Although the number of protein-coding genes is not highly variable between plant taxa, the DNA content in their genomes is highly variable, by as much as 2,056-fold from a 1C amount of 0.0648 pg to 132.5 pg. The mean 1C-value in plants is 2.4 pg, and genome size expansion/contraction is lineage-specific in plant taxonomy. Transposable element fractions in plant genomes are also variable, as low as ~3% in small genomes and as high as ~85% in large genomes, indicating that genome size is a linear function of transposable element content. Of the 2 classes of transposable elements, the dynamics of class 1 long terminal repeat (LTR) retrotransposons is a major contributor to the 1C value differences among plants. The activity of LTR retrotransposons is under the control of epigenetic suppressing mechanisms. Also, genome-purging mechanisms have been adopted to counter-balance the genome size amplification. With a wealth of information on whole-genome sequences in plant genomes, it was revealed that several genome-purging mechanisms have been employed, depending on plant taxa. Two genera, Lilium and Fritillaria, are known to have large genomes in angiosperms. There were twice times of concerted genome size evolutions in the family Liliaceae during the divergence of the current genera in Liliaceae. In addition to the LTR retrotransposons, non-LTR retrotransposons and satellite DNAs contributed to the huge genomes in the two genera by possible failure of genome counter-balancing mechanisms.
Angiosperms ; Classification ; DNA ; DNA Transposable Elements* ; DNA, Satellite ; Epigenomics ; Fritillaria ; Genome ; Genome Size* ; Genome, Plant ; Humans ; Liliaceae ; Lilium ; Plants ; Retroelements ; Terminal Repeat Sequences

Ralstonia solanacearum strain PRS-84 used in this study was isolated from diseased Pogostemon cablin plants in our previous study.The competent cells of R.solanacearum strain PRS-84 were transformed by electroporation with Tn5 transposon and then were plated on TTC agar plates containing kanamycin to select for kanamycin-resistant colonies.The detection of kanamycin-resistant gene in kanamycin-resistant colonies was performed by PCR.Further,the flanking fragments of Tn5 transposon insertion site in the mutants were amplified by inverse PCR,and the flanking fragments were sequenced and analyzed.The results indicated that the kanamycin-resistant colonies were obtained in the transformation experiment of R.solanacearum strain PRS-84 by electroporation with Tn5 transposon.A specific band of approximately 700 bp was amplified by PCR from kanamycin-resistant colonies.The flanking sequences of Tn5 transposon insertion site in the transformants were obtained by inverse PCR.After sequencing and sequence analysis of Tn5 transposon insertion site in mutants,we preliminarily speculated that the Tn5 transposon inserted in the typ A gene,rec O gene and gid A gene in three mutants,respectively.A random mutagenesis system of R.solanacearum strain PRS-84 by electroporation with Tn5 transposon has been established,and the Tn5 insertion mutants have been obtained.This study might facilitate the creation of mutant library and the discovery of the virulence gene of R.solanacearum isolated from P.cablin.
DNA Transposable Elements ; Electroporation ; Genes, Bacterial ; Mutagenesis, Insertional ; Pogostemon ; microbiology ; Ralstonia solanacearum ; genetics ; Virulence

Foldback intercoil (FBI) DNA is formed by the folding back at one point of a non-helical parallel track of double-stranded DNA at as sharp as 180degrees and the intertwining of two double helixes within each other's major groove to form an intercoil with a diameter of 2.2 nm. FBI DNA has been suggested to mediate intra-molecular homologous recombination of a deletion and inversion. Inter-molecular homologous recombination, known as site-specific insertion, on the other hand, is mediated by the direct perpendicular approach of the FBI DNA tip, as the attP site, onto the target DNA, as the attB site. Transposition of DNA transposons involves the pairing of terminal inverted repeats and 5-7-bp tandem target duplication. FBI DNA configuration effectively explains simple as well as replicative transposition, along with the involvement of an enhancer element. The majority of diverse retrotransposable elements that employ a target site duplication mechanism is also suggested to follow the FBI DNA-mediated perpendicular insertion of the paired intercoil ends by non-homologous end-joining, together with gap filling. A genome-wide perspective of transposable elements in light of FBI DNA is discussed.
DNA End-Joining Repair ; DNA Transposable Elements ; DNA* ; Enhancer Elements, Genetic ; Hand ; Homologous Recombination ; Retroelements

The mPing family is the first active MITE TE family identified in rice genome. In order to compare the compositions and distributions of mPing family in the genomes of two rice subspecies japonica (cv. Nipponbare) and indica (cv. 93-11), we initially estimated the copy numbers of mPing family in those two subspecies using Southern blot and then confirmed the results by searching homologous copies in each reference genome using Blastn program, which turned out to have 52 and 14 mPing copies in corresponding reference genome, respectively. All mPing members in Nipponbare genome belong to mPing-1, while there are 3 mPing-1 and 11 mPing-2 copies in 93-11 genome. By further investigating the 5-kb flanking sequences of those mPing copies, it was found that 23 and 3 protein-coding genes in Nipponbare and 93-11 genome are residing adjacent to those mPing copies respectively. These results establish the preliminary theoretical foundation for further dissecting the genetic differences of japonica and indica rice in terms of the diversities and distributions of their component mPing.
Animals ; DNA Transposable Elements ; genetics ; Genome, Plant ; Oryza ; classification ; genetics

Approximately 45% of the human genome is comprised of transposable elements (TEs). Results from the Human Genome Project have emphasized the biological importance of TEs. Many studies have revealed that TEs are not simply "junk" DNA, but rather, they play various roles in processes, including genome evolution, gene expression regulation, genetic instability, and cancer disposition. The effects of TE insertion in the genome varies from negligible to disease conditions. For the past two decades, many studies have shown that TEs are the causative factors of various genetic disorders and cancer. TEs are a subject of interest worldwide, not only in terms of their clinical aspects but also in basic research, such as evolutionary tracking. Although active TEs contribute to genetic instability and disease states, non-long terminal repeat transposons are well studied, and their roles in these processes have been confirmed. In this review, we will give an overview of the importance of TEs in studying genome evolution and genetic instability, and we suggest that further in-depth studies on the mechanisms related to these phenomena will be useful for both evolutionary tracking and clinical diagnostics.
DNA ; DNA Transposable Elements* ; Gene Expression ; Gene Expression Regulation ; Genome* ; Genome, Human ; Human Genome Project ; Humans ; Terminal Repeat Sequences

Since the advent of whole-genome sequencing, transposable elements (TEs), just thought to be 'junk' DNA, have been noticed because of their numerous copies in various eukaryotic genomes. Many studies about TEs have been conducted to discover their functions in their host genomes. Based on the results of those studies, it has been generally accepted that they have a function to cause genomic and genetic variations. However, their infinite functions are not fully elucidated. Through various mechanisms, including de novo TE insertions, TE insertion-mediated deletions, and recombination events, they manipulate their host genomes. In this review, we focus on Alu, L1, human endogenous retrovirus, and short interspersed element/variable number of tandem repeats/Alu (SVA) elements and discuss how they have affected primate genomes, especially the human and chimpanzee genomes, since their divergence.
Alu Elements ; Coat Protein Complex I ; DNA ; DNA Transposable Elements ; Endogenous Retroviruses ; Genetic Variation ; Genome ; Humans ; Long Interspersed Nucleotide Elements ; Pan troglodytes ; Primates ; Recombination, Genetic ; Tromethamine

Southern blot analysis with probe from mini-Tn5 gfp-km transposon indicated that 5 non-pathogenic mutants which were generated by insertion of mini-Tn5 gfp-km mutagenesis contained a single copy of the transposon. Using genomic DNA of each mutant as a template, TAIL-PCR was performed with seven arbitrary degenerate (AD) primers pairing with 3 nested specific primers designed based on the sequence of GFP toward outside in mini-Tn5 gfp-km. After 3-step PCR reactions, the flanking sequence of each mutant was obtained. The PCR product was ligated with pGEM-T EASY vector and then was transformed into E. coli DH5 alpha by electroporation. Positive clones were selected by white/blue colony and plasmid was isolated, then digested with EcoRI. Plasmid was sequenced if its insert was longer than 300 bp. Our results indicated that TAIL-PCR was proved to be a simple and efficient approach in identification of gene using insertion mutagenesis.
Base Sequence ; Cloning, Molecular ; methods ; DNA Transposable Elements ; DNA, Bacterial ; isolation & purification ; Genes, Bacterial ; Green Fluorescent Proteins ; Luminescent Proteins ; genetics ; Molecular Sequence Data ; Mutagenesis ; Polymerase Chain Reaction ; methods ; Xanthomonas campestris ; genetics ; pathogenicity

Constructing robust gene circuits is a fundamental work for synthetic biology. Bacteria with suicide gene circuit based on quorum-sensing will kill themselves in a controllable pattern upon certain cell density. In the media of different IPTG inducer concentration, we observed the growth and suicidal behavior of the Escherichia coli. Top10F' with such gene circuit, screened the mutants and determined their mutated loci. The results show that, with higher IPTG concentration, the more wild type bacteria were killed; as well the mutants emerged earlier and spread over the population more quickly. The sequence of plasmids in those mutants revealed that a transposon inserted into the luxR gene and therefore disrupted Quorum-Sensing of these individuals. Furthermore, the insertion sequence of the plasmid can solely result in the mutants escaping from suicide.
Culture Media ; chemistry ; DNA Transposable Elements ; genetics ; Escherichia coli ; genetics ; growth & development ; Gene Expression Regulation, Bacterial ; Genes, Synthetic ; genetics ; Genes, Transgenic, Suicide ; Isopropyl Thiogalactoside ; chemistry ; Mutation ; Quorum Sensing ; genetics ; Repressor Proteins ; genetics ; Trans-Activators ; genetics

Transposable elements are one of major sources to cause genomic instability through various mechanisms including de novo insertion, insertion-mediated genomic deletion, and recombination-associated genomic deletion. Among them is Alu element which is the most abundant element, composing ~10% of the human genome. The element emerged in the primate genome 65 million years ago and has since propagated successfully in the human and non-human primate genomes. Alu element is a non-autonomous retrotransposon and therefore retrotransposed using L1-enzyme machinery. The 'master gene' model has been generally accepted to explain Alu element amplification in primate genomes. According to the model, different subfamilies of Alu elements are created by mutations on the master gene and most Alu elements are amplified from the hyperactive master genes. Alu element is frequently involved in genomic rearrangements in the human genome due to its abundance and sequence identity between them. The genomic rearrangements caused by Alu elements could lead to genetic disorders such as hereditary disease, blood disorder, and neurological disorder. In fact, Alu elements are associated with approximately 0.1% of human genetic disorders. The first part of this review discusses mechanisms of Alu amplification and diversity among different Alu subfamilies. The second part discusses the particular role of Alu elements in generating genomic rearrangements as well as human genetic disorders.
Alu Elements* ; DNA Transposable Elements ; Genetic Diseases, Inborn ; Genome ; Genome, Human ; Genomic Instability ; Humans* ; Nervous System Diseases ; Primates ; Recombination, Genetic ; Retroelements

The mutant population of Xanthomonas oryzae pv oryzae strain differential to rice bacterial blight resistance gene Xa23 has been constructed mediated by transposon in vivo . The results of PCR amplification with specific primers and analysis of flanking sequence of mutants indicated that the foreign DNA has been integrated into X. oryzae pv oryzae genome. Four mutants with changed avirulent activity to Xa23 gene have been identified by artificial inoculation. It is possible to clone genes that are required for AvrXa23 avirulence activity using this new strategy.
Bacterial Proteins ; genetics ; Base Sequence ; DNA Transposable Elements ; Gene Expression Regulation, Plant ; Genes, Plant ; Molecular Sequence Data ; Mutation ; Oryza ; genetics ; microbiology ; Plant Diseases ; microbiology ; Plants, Genetically Modified ; genetics ; microbiology ; Virulence ; Xanthomonas ; genetics ; pathogenicity ; physiology