Survey of long terminal repeat retrotransposons of domesticated silkworm (Bombyx mori)

Long terminal retrotransposons are major components of eukaryotic transposable elements. We have surveyed the long terminal repeats (LTR) retrotransposons of domesticated silkworm (Bombyx mori) by mining the data produced by Bombyx mori Genome Sequencing Project. At least 29 separate families of LTR retrotransposons are identified in this survey, comprising of 11.8% of the complete sequence. Families of domesticated silkworm LTR retrotransposons can be mainly classified into three groups: gypsy-like, copia-like, Pao-Bel. Fourteen families identified consist of gypsy-like elements, four families consist of copia-like elements and seven families consist of Pao-Bel elements. In addition to the three groups of LTR retrotransposons, two families of unusual non-coding elements are identified in the genome of this species. Further phylogenetic analysis of RT domain indicates that the elements of B.mori show high diversity and can form different clades in each group. An analysis of sequence variation from different families reveals distinct patterns of variation for the elements belonging to three groups. The analysis of the domesticated silkworm LTR retrotransposons should assist in our understanding of the roles of retroelement in lepidopteron insect genome evolution.     

Evidence for horizontal transfer of the LTR retrotransposon mdg3, which lacks an env gene

Horizontal (interspecific) transfer is regarded as a possible strategy for the propagation of transposable elements through evolutionary time. To date, however, conclusive evidence that transposable elements are capable of horizontal transfer from one species to another has been limited to class II or DNA-type elements. We tested the possibility of such transfer for several Drosophila melanogaster LTR retrotransposons of the gypsy group in an experiment in which D. melanogaster and D. virilis somatic cell lines were used as donor and recipient cells, respectively. This approach was chosen in light of the high levels of LTR retrotransposon amplification and expression observed in cultured D. melanogaster cells. In the course of the experiment, parallel analysis for mdg1, mdg3, 17.6, 297, 412 and B104/roo retrotransposons was performed to detect their presence in the genome of recipient cells. Only the mdg3 retrotransposon, which lacks an env gene, was found to be transmitted into recipient cells. This model, based on the use of cultured cells, is a promising system for further investigating the mechanisms of LTR retrotransposon transfer.     

Revisiting horizontal transfer of transposable elements in Drosophila

Horizontal transfer (HT), defined as the transfer of genetic material between species, is considered to be an essential step in the 'life cycle' of transposable elements. We present a broad overview of suspected cases of HT of transposable elements in Drosophila. Hundred-one putative events of HT have been proposed in Drosophila for 21 different elements (5.0% refer to non-long terminal repeat (LTR) retrotransposons, 42.6% to LTR retrotransposons and 52.4% to DNA transposons). We discuss the methods used to infer HT, their limits and the putative vectors of transposable elements. We outline all the alternative hypotheses and ask how we can be almost certain that phylogenetic inconsistencies are due to HT.     

植物反转录转座子及其分子标记

反转录转座子(retrotransposon)是真核生物中一类可移动因子,可分为m反转录转座子和非LTR反转录转座子。反转录转座子以高拷贝在植物界广泛分布,可以通过纵向和横向分别在世代之间和不同种之间进行传递,同一家族的反转录转座子具有高度的异质性．在一些生物的和非生物的逆境条件下,反转录转座子的转录可以被激活。由于反转录转座子的特点,使其作为一种分子标记得以应用。SSAP、IRAP、REMAP和RBIP等分子标记相继发展起来,在基因作图、生物遗传多样性与系统进化、品种鉴定等方面具有广泛的应用前景。     

RIRE2, a novel gypsy-type retrotransposon from rice

The 441-bp DNA segment in a PCR-amplified fragment from Oryza sativa cv. IR36 was found to have a sequence with features characteristic of LTRs of retroelements, which was named RIRE2 (Rice retroelement #2) and further analyzed. Cloning and sequencing analyses of the DNA segments connected to LTR-like sequence showed that RIRE2 has a long internal region almost 10 kb long that is flanked by LTR-like sequences. This internal region carries a primer binding site (PBS) and polypurine tract (PPT) which are necessary for cDNA synthesis of retroelements. The PBS sequence is complementary to the 3' end region of tRNA(Arg). The internal region has an rt gene homologous to that of gypsy-type retrotransposons, evidence that RIRE2 is indeed a retrotransposon related to gypsy from Drosophila. RIRE2 has an extra sequence more than 4 kb long in the region downstream of gag-pol. Phylogenetic analysis of the putative amino-acid sequences of the rt gene as well as the int gene showed that RIRE2 is related to a group of gypsy-type retrotransposons of a large size that include Grande1-4 of teosinte, Tat4-1 and Athila1-1 of Arabidopsis thaliana, and Cyclops-2 of pea, but distantly related to any other group of gypsy-type retrotransposons, including RIRE3 and RIRE8 of rice. RIRE2 and Grande1-4 had the highest homology in the gag-pol region, but the nucleotide sequences of the LTR regions differed. Both elements had significant homology in the middle area of the extra regions downstream of gag-pol, in which they had an open reading frame encoding a protein with no known function on the opposite strand from that coding for gag-pol.     

植物反转录转座子及其分子标记

反转录转座子（retrotransposon）是真核生物中一类可移动因子,可分为LTR反转录转座子和非LTR反转录转座子。反转录转座子以高拷贝在植物界广泛分布,可以通过纵向和横向分别在世代之间和不同种之间进行传递,同一家族的反转录转座子具有高度的异质性. 在一些生物的和非生物的逆境条件下,反转录转座子的转录可以被激活。由于反转录转座子的特点,使其作为一种分子标记得以应用。S-SAP、IRAP、REMAP和RBIP等分子标记相继发展起来,在基因作图、生物遗传多样性与系统进化、品种鉴定等方面具有广泛的应用前景。     

Formation of solo-LTRs through unequal homologous recombination counterbalances amplifications of LTR retrotransposons in rice Oryza sativa L

We studied the dynamics of hopi, Retrosat1, and RIRE3, three gypsy-like long terminal repeat (LTR) retrotransposons, in Oryza sativa L. genome. For each family, we assessed the phenetic relationships of the copies and estimated the date of insertion of the complete copies through the evaluation of their LTR divergence. We show that within each family, distinct phenetic groups have inserted at significantly different times, within the past 5 Myr and that two major amplification events may have occurred during this period. We show that solo-LTR formation through homologous unequal recombination has occurred in rice within the past 5 Myr for the three elements. We thus propose an increase/decrease model for rice genome evolution, in which both amplification and recombination processes drive variations in genome size.     

Mechanisms regulating the copy numbers of six LTR retrotransposons in the genome of Drosophila melanogaster

There has been debate over the mechanisms that control the copy number of transposable elements in the genome of Drosophila melanogaster. Target sites in D. melanogaster populations are occupied at low frequencies, suggesting that there is some form of selection acting against transposable elements. Three main theories have been proposed to explain how selection acts against transposable elements: insertions of a copy of a transposable element are selected against; chromosomal rearrangements caused by ectopic exchange between element copies are selected against; or the process of transposition itself is selected against. The three theories give different predictions for the pattern of transposable element insertions in the chromosomes of D. melanogaster. We analysed the abundance of six LTR (long terminal repeat) retrotransposons on the X and fourth chromosomes of multiple strains of D. melanogaster, which we compare with the predictions of each theory. The data suggest that no one theory can account for the insertion patterns of all six retrotransposons. Comparing our results with earlier work using these transposable element families, we find a significant correlation between studies in the particular model of copy number regulation supported by the proportion of elements on the X for the different transposable element families. This suggests that different retrotransposon families are regulated by different mechanisms.     

Characterization of transposable elements in the genome of rice (Oryza sativa L.) using Representational Difference Analysis (RDA)

Representational Difference Analysis was applied to characterize genomic differentiations between rice ( Oryza sativa) and foxtail millet ( Setaria italica) and subsequently to identify rice transposable elements. Rice was used as the tester and millet as the driver. A total of eleven, non-redundant, positive clones were isolated from the library. Their analysis revealed that they all represent dispersed repetitive DNA sequences. In addition, homology searches using the BLAST procedure showed that they correspond to seven distinct rice transposable elements. Three had been previously identified as gypsy-like retroelements ( Retrosat1, RIRE3 and RIRE8). The remaining four are novel: we named them hipa (a CACTA-like transposon), houba (a copia-like retroelement), hopi and dagul (two gypsy-like retroelements). The RDA clones were used as probes in Southern hybridization experiments with genomic DNAs of several species from the family Poaceae. The results suggest that the genomic differentiations associated with the activity of these transposable elements are of relatively recent origin. In addition, comparison of the hybridization patterns obtained for several Oryza species suggests that several independent amplifications of these transposable elements might have occurred within the genus.     

Evolution of Tom, 297, 17.6 and rover retrotransposons in Drosophilidae species

LTR retrotransposons are the most abundant transposable elements in Drosophila and are believed to have contributed significantly to genome evolution. Different reports have shown that many LTR retrotransposon families in Drosophila melanogaster emerged from recent evolutionary episodes of transpositional activity. To contribute to the knowledge of the evolutionary history of Drosophila LTR retrotransposons and the mechanisms that control their abundance, distribution and diversity, we conducted analyses of four related families of LTR retrotransposons, 297, 17.6, rover and Tom. Our results show that these elements seem to be restricted to species from the D. melanogaster group, except for 17.6, which is also present in D. virilis and D. mojavensis. Genetic divergences and phylogenetic analyses of a 1-kb fragment region of the pol gene illustrate that the evolutionary dynamics of Tom, 297, 17.6 and rover retrotransposons are similar in several aspects, such as low codon bias, the action of purifying selection and phylogenies that are incongruent with those of the host species. We found an extremely complex association among the retrotransposon sequences, indicating that different processes shaped the evolutionary history of these elements, and we detected a very high number of possible horizontal transfer events, corroborating the importance of lateral transmission in the evolution and maintenance of LTR retrotransposons.     

家蚕LTR逆转录转座子的鉴定、分类及系统发育分析

转座子是真核生物基因组的重要组成成分。为了研究家蚕Bombyx mori长末端重复序列 (long terminal repeat, LTR)逆转录转座子的分类及进化, 本研究采用de novo预测和同源性搜索相结合的方法, 在家蚕基因组中共鉴定出了38个LTR逆转录转座子家族, 序列长度占整个基因组的0.64%, 远小于先前预测的11.8%, 其中有6个家族为本研究的新发现。38个家族中, 26个家族有表达序列标签 (expression sequence tag, EST)证据, 表明这些家族具有潜在的活性。对有EST证据的6个家族和没有EST证据的5个家族用RT-PCR进行了组织表达谱实验, 结果表明这11个家族在一些组织中有表达, 这进一步证实了这些家族具有转录活性, 基于此我们推测家蚕中大部分的LTR逆转录转座子家族很可能具有潜在活性。对转座子的插入时间进行估计, 结果表明绝大部分元件都是最近1百万年内插入到家蚕基因组中的。我们还比较了黑腹果蝇Drosophila melanogaster、 冈比亚按蚊Anopheles gambiae和家蚕B. mori中Ty3/Gypsy超家族分支的差异, 结果表明不同枝在不同昆虫中有着不同的扩张。家蚕中LTR逆转录转座子的鉴定和系统分析有助于我们理解逆转录转座子在昆虫进化中的作用。     

水稻逆转录转座子RIRE10拷贝数与LTR区转录活性的鉴定

在水稻第四号染色体的长臂上鉴定了一个结构完整的Ty3型逆转录转座子RIRE10。RIRE10两LTR间的中间区域在gag pol的上游还包含另一个开放阅读框。通过RT PCR与Northern印迹杂交检测到来自LTR区的转录产物 ;根据点杂交结果 ,鉴定出包含中间区域的RIRE10成员的个数以及LTR区的拷贝数。除了 6 5个完整的逆转录转座子所具备的两个LTR外 ,水稻基因组还含有近 90 0个RIRE10的solo LTR。LTR区的转录以及导致solo LTR产生的同源重组可能影响了RIRE10成员在水稻基因组中的转座活性     

Long terminal repeat retrotransposons of <Emphasis Type="Italic">Mus musculus</Emphasis>

Background

Long terminal repeat (LTR) retrotransposons make up a large fraction of the typical mammalian genome. They comprise about 8% of the human genome and approximately 10% of the mouse genome. On account of their abundance, LTR retrotransposons are believed to hold major significance for genome structure and function. Recent advances in genome sequencing of a variety of model organisms has provided an unprecedented opportunity to evaluate better the diversity of LTR retrotransposons resident in eukaryotic genomes.

Results

Using a new data-mining program, LTR_STRUC, in conjunction with conventional techniques, we have mined the GenBank mouse (Mus musculus) database and the more complete Ensembl mouse dataset for LTR retrotransposons. We report here that the M. musculus genome contains at least 21 separate families of LTR retrotransposons; 13 of these families are described here for the first time.

Conclusions

All families of mouse LTR retrotransposons are members of the gypsy-like superfamily of retroviral-like elements. Several different families of unrelated non-autonomous elements were identified, suggesting that the evolution of non-autonomy may be a common event. High sequence similarity between several LTR retrotransposons identified in this study and those found in distantly-related species suggests that horizontal transfer has been a significant factor in the evolution of mouse LTR retrotransposons.

     

Evolutionary Genomics of Transposable Elements in Saccharomyces cerevisiae

Saccharomyces cerevisiae is one of the premier model systems for studying the genomics and evolution of transposable elements. The availability of the S. cerevisiae genome led to unprecedented insights into its five known transposable element families (the LTR retrotransposons Ty1-Ty5) in the years shortly after its completion. However, subsequent advances in bioinformatics tools for analysing transposable elements and the recent availability of genome sequences for multiple strains and species of yeast motivates new investigations into Ty evolution in S. cerevisiae. Here we provide a comprehensive phylogenetic and population genetic analysis of all Ty families in S. cerevisiae based on a systematic re-annotation of Ty elements in the S288c reference genome. We show that previous annotation efforts have underestimated the total copy number of Ty elements for all known families. In addition, we identify a new family of Ty3-like elements related to the S. paradoxus Ty3p which is composed entirely of degenerate solo LTRs. Phylogenetic analyses of LTR sequences identified three families with short-branch, recently active clades nested among long branch, inactive insertions (Ty1, Ty3, Ty4), one family with essentially all recently active elements (Ty2) and two families with only inactive elements (Ty3p and Ty5). Population genomic data from 38 additional strains of S. cerevisiae show that the majority of Ty insertions in the S288c reference genome are fixed in the species, with insertions in active clades being predominantly polymorphic and insertions in inactive clades being predominantly fixed. Finally, we use comparative genomic data to provide evidence that the Ty2 and Ty3p families have arisen in the S. cerevisiae genome by horizontal transfer. Our results demonstrate that the genome of a single individual contains important information about the state of TE population dynamics within a species and suggest that horizontal transfer may play an important role in shaping the genomic diversity of transposable elements in unicellular eukaryotes.     

Transposable elements in mosquitoes

We describe the current state of knowledge about transposable elements (TEs) in different mosquito species. DNA-based elements (class II elements), non-LTR retrotransposons (class I elements), and MITEs (Miniature Inverted Repeat Transposable Elements) are found in the three genera, Anopheles, Aedes and Culex, whereas LTR retrotransposons (class I elements) are found only in Anopheles and Aedes. Mosquitoes were the first insects in which MITEs were reported; they have several LTR retrotransposons belonging to the Pao family, which is distinct from the Gypsy-Ty3 and Copia-Ty1 families. The number of TE copies shows huge variations between classes of TEs within a given species (from 1 to 1000), in sharp contrast to Drosophila, which shows only relatively minor differences in copy number between elements (from 1 to 100). The genomes of these insects therefore display major differences in the amount of TEs and therefore in their structure and global composition. We emphasize the need for more population genetic data about the activity of TEs, their distribution over chromosomes and their frequencies in natural populations of mosquitoes, to further the current attempts to develop a transgenic mosquito unable to transmit malaria that is intended to replace the natural populations.     

Structure and evolution of full-length LTR retrotransposons in rice genome

The long terminal repeat (LTR) retrotransposons are the most abundant class of transposable elements in plant genomes and play important roles in genome divergence and evolution. Their accumulation is the main factor influencing genome size increase in plants. Rice (Oryza sativa L.) is a model monocot and is the focus of much biological research due to its economic importance. We conducted a comprehensive survey of full-length LTR retrotransposons based on the completed genome of japonica rice variety Nipponbare (TIGR Release 5), with the newly published tool LTR-FINDER. The elements could be categorized into 29 structural domain categories (SDCs), and their total copy number identified was estimated at >6,000. Most of them were relatively young: more than 90% were less than 10 My. There existed a high level of activity among them as a whole at 0–1 Mya, but different categories possessed distinct amplification patterns. Most recently inserted elements were specific to the rice genome, while a few were conserved across species. This study provides new insights into the structure and evolutionary history of the full-length retroelements in the rice genome.     

植物LTR反转录转座子的研究进展

反转录转座子是真核生物基因组中普遍存在的一类可移动的遗传因子,它们以RNA为媒介,在基因组中不断自我复制。在高等植物中,反转录转座子是基因组的重要成分之一。反转录转座子可以分为5大类型,其中以长末端重复（LTR）类型报道较多。LTR类型由于其首尾具有长末端重复序列,内部含有PBS、PPT、GAG和POL开放阅读框、TSD等结构,可以采用生物信息学软件进行预测。LTR反转录转座子的活性受到自身甲基化和环境因素的影响,DNA甲基化抑制反转录转座子转座,而外界环境的刺激能够激活转座子,从而影响插入位点周边基因的表达。同时由于LTR反转录转座子在植物中普遍存在,丰富的拷贝数以及多态性为新型分子标记（RBIP、SSAP、IRAP、REMAP）的开发提供了良好的素材。该文对近年来国内外有关植物反转录转座子的类型、结构特征、 LTR反转录转座子的活性及其影响因素、 LTR反转录转座子的预测以及标记开发等方面的研究进展进行综述。     

Diversity of LTR retrotransposons and their role in genome reorganization

Current views of retrotransposons possessing long terminal repeats (LTRs) are described. The existing classification and element types isolated by genome organization are considered. Experimental data are summarized to demonstrate that the replicative cycle of a retrotransposon is not restricted to a single cell and that LTR retrotransposons are transferred between somatic cells with a rate comparable with the element transposition rate within the genome of one cell. The major mechanisms mediating the role of LTR retrotransposons in reorganization of the genome are considered with regard to the strategies of their horizontal and vertical transfer.