Computational tools to unmask transposable elements

P Goerner-Potvin, G Bourque - Nature Reviews Genetics, 2018 - nature.com
A substantial proportion of the genome of many species is derived from transposable
elements (TEs). Moreover, through various self-copying mechanisms, TEs continue to …

Twenty years of transposable element analysis in the Arabidopsis thaliana genome

H Quesneville - Mobile DNA, 2020 - Springer
Transposable elements (TEs) are mobile repetitive DNA sequences shown to be major
drivers of genome evolution. As the first plant to have its genome sequenced and analyzed …

Transposition favors the generation of large effect mutations that may facilitate rapid adaption

L Quadrana, M Etcheverry, A Gilly, E Caillieux… - Nature …, 2019 - nature.com
Transposable elements (TEs) are mobile parasitic sequences that have been repeatedly
coopted during evolution to generate new functions and rewire gene regulatory networks …

The role of transposable elements in speciation

A Serrato-Capuchina, DR Matute - Genes, 2018 - mdpi.com
Understanding the phenotypic and molecular mechanisms that contribute to genetic
diversity between and within species is fundamental in studying the evolution of species. In …

Plant transgenerational epigenetics

L Quadrana, V Colot - Annual Review of Genetics, 2016 - annualreviews.org
Transgenerational epigenetics is defined in opposition to developmental epigenetics and
implies an absence of resetting of epigenetic states between generations. Unlike mammals …

Transposable element detection from whole genome sequence data

AD Ewing - Mobile DNA, 2015 - Springer
The number of software tools available for detecting transposable element insertions from
whole genome sequence data has been increasing steadily throughout the last~ 5 years …

Identification and characterisation of hypomethylated DNA loci controlling quantitative resistance in Arabidopsis

L Furci, R Jain, J Stassen, O Berkowitz, J Whelan… - Elife, 2019 - elifesciences.org
Variation in DNA methylation enables plants to inherit traits independently of changes to
DNA sequence. Here, we have screened an Arabidopsis population of epigenetic …

TransposonUltimate: software for transposon classification, annotation and detection

K Riehl, C Riccio, EA Miska… - Nucleic Acids Research, 2022 - academic.oup.com
Most genomes harbor a large number of transposons, and they play an important role in
evolution and gene regulation. They are also of interest to clinicians as they are involved in …

PoPoolationTE2: comparative population genomics of transposable elements using Pool-Seq

R Kofler, D Gómez-Sánchez… - Molecular biology and …, 2016 - academic.oup.com
The evolutionary dynamics of transposable elements (TEs) are still poorly understood. One
reason is that TE abundance needs to be studied at the population level, but sequencing …

McClintock: an integrated pipeline for detecting transposable element insertions in whole-genome shotgun sequencing data

MG Nelson, RS Linheiro… - G3: Genes, Genomes …, 2017 - academic.oup.com
Transposable element (TE) insertions are among the most challenging types of variants to
detect in genomic data because of their repetitive nature and complex mechanisms of …