT and AACA: two transcriptionally active LTR retrotransposon subfamilies with a specific LTR structure and horizontal transfer in four Rosaceae species

BACKGROUND

Long terminal repeat retrotransposons (LTR-RTs) are major components of plant genomes. Common LTR-RTs contain the palindromic dinucleotide 5'-'TG'-'CA'-3' motif at the ends. Thus, further analyses of non-canonical LTR-RTs with non-palindromic motifs will enhance our understanding of their structures and evolutionary history.

RESULTS

Here, we report two new LTR-RT subfamilies (TGTT and AACA) with atypical dinucleotide ends of 5'-'TG'-'TT'-3', and 5'-'AA'-'CA'-3' in pear, apple, peach and mei. In total, 91 intact LTR-RTs were identified and classified into four TGTT and four AACA families. A structural annotation analysis showed that the four TGTT families, together with AACA1 and AACA2, belong to the Copia-like superfamily, whereas AACA3 and AACA4 appeared to be TRIM elements. The average amplification time frames for the eight families ranged from 0.05 to 2.32 million years. Phylogenetics coupled with sequence analyses revealed that the TGTT1 elements of peach were horizontally transferred from apple. In addition, 32 elements from two TGTT and three AACA families had detectable transcriptional activation, and a qRT-PCR analysis indicated that their expression levels varied dramatically in different species, organs and stress treatments.

CONCLUSIONS

Two novel LTR-RT subfamilies that terminated with non-palindromic dinucleotides at the ends of their LTRs were identified in four Rosaceae species, and a deep analysis showed their recent activity, horizontal transfer and varied transcriptional levels in different species, organs and stress treatments. This work enhances our understanding of the structural variation and evolutionary history of LTR-RTs in plants and also provides a valuable resource for future investigations of LTR-RTs having specific structures in other species.

Identification and characterization of mobile genetic elements LINEs from Brassica genome

Among transposable elements (TEs), the LTR retrotransposons are abundant followed by non-LTR retrotransposons in plant genomes, the lateral being represented by LINEs and SINEs. Computational and molecular approaches were used for the characterization of Brassica LINEs, their diversity and phylogenetic relationships. Four autonomous and four non-autonomous LINE families were identified and characterized from Brassica. Most of the autonomous LINEs displayed two open reading frames, ORF1 and ORF2, where ORF1 is a gag protein domain, while ORF2 encodes endonuclease (EN) and a reverse transcriptase (RT). Three of four families encoded an additional RNase H (RH) domain in pol gene common to 'R' and 'I' type of LINEs. The PCR analyses based on LINEs RT fragments indicate their high diversity and widespread occurrence in tested 40 Brassica cultivars. Database searches revealed the homology in LINE sequences in closely related genera Arabidopsis indicating their origin from common ancestors predating their separation. The alignment of 58 LINEs RT sequences from Brassica, Arabidopsis and other plants depicted 4 conserved domains (domain II-V) showing similarity to previously detected domains. Based on RT alignment of Brassica and 3 known LINEs from monocots, Brassicaceae LINEs clustered in separate clade, further resolving 4 Brassica-Arabidopsis specific families in 2 sub-clades. High similarities were observed in RT sequences in the members of same family, while low homology was detected in members across the families. The investigation led to the characterization of Brassica specific LINE families and their diversity across Brassica species and their cultivars.

The Variation Analysis of DNA Methylation in Wheat Carrying Gametocidal Chromosome 3C from Aegilops triuncialis

Gametocidal (Gc) chromosomes can ensure their preferential transmission by killing the gametes without themselves through causing chromosome breakage and therefore have been exploited as an effective tool for genetic breeding. However, to date very little is known about the molecular mechanism of Gc action. In this study, we used methylation-sensitive amplified polymorphism (MSAP) technique to assess the extent and pattern of cytosine methylation alterations at the whole genome level between two lines of wheat Gc addition line and their common wheat parent. The results indicated that the overall levels of cytosine methylation of two studied Gc addition lines (CS–3C and CS–3C3C, 48.68% and 48.65%, respectively) were significantly increased when compared to common wheat CS (41.31%) and no matter fully methylated or hemimethylated rates enhanced in Gc addition lines. A set of 30 isolated fragments that showed different DNA methylation or demethylation patterns between the three lines were sequenced and the results indicated that 8 fragments showed significant homology to known sequences, of which three were homologous to MITE transposon (Miniature inverted–repeat transposable elements), LTR-retrotransposon WIS-1p and retrotransposon Gypsy, respectively. Overall, our results showed that DNA methylation could play a role in the Gc action.

Transcriptional activity of PIF and Pong-like Class II transposable elements in Triticeae

Background

Transposable elements are major contributors to genome size and variability, accounting for approximately 70–80% of the maize, barley, and wheat genomes. PIF and Pong-like elements belong to two closely-related element families within the PIF/Harbinger superfamily of Class II (DNA) transposons. Both elements contain two open reading frames; one encodes a transposase (ORF2) that catalyzes transposition of the functional elements and their related non-autonomous elements, while the function of the second is still debated. In this work, we surveyed for PIF- and Pong-related transcriptional activity in 13 diploid Triticeae species, all of which have been previously shown to harbor extensive within-genome diversity of both groups of elements.

Results

The results revealed that PIF elements have considerable transcriptional activity in Triticeae, suggesting that they can escape the initial levels of plant cell control and are regulated at the post-transcriptional level. Phylogenetic analysis of 156 PIF cDNA transposase fragments along with 240 genomic partial transposase sequences showed that most, if not all, PIF clades are transcriptionally competent, and that multiple transposases coexisting within a single genome have the potential to act simultaneously. In contrast, we did not detect any transcriptional activity of Pong elements in any sample.

Conclusions

The lack of Pong element transcription shows that even closely related transposon families can exhibit wide variation in their transposase transcriptional activity within the same genome.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-1028-6) contains supplementary material, which is available to authorized users.

Genomic fossils reveal adaptation of non-autonomous pararetroviruses driven by concerted evolution of noncoding regulatory sequences

The interplay of different virus species in a host cell after infection can affect the adaptation of each virus. Endogenous viral elements, such as endogenous pararetroviruses (PRVs), have arisen from vertical inheritance of viral sequences integrated into host germline genomes. As viral genomic fossils, these sequences can thus serve as valuable paleogenomic data to study the long-term evolutionary dynamics of virus-virus interactions, but they have rarely been applied for this purpose. All extant PRVs have been considered autonomous species in their parasitic life cycle in host cells. Here, we provide evidence for multiple non-autonomous PRV species with structural defects in viral activity that have frequently infected ancient grass hosts and adapted through interplay between viruses. Our paleogenomic analyses using endogenous PRVs in grass genomes revealed that these non-autonomous PRV species have participated in interplay with autonomous PRVs in a possible commensal partnership, or, alternatively, with one another in a possible mutualistic partnership. These partnerships, which have been established by the sharing of noncoding regulatory sequences (NRSs) in intergenic regions between two partner viruses, have been further maintained and altered by the sequence homogenization of NRSs between partners. Strikingly, we found that frequent region-specific recombination, rather than mutation selection, is the main causative mechanism of NRS homogenization. Our results, obtained from ancient DNA records of viruses, suggest that adaptation of PRVs has occurred by concerted evolution of NRSs between different virus species in the same host. Our findings further imply that evaluation of within-host NRS interactions within and between populations of viral pathogens may be important.

Two new miniature inverted-repeat transposable elements in the genome of the clam Donax trunculus

Repetitive sequences are important components of eukaryotic genomes that drive their evolution. Among them are different types of mobile elements that share the ability to spread throughout the genome and form interspersed repeats. To broaden the generally scarce knowledge on bivalves at the genome level, in the clam Donax trunculus we described two new non-autonomous DNA transposons, miniature inverted-repeat transposable elements (MITEs), named DTC M1 and DTC M2. Like other MITEs, they are characterized by their small size, their A + T richness, and the presence of terminal inverted repeats (TIRs). DTC M1 and DTC M2 are 261 and 286 bp long, respectively, and in addition to TIRs, both of them contain a long imperfect palindrome sequence in their central parts. These elements are present in complete and truncated versions within the genome of the clam D. trunculus. The two new MITEs share only structural similarity, but lack any nucleotide sequence similarity to each other. In a search for related elements in databases, blast search revealed within the Crassostrea gigas genome a larger element sharing sequence similarity only to DTC M1 in its TIR sequences. The lack of sequence similarity with any previously published mobile elements indicates that DTC M1 and DTC M2 elements may be unique to D. trunculus.

Isolation of two new retrotransposon sequences and development of molecular and cytological markers for Dasypyrum villosum (L.)

Dasypyrum villosum is a valuable genetic resource for wheat improvement. With the aim to efficiently monitor the D. villosum chromatin introduced into common wheat, two novel retrotransposon sequences were isolated by RAPD, and were successfully converted to D. villosum-specific SCAR markers. In addition, we constructed a chromosomal karyotype of D. villosum. Our results revealed that different accessions of D. villosum showed slightly different signal patterns, indicating that distribution of repeats did not diverge significantly among D. villosum accessions. The two SCAR markers and FISH karyotype of D. villosum could be used for efficient and precise identification of D. villosum chromatin in wheat breeding.

Wild tobacco genomes reveal the evolution of nicotine biosynthesis

Nicotine, the signature alkaloid of Nicotiana species responsible for the addictive properties of human tobacco smoking, functions as a defensive neurotoxin against attacking herbivores. However, the evolution of the genetic features that contributed to the assembly of the nicotine biosynthetic pathway remains unknown. We sequenced and assembled genomes of two wild tobaccos, Nicotiana attenuata (2.5 Gb) and Nicotiana obtusifolia (1.5 Gb), two ecological models for investigating adaptive traits in nature. We show that after the Solanaceae whole-genome triplication event, a repertoire of rapidly expanding transposable elements (TEs) bloated these Nicotiana genomes, promoted expression divergences among duplicated genes, and contributed to the evolution of herbivory-induced signaling and defenses, including nicotine biosynthesis. The biosynthetic machinery that allows for nicotine synthesis in the roots evolved from the stepwise duplications of two ancient primary metabolic pathways: the polyamine and nicotinamide adenine dinucleotide (NAD) pathways. In contrast to the duplication of the polyamine pathway that is shared among several solanaceous genera producing polyamine-derived tropane alkaloids, we found that lineage-specific duplications within the NAD pathway and the evolution of root-specific expression of the duplicated Solanaceae-specific ethylene response factor that activates the expression of all nicotine biosynthetic genes resulted in the innovative and efficient production of nicotine in the genus Nicotiana Transcription factor binding motifs derived from TEs may have contributed to the coexpression of nicotine biosynthetic pathway genes and coordinated the metabolic flux. Together, these results provide evidence that TEs and gene duplications facilitated the emergence of a key metabolic innovation relevant to plant fitness.

Resolving fine-grained dynamics of retrotransposons: comparative analysis of inferential methods and genomic resources

Transposable elements support genome diversification, but comparison of their proliferation and genomic distribution within and among species is necessary to characterize their role in evolution. Such inferences are challenging because of potential bias with incomplete sampling of repetitive genome regions. Here, using the assembled genome as well as genome skimming datasets in Arabis alpina, we assessed the limits of current approaches inferring the biology of transposable elements. Long terminal repeat retrotransposons (LTR-RTs) identified in the assembled genome were classified into monophyletic lineages (here called tribes), including families of similar copies in Arabis along with elements from related Brassicaceae. Inference of their dynamics using divergence of LTRs in full-length copies and mismatch distribution of genetic variation among all copies congruently highlighted recent transposition bursts, although ancient proliferation events were apparent only with mismatch distribution. Similar inferences of LTR-RT dynamics based on random sequences from genome skimming were highly correlated with assembly-based estimates, supporting accurate analyses from shallow sequencing. Proportions of LTR-RT copies next to genes from both assembled genomes and genome skimming were congruent, pointing to tribes being over- or under-represented in the vicinity of genes. Finally, genome skimming at low coverage revealed accurate inferences of LTR-RT dynamics and distribution, although only the most abundant families appeared robustly analysed at 0.1X. Examining the pitfalls and benefits of approaches relying on different genomic resources, we highlight that random sequencing reads represent adequate data suitably complementing biased samples of LTR-RT copies retrieved from assembled genomes towards comprehensive surveys of the biology of transposable elements.

Comparative genomics of Eucalyptus and Corymbia reveals low rates of genome structural rearrangement

BACKGROUND

Previous studies suggest genome structure is largely conserved between Eucalyptus species. However, it is unknown if this conservation extends to more divergent eucalypt taxa. We performed comparative genomics between the eucalypt genera Eucalyptus and Corymbia. Our results will facilitate transfer of genomic information between these important taxa and provide further insights into the rate of structural change in tree genomes.

RESULTS

We constructed three high density linkage maps for two Corymbia species (Corymbia citriodora subsp. variegata and Corymbia torelliana) which were used to compare genome structure between both species and Eucalyptus grandis. Genome structure was highly conserved between the Corymbia species. However, the comparison of Corymbia and E. grandis suggests large (from 1-13 MB) intra-chromosomal rearrangements have occurred on seven of the 11 chromosomes. Most rearrangements were supported through comparisons of the three independent Corymbia maps to the E. grandis genome sequence, and to other independently constructed Eucalyptus linkage maps.

CONCLUSIONS

These are the first large scale chromosomal rearrangements discovered between eucalypts. Nonetheless, in the general context of plants, the genomic structure of the two genera was remarkably conserved; adding to a growing body of evidence that conservation of genome structure is common amongst woody angiosperms.

LTR-retrotransposons in plants: Engines of evolution

LTR retrotransposons are the most abundant group of transposable elements (TEs) in plants. These elements can fall inside or close to genes, and therefore influence their expression and evolution. This review aims to examine how LTR retrotransposons, especially Ty1-copia elements, mediate gene regulation and evolution. Various stimuli, including polyploidization and biotic and abiotic elicitors, result in the transcription and movement of these retrotransposons, and can facilitate adaptation. The presence of cis-regulatory motifs in the LTRs are central to their stress-mediated responses and are shared with host stress-responsive genes, showing a complex evolutionary history in which TEs provide new regulatory units to genes. The presence of retrotransposon remnants in genes that are necessary for normal gene function, demonstrates the importance of exaptation and co-option, and is also a consequence of the abundance of these elements in plant genomes. Furthermore, insertions of LTR retrotransposons in and around genes provide potential for alternative splicing, epigenetic control, transduction, duplication and recombination. These characteristics can become an active part of the evolution of gene families as in the case of resistance genes (R-genes). The character of TEs as exclusively selfish is now being re-evaluated. Since genome-wide reprogramming via TEs is a long evolutionary process, the changes we can examine are case-specific and their fitness advantage may not be evident until TE-derived motifs and domains have been completely co-opted and fixed. Nevertheless, the presence of LTR retrotransposons inside genes and as part of gene promoter regions is consistent with their roles as engines of plant genome evolution.

Obtaining retrotransposon sequences, analysis of their genomic distribution and use of retrotransposon-derived genetic markers in lentil (Lens culinaris Medik.)

Retrotransposons with long terminal repeats (LTR-RTs) are widespread mobile elements in eukaryotic genomes. We obtained a total of 81 partial LTR-RT sequences from lentil corresponding to internal retrotransposon components and LTRs. Sequences were obtained by PCR from genomic DNA. Approximately 37% of the LTR-RT internal sequences presented premature stop codons, pointing out that these elements must be non-autonomous. LTR sequences were obtained using the iPBS technique which amplifies sequences between LTR-RTs. A total of 193 retrotransposon-derived genetic markers, mainly iPBS, were used to obtain a genetic linkage map from 94 F₇ inbred recombinant lines derived from the cross between the cultivar Lupa and the wild ancestor L. culinaris subsp. orientalis. The genetic map included 136 markers located in eight linkage groups. Clusters of tightly linked retrotransposon-derived markers were detected in linkage groups LG1, LG2, and LG6, hence denoting a non-random genomic distribution. Phylogenetic analyses identified the LTR-RT families in which internal and LTR sequences are included. Ty3-gypsy elements were more frequent than Ty1-copia, mainly due to the high Ogre element frequency in lentil, as also occurs in other species of the tribe Vicieae. LTR and internal sequences were used to analyze in silico their distribution among the contigs of the lentil draft genome. Up to 8.8% of the lentil contigs evidenced the presence of at least one LTR-RT similar sequence. A statistical analysis suggested a non-random distribution of these elements within of the lentil genome. In most cases (between 97% and 72%, depending on the LTR-RT type) none of the internal sequences flanked by the LTR sequence pair was detected, suggesting that defective and non-autonomous LTR-RTs are very frequent in lentil. Results support that LTR-RTs are abundant and widespread throughout of the lentil genome and that they are a suitable source of genetic markers useful to carry out further genetic analyses.

Useful parasites: the evolutionary biology and biotechnology applications of transposable elements

Transposable elements usually comprise the most abundant nongenic fraction of eukaryotic genomes. Because of their capacity to selfreplicate and to induce a wide range of mutations, transposable elements have long been considered as 'parasitic' or 'selfish'. Today, we recognize that the findings about genomic changes affected by transposable elements have considerably altered our view of the ways in which genomes evolve and work. Numerous studies have provided evidences that mobile elements have the potential to act as agents of evolution by increasing, rearranging and diversifying the genetic repertoire of their hosts. With large-scale sequencing becoming increasingly available, more and more scientists come across transposable element sequences in their data. I will provide examples that transposable elements, although having signatures of 'selfish' DNA, play a significant biological role in the maintainance of genome integrity and providing novel regulatoty networks. These features, along with the transpositional and mutagenic capacity to produce a raw genetic diversity, make the genome mobile fraction, a key player in species adaptation and microevolution. The last but not least, transposable elements stand as informative DNA markers that may complement other conventional DNA markers. Altogether, transposable elements represent a promising, but still largely unexplored research niche and deserve to be included into the agenda of molecular ecologists, evolutionary geneticists, conservation biologists and plant breeders.

Laser Irradiation-Induced DNA Methylation Changes Are Heritable and Accompanied with Transpositional Activation of mPing in Rice

DNA methylation is an integral component of the epigenetic code in most higher eukaryotes. Exploring the extent to which DNA methylation can be altered under a specific condition and its heritability is important for elucidating the biological functions of this epigenetic modification. Here, we conducted MSAP analysis of rice plants with altered phenotypes subsequent to a low-dose Nd³⁺YAG laser irradiation. We found that all four methylation patterns at the 5'-CCGG sites that are analyzable by MSAP showed substantial changes in the immediately treated M0 plants. Interestingly, the frequencies of hypo- and hypermethylation were of similar extents, which largely offset each other and render the total methylation levels unchanged. Further analysis revealed that the altered methylation patterns were meiotically heritable to at least the M2 generation but accompanied with further changes in each generation. The methylation changes and their heritability of the metastable epigenetic state were verified by bisulfite sequencing of portion of the retrotranspon, Tos17, an established locus for assessing DNA methylation liability in rice. Real-time PCR assay indicated that the expression of various methylation-related chromatin genes was perturbed, and a Pearson correlation analysis showed that many of these genes, especially two AGOs (AGO4-1 and AGO4-2), were significantly correlated with the methylation pattern alterations. In addition, excisions of a MITE transposon, mPing, occurred rampantly in the laser irradiated plants and their progenies. Together, our results indicate that heritable DNA methylation changes can be readily induced by low-dose laser irradiation, and which can be accompanied by transpostional activation of transposable elements.

The Diversity of Sequence and Chromosomal Distribution of New Transposable Element-Related Segments in the Rye Genome Revealed by FISH and Lineage Annotation

Transposable elements (TEs) in plant genomes exhibit a great variety of structure, sequence content and copy number, making them important drivers for species diversity and genome evolution. Even though a genome-wide statistic summary of TEs in rye has been obtained using high-throughput DNA sequencing technology, the accurate diversity of TEs in rye, as well as their chromosomal distribution and evolution, remains elusive due to the repetitive sequence assembling problems and the high dynamic and nested nature of TEs. In this study, using genomic plasmid library construction combined with dot-blot hybridization and fluorescence in situ hybridization (FISH) analysis, we successfully isolated 70 unique FISH-positive TE-related sequences including 47 rye genome specific ones: 30 showed homology or partial homology with previously FISH characterized sequences and 40 have not been characterized. Among the 70 sequences, 48 sequences carried Ty3/gypsy-derived segments, 7 sequences carried Ty1/copia-derived segments and 15 sequences carried segments homologous with multiple TE families. 26 TE lineages were found in the 70 sequences, and among these lineages, Wilma was found in sequences dispersed in all chromosome regions except telomeric positions; Abiba was found in sequences predominantly located at pericentromeric and centromeric positions; Wis, Carmilla, and Inga were found in sequences displaying signals dispersed from distal regions toward pericentromeric positions; except DNA transposon lineages, all the other lineages were found in sequences displaying signals dispersed from proximal regions toward distal regions. A high percentage (21.4%) of chimeric sequences were identified in this study and their high abundance in rye genome suggested that new TEs might form through recombination and nested transposition. Our results also gave proofs that diverse TE lineages were arranged at centromeric and pericentromeric positions in rye, and lineages like Abiba might play a role in their structural organization and function. All these results might help in understanding the diversity and evolution of TEs in rye, as well as their driving forces in rye genome organization and evolution.

iMITEdb: the genome-wide landscape of miniature inverted-repeat transposable elements in insects

Miniature inverted-repeat transposable elements (MITEs) have attracted much attention due to their widespread occurrence and high copy numbers in eukaryotic genomes. However, the systematic knowledge about MITEs in insects and other animals is still lacking. In this study, we identified 6012 MITE families from 98 insect species genomes. Comparison of these MITEs with known MITEs in the NCBI non-redundant database and Repbase showed that 5701(∼95%) of 6012 MITE families are novel. The abundance of MITEs varies drastically among different insect species, and significantly correlates with genome size. In general, larger genomes contain more MITEs than small genomes. Furthermore, all identified MITEs were included in a newly constructed database (iMITEdb) (http://gene.cqu.edu.cn/iMITEdb/), which has functions such as browse, search, BLAST and download. Overall, our results not only provide insight on insect MITEs but will also improve assembly and annotation of insect genomes. More importantly, the results presented in this study will promote studies of MITEs function, evolution and application in insects.

Database URL: http://gene.cqu.edu.cn/iMITEdb/

Genomic skimming for identification of medium/highly abundant transposable elements in Arundo donax and Arundo plinii

Transposable elements (TEs) are the most abundant genetic material for almost all eukaryotic genomes. Their effects on the host genomes range from an extensive size variation to the regulation of gene expression, altering gene function and creating new genes. Because of TEs pivotal contribute to the host genome structure and regulation, their identification and characterization provide a wealth of useful data for gaining an in-depth understanding of host genome functioning. The giant reed (Arundo donax) is a perennial rhizomatous C₃ grass, octadecaploid, with an estimated nuclear genome size of 2744 Mbp. It is a promising feedstock for second-generation biofuels and biomethane production. To identify and characterize the most repetitive TEs in the genomes of A. donax and its ancestral A. plinii species, we carried out low-coverage whole genome shotgun sequencing for both species. Using a de novo repeat identification approach, 33,041 and 28,237 non-redundant repetitive sequences were identified and characterized in A. donax and A. plinii genomes, representing 37.55 and 31.68% of each genome, respectively. Comparative phylogenetic analyses, including the major TE classes identified in A. donax and A. plinii, together with rice and maize TE paralogs, were carried out to understand the evolutionary relationship of the most abundant TE classes. Highly conserved copies of RIRE1-like Ty1-Copia elements were discovered in two Arundo spp. in which they represented nearly 3% of each genomic sequence. We identified and characterized the medium/highly repetitive TEs in two unexplored polyploid genomes, thus generating useful information for the study of the genomic structure, composition, and functioning of these two non-model species. We provided a valuable resource that could be exploited in any effort aimed at sequencing and assembling these two genomes.

Epigenetic regulation and epigenomic landscape in rice

Epigenetic regulation has been implicated in the control of complex agronomic traits in rice (Oryza sativa), a staple food crop and model monocot plant. Recent advances in high-throughput sequencing and the moderately complex genome of rice have made it possible to study epigenetic regulation in rice on a genome-wide scale. This review discusses recent advances in our understanding of epigenetic regulation in rice, with an emphasis on the roles of key epigenetic regulators, the epigenomic landscape, epigenetic variation, transposon repression, and plant development.

To be or not to be alive: How recent discoveries challenge the traditional definitions of viruses and life

Three major discoveries have recently profoundly modified our perception of the viral world: molecular ecologists have shown that viral particles are more abundant than cells in natural environments; structural biologists have shown that some viruses from the three domains of life, Bacteria, Eukarya and Archaea, are evolutionarily related, and microbiologists have discovered giant viruses that rival with cells in terms of size and gene content. I discuss here the scientific and philosophical impact of these discoveries on the debates over the definition, nature (living or not), and origin of viruses. I suggest that viruses have often been considered non-living, because they are traditionally assimilated to their virions. However, the term virus describes a biological process and should integrate all aspects of the viral reproduction cycle. It is especially important to focus on the intracellular part of this cycle, the virocell, when viral information is actively expressed and reproduced, allowing the emergence of new viral genes. The virocell concept theoretically removes roadblocks that prevent defining viruses as living organisms. However, defining a "living organism" remains challenging, as indicated by the case of organelles that evolved from intracellular bacteria. To bypass this problem, I suggest considering that all biological entities that actively participate in the process of life are living.

Structural and functional liaisons between transposable elements and satellite DNAs

Transposable elements (TEs) and satellite DNAs (satDNAs) are typically identified as major repetitive DNA components in eukaryotic genomes. TEs are DNA segments able to move throughout a genome while satDNAs are tandemly repeated sequences organized in long arrays. Both classes of repetitive sequences are extremely diverse, and many TEs and satDNAs exist within a genome. Although they differ in structure, genomic organization, mechanisms of spread, and evolutionary dynamics, TEs and satDNAs can share sequence similarity and organizational patterns, thus indicating that complex mutual relationships can determine their evolution, and ultimately define roles they might have on genome architecture and function. Motivated by accumulating data about sequence elements that incorporate features of both TEs and satDNAs, here we present an overview of their structural and functional liaisons.