Functional characterization of sugarcane mustang domesticated transposases and comparative diversity in sugarcane, rice, maize and sorghum

Kajihara, Daniela; Godoy, Fabiana; Hamaji, Thais Alves; Blanco, Silvia R.; Sluys, Marie‐Anne Van; Rossi, Magdalena

doi:10.1590/s1415-47572012005000038

Cited by 10 publications

(6 citation statements)

References 38 publications

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“…One such clade includes genes called MUSTANG elements (151). Although the function of these genes has not been established, at least some of them appear to be negatively modulated by phytohormones and by auxin, and their expression shows some tissue specificity (152). Further, mutations in some combinations of these genes have defects in growth, flowering and reproduction (153).…”

Section: Mule Domesticationmentioning

confidence: 99%

Mutator and MULE Transposons

Lisch

2015

Microbiol Spectr

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The Mutator system of transposable elements (TEs) is a highly mutagenic family of transposons in maize. Because they transpose at high rates and target genic regions, these transposons can rapidly generate large numbers of new mutants, which has made the Mutator system a favored tool for both forward and reverse mutagenesis in maize. Low copy number versions of this system have also proved to be excellent models for understanding the regulation and behavior of Class II transposons in plants. Notably, the availability of a naturally occurring locus that can heritably silence autonomous Mutator elements has provided insights into the means by which otherwise active transposons are recognized and silenced. This chapter will provide a review of the biology, regulation, evolution and uses of this remarkable transposon system, with an emphasis on recent developments in our understanding of the ways in which this TE system is recognized and epigenetically silenced as well as recent evidence that Mu-like elements (MULEs) have had a significant impact on the evolution of plant genomes.

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Section: Mule Domesticationmentioning

confidence: 99%

Mutator and MULE Transposons

Lisch

2015

Microbiol Spectr

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“…Nevertheless, in some cases the excision may leave behind parts of the element that are not removed and can modify the coding capacity of the gene, and in some cases provide new gene functions (Lisch 2013;Oliver et al 2013). This process by which a TE, or a part of it, is established in a specific region and gains a cellular function is known as molecular domestication (Kajihara et al 2012).…”

Section: Transposable Elements As a Source Of New Functionsmentioning

confidence: 99%

Evolutionary Biology: Biodiversification from Genotype to Phenotype

Pontarotti¹

2015

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“…Under stressful conditions, they can rearrange a genome [9–11]. TEs play roles in relocating genes [12, 13] and generating new genes [14, 15] and new pseudo genes [16, 17]. They can contribute to centromere function [18, 19].…”

Section: Introductionmentioning

confidence: 99%

LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo

Valencia

Girgis

2019

BMC Genomics

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Background: Long terminal repeat retrotransposons are the most abundant transposons in plants. They play important roles in alternative splicing, recombination, gene regulation, and defense mechanisms. Large-scale sequencing projects for plant genomes are currently underway. Software tools are important for annotating long terminal repeat retrotransposons in these newly available genomes. However, the available tools are not very sensitive to known elements and perform inconsistently on different genomes. Some are hard to install or obsolete. They may struggle to process large plant genomes. None can be executed in parallel out of the box and very few have features to support visual review of new elements. To overcome these limitations, we developed LtrDetector, which uses techniques inspired by signal-processing. Results: We compared LtrDetector to LTR_Finder and LTRharvest, the two most successful predecessor tools, on six plant genomes. For each organism, we constructed a ground truth data set based on queries from a consensus sequence database. According to this evaluation, LtrDetector was the most sensitive tool, achieving 16-23% improvement in sensitivity over LTRharvest and 21% improvement over LTR_Finder. All three tools had low false positive rates, with LtrDetector achieving 98.2% precision, in between its two competitors. Overall, LtrDetector provides the best compromise between high sensitivity and low false positive rate while requiring moderate time and utilizing memory available on personal computers. Conclusions: LtrDetector uses a novel methodology revolving around k-mer distributions, which allows it to produce high-quality results using relatively lightweight procedures. It is easy to install and use. It is not species specific, performing well using its default parameters on genomes of varying size and repeat content. It is automatically configured for parallel execution and runs efficiently on an ordinary personal computer. It includes a k-mer scores visualization tool to facilitate manual review of the identified elements. These features make LtrDetector an attractive tool for future annotation projects involving long terminal repeat retrotransposons.

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Functional characterization of sugarcane mustang domesticated transposases and comparative diversity in sugarcane, rice, maize and sorghum

Cited by 10 publications

References 38 publications

Mutator and MULE Transposons

Mutator and MULE Transposons

Evolutionary Biology: Biodiversification from Genotype to Phenotype

LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo

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