Ty1-copia Group Retrotransposons Research Articles

LTR-retrotransposon activation, IRAP marker development and its potential in genetic diversity assessment of masson pine (Pinus massoniana)

Activation of retrotransposon is the pivotal factor for the genesis of genetic polymorphism. Retrotransposon-based molecular markers are excellent tools for detecting genetic diversity and genomic changes associated with retrotransposon activity. The scarcity of retrotransposon long terminal repeat (LTR) sequence limits the application of retrotransposon-based molecular marker systems. In this study, retrotransposon 3′-LTR segments were firstly isolated and characterized from the masson pine genome using a genome walking strategy, subsequently inter-retrotransposon amplified polymorphism (IRAP) markers were explored for genetic diversity assessment. These were shown to have clearly distinguishable amplification bands and high levels of polymorphism for masson pine. Dendrogram of our IRAP data highlighted that IRAP markers for individual elements are distinguishable and will shed light on the usage in genetic diversity studies of the masson pine. Transcription activation of Ty1-copia and Ty3-gypsy group retrotransposons in masson pine was investigated with exposure to various abiotic stresses. The insertional polymorphism and the transposition activation were detected by IRAP. Results revealed that none of the analyzed materials in the course of 2-month trials displayed fingerprint changes.

Isolation, identification, and characterization of genomic LTR retrotransposon sequences from masson pine (Pinus massoniana)

Long terminal repeat (LTR) retrotransposons are ubiquitous in the plant kingdom and play an important role in plant genome evolution. Masson pine (Pinus massoniana) is one of the most economically important forest trees. However, the masson pine genome is poorly understood. Conserved domains of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy LTR retrotransposons were amplified from masson pine using degenerate primers. Sequence analysis showed less heterogeneity among Ty1-copia group retrotransposons than among Ty3-gypsy group retrotransposons. Phylogenetic analysis demonstrated that Ty1-copia and Ty3-gypsy RT sequences had considerable homology with other species, indicating that both vertical transmission and horizontal transmission may probably be the source of LTR retrotransposons in masson pine. Southern dot blot hybridization results suggested that both types of LTR retrotransposons are present in the genome of masson pine with high copy number. These results contribute to further understanding about the organization and evolution of the masson pine genome and provide fundamental genetic information for the utilization of retrotransposons in masson pine.

Ty1-copia group retrotransposons and the evolution of retroelements in several angiosperm plants: evidence of horizontal transmission.

The phylogenetic relationships among thirty-seven new Ty1-copia group retrotransposons in seven angiosperm plants were examined by reverse transcriptase and ribonuclease H sequence analysis. Distribution pattern of the retrotransposons of closely related plant species generally reflects a close phylogenetic relationship. In contrast, we found that several retrotransposon sequences from the same genome exhibited a high degree of divergence and had a relatively high degree of identity versus retrotransposon sequences from widely divergent species, including an ancestral phytopathogen fungus. This finding supports the hypothesis that the horizontal transmission from phytopatogen organism to the host flowering plants could have played a role in the evolutionary dynamics of Ty1-copia group retrotransposons.

Genome-wide detection of Ty1-copia and Ty3-gypsy group retrotransposons in Japanese apricot ( Prunus mume Sieb. et Zucc.)

The conserved domains of reverse transcriptase (RT) genes of approximately 260 bp for Ty1-copia and 430 bp for Ty3-gypsy groups of long terminal repeat (LTR) retrotransposons were amplified from Japanese apricot ( Prunus mume Sieb. et Zucc.) using degenerate oligonucleotide primers. Sequence analysis showed that 32.3% of Ty1-copia and 27.5% of Ty3-gypsy RT sequences possessed stop codons and/or frameshifts, and all sequences were AT-rich. Ty1-copia retrotransposon has higher heterogeneity than Ty3-gypsy retrotransposon, but the latter has a higher copy number revealed by southern dot blot hybridization. Phylogenetic analysis illustrated that some of the clones were more closely related to the representative elements present in other plant species than to other clones of Japanese apricot. Transcription was not detected by reverse transcription-polymerase chain reaction amplification for either Ty1-copia or Ty3-gypsy retrotransposons in young leaves of plants treated with UV light and 2,4-dichlorophenoxyacetic acid either individually or in both combinations, even though the ratios of dN/dS of the open reading frames among members of each subgroup of both group retrotransposons were less than 1. This is the first report on the presence of RT sequences of Ty1-copia and Ty3-gypsy group retrotransposons in Japanese apricot genome. Keywords: Prunus mume , retrotransposon, heterogeneity, copy number, transcriptional activity

Genome‐wide Characterization of Long Terminal Repeat ‐retrotransposons in Apple Reveals the Differences in Heterogeneity and Copy Number between Ty1‐copiaand Ty3‐gypsyRetrotransposons

The conserved domains of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy groups of long terminal repeat (LTR) retrotransposons were isolated from the Malus domestica genome using degenerate oligonucleotide primers. Sequence analysis showed that 45% of Ty1-copia and 63% of Ty3-gypsy RT sequences contained premature stop codons and/or indels disrupting the reading frame. High heterogeneity among RT sequences of both Ty1-copia and Ty3-gypsy group retrotransposons was observed, but Ty3-gypsy group retrotransposons in the apple genome are less heterogeneous than Ty1-copia elements. Retrotransposon copy number was estimated by dot blot hybridizations for Ty1-copia (approximately 5,000) and Ty3-gypsy (approximately 26,000). All elements of the two types of LTR retrotransposons comprise approximately 38% of the M. domestica genome, with the Ty3-gypsy group contribution being higher (33.5%) than the Ty1-copia one (4.6%). Transcription was not detected by reverse transcription-polymerase chain reaction for either Ty1-copia or Ty3-gypsy retrotransposons in the leaves of plants in vitro or in leaf explants cultured on medium supplemented with high concentration benzylaminopurine. This research reveals the differences in heterogeneity and copy number between Ty1-copia and Ty3-gypsy retrotransposons in the apple genome. Ty1-copia retrotransposon has higher heterogeneity than Ty3-gypsy retrotransposon, but the latter has a higher copy number, which implies that Ty3-gypsy retrotransposons may play a more important role in the apple genome evolution.

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

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

SIRE-1, a putative plant retrovirus is closely related to a legume TY1-copia retrotransposon family.

SIRE-1 is a potential soybean retrovirus which has a gene order similar to Ty1-copia retrotransposons but also contains an envelope-like open reading frame (ORF), which is characteristic of retroviruses. PCR and Southern analysis reveals that SIRE-1 is closely related to a legume-wide family of envelope-lacking Ty1-copia group retrotransposons which suggests that SIRE-1 was formed by the recent acquisition of an envelope gene by a Ty1-copia retrotransposon.

Phylogenetic and molecular evolutionary analyses of Ty1-copia group retrotransposons in cultivated Egyptian cotton, Gossypium barbadense L.

The Ty1-copia group retrotransposons have been characterized in cultivated Egyptian cotton, G.barbadense L., using degenerate PCR primers for their reverse transcriptase (RT) domains. Comparative nucleotide and amino acid sequences analyses showed that G. barbadense Ty1-copia RT sequences are heterogeneous and this heterogeneity is resolved into 11 distinct families. The high ratio of synonymous to nonsynonymous changes indicates that there is a strong selection for the RT domain of these families. Phylogenetic analysis revealed that two cultivated G. barbadense RT families are closely related to Ty1-copia group retrotransposons present in other plant species. In other words, these families mirror their own phylogenies rather than that of their host cultivars. On the other hand, the remaining G. barbadense RT families are closely related to their respective Gossypium species. These data show that Ty1-copia group retrotransposons tend to span species boundaries, suggesting that they existed early in plant evolution, and were diverged into heterogeneous sequences prior to modern plant species divergence.

Ty1-copiagroup retrotransposon families in cultivated cottonsG. barbadenseL. identified by reverse transcriptase domain analysis

The objective of the current study was to analyze Ty1-copia group retrotransposons in cultivated G. barbadense L. cottons. DNA sequence analysis of 27 partial reverse transcriptase sequences revealed that these elements are heterogeneous and this heterogeneity is resolved into 11 distinct families. Phylogenetic analyses provided strong bootstrap support for a monophyletic origin of plant Ty1-copia group retrotransposons, yet showed high diversity within and between Gossypium species. Furthermore, G. Barbadense element topologies are incongruent with Gossypium phylogeny. The high ratio of synonymous to nonsynonymous changes indicates that the reverse transcriptase domain of these families is evolving under purifying selection. The antiquity and wide distribution of Ty1-copia group retrotransposons illustrate their active role in shaping and evolution of the Gossypium genome.

Ty1-copia group retrotransposons in persimmon (Diospyros kaki Thunb.).

We cloned and characterized Ty1-copia group retrotransposons in persimmon (Diospyros kaki Thunb.). Genomic DNA or methyl jasmonate (MJA)-treated cDNA were used as templates to amplify the reverse transcriptase region of Ty1-copia group retrotransposons. About 280 bp fragments were amplified and cloned, and 97 clones were sequenced. Forty-nine clones included frameshift or the stop codon, or both. Among 48 clones containing complete reading frames, 42 clones had unique nucleotide sequences. Alignment and phylogenetic analysis of putative amino acid sequences in the 42 clones indicated that these clones (named Tdk; retroTransposon in Diospyros kaki) fell into seven subgroups and six ungrouped sequences, indicating high sequence heterogeneity in Tdk clones. Phylogenetic analysis comparing unrelated plant species shows that some Tdk clones are more closely related to Ty1-copia group retrotransposons in the orders Solanales and Sapindales rather than to other Tdk clones. Southern blot analysis using Tdk2B, Tdk4c, Tdk6Ac, Tdk12K and Tdk13G clones as probes showed that persimmon and its related species, D. lotus, D. lotus var. glabba, D. oleifera, D. rhombifolia and D. virginiana, contained multiple Tdk-like sequences, indicating that homologous elements exist in other Diospyros species.

Pea Ty1-copia group retrotransposons: transpositional activity and use as markers to study genetic diversity in Pisum.

The variation in transposition history of different Ty1-copia group LTR retrotransposons in the species lineages of the Pisum genus has been investigated. A heterogeneous population of Ty1-copia elements was isolated by degenerate PCR and two of these (Tps12 and Tps19) were selected on the basis of their copy number and sequence conservation between closely related species for further in-depth study of their transpositional history in Pisum species. The insertional polymorphism of these elements and the previously characterised PDR1 element was studied by sequence-specific amplification polymorphism (SSAP). Each of these elements reveals a unique transpositional history within 55 diverse Pisum accessions. Phylogenetic trees based on the SSAP data show that SSAP markers for individual elements are able to resolve different species lineages within the Pisum genus. Finally, the SSAP data from all of these retrotransposon markers were combined to reveal a detailed picture of the intra and interspecies relationships within Pisum.

Phylogeny and transpositional activity of Ty1-copia group retrotransposons in cereal genomes.

The Ty1-copia group retrotransposon populations of barley (Hordeum vulgare) and bread wheat (Triticum aestivum) have been characterised by degenerate PCR and sequence analysis of fragments of the reverse transcriptase genes. The barley population is comprised of a highly heterogeneous set of retrotransposons, together with a collection of sequences that are closely related to the BARE-1 element. Wheat also contains a highly diverse Ty1-copia retrotransposon population, together with a less prominent BARE-1 subgroup. These data have been combined with previously published Gramineae sequences to construct a composite phylogenetic tree for this class of retrotransposons in cereal grasses. The analysis indicates that the ancestral Gramineae genome contained a heterogeneous population of Ty1-copia group retrotransposons, the descendants of which have proliferated to differing degrees in present-day species. Lastly, the level of recent transpositional activity of two Ty1-copia elements has been estimated by measuring their insertional polymorphism within species. Both transposons are highly polymorphic within all species tested. These data suggest that transposition proficiency may be a common and evolutionarily stable feature of the Ty1-copia group retrotransposons of cereal grasses.

Evolutionary dynamics of Ty1-copia group retrotransposons in grass shown by reverse transcriptase domain analysis.

The evolutionary dynamics of Ty1-copia group retrotransposons in grass were examined by reverse transcriptase (RT) domain analysis. Twenty-three rice RT sequences were newly determined for this report. Phylogenetic analysis of 177 RT sequences, mostly derived from wheat, rice, and, maize, showed four distinct families, which were designated G1, G2, G3, and G4. Three of these families have elements obtained from distantly related species, indicative of origins prior to the radiation of grass species. Results of Southern hybridization and detailed comparisons between the wheat and rice sequences indicated that each of the families had undergone a distinct pattern of evolution. Multiple families appear to have evolved in parallel in a host species. Analyses of synonymous and nonsynonymous substitutions suggested that there is a low percentage of elements carrying functional RT domains in the G4 family, indicating that the production of new G4 elements has been controlled by a small number of elements carrying functional RT domains.

Characterization and genomic organization of Ty1-copia group retrotransposons in rye (Secale cereale).

The genomic organisation of the Ty1-copia retrotransposons in rye (Secale cereale) has been studied. We have used the polymerase chain reaction (PCR) to amplify sequences from a conserved domain of the reverse transcriptase gene of the Ty1-copia retrotransposons in this species. Sequence analysis of 26 of these PCR products shows them to be a highly heterogeneous population, a feature that is common in plants. Slot blot analysis shows that there are about 100,000 individual Ty1-copia retrotransposons in rye. In situ hybridization of a heterogeneous probe, representing the whole population of rye Ty1-copia retrotransposon sequences, to chromosome spreads of triticale (xTriticosecale), a rye-wheat hybrid, shows that these sequences are present throughout all the rye chromosomes but absent from the centromeric regions and, in particular, from the terminal heterochromatin. Southern analysis of oat, barley, wheat, and rye, using as a probe R9, one of the rye sequences that is closely similar to the BARE-1 element of barley, shows that close relatives of this retrotransposon subgroup are present in all these species in high copy number. Northern analysis on RNAs from seedlings shows that the BARE-1 subgroup is transcribed in all these cereal plants but in variable amounts: high in barley, moderate in wheat and rye, and extremely low in oat.

Activation of the Ty1-copia group retrotransposons of potato (Solatium tuberosum) during protoplast isolation

The potato (Solanum tuberosum) genome contains a highly heterogeneous population of Ty1-copia group retrotransposons. Here we identify the first such transposable element known to be transcribed in this species. The elements are transcriptionally activated during protoplast isolation. The majority of the activated Ty1-copia sequences are similar to elements which are transcriptionally induced under the same conditions in tobacco (Nicotiana tabacum). We also show that a previously identified potato element M166, which has no known equivalent in tobacco is also transcribed under these conditions. It appears that the control of transcription of this particular Ty1-copia group retrotransposons has been broadly conserved between these two species.

Ty1-copia group retrotransposon sequences in amphibia and reptilia.

We have isolated sequences belonging to Ty1-copia group retrotransposons from the genomes of an amphibian (Pyxicephalus adspersa) and three reptiles (Conolophus subscristatus, Amblyrynchus cristatus and Pytas mucosus). Two different sequences were found in the amphibian (Tpa1 and Tpa2). Each is present in several copies per genome and absent from the genomes of two other amphibian species. The C. subcristatus sequence Tcs1 is present in multiple copies in both its host genome (Galapagos land iguana) and the genome of the related Galapagos marine iguana (A. cristatus). There is little or no polymorphism in Tcs1 insertions between different individual animals, suggesting that this sequence is not transposing rapidly in either iguana genome. The P. mucosus sequence Tpm1 shows a discontinuous distribution in snake species, suggesting that it has either been lost from many lineages during vertical germline transmission or has been transferred horizontally in some snake species. Phylogenetic comparisons of all these sequences with each other and with other members of this retrotransposon group from other animals and plants show that sequences within a particular vertebrate species are most closely related to each other, consistent with a vertical transmission model for their evolution.

Ty1-copia group retrotransposons as ubiquitous components of plant genomes.

Ty1-copia group retrotransposons were searched for in 35 plant species by amplification of the reverse transcriptase coding region using the polymerase chain reaction. Sequences of the expected size were amplified from all of these plant species, including a liverwort, a horsetail, a bracken, gymnosperms and angiosperms. Sequences of 72 clones from 17 species were determined, all of which showed clear homology to the reverse transcriptase sequence of Ty1-copia type retrotransposons. More than half of the sequences carried stop codons or frame shifts. Twenty three new retrotransposon sequences with no interruption by these mutations were revealed. The mechanisms of the evolution of retrotransposons and accumulation of mutations were discussed.

Ty1-copia group retrotransposons as ubiquitous components of plant genomes

Ty1-copia group retrotransposons as ubiquitous components of plant genomes

A Ty1-copia group retrotransposon sequence in a vertebrate.

We have used the polymerase chain reaction (PCR) to isolate a sequence characteristic of a Ty1-copia group retrotransposon from the genome of the herring (Clupea harengus). This is the first Ty1-copia group retrotransposon sequence described in a vertebrate. Phylogenetic comparison of this sequence with other members of this group of retrotransposons shows that it resembles more closely some Ty1-copia group members from Drosophila melanogaster than other group members in plants and fungi. These observations provide further evidence that the Ty1-copia group LTR retrotransposons span many of the major eukaryote species boundaries, suggesting that horizontal transmission between different species has played a role in the evolution of this retrotransposon group.

Extreme heterogeneity of Ty1-copia group retrotransposons in plants.

We have used the polymerase chain reaction to analyse Ty1-copia group retrotransposons of flowering plants. All eight species studied contain reverse transcriptase fragments from Ty1-copia group retrotransposons. Sequence analysis of 31 subcloned fragments from potato reveals that each is different from the others, with predicted amino acid diversities between individual fragments varying between 5% and 75%. Such sequence heterogeneity within a single species contrasts strongly with the limited diversity seen in such retrotransposons in yeast and Drosophila. The fragments from the other seven plant species examined are also heterogeneous, both within and between species, showing that this is a general property of this transposon group in plants. Phylogenetic analysis of all these sequences reveals that many of them fall into subgroups which span species boundaries, such that the closest homologue of one sequence is often from a different species. We suggest that both vertical transmission of Ty1-copia group retrotransposons within plant lineages and horizontal transmission between different species have played roles in the evolution of Ty1-copia group retrotransposons in flowering plants.