The BARE-1 retrotransposon is transcribed in barley from an LTR promoter active in transient assays

Transposable elements: multifunctional players in the plant genome

Transposable elements (TEs) are indispensable components of eukaryotic genomes that play diverse roles in gene regulation, recombination, and environmental adaptation. Their ability to mobilize within the genome leads to gene expression and DNA structure changes. TEs serve as valuable markers for genetic and evolutionary studies and facilitate genetic mapping and phylogenetic analysis. They also provide insight into how organisms adapt to a changing environment by promoting gene rearrangements that lead to new gene combinations. These repetitive sequences significantly impact genome structure, function and evolution. This review takes a comprehensive look at TEs and their applications in biotechnology, particularly in the context of plant biology, where they are now considered "genomic gold" due to their extensive functionalities. The article addresses various aspects of TEs in plant development, including their structure, epigenetic regulation, evolutionary patterns, and their use in gene editing and plant molecular markers. The goal is to systematically understand TEs and shed light on their diverse roles in plant biology.

Drought and recovery in barley: key gene networks and retrotransposon response

Introduction

During drought, plants close their stomata at a critical soil water content (SWC), together with making diverse physiological, developmental, and biochemical responses.

Methods

Using precision-phenotyping lysimeters, we imposed pre-flowering drought on four barley varieties (Arvo, Golden Promise, Hankkija 673, and Morex) and followed their physiological responses. For Golden Promise, we carried out RNA-seq on leaf transcripts before and during drought and during recovery, also examining retrotransposon BARE1expression. Transcriptional data were subjected to network analysis.

Results

The varieties differed by their critical SWC (ϴ_crit), Hankkija 673 responding at the highest and Golden Promise at the lowest. Pathways connected to drought and salinity response were strongly upregulated during drought; pathways connected to growth and development were strongly downregulated. During recovery, growth and development pathways were upregulated; altogether, 117 networked genes involved in ubiquitin-mediated autophagy were downregulated.

Discussion

The differential response to SWC suggests adaptation to distinct rainfall patterns. We identified several strongly differentially expressed genes not earlier associated with drought response in barley. BARE1 transcription is strongly transcriptionally upregulated by drought and downregulated during recovery unequally between the investigated cultivars. The downregulation of networked autophagy genes suggests a role for autophagy in drought response; its importance to resilience should be further investigated.

The role of LTR retrotransposons in plant genetic engineering: how to control their transposition in the genome

We briefly discuss that the similarity of LTR retrotransposons to retroviruses is a great opportunity for the development of a genetic engineering tool that exploits intragenic elements in the plant genome for plant genetic improvement. Long terminal repeat (LTR) retrotransposons are very similar to retroviruses but do not have the property of being infectious. While spreading between its host cells, a retrovirus inserts a DNA copy of its genome into the cells. The ability of retroviruses to cause infection with genome integration allows genes to be delivered to cells and tissues. Retrovirus vectors are, however, only specific to animals and insects, and, thus, are not relevant to plant genetic engineering. However, the similarity of LTR retrotransposons to retroviruses is an opportunity to explore the former as a tool for genetic engineering. Although recent long-read sequencing technologies have advanced the knowledge about transposable elements (TEs), the integration of TEs is still unable either to control them or to direct them to specific genomic locations. The use of existing intragenic elements to achieve the desired genome composition is better than using artificial constructs like vectors, but it is not yet clear how to control the process. Moreover, most LTR retrotransposons are inactive and unable to produce complete proteins. They are also highly mutable. In addition, it is impossible to find a full active copy of a LTR retrotransposon out of thousands of its own copies. Theoretically, if these elements were directly controlled and turned on or off using certain epigenetic mechanisms (inducing by stress or infection), LTR retrotransposons could be a great opportunity to develop a genetic engineering tool using intragenic elements in the plant genome. In this review, the recent developments in uncovering the nature of LTR retrotransposons and the possibility of using these intragenic elements as a tool for plant genetic engineering are briefly discussed.

Functional characterization of a strong promoter of the early light-inducible protein gene from tomato

The tomato ELIP gene promoter is mainly active in the ripening fruit. Considering its high activity, the promoter could be used for molecular breeding of plants in the future. The ability to obtain new varieties of transgenic plants with economically valuable traits relies on a high level of target gene expression, which is largely controlled by a gene promoter. Hence, research aimed at finding and characterizing new tissue-specific promoters that direct gene expression in specific plant tissues or at certain developmental stages has become the most important field of plant biotechnology. Here, we cloned and characterized the promoter of the early light-inducible protein (ELIP) gene from tomato (Solanum lycopersicum cv. Yalf). ELIPs are produced in the presence of light and putatively function in the chloroplast-to-chromoplast conversion, playing a photorepairing role in the photosynthetic system. Analysis of the promoter sequence revealed multiple cis-acting elements related to light responsiveness, and other motifs involved in plant hormone response and circadian control. To determine the functionality of the promoter, seven 5'-deletion variants were fused with the β-glucuronidase (GUS) reporter gene and introduced into tomato. Histochemical analysis of transgenic tomato plants revealed different levels of GUS activity in most analyzed tissues, depending on the promoter fragment used. The intensity of staining was considerably higher in ripening fruits than in unripe and non-fruit tissues. Quantitative analysis indicated that the level of GUS activity with the longest (full-length) version of the ELIP promoter in ripened fruits was comparable to that in plants expressing the constitutive CaMV35S promoter. Further, the location of both negative and positive regulatory motifs was identified. The described ELIP promoter is a potential tool for various applications in plant biotechnology.

Cloning of the wheat Yr15 resistance gene sheds light on the plant tandem kinase-pseudokinase family

Yellow rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating fungal disease threatening much of global wheat production. Race-specific resistance (R)-genes are used to control rust diseases, but the rapid emergence of virulent Pst races has prompted the search for a more durable resistance. Here, we report the cloning of Yr15, a broad-spectrum R-gene derived from wild emmer wheat, which encodes a putative kinase-pseudokinase protein, designated as wheat tandem kinase 1, comprising a unique R-gene structure in wheat. The existence of a similar gene architecture in 92 putative proteins across the plant kingdom, including the barley RPG1 and a candidate for Ug8, suggests that they are members of a distinct family of plant proteins, termed here tandem kinase-pseudokinases (TKPs). The presence of kinase-pseudokinase structure in both plant TKPs and the animal Janus kinases sheds light on the molecular evolution of immune responses across these two kingdoms.

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.

Ty1-copia elements reveal diverse insertion sites linked to polymorphisms among flax (Linum usitatissimum L.) accessions

BACKGROUND

Initial characterization of the flax genome showed that Ty1-copia retrotransposons are abundant, with several members being recently inserted, and in close association with genes. Recent insertions indicate a potential for ongoing transpositional activity that can create genomic diversity among accessions, cultivars or varieties. The polymorphisms generated constitute a good source of molecular markers that may be associated with phenotype if the insertions alter gene activity. Flax, where accessions are bred mainly for seed nutritional properties or for fibers, constitutes a good model for studying the relationship of transpositional activity with diversification and breeding. In this study, we estimated copy number and used a type of transposon display known as Sequence-Specific Amplification Polymorphisms (SSAPs), to characterize six families of Ty1-copia elements across 14 flax accessions. Polymorphic insertion sites were sequenced to find insertions that could potentially alter gene expression, and a preliminary test was performed with selected genes bearing transposable element (TE) insertions.

RESULTS

Quantification of six families of Ty1-copia elements indicated different abundances among TE families and between flax accessions, which suggested diverse transpositional histories. SSAPs showed a high level of polymorphism in most of the evaluated retrotransposon families, with a trend towards higher levels of polymorphism in low-copy number families. Ty1-copia insertion polymorphisms among cultivars allowed a general distinction between oil and fiber types, and between spring and winter types, demonstrating their utility in diversity studies. Characterization of polymorphic insertions revealed an overwhelming association with genes, with insertions disrupting exons, introns or within 1 kb of coding regions. A preliminary test on the potential transcriptional disruption by TEs of four selected genes evaluated in three different tissues, showed one case of significant impact of the insertion on gene expression.

CONCLUSIONS

We demonstrated that specific Ty1-copia families have been active since breeding commenced in flax. The retrotransposon-derived polymorphism can be used to separate flax types, and the close association of many insertions with genes defines a good source of potential mutations that could be associated with phenotypic changes, resulting in diversification processes.

Genome-wide analysis of LTR-retrotransposons in oil palm

BACKGROUND

The oil palm (Elaeis guineensis Jacq.) is a major cultivated crop and the world's largest source of edible vegetable oil. The genus Elaeis comprises two species E. guineensis, the commercial African oil palm and E. oleifera, which is used in oil palm genetic breeding. The recent publication of both the African oil palm genome assembly and the first draft sequence of its Latin American relative now allows us to tackle the challenge of understanding the genome composition, structure and evolution of these palm genomes through the annotation of their repeated sequences.

METHODS

In this study, we identified, annotated and compared Transposable Elements (TE) from the African and Latin American oil palms. In a first step, Transposable Element databases were built through de novo detection in both genome sequences then the TE content of both genomes was estimated. Then putative full-length retrotransposons with Long Terminal Repeats (LTRs) were further identified in the E. guineensis genome for characterization of their structural diversity, copy number and chromosomal distribution. Finally, their relative expression in several tissues was determined through in silico analysis of publicly available transcriptome data.

RESULTS

Our results reveal a congruence in the transpositional history of LTR retrotransposons between E. oleifera and E. guineensis, especially the Sto-4 family. Also, we have identified and described 583 full-length LTR-retrotransposons in the Elaeis guineensis genome. Our work shows that these elements are most likely no longer mobile and that no recent insertion event has occurred. Moreover, the analysis of chromosomal distribution suggests a preferential insertion of Copia elements in gene-rich regions, whereas Gypsy elements appear to be evenly distributed throughout the genome.

CONCLUSIONS

Considering the high proportion of LTR retrotransposon in the oil palm genome, our work will contribute to a greater understanding of their impact on genome organization and evolution. Moreover, the knowledge gained from this study constitutes a valuable resource for both the improvement of genome annotation and the investigation of the evolutionary history of palms.

Identification of a retroelement from the resurrection plant Boea hygrometrica that confers osmotic and alkaline tolerance in Arabidopsis thaliana

Functional genomic elements, including transposable elements, small RNAs and non-coding RNAs, are involved in regulation of gene expression in response to plant stress. To identify genomic elements that regulate dehydration and alkaline tolerance in Boea hygrometrica, a resurrection plant that inhabits drought and alkaline Karst areas, a genomic DNA library from B. hygrometrica was constructed and subsequently transformed into Arabidopsis using binary bacterial artificial chromosome (BIBAC) vectors. Transgenic lines were screened under osmotic and alkaline conditions, leading to the identification of Clone L1-4 that conferred osmotic and alkaline tolerance. Sequence analyses revealed that L1-4 contained a 49-kb retroelement fragment from B. hygrometrica, of which only a truncated sequence was present in L1-4 transgenic Arabidopsis plants. Additional subcloning revealed that activity resided in a 2-kb sequence, designated Osmotic and Alkaline Resistance 1 (OAR1). In addition, transgenic Arabidopsis lines carrying an OAR1-homologue also showed similar stress tolerance phenotypes. Physiological and molecular analyses demonstrated that OAR1-transgenic plants exhibited improved photochemical efficiency and membrane integrity and biomarker gene expression under both osmotic and alkaline stresses. Short transcripts that originated from OAR1 were increased under stress conditions in both B. hygrometrica and Arabidopsis carrying OAR1. The relative copy number of OAR1 was stable in transgenic Arabidopsis under stress but increased in B. hygrometrica. Taken together, our results indicated a potential role of OAR1 element in plant tolerance to osmotic and alkaline stresses, and verified the feasibility of the BIBAC transformation technique to identify functional genomic elements from physiological model species.

Environmental stress activation of plant long-terminal repeat retrotransposons

Genomic retrotransposons (RTs) are major components of most plant genomes. They spread throughout the genomes by a process termed retrotransposition, which consists of reverse transcription and reinsertion of the copied element into a new genomic location (a copy-and-paste system). Abiotic and biotic stresses activate long-terminal repeat (LTR) RTs in photosynthetic eukaryotes from algae to angiosperms. LTR RTs could represent a threat to the integrity of host genomes because of their activity and mutagenic potential by epigenetic regulation. Host genomes have developed mechanisms to control the activity of the retroelements and their mutagenic potential. Some LTR RTs escape these defense mechanisms, and maintain their ability to be activated and transpose as a result of biotic or abiotic stress stimuli. These stimuli include pathogen infection, mechanical damage, in vitro tissue culturing, heat, drought and salt stress, generation of doubled haploids, X-ray irradiation and many others. Reactivation of LTR RTs differs between different plant genomes. The expression levels of reactivated RTs are influenced by the transcriptional and post-transcriptional gene silencing mechanisms (e.g. DNA methylation, heterochromatin formation and RNA interference). Moreover, the insertion of RTs (e.g. Triticum aestivum L. Wis2-1A) into or next to coding regions of the host genome can generate changes in the expression of adjacent host genes of the host. In this paper, we review the ways that plant genomic LTR RTs are activated by environmental stimuli to affect restructuring and diversification of the host genome.

Major repeat components covering one-third of the ginseng (Panax ginseng C.A. Meyer) genome and evidence for allotetraploidy

Ginseng (Panax ginseng) is a famous medicinal herb, but the composition and structure of its genome are largely unknown. Here we characterized the major repeat components and inspected their distribution in the ginseng genome. By analyzing three repeat-rich bacterial artificial chromosome (BAC) sequences from ginseng, we identified complex insertion patterns of 34 long terminal repeat retrotransposons (LTR-RTs) and 11 LTR-RT derivatives accounting for more than 80% of the BAC sequences. The LTR-RTs were classified into three Ty3/gypsy (PgDel, PgTat and PgAthila) and two Ty1/Copia (PgTork and PgOryco) families. Mapping of 30-Gbp Illumina whole-genome shotgun reads to the BAC sequences revealed that these five LTR-RT families occupy at least 34% of the ginseng genome. The Ty3/Gypsy families were predominant, comprising 74 and 33% of the BAC sequences and the genome, respectively. In particular, the PgDel family accounted for 29% of the genome and presumably played major roles in enlargement of the size of the ginseng genome. Fluorescence in situ hybridization (FISH) revealed that the PgDel1 elements are distributed throughout the chromosomes along dispersed heterochromatic regions except for ribosomal DNA blocks. The intensity of the PgDel2 FISH signals was biased toward 24 out of 48 chromosomes. Unique gene probes showed two pairs of signals with different locations, one pair in subtelomeric regions on PgDel2-rich chromosomes and the other in interstitial regions on PgDel2-poor chromosomes, demonstrating allotetraploidy in ginseng. Our findings promote understanding of the evolution of the ginseng genome and of that of related species in the Araliaceae.

Retrotransposon BARE displays strong tissue-specific differences in expression

The BARE retrotransposon comprises c. 10% of the barley (Hordeum vulgare) genome. It is actively transcribed, translated and forms virus-like particles (VLPs). For retrotransposons, the inheritance of new copies depends critically on where in the plant replication occurs. In order to shed light on the replication strategy of BARE in the plant, we have used immunolocalization and in situ hybridization to examine expression of the BARE capsid protein, Gag, at a tissue-specific level. Gag is expressed in provascular tissues and highly localized in companion cells surrounding the phloem sieve tubes in mature vascular tissues. BARE Gag and RNA was not seen in the shoot apical meristem of young seedlings, but appeared, following transition to flowering, in the developing floral spike. Moreover, Gag has a highly specific localization in pre-fertilization ovaries. The strong presence of Gag in the floral meristems suggests that newly replicated copies there will be passed to the next generation. BARE expression patterns are consistent with transcriptional regulation by predicted response elements in the BARE promoter, and in the ovary with release from epigenetic transcriptional silencing. To our knowledge, this is the first analysis of the expression of native retrotransposon proteins within a plant to be reported.

BARE retrotransposons are translated and replicated via distinct RNA pools

The replication of Long Terminal Repeat (LTR) retrotransposons, which can constitute over 80% of higher plant genomes, resembles that of retroviruses. A major question for retrotransposons and retroviruses is how the two conflicting roles of their transcripts, in translation and reverse transcription, are balanced. Here, we show that the BARE retrotransposon, despite its organization into just one open reading frame, produces three distinct classes of transcripts. One is capped, polyadenylated, and translated, but cannot be copied into cDNA. The second is not capped or polyadenylated, but is destined for packaging and ultimate reverse transcription. The third class is capped, polyadenylated, and spliced to favor production of a subgenomic RNA encoding only Gag, the protein forming virus-like particles. Moreover, the BARE2 subfamily, which cannot synthesize Gag and is parasitic on BARE1, does not produce the spliced sub-genomic RNA for translation but does make the replication competent transcripts, which are packaged into BARE1 particles. To our knowledge, this is first demonstration of distinct RNA pools for translation and transcription for any retrotransposon.

Transposon-mediated alteration of TaMATE1B expression in wheat confers constitutive citrate efflux from root apices

The TaMATE1B gene (for multidrug and toxic compound extrusion) from wheat (Triticum aestivum) was isolated and shown to encode a citrate transporter that is located on the plasma membrane. TaMATE1B expression in roots was induced by iron deficiency but not by phosphorus deficiency or aluminum treatment. The coding region of TaMATE1B was identical in a genotype showing citrate efflux from root apices (cv Carazinho) to one that lacked citrate efflux (cv Egret). However, sequence upstream of the coding region differed between these two genotypes in two ways. The first difference was a single-nucleotide polymorphism located approximately 2 kb upstream from the start codon in cv Egret. The second difference was an 11.1-kb transposon-like element located 25 bp upstream of the start codon in cv Carazinho that was absent from cv Egret. The influence of these polymorphisms on TaMATE1B expression was investigated using fusions to green fluorescent protein expressed in transgenic lines of rice (Oryza sativa). Fluorescence measurements in roots of rice indicated that 1.5- and 2.3-kb regions upstream of TaMATE1B in cv Carazinho (which incorporated 3' regions of the transposon-like element) generated 20-fold greater expression in the apical 1 mm of root compared with the native promoter in cv Egret. By contrast, fluorescence in more mature tissues was similar in both cultivars. The presence of the single-nucleotide polymorphism alone consistently generated 2-fold greater fluorescence than the cv Egret promoter. We conclude that the transposon-like element in cv Carazinho extends TaMATE1B expression to the root apex, where it confers citrate efflux and enhanced aluminum tolerance.

Genomic, RNA, and ecological divergences of the Revolver transposon-like multi-gene family in Triticeae

Background

Revolver is a newly discovered multi-gene family of transposable elements in the Triticeae genome. Revolver encompasses 2929 to 3041 bp, has 20 bp of terminal inverted repeated sequences at both ends, and contains a transcriptionally active gene encoding a DNA-binding-like protein. A putative TATA box is located at base 221, with a cap site at base 261 and a possible polyadenylation signal AATAAA at base 2918. Revolver shows considerable quantitative variation in wheat and its relatives.

Results

Revolver cDNAs varied between 395 and 2,182 bp in length. The first exon exhibited length variation, but the second and third exons were almost identical. These variants in the Revolver family shared the downstream region of the second intron, but varied structurally at the 5' first exon. There were 58 clones, which showed partial homology to Revolver, among 440,000 expressed sequence tagged (EST) clones sourced from Triticeae. In these Revolver homologues with lengths of 360-744 bp, the portion after the 2nd exon was conserved (65-79% homology), but the 1st exon sequences had mutually low homology, with mutations classified into 12 types, and did not have EST sequences with open reading frames (ORFs). By PCR with the 3'-flanking region of a typical genomic clone of Revolver-2 used as a single primer, rye chromosomes 1R and 5R could be simultaneously identified. Extensive eco-geographic diversity and divergence was observed among 161 genotypes of the single species Triticum dicoccoides collected from 18 populations in Israel with varying exposures to abiotic and biotic stresses (soil, temperature, altitude, water availability, and pathogens).

Conclusions

On the base of existing differences between Revolver variants, the molecular markers that can distinguish different rye chromosomes were developed. Eco-geographic diversification of wild emmer T. dicoccoides in Israel and high Revolver copy numbers are associated with higher rainfall and biotic stresses. The remarkable quantitative differences among copy numbers of Revolver in the same species from different ecosystems suggest strong amplification activity within the last 10,000 years. It is the interesting finding because the majority of Triticeae high-copy transposable elements seem to be inactive at the recent time except for BARE-1 element in Hordeum and the fact might be interesting to perceive the processes of plant adaptive evolution.

Revolver and superior: novel transposon-like gene families of the plant kingdom

High-throughput sequencing of eukaryotic genomes has revived interest in the structure and function of repetitive genomic sequences, previously referred to as junk DNA. Repetitive sequences, including transposable elements, are now believed to play a significant role in genomic differentiation and evolution. Some are also expressed as regulatory noncoding RNAs. Vast DNA databases exist for higher eukaryotes; however, with the exception of homologues of known repetitive-sequence-families and transposable elements, most repetitive elements still need to be annotated. Revolver and Superior, both discovered in the Triticeae, are novel classes of transposon-like genes and major components of large cereal genomes. Revolver was isolated from rye via genome subtraction of sequences common to rye and wheat. Superior was isolated from rye by cleavage with EcoO109I, the recognition sites of which consist of a 5'- PuGGNCCPy-3' multi-sequence. Revolver is 2929-3041 bp long with an inverted repeat sequence on each end. The Superior family elements are 1292-1432 bp in length, with divergent 5' regions, indicating the presence of considerable structural diversity. Revolver and Superior are transcriptionally active elements; Revolver harbors a single gene consisting of three exons and two introns, encoding a protein of 139 amino acid residues. Revolver variants range in size from 2665 bp to 4269 bp, with some variants lacking the 5' region, indicating structural diversity around the first exon. Revolver and Superior are dispersed across all seven chromosomes of rye. Revolver has existed since the diploid progenitor of wheat, and has been amplified or lost in several species during the evolution of the Triticeae. This article reviews the recently discovered Revolver and Superior families of plant transposons, which do not share identity with any known autonomous transposable elements or repetitive elements from any living species.

Identification and characterization of jute LTR retrotransposons:: Their abundance, heterogeneity and transcriptional activity

Long Terminal Repeat (LTR) retrotransposons constitute a significant part of eukaryotic genomes and play an important role in genome evolution especially in plants. Jute is an important fiber crop with a large genome of 1,250 Mbps. This genome is still mostly unexplored. In this study we aimed at identifying and characterizing the LTR retrotransposons of jute with a view to understanding the jute genome better. In this study, the Reverse Transcriptase domain of Ty1-copia and Ty3-gypsy LTR retrotransposons of jute were amplified by degenerate primers and their expressions were examined by reverse transcription PCR. Copy numbers of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy elements were determined by dot blot analysis. Sequence analysis revealed higher heterogeneity among Ty1-copia retrotransposons than Ty3-gypsy and clustered each of them in three groups. Copy number of RT genes in Ty1-copia was found to be higher than that of Ty3-gypsy elements from dot blot hybridization. Cumulatively Ty1-copia and Ty3-gypsy may constitute around 19% of the jute genome where two groups of Ty1-copia were found to be transcriptionally active. Since the LTR retrotransposons constitute a large portion of jute genome, these findings imply the importance of these elements in the evolution of jute genome.

Transcriptional activity of transposable elements in maize

BACKGROUND

Mobile genetic elements represent a high proportion of the Eukaryote genomes. In maize, 85% of genome is composed by transposable elements of several families. First step in transposable element life cycle is the synthesis of an RNA, but few is known about the regulation of transcription for most of the maize transposable element families. Maize is the plant from which more ESTs have been sequenced (more than two million) and the third species in total only after human and mice. This allowed us to analyze the transcriptional activity of the maize transposable elements based on EST databases.

RESULTS

We have investigated the transcriptional activity of 56 families of transposable elements in different maize organs based on the systematic search of more than two million expressed sequence tags. At least 1.5% maize ESTs show sequence similarity with transposable elements. According to these data, the patterns of expression of each transposable element family is variable, even within the same class of elements. In general, transcriptional activity of the gypsy-like retrotransposons is higher compared to other classes. Transcriptional activity of several transposable elements is specially high in shoot apical meristem and sperm cells. Sequence comparisons between genomic and transcribed sequences suggest that only a few copies are transcriptionally active.

CONCLUSIONS

The use of powerful high-throughput sequencing methodologies allowed us to elucidate the extent and character of repetitive element transcription in maize cells. The finding that some families of transposable elements have a considerable transcriptional activity in some tissues suggests that, either transposition is more frequent than previously expected, or cells can control transposition at a post-transcriptional level.

Transcriptional activity of transposable elements in maize

BACKGROUND

Mobile genetic elements represent a high proportion of the Eukaryote genomes. In maize, 85% of genome is composed by transposable elements of several families. First step in transposable element life cycle is the synthesis of an RNA, but few is known about the regulation of transcription for most of the maize transposable element families. Maize is the plant from which more ESTs have been sequenced (more than two million) and the third species in total only after human and mice. This allowed us to analyze the transcriptional activity of the maize transposable elements based on EST databases.

RESULTS

We have investigated the transcriptional activity of 56 families of transposable elements in different maize organs based on the systematic search of more than two million expressed sequence tags. At least 1.5% maize ESTs show sequence similarity with transposable elements. According to these data, the patterns of expression of each transposable element family is variable, even within the same class of elements. In general, transcriptional activity of the gypsy-like retrotransposons is higher compared to other classes. Transcriptional activity of several transposable elements is specially high in shoot apical meristem and sperm cells. Sequence comparisons between genomic and transcribed sequences suggest that only a few copies are transcriptionally active.

CONCLUSIONS

The use of powerful high-throughput sequencing methodologies allowed us to elucidate the extent and character of repetitive element transcription in maize cells. The finding that some families of transposable elements have a considerable transcriptional activity in some tissues suggests that, either transposition is more frequent than previously expected, or cells can control transposition at a post-transcriptional level.

FaRE1: a transcriptionally active Ty1-copia retrotransposon in strawberry

Retrotransposons are ubiquitous in the plant kingdom and constitute a large fraction of many plant genomes. Although most retrotransposons from plants were thought to be transcriptionally silent in somatic tissues, evidence of activity under certain conditions is available in some cases. In this study, a complete LTR retrotransposon was isolated from the cultivated strawberry (Fragaria x ananassa) genome using genome walking. The element, named FaRE1, has all the features of a typical Ty1-copia retrotransposon. Its total length was 5,104 bp, comprising a single 3,891 bp open reading frame. It is represented by approximately 96 copies per genome, equivalent to approximately 0.33% of the genome. Transcription of FaRE1 was detected in leaf tissue treated with various phytohormones, such as naphthalene acetic acid, 2,4-dichlorophenoxyacetic acid or abscisic acid . To our knowledge, this is the first report of the isolation of a complete LTR retrotransposon with transcriptional activity in strawberry.

Polymorphism of a new Ty1-copia retrotransposon in durum wheat under salt and light stresses

Long terminal repeat retrotransposons are the most abundant mobile elements in the plant genome and play an important role in the genome reorganization induced by environmental challenges. Their success depends on the ability of their promoters to respond to different signaling pathways that regulate plant adaptation to biotic and abiotic stresses. We have isolated a new Ty1-copia-like retrotransposon, named Ttd1a from the Triticum durum L. genome. To get insight into stress activation pathways in Ttd1a, we investigated the effect of salt and light stresses by RT-PCR and S-SAP profiling. We screened for Ttd1a insertion polymorphisms in plants grown to stress and showed that one new insertion was located near the resistance gene. Our analysis showed that the activation and mobilization of Ttd1a was controlled by salt and light stresses, which strengthened the hypothesis that stress mobilization of this element might play a role in the defense response to environmental stresses.

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

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

Refunctionalization of the ancient rice blast disease resistance gene Pit by the recruitment of a retrotransposon as a promoter

The plant genome contains a large number of disease resistance (R) genes that have evolved through diverse mechanisms. Here, we report that a long terminal repeat (LTR) retrotransposon contributed to the evolution of the rice blast resistance gene Pit. Pit confers race-specific resistance against the fungal pathogen Magnaporthe grisea, and is a member of the nucleotide-binding site leucine-rich repeat (NBS-LRR) family of R genes. Compared with the non-functional allele Pit(Npb), the functional allele Pit(K59) contains four amino acid substitutions, and has the LTR retrotransposon Renovator inserted upstream. Pathogenesis assays using chimeric constructs carrying the various regions of Pit(K59) and Pit(Npb) suggest that amino acid substitutions might have a potential effect in Pit resistance; more importantly, the upregulated promoter activity conferred by the Renovator sequence is essential for Pit function. Our data suggest that transposon-mediated transcriptional activation may play an important role in the refunctionalization of additional 'sleeping' R genes in the plant genome.

BARE retrotransposons produce multiple groups of rarely polyadenylated transcripts from two differentially regulated promoters

The BARE retrotransposon family comprises more than 10(4) copies in the barley (Hordeum vulgare) genome. The element is bounded by long terminal repeats (LTRs, 1829 bp) containing promoters and RNA-processing motifs required for retrotransposon replication. Members of the BARE1 subfamily are transcribed, translated, and form virus-like particles. Very similar retrotransposons are expressed as RNA and protein in other cereals and grasses. The BARE2 subfamily is, however, non-autonomous because it cannot produce the GAG capsid protein. The pattern of plant development implies that inheritance of integrated copies should critically depend, in the first instance, on cell-specific and tissue-specific expression patterns. We examined transcription of BARE within different barley tissues and analyzed the promoter function of the BARE LTR. The two promoters of the LTR vary independently in activity by tissue. In embryos TATA1 was almost inactive, whereas transcription in callus appears to be less tightly regulated than in other tissues. Deletion analyses of the LTR uncovered strong positive and negative regulatory elements. The promoters produce multiple groups of transcripts that are distinct by their start and stop points, by their sequences, and by whether they are polyadenylated. Some of these groups do not share the common end structures needed for template switching during replication. Only about 15% of BARE transcripts are polyadenylated. The data suggest that distinct subfamilies of transcripts may play independent roles in providing the proteins and replication templates for the BARE retrotransposon life cycle.

Identification and characterization of novel senescence-associated genes from barley (Hordeum vulgare) primary leaves

Leaf senescence is the final developmental stage of a leaf. The progression of barley primary leaf senescence was followed by measuring the senescence-specific decrease in chlorophyll content and photosystem II efficiency. In order to isolate novel factors involved in leaf senescence, a differential display approach with mRNA populations from young and senescing primary barley leaves was applied. In this approach, 90 senescence up-regulated cDNAs were identified. Nine of these clones were, after sequence analyses, further characterized. The senescence-associated expression was confirmed by Northern analyses or quantitative RealTime-PCR. In addition, involvement of the phytohormones ethylene and abscisic acid in regulation of these nine novel senescence-induced cDNA fragments was investigated. Two cDNA clones showed homologies to genes with a putative regulatory function. Two clones possessed high homologies to barley retroelements, and five clones may be involved in degradation or transport processes. One of these genes was further analysed. It encodes an ADP ribosylation factor 1-like protein (HvARF1) and includes sequence motifs representing a myristoylation site and four typical and well conserved ARF-like protein domains. The localization of the protein was investigated by confocal laser scanning microscopy of onion epidermal cells after particle bombardment with chimeric HvARF1-GFP constructs. Possible physiological roles of these nine novel SAGs during barley leaf senescence are discussed.

Revolver is a new class of transposon-like gene composing the triticeae genome

Revolver discovered in the Triticeae plant is a novel class of transposon-like gene and a major component of the large cereal genome. An 89 bp segment of Revolver that is enriched in the genome of rye was isolated by deleting the DNA sequences common to rye and wheat. The entire structure of Revolver was determined by using rye genomic clones, which were screened by the 89 bp probe. Revolver consists of 2929-3041 bp with an inverted repeated sequence on each end and is dispersed through all seven chromosomes of the rye genome. Revolver is transcriptionally active, and the isolated full-length cDNA (726 bp) reveals that Revolver harbors a single gene consisting of three exons (342, 88, and 296 bp) and two introns (750 and 1237 bp), and encodes 139 amino acid residues of protein, which shows similarity to some transcriptional regulators. Revolver variants ranging from 2665 to 4269 bp, in which 5' regions were destructed, indicate structural diversities around the first exon. Revolver does not share identity with any known class I or class II autonomous transposable elements of any living species. DNA blot analysis of Triticeae plants shows that Revolver has existed since the diploid progenitor of wheat, and has been amplified or lost in several species during the evolution of the Triticeae.

Reme1, a Copia retrotransposon in melon, is transcriptionally induced by UV light

For the first time, numerous sequences of Copia and Gypsy retrotransposons from the Cucumis melo genome have been obtained and analyzed. Phylogenetic analyses of sequences of both types of long terminal repeat (LTR) retrotransposons were carried out. The melon genome contains approximately 20,000 Gypsy and 6,800 Copia elements, comprising about 26% of its total size. Starting from a retrotransposon fragment, we have cloned and characterized an entire melon retrotransposon, named Reme1, which is 5,149 bp long. Reme1 belongs to the Superfamily Copia retrotransposons by its protein domain order and sequence similarity to other Copia elements of dicotyledons. The haploid genome of melon (var. "Piel de Sapo") contains about 120 copies of Reme1. Several copies of Reme1 are transcriptionally active, although at low levels, in melon leaves as analyzed by reverse-transcription PCR (RT-PCR) and sequencing. However, the transcript pool is considerably increased when melon leaves are treated with UV light, as has been seen for various retroelements in many organisms. The cDNAs of Reme1 transcripts showed less diversity than do Reme1 genomic sequences, suggesting that a subfamily of these elements is differentially responsive to UV.

A genome-wide transcriptional activity survey of rice transposable element-related genes

A genome-wide survey of the transcriptional activity of TE-related genes that were associated with fifteen developmental stages and stress conditions revealed clear, albeit low, general transcription of TE-related genes.

Background

Transposable element (TE)-related genes comprise a significant portion of the gene catalog of grasses, although their functions are insufficiently characterized. The recent availability of TE-related gene annotation from the complete genome sequence of rice (Oryza sativa) has created an opportunity to conduct a comprehensive evaluation of the transcriptional activities of these potentially mobile elements and their related genes.

Results

We conducted a genome-wide survey of the transcriptional activity of TE-related genes associated with 15 developmental stages and stress conditions. This dataset was obtained using a microarray encompassing 2,191 unique TE-related rice genes, which were represented by oligonucleotide probes that were free from cross-hybridization. We found that TE-related genes exhibit much lower transcriptional activities than do non-TE-related genes, although representative transcripts were detected from all superfamilies of both type I and II TE-related genes. The strongest transcriptional activities were detected in TE-related genes from among the MULE and CACTA superfamilies. Phylogenetic analyses suggest that domesticated TE-related genes tend to form clades with active transcription. In addition, chromatin-level regulations through histone and DNA modifications, as well as enrichment of certain cis elements in the promoters, appear to contribute to the transcriptional activation of representative TE-related genes.

Conclusion

Our findings reveal clear, albeit low, general transcription of TE-related genes. In combination with phylogenetic analysis, transcriptional analysis has the potential to lead to the identification of domesticated TEs with adapted host functions.

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.

CIRE1, a novel transcriptionally active Ty1-copia retrotransposon from Citrus sinensis

LTR retrotransposons (LTR-RTNs) are widespread constituents of eukaryote genomes, particularly plant genomes. Although LTR-RTNs from plants were thought to be transcriptionally silent in somatic tissues, evidences of activity under certain conditions are available for some of them. In order to investigate LTR-RTNs in the Citrus sinensis genome, we analysed them by PCR using degenerate primers corresponding to highly conserved domains. All elements of the two types of LTR-RTN comprise about 23% of the genome, the copia group contribution being higher (13%) than the gypsy one (10%). From dendogram analysis, we report seven new copia RTN families, named CIRE1 to CIRE7. Here, we report on the first complete retrotransposon identified in Citrus (named CIRE1), which has all the features of a typical copia RTN. CIRE1 retrotransposon has around 2,200 full-length copies, contributing to 2.9% of the C. sinensis genome. CIRE1 has a root-specific expression in sweet orange plants. We have also determined that wounding and exogenous application of plant hormones, as methyl jasmonate and auxin, increase the transcription level of CIRE1 in leaf tissues. In addition, we show that CIRE1 5'LTR promoter can drive transient expression of the gus reporter gene in heterologous plant systems. These findings confirm CIRE1 as one of the few transcriptionally active RTNs described in plants and to our knowledge the first one to be reported in Citrus species.

The evolution of retrotransposon regulatory regions and its consequences on the Drosophila melanogaster and Homo sapiens host genomes

It has now been established that transposable elements (TEs) make up a variable, but significant proportion of the genomes of all organisms, from Bacteria to Vertebrates. However, in addition to their quantitative importance, there is increasing evidence that TEs also play a functional role within the genome. In particular, TE regulatory regions can be viewed as a large pool of potential promoter sequences for host genes. Studying the evolution of regulatory region of TEs in different genomic contexts is therefore a fundamental aspect of understanding how a genome works. In this paper, we first briefly describe what is currently known about the regulation of TE copy number and activity in genomes, and then focus on TE regulatory regions and their evolution. We restrict ourselves to retrotransposons, which are the most abundant class of eukaryotic TEs, and analyze their evolution and the subsequent consequences for host genomes. Particular attention is paid to much-studied representatives of the Vertebrates and Invertebrates, Homo sapiens and Drosophila melanogaster, respectively, for which high quality sequenced genomes are available.

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.

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.

Identification of transposons, retroelements, and a gene family predominantly expressed in floral tissues in chromosome 3DS of the hexaploid wheat progenitor Aegilops tauschii

A multigene family expressed during early floral development was identified on the short arm of wheat chromosome 3D in the region of the Ph2 locus, a locus controlling homoeologous chromosome pairing in allohexaploid wheat. Physical, genetic and molecular characterisation of the Wheat Meiosis 1 (WM1) gene family identified seven members that localised within a region of 173-kb. WM1 gene family members were sequenced and they encode mainly type Ia plasma membrane-anchored leucine rich repeat-like receptor proteins. In situ expression profiling suggests the gene family is predominantly expressed in floral tissue. In addition to the WM1 gene family, a number of other genes, gene fragments and pseudogenes were identified. It has been predicted that there is approximately one gene every 19-kb and that this region of the wheat genome contains 23 repetitive elements including BARE-1 and Wis2-1 like sequences. Nearly 50% of the repetitive elements identified were similar to known transposons from the CACTA superfamily. Ty1-copia, Ty3-gypsy and Athila LTR retroelements were also prevalent within the region. The WM1 gene cluster is present on 3DS and on barley 3HS but missing from the A and B genomes of hexaploid wheat. This suggests either recent generation of the cluster or specific deletion of the cluster during wheat polyploidisation. The evolutionary significance of the cluster, its possible roles in disease response or floral and early meiotic development and its location at or near the Ph2 locus are discussed.

A movable feast: diverse retrotransposons and their contribution to barley genome dynamics

Cellular genes comprise at most 5% of the barley genome; the rest is occupied primarily by retrotransposons. Retrotransposons move intracellularly by a replicative mechanism similar to that of retroviruses. We describe the major classes of retrotransposons in barley, including the two nonautonomous groups that were recently identified, and detail the evidence supporting our current understanding of their life cycle. Data from analyses of long contiguous segments of the barley genome, as well as surveys of the prevalence of full-length retrotransposons and their solo LTR derivatives in the genus Hordeum, indicate that integration and recombinational loss of retrotransposons are major factors shaping the genome. The sequence conservation and integrative capacity of barley retrotransposons have made them excellent sources for development of molecular marker systems.

Involvement of ethylene in stress-induced expression of the TLC1.1 retrotransposon from Lycopersicon chilense Dun

The TLC1 family is one of the four families of long terminal repeat (LTR) retrotransposons identified in the genome of Lycopersicon chilense. Here, we show that this family of retroelements is transcriptionally active and its expression is induced in response to diverse stress conditions such as wounding, protoplast preparation, and high salt concentrations. Several stress-associated signaling molecules, including ethylene, methyl jasmonate, salicylic acid, and 2,4-dichlorophenoxyacetic acid, are capable of inducing TLC1 family expression in vivo. A representative of this family, named TLC1.1, was isolated from a genomic library from L. chilense. Transient expression assays in leaf protoplasts and stably transformed tobacco (Nicotiana tabacum) plants demonstrate that the U3 domain of the 5'-LTR region of this element can drive stress-induced transcriptional activation of the beta-glucuronidase reporter gene. Two 57-bp tandem repeated sequences are found in this region, including an 8-bp motif, ATTTCAAA, previously identified as an ethylene-responsive element box in the promoter region of ethylene-induced genes. Expression analysis of wild-type LTR and single and double ethylene-responsive element box mutants fused to the beta-glucuronidase gene shows that these elements are required for ethylene-responsive gene expression in protoplasts and transgenic plants. We suggest that ethylene-dependent signaling is the main signaling pathway involved in the regulation of the expression of the TLC1.1 element from L. chilense.

Variability, Recombination, and Mosaic Evolution of the Barley BARE-1 Retrotransposon

BARE-1 is a highly abundant, copia-like, LTR (long terminal repeat) retrotransposon in the genus Hordeum. The LTRs provide the promoter, terminator, and polyadenylation signals necessary for the replicational life cycle of retrotransposons. We have examined the variability and evolution of BARE-1-like elements, focusing on the LTRs. Three groups were found, corresponding to each of the Hordeum genome types analyzed, which predate the divergence of these types. The most variable LTR regions are tandem repeats near the 3' end and the promoter. In barley (H. vulgare L.), two main classes of LTR promoters were defined, corresponding to BARE-1 and to a new class we call BARE-2. These can be considered as families within the group I BARE elements. Although less abundant in cultivated barley than is BARE-1, BARE-2 is transcriptionally active in leaves and calli. A sequenced BARE-2 has more than 99% similar LTRs and perfect terminal direct repeats (TDRs), indicating it is a recent insertion, but the coding region, especially gag, is disrupted by frameshifts and stop codons. BARE-2 appears to be a chimeric element resulting from retrotransposon recombination by strand switching during replication, with LTRs and 5'UTR more similar to BARE-1 and the rest more similar to Wis-2. We provide evidence as well for another form of recombination, where LTR-LTR recombination has generated tandem multimeric BARE-1 elements in which internal coding domains are interspersed with shared LTRs. The data indicate that recombination contributes to the complexity and plasticity of retroelement evolution in plant genomes.

Genetic diversity among barley cultivars assessed by sequence-specific amplification polymorphism

We analyzed the genetic structure and relationships among barley cultivars (Hordeum vulgare L.) with sequence-specific amplification polymorphisms (S-SAPs). Polymorphisms were identified in 824 individual barley plants representing 103 cultivars (eight plants per cultivar) widely grown in Canada and the United States, using PCR primers designed from the long terminal repeat of the barley retrotransposon BARE-1 and a subset of four selective MseI primers. From the 404 bands scored, 150 were polymorphic either within or between cultivars. Genetic structure assessed with analysis of molecular variance attributed the largest component of variation to the within groups of cultivars (69-86%). Within-cultivar genetic variation was estimated as average gene diversity over loci and ranged from 0 (completely homogenous) to 0.076 (most heterogeneous cultivar). Only 17 out of 103 cultivars (16%) were judged to be homogenous by this criterion. Relationships among cultivars were analyzed by cluster analysis using unweighted pair-groups using arithmetic averages and found groups similar to those determined by agriculturally significant phenotypic traits such as spike morphology (two-rowed or six-rowed), cultivar type (malting or feed), seed characteristic (hull-less or hulled), and growth habit (winter or spring), with minor overlaps. Discriminant analysis of groups determined by these phenotypic traits fully supported the different groups with minor overlaps between the malting/feed. S-SAP markers generated from retrotransposons such as BARE-1 are invaluable tools for the study of genetic diversity in organisms with a narrow genetic base such as barley. In this study, S-SAP analysis revealed significant amounts of cryptic variation in closely related cultivars including somaclonal variation, which could not be inferred by the pedigree analysis.

Isolation of an active element from a high-copy-number family of retrotransposons in the sweetpotato genome

A large number of plant retrotransposons have been characterized, but only three families ( Tnt1, Tto1 and Tos17) have been demonstrated to be transpositionally competent. We have used a novel approach to identify an active member of the Ty1- copia retrotransposon family with estimated 400 copies in the sweetpotato genome. Ty1- copia reverse transcriptase (RTase) sequences from the sweetpotato genome were analyzed, and a group of retrotransposon copies that probably arose by recent transposition events was identified and analyzed further. Transcripts containing long terminal repeats (LTRs) of this group were amplified from callus cDNA by the 3'RACE technique. Patterns of sequence-specific amplification polymorphism (S-SAP) of the LTR sequences in genomic DNA were compared between a normal plant and callus lines derived from it. In this way, a callus-specific S-SAP product was identified, which apparently resulted from the insertion of the retrotransposon detected by 3'RACE during cell culture. We conclude that our approach provides an effective way to identify active elements among the members of high-copy-number retrotransposon families.

Isolation and characterization of genomic and transcribed retrotransposon sequences from sorghum

Reverse transcriptase sequences from both major classes of retrotransposons were amplified from sorghum genomic DNA, leaf mRNA and callus protoplast mRNA. Sequence analysis of clones derived from genomic DNA demonstrated the presence of a wide variety of copia-like and gypsy-like elements. Twenty-four families of copia-like elements were found, of which at least thirteen were expressed in callus protoplasts. Two families (containing forty-eight subfamilies) of gypsy-like elements were discovered, both closely related to Huck of maize. At least twenty-seven of these subfamilies were expressed in callus protoplasts. Most of these elements were expressed at high levels in protoplasts derived from embryogenic callus, but expression of only a few was detected (at low levels) in leaves. Sequence divergence within individual families was quite high, and all relatedness profiles were consistent with vertical transmission of these elements. These data indicate that sorghum contains a large number and diversity of retrotransposons, and that some may be useful as transposon tagging systems in callus protoplasts.

Comparison of the utility of barley retrotransposon families for genetic analysis by molecular marker techniques

The Sequence-Specific Amplification Polymorphism (S-SAP) method, and the related molecular marker techniques IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism), are based on retrotransposon activity, and are increasingly widely used. However, there have been no systematic analyses of the parameters of these methods or of the utility of different retrotransposon families in producing polymorphic, scorable fingerprints. We have generated S-SAP, IRAP, and REMAP data for three barley (Hordeum vulgare L.) varieties using primers based on sequences from six retrotransposon families (BARE-1, BAGY-1, BAGY-2, Sabrina, Nikita and Sukkula). The effect of the number of selective bases on the S-SAP profiles has been examined and the profiles obtained with eight MseI+3 selective primers compared for all the elements. Polymorphisms detected in the insertion pattern of all the families show that each can be used for S-SAP. The uniqueness of each transposition event and differences in the historic activity of each family suggest that the use of multiple retrotransposon families for genetic analysis will find applications in mapping, fingerprinting, and marker-assisted selection and evolutionary studies, not only in barley and other Hordeum species and related taxa, but also more generally.

Characterization of high-copy-number retrotransposons from the large genomes of the louisiana iris species and their use as molecular markers

The Louisiana iris species Iris brevicaulis and I. fulva are morphologically and karyotypically distinct yet frequently hybridize in nature. A group of high-copy-number TY3/gypsy-like retrotransposons was characterized from these species and used to develop molecular markers that take advantage of the abundance and distribution of these elements in the large iris genome. The copy number of these IRRE elements (for iris retroelement), is approximately 1 x 10(5), accounting for approximately 6-10% of the approximately 10,000-Mb haploid Louisiana iris genome. IRRE elements are transcriptionally active in I. brevicaulis and I. fulva and their F(1) and backcross hybrids. The LTRs of the elements are more variable than the coding domains and can be used to define several distinct IRRE subfamilies. Transposon display or S-SAP markers specific to two of these subfamilies have been developed and are highly polymorphic among wild-collected individuals of each species. As IRRE elements are present in each of 11 iris species tested, the marker system has the potential to provide valuable comparative data on the dynamics of retrotransposition in large plant genomes.

Dasheng: a recently amplified nonautonomous long terminal repeat element that is a major component of pericentromeric regions in rice

A new and unusual family of LTR elements, Dasheng, has been discovered in the genome of Oryza sativa following database searches of approximately 100 Mb of rice genomic sequence and 78 Mb of BAC-end sequence information. With all of the cis-elements but none of the coding domains normally associated with retrotransposons (e.g., gag, pol), Dasheng is a novel nonautonomous LTR element with high copy number. Over half of the approximately 1000 Dasheng elements in the rice genome are full length (5.6-8.6 kb), and 60% are estimated to have amplified in the past 500,000 years. Using a modified AFLP technique called transposon display, 215 elements were mapped to all 12 rice chromosomes. Interestingly, more than half of the mapped elements are clustered in the heterochromatic regions around centromeres. The distribution pattern was further confirmed by FISH analysis. Despite clustering in heterochromatin, Dasheng elements are not nested, suggesting their potential value as molecular markers for these marker-poor regions. Taken together, Dasheng is one of the highest-copy-number LTR elements and one of the most recent elements to amplify in the rice genome.

Plant transposable elements: where genetics meets genomics

Transposable elements are the single largest component of the genetic material of most eukaryotes. The recent availability of large quantities of genomic sequence has led to a shift from the genetic characterization of single elements to genome-wide analysis of enormous transposable-element populations. Nowhere is this shift more evident than in plants, in which transposable elements were first discovered and where they are still actively reshaping genomes.

T-DNA integration into the barley genome from single and double cassette vectors

Patterns and sites of T-DNA integrations into the barley genome from single and double cassette vectors are of interest for the identification of cultivars with value added properties as well as for the production of selection marker-free transgenic lines that can be retransformed. T-DNA/Plant DNA junctions were obtained by capturing a single-stranded DNA with a biotinylated primer annealing to the vector adjacent to the border and an adaptor ligated to a restriction site overhang in the flanking barley DNA. The captured junction was converted into a double strand and sequenced. Fifty left and right border junctions from plants transgenic for one of five human genes were analyzed. Primers of 15-30 nucleotides designed from the genomic DNA at the insertion site can PCR amplify fragments that identify unequivocally any transformant. Adjacent transgene insertions with single cassette vectors were always in tandem direct repeat configuration. With regard to T-DNA integration the patterns were comparable to the variations found in dicotyledonous plants. Twelve of the 46 integrations characterized by blast searches were within different regions of the BARE-1 retrotransposon element occurring with a frequency of 2 x 10(5) copies in the barley genome. The use of border junctions to identify number of copies and loci of integrates in transformants is discussed.

Three Tnt1 subfamilies show different stress-associated patterns of expression in tobacco. Consequences for retrotransposon control and evolution in plants

The genomes of most Nicotiana species contain three different subfamilies of the Tnt1 retrotransposon, which differ completely in their U3 sequence, whereas the rest of the sequence is relatively constant. The results presented here show that all three Tnt1 subfamilies are expressed in tobacco (Nicotiana tabacum) and that the U3 sequence variability correlates with differences in the pattern of expression of the Tnt1 elements. Each of the three Tnt1 subfamilies is induced by stress, but their promoters have a different response to different stress-associated signaling molecules. The Tnt1A subfamily is particularly strongly induced by elicitors and methyl jasmonate, whereas expression of the Tnt1C subfamily is more sensitive to salicylic acid and auxins. The direct relationship between U3 sequence variability and differences in the stress-associated expression of the Tnt1 elements present in a single host species gives support to our model that postulates that retrotransposons have adapted to their host genomes through the evolution of highly regulated promoters that mimic those of the stress-induced plant genes. Moreover, here we show that the analysis of the transcriptional control of a retrotransposon population such as Tnt1 provides new insights into the study of the complex and still poorly understood network of defense- and stress-induced plant signal transduction pathways.