Role of Miniature Inverted-Repeat Transposable Elements in Genome Evolution of Potamopyrgus antipodarum

Transposable elements are genomic parasites that move within the genome and can cause gene and genome evolution. Transposable elements make up significant portions of many eukaryotic genomes but have been little studied in animals. This research study focuses on characterizing and identifying a type of transposable element, called miniature inverted-repeat transposable elements (MITEs) within the Potamopyrgus antipodarum genome. MITEs are particularly small transposable elements which can occur in thousands of copies within a genome. This research is conducted using the genome of P. antipodarum, a species of mud snail that is native to New Zealand. This genome is currently being annotated by the Neiman Lab. My research focuses primarily on identifying and characterizing the MITEs that are present within this genome. Whenever assembling a new genome, the transposable element content of that genome should be assessed, which can only be done after these elements are identified and characterized. I identified the likely superfamilies and key characteristics of these MITEs. In my research I also assessed the genomic locations of these MITEs, determining if they are inserted in exons, introns, or intergenic regions. I discuss the proportions of MITEs inserted in these genomic locations and the implications of these insertions. Finally, these genomic insertions are assessed both based on MITE families and on all MITE sequences

Tools and databases for solving problems in detection and identification of repetitive DNA sequences

Genome compartments known to carry out very important biological functions (e.g. centromeres and telomeres) are mostly constituted of repetitive sequences. At the same time, regions of the genomes enriched in repetitive sequences have always presented great technical challenges for sequence alignments and genome assemblies. Fast evolving sequencing technologies and the increasing accessibility of genomic datasets have opened the opportunity to gain new insights into poorly explored genome fractions, built of repetitive DNA. Comprehensive and accurate annotation and characterization of these sequences is therefore an important contribution to the understanding of genomic architecture and function as a whole. In order to attend the emerging needs in repeat analysis and characterization, many bioinformatics tools, databases and pipelines have been generated. This review is intended to draw attention to the problems encountered in the genomic studies of repetitive sequences and to provide an overview of a spectrum of most prominent bioinformatics tools used for gaining better insight into these important genomic components. Some of the described assets are focused on detection of a wide range of repeats while the others are focused on a specific type of repetitive DNA sequences, generated as an answer to specific research interests and needs of the scientific community.</p

PLOTREP: a web tool for defragmentation and visual analysis of dispersed genomic repeats

Identification of dispersed or interspersed repeats, most of which are derived from transposons, retrotransposons or retrovirus-like elements, is an important step in genome annotation. Software tools that compare genomic sequences with precompiled repeat reference libraries using sensitive similarity-based methods provide reliable means of finding the positions of fragments homologous to known repeats. However, their output is often incomplete and fragmented owing to the mutations (nucleotide substitutions, deletions or insertions) that can result in considerable divergence from the reference sequence. Merging these fragments to identify the whole region that represents an ancient copy of a mobile element is challenging, particularly if the element is large and suffered multiple deletions or insertions. Here we report PLOTREP, a tool designed to post-process results obtained by sequence similarity search and merge fragments belonging to the same copy of a repeat. The software allows rapid visual inspection of the results using a dot-plot like graphical output. The web implementation of PLOTREP is available at

Diversity and structure of PIF/Harbinger-like elements in the genome of Medicago truncatula

<p>Abstract</p> <p>Background</p> <p>Transposable elements constitute a significant fraction of plant genomes. The <it>PIF/Harbinger </it>superfamily includes DNA transposons (class II elements) carrying terminal inverted repeats and producing a 3 bp target site duplication upon insertion. The presence of an ORF coding for the DDE/DDD transposase, required for transposition, is characteristic for the autonomous <it>PIF/Harbinger</it>-like elements. Based on the above features, <it>PIF/Harbinger</it>-like elements were identified in several plant genomes and divided into several evolutionary lineages. Availability of a significant portion of <it>Medicago truncatula </it>genomic sequence allowed for mining <it>PIF/Harbinger</it>-like elements, starting from a single previously described element <it>MtMaster</it>.</p> <p>Results</p> <p>Twenty two putative autonomous, i.e. carrying an ORF coding for TPase and complete terminal inverted repeats, and 67 non-autonomous <it>PIF/Harbinger</it>-like elements were found in the genome of <it>M. truncatula</it>. They were divided into five families, <it>MtPH-A5</it>, <it>MtPH-A6</it>, <it>MtPH-D</it>,<it>MtPH-E</it>, and <it>MtPH-M</it>, corresponding to three previously identified and two new lineages. The largest families, <it>MtPH-A6 </it>and <it>MtPH-M </it>were further divided into four and three subfamilies, respectively. Non-autonomous elements were usually direct deletion derivatives of the putative autonomous element, however other types of rearrangements, including inversions and nested insertions were also observed. An interesting structural characteristic – the presence of 60 bp tandem repeats – was observed in a group of elements of subfamily <it>MtPH-A6-4</it>. Some families could be related to miniature inverted repeat elements (MITEs). The presence of empty <it>loci </it>(RESites), paralogous to those flanking the identified transposable elements, both autonomous and non-autonomous, as well as the presence of transposon insertion related size polymorphisms, confirmed that some of the mined elements were capable for transposition.</p> <p>Conclusion</p> <p>The population of <it>PIF/Harbinger</it>-like elements in the genome of <it>M. truncatula </it>is diverse. A detailed intra-family comparison of the elements' structure proved that they proliferated in the genome generally following the model of abortive gap repair. However, the presence of tandem repeats facilitated more pronounced rearrangements of the element internal regions. The insertion polymorphism of the <it>MtPH </it>elements and related MITE families in different populations of <it>M. truncatula</it>, if further confirmed experimentally, could be used as a source of molecular markers complementary to other marker systems.</p

Miniature inverted repeat transposable elements in rice - origin and function

Transposable elements (TEs) are interspersed repetitive sequences that are present in most genomes. Miniature inverted repeat transposable elements (MITEs) are the most numerous Class II elements in higher eukaryotes. Little is known about their origin, transposition and function. In this study, three novel MITE families (Kiddo, MDM1 and MDM2) were identified in the rice genome. They bear terminal inverted repeats (TIRs) and show target site duplications (TSDs) at the insertion sites. Each family is present in hundreds of copies with length that range from 200 bp to 400 bp. An evolutionary relationship between Mutator elements and MDM1 and MDM2 family was established. The absence of an observed transposition event, together with the mutated ancestral elements identified by in silico analysis, led to a conclusion that Kiddo and its autonomous elements are not presently active. To overcome laborious and time consuming manual analysis of MITEs on a genomic scale, MAK, a computational tool kit, was developed to automatically retrieve MITE sequences, their neighboring genes and ancestral elements from genome sequences. MAK has been functionally tested and is now available to the research community. Studies on the effect of MITE (Kiddo and MDM1) insertions into a rice ubiquitin (rubq2) promoter revealed a two-edged role of MITEs on gene regulation. While Kiddo and MDM1 contribute ~40% to rubq2 promoter activity, they also induce progressive silencing of this promoter. The evolutionary implications of the two-edged role of MITEs in gene regulation are discussed

Miniature Inverted–Repeat Transposable Elements (MITEs) Have Been Accumulated through Amplification Bursts and Play Important Roles in Gene Expression and Species Diversity in Oryza sativa

Miniature inverted–repeat transposable elements (MITEs) are predicted to play important roles on genome evolution. We developed a BLASTN-based approach for de novo identification of MITEs and systematically analyzed MITEs in rice genome. The genome of rice cultivar Nipponbare (Oryza sativa ssp. japonica) harbors 178,533 MITE-related sequences classified into 338 families. Pairwise nucleotide diversity and phylogenetic tree analysis indicated that individual MITE families were resulted from one or multiple rounds of amplification bursts. The timing of amplification burst varied considerably between different MITE families or subfamilies. MITEs are associated with 23,623 (58.2%) genes in rice genome. At least 7,887 MITEs are transcribed and more than 3,463 were transcribed with rice genes. The MITE sequences transcribed with rice coding genes form 1,130 pairs of potential natural sense/antisense transcripts. MITEs generate 23.5% (183,837 of 781,885) of all small RNAs identified from rice. Some MITE families generated small RNAs mainly from the terminals, while other families generated small RNAs predominantly from the central region. More than half (51.8%) of the MITE-derived small RNAs were generated exclusively by MITEs located away from genes. Genome-wide analysis showed that genes associated with MITEs have significantly lower expression than genes away from MITEs. Approximately 14.8% of loci with full-length MITEs have presence/absence polymorphism between rice cultivars 93-11 (O. sativa ssp. indica) and Nipponbare. Considering that different sets of genes may be regulated by MITE-derived small RNAs in different genotypes, MITEs provide considerable diversity for O. sativa

Entomopathogenic potential of bacteria associated with soil-borne nematodes and insect immune responses to their infection

Soil-borne nematodes establish close associations with several bacterial species. Whether they confer benefits to their hosts has been investigated in only a few nematode-bacteria systems. Their ecological function, therefore, remains poorly understood. In this study, we isolated several bacterial species from rhabditid nematodes, molecularly identified them, evaluated their entomopathogenic potential on Galleria mellonella larvae, and measured immune responses of G. mellonella larvae to their infection. Bacteria were isolated from Acrobeloides sp., A. bodenheimeri, Heterorhabditis bacteriophora, Oscheius tipulae, and Pristionchus maupasi nematodes. They were identified as Acinetobacter sp., Alcaligenes sp., Bacillus cereus, Enterobacter sp., Kaistia sp., Lysinibacillus fusiformis, Morganella morganii subsp. morganii, Klebsiella quasipneumoniae subsp. quasipneumoniae, and Pseudomonas aeruginosa. All bacterial strains were found to be highly entomopathogenic as they killed at least 53.33% G. mellonella larvae within 72h post-infection, at a dose of 106 CFU/larvae. Among them, Lysinibacillus fusiformis, Enterobacter sp., Acinetobacter sp., and K. quasipneumoniae subsp. quasipneumoniae were the most entomopathogenic bacteria. Insects strongly responded to bacterial infection. However, their responses were apparently little effective to counteract bacterial infection. Our study, therefore, shows that bacteria associated with soil-borne nematodes have entomopathogenic capacities. From an applied perspective, our study motivates more research to determine the potential of these bacterial strains as biocontrol agents in environmentally friendly and sustainable agriculture

Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea

<p>Abstract</p> <p>Background</p> <p>Mobile genetic elements (MGEs) play an essential role in genome rearrangement and evolution, and are widely used as an important genetic tool.</p> <p>Results</p> <p>In this article, we present genetic maps of recently active <it>Insertion Sequence </it>(IS) elements, the simplest form of MGEs, for all sequenced cyanobacteria and archaea, predicted based on the previously identified ~1,500 IS elements. Our predicted IS maps are consistent with the NCBI annotations of the IS elements. By linking the predicted IS elements to various characteristics of the organisms under study and the organism's living conditions, we found that (a) the activities of IS elements heavily depend on the environments where the host organisms live; (b) the number of recently active IS elements in a genome tends to increase with the genome size; (c) the flanking regions of the recently active IS elements are significantly enriched with genes encoding DNA binding factors, transporters and enzymes; and (d) IS movements show no tendency to disrupt operonic structures.</p> <p>Conclusion</p> <p>This is the first genome-scale maps of IS elements with detailed structural information on the sequence level. These genetic maps of recently active IS elements and the several interesting observations would help to improve our understanding of how IS elements proliferate and how they are involved in the evolution of the host genomes.</p