Transposable Elements as Tools for Reshaping the Genome: It Is a Huge World After All!

Bire, Solenne; Rouleux‐Bonnin, Florence

doi:10.1007/978-1-61779-603-6_1

Cited by 25 publications

(26 citation statements)

References 213 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…TE-based markers have been successfully utilized for various genomics purposes, such as the analysis of genetic diversity, inspection of clonal variation, and breeding. TE markers are also useful to identify unambiguous gene flow between closely related species (Bire and Rouleux-Bonnin 2012;Carrier et al 2012). The principle characteristics of mTEs, namely their abundance, small size, stability, and distribution in genic regions, are advantageous for DNA marker development in both plants and animals.…”

Section: Utility Of Mites As Molecular Markersmentioning

confidence: 99%

“…Amplification of TEs in the genome can not only cause an increase in genome size, but also help to drive the evolution of genes and genomes (Arkhipova et al 2012), although most TEs are inactive, and are mainly controlled by epigenetic mechanisms (e.g., DNA and histone methylation) (Alzohairy et al 2013;Bire and Rouleux-Bonnin 2012;Fedoroff 2012;Feschotte 2008;Hollister and Gaut 2009;Lisch 2009). TEs containing their own functional genes for transposition are referred to as autonomous transposable elements (aTEs); whereas, TEs that lack coding genes, and therefore cannot produce their own transposase or reverse transcriptase, are termed non-autonomous or noncoding transposable elements (nTEs).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Miniature Inverted-repeat Transposable Elements (MITEs) as Valuable Genomic Resources for the Evolution and Breeding of Brassica Crops

Sampath¹,

Yang²

2014

Plant Breed. Biotech.

View full text Add to dashboard Cite

This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. ABSTRACT Transposable elements (TEs) play important roles in structural and functional diversification, genome enlargement, and speciation in plant genome. Their derivatives or small non-autonomous TEs play important roles in the alteration of homologous genes by epigenetic control or structural modification. The miniature inverted-repeat transposable element (MITE) is one of the representative non-autonomous class II TEs. MITEs include high copy members that are widely distributed and in close association with genic regions, which make MITEs useful targets and resources for in-depth understanding of genome evolution, as well as practical applications in molecular breeding. Here, we discuss the important features of MITEs, such as the identification tools of a novel MITE family, structural characterization, distribution pattern analysis, and impact on evolution in highly duplicated Brassica genome. We show the characteristics, copy numbers, and distribution patterns of 20 novel MITE families, and represent their putative roles in the evolution of the triplicated Brassica genome. We also introduce our MITE database, and discuss the utility of MITEs for developing MITE-derived markers that are useful for molecular breeding of Brassica crops.

show abstract

Section: Utility Of Mites As Molecular Markersmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Miniature Inverted-repeat Transposable Elements (MITEs) as Valuable Genomic Resources for the Evolution and Breeding of Brassica Crops

Sampath¹,

Yang²

2014

Plant Breed. Biotech.

View full text Add to dashboard Cite

show abstract

“…Transposable elements (TEs) account for the largest fraction (up to 85%) of most plant genomes and play tremendous control on the genome function and evolution (Feschotte 2008;Arkhipova et al 2012;Bire and Rouleux-Bonnin 2012). TEs are classified into either DNA transposon or retrotransposon based on their transposition mechanisms.…”

Section: Introductionmentioning

confidence: 99%

“…TE-based molecular markers such as inter-retrotransposon amplified polymorphism, retrotransposon-microsatellite amplified polymorphism, sequence-specific amplification polymorphism, insertion polymorphism based on retrotransposon and DNA transposon, inter-MITE polymorphism and transposon display (TD) (Agarwal et al 2008;Kalendar et al 2011;Shirasawa et al 2012) have been successfully applied for the various genomics purposes such as genetic diversity, inspection of clonal variation, identifying unambiguous gene flow between closely related species and breeding (Deragon and Zhang 2006;Bire and Rouleux-Bonnin 2012;Carrier et al 2012). DNA polymorphisms are used to identify molecular markers for important agronomic traits controlled by single gene or quantitative trait loci (Monden et al 2009;Kalendar et al 2011;Fattash et al 2013).…”

Section: Introductionmentioning

confidence: 99%

Next-Generation Sequencing Based Transposon Display to Detect High-Throughput Insertion Polymorphism Markers in Brassica

Perumal¹,

Waminal²,

Lee³

et al. 2016

Plant Breed. Biotech.

View full text Add to dashboard Cite

This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang 25354, Korea ABSTRACT Miniature transposable elements (mTEs) such as miniature inverted-repeat transposable element (MITE), terminal repeat retrotransposon in miniature, and short interspersed element are exquisite sources for marker development. mTEs are short, non-autonomous and stably inherited. The high-copy members are widely distributed into the gene rich euchromatic regions. Here, we conducted a modified transposon display (TD) for a high-copy MITE family, BraSto-2 (Bs2). The Bs2-specific primers derived from conserved sequences of Bs2 members as well as MseI adapter primers were used for polymerase chain reaction (PCR) in two Brassica rapa accessions, 'Chiifu' and 'Kenshin'. The pooled PCR products were sequenced by Illumina sequencing platform instead of high-resolution gel electrophoresis. Subsequent in silico-based insertion polymorphism (IP) analysis (next-generation sequencing [NGS]-based Bs2 transposon display) was conducted, which generated more than 99 putative polymorphic insertion sites between 'Chiifu' and 'Kenshin'. Among 90 successful PCR amplification, 34 showed Bs2 IP (IP-Bs2) between 'Chiifu' and 'Kenshin' accessions, 27 and seven 'Chiifu'-and 'Kenshin'-unique insertions, respectively. When the 90 IP-Bs2 primer sets were applied to 10 Brassica accessions, including four additional B. rapa and B. oleracea accessions, 69 (76%) showed insertion olymorphism among accessions. The IP-Bs2 were evenly distributed through all the chromosomes and provide rich polymorphism among various B. rapa and B. oleracea accessions demonstrating the usefulness of these markers for various genetic diversity and molecular breeding studies in Brassica. In addition, NGS-based TD will be applicable to various high copy transposable elements family for high throughput and rapid polymorphic marker development which will be helpful for efficient plant genomics and breeding purposes.

show abstract

“…Thus, one challenge in using NGS technologies in such applications lies in preserving sample identity while sequencing many samples simultaneously. This challenge can be addressed by encoding sample identity through either DNA barcoding or directed pooling (Mazurkiewicz et al 2006;Erlich et al 2009;Goodman et al 2009;Prabhu and Pe'er 2009).Transposable elements represent powerful tools for manipulating the genomes of many model organisms (Bellen et al 2011;Bire and Rouleux-Bonnin 2012). Thus, determining the genomic location of transposon insertion sites is a common experimental goal.…”

mentioning

confidence: 99%

Large-Scale Mapping of Transposable Element Insertion Sites Using Digital Encoding of Sample Identity

et al. 2014

View full text Add to dashboard Cite

Determining the genomic locations of transposable elements is a common experimental goal. When mapping large collections of transposon insertions, individualized amplification and sequencing is both time consuming and costly. We describe an approach in which large numbers of insertion lines can be simultaneously mapped in a single DNA sequencing reaction by using digital error-correcting codes to encode line identity in a unique set of barcoded pools. N EXT-generation sequencing (NGS) technologies have greatly reduced the cost of DNA sequence analysis through the parallel sequencing of many short fragments. However, many applications, including molecular cloning and mutational analysis continue to rely on conventional capillary electrophoresis Sanger sequencing methods, as these are well-suited to sequencing individual fragments. Thus, one challenge in using NGS technologies in such applications lies in preserving sample identity while sequencing many samples simultaneously. This challenge can be addressed by encoding sample identity through either DNA barcoding or directed pooling (Mazurkiewicz et al. 2006;Erlich et al. 2009;Goodman et al. 2009;Prabhu and Pe'er 2009).Transposable elements represent powerful tools for manipulating the genomes of many model organisms (Bellen et al. 2011;Bire and Rouleux-Bonnin 2012). Thus, determining the genomic location of transposon insertion sites is a common experimental goal. Several methods, such as inverse PCR and splinkerette PCR, are used to amplify a short fragment of the genome directly adjacent to an insertion (Ochman et al. 1988;Devon et al. 1995). Subsequently, capillary electrophoresis Sanger sequencing is used to sequence each amplicon. As a result, all processing reactions must be performed independently on each sample, making the cost and labor associated with mapping collections of thousands of insertion lines significant. Several techniques have used NGS to map transposons in large populations of bacteria or yeast (Goodman et al. 2009;Uren et al. 2009;Iskow et al. 2010;Febrer et al. 2011). However, most of these approaches do not allow the insertion site to be associated with the identity of the original sample.While DNA barcoding can be used to encode sample identity prior to NGS, adding the barcode requires either individualized molecular manipulation of each sample or prior construction of a sequence-tagged transposon library (Mazurkiewicz et al. 2006;Hamady et al. 2008). As an alternative, pooling strategies can be used to encode sample identity, and several recent studies have reported strategies for efficient, error-resistant encoding in pooled DNA samples (Erlich et al. 2009;Goodman et al. 2009;Prabhu and Pe'er 2009). However, none of these approaches have been applied to the large genomes of multicellular eukaryotes, which present unique challenges due to repetitive sequences, increased sequence complexity, and an 100-to 1000-fold reduction in the ratio of transposon sequence to genome sequence.We have developed a method for mapping transposo...

show abstract

Transposable Elements as Tools for Reshaping the Genome: It Is a Huge World After All!

Cited by 25 publications

References 213 publications

Miniature Inverted-repeat Transposable Elements (MITEs) as Valuable Genomic Resources for the Evolution and Breeding of Brassica Crops

Miniature Inverted-repeat Transposable Elements (MITEs) as Valuable Genomic Resources for the Evolution and Breeding of Brassica Crops

Next-Generation Sequencing Based Transposon Display to Detect High-Throughput Insertion Polymorphism Markers in Brassica

Large-Scale Mapping of Transposable Element Insertion Sites Using Digital Encoding of Sample Identity

Contact Info

Product

Resources

About