Genomic re-assessment of the transposable element landscape of the potato genome

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

(2019) Leandro Quadrana et al.   Nature Communications

Dynamic regulation of chromatin topology and transcription by inverted repeat-derived small RNAs in sunflower

(2019) Delfina Gagliardi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The impact of transposable elements on the structure, evolution and function of the rice genome

(2019) Roland Akakpo et al.   NEW PHYTOLOGIST

A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea

(2018) Jérémy Berthelier et al.   BMC GENOMICS

Transposable elements, genome evolution and transgenerational epigenetic variation

(2018) Aoi Hosaka et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Transposons: a blessing curse

(2018) Manu J Dubin et al.   CURRENT OPINION IN PLANT BIOLOGY

Modeling Interactions between Transposable Elements and the Plant Epigenetic Response: A Surprising Reliance on Element Retention

(2018) Kyria Roessler et al.   Genome Biology and Evolution

Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes

(2018) Silong Sun et al.   NATURE GENETICS

Immune receptor genes and pericentromeric transposons as targets of common epigenetic regulatory elements

(2018) Damián A Cambiagno et al.   PLANT JOURNAL

Shifting the limits in wheat research and breeding using a fully annotated reference genome

(2018) et al.   SCIENCE

Transposons take remote control

(2018) Julius Judd et al.   eLife

MITE Tracker: an accurate approach to identify miniature inverted-repeat transposable elements in large genomes

(2018) Juan Manuel Crescente et al.   BMC BIOINFORMATICS

Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum

(2017) Rosalía Cristina Paz et al.   GENETICA

Genome sequence of the progenitor of the wheat D genome Aegilops tauschii

(2017) Ming-Cheng Luo et al.   NATURE

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

(2017) Hélène Badouin et al.   NATURE

Integration site selection by retroviruses and transposable elements in eukaryotes

(2017) Tania Sultana et al.   NATURE REVIEWS GENETICS

Accurate Transposable Element Annotation Is Vital When Analyzing New Genome Assemblies

(2016) Roy N. Platt et al.   Genome Biology and Evolution

The First Rule of Plant Transposable Element Silencing: Location, Location, Location

(2016) Meredith J. Sigman et al.   PLANT CELL

RiTE database: a resource database for genus-wide rice genomics and evolutionary biology

(2015) Dario Copetti et al.   BMC GENOMICS

Comparative Analysis of Transposable Elements Highlights Mobilome Diversity and Evolution in Vertebrates

(2015) Domitille Chalopin et al.   Genome Biology and Evolution

Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm

(2015) Meilina Ong-Abdullah et al.   NATURE

A new approach for annotation of transposable elements using small RNA mapping

(2015) Moaine El Baidouri et al.   NUCLEIC ACIDS RESEARCH

MaizeGDB update: new tools, data and interface for the maize model organism database

(2015) Carson M. Andorf et al.   NUCLEIC ACIDS RESEARCH

Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress

(2015) Irina Makarevitch et al.   PLoS Genetics

A call for benchmarking transposable element annotation methods

(2015) Douglas R. Hoen et al.   Mobile DNA

A Deluge of Complex Repeats: The Solanum Genome

(2015) Mrigaya Mehra et al.   PLoS One

Profiling of extensively diversified plant LINEs reveals distinct plant-specific subclades

(2014) Tony Heitkam et al.   PLANT JOURNAL

PASTEC: An Automatic Transposable Element Classification Tool

(2014) Claire Hoede et al.   PLoS One

HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes

(2014) W. Xiong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Natural occurring epialleles determine vitamin E accumulation in tomato fruits

(2014) Leandro Quadrana et al.   Nature Communications

Potatoes for Sustainable Global Food Security

(2014) André Devaux et al.   POTATO RESEARCH

Improving prokaryotic transposable elements identification using a combination of de novo and profile HMM methods

(2013) Choumouss Kamoun et al.   BMC GENOMICS

GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations

(2013) Gordon Gremme et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Naturally occurring allele diversity allows potato cultivation in northern latitudes

(2013) Bjorn Kloosterman et al.   NATURE

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

Mechanism for full-length RNA processing of Arabidopsis genes containing intragenic heterochromatin

(2013) Hidetoshi Saze et al.   Nature Communications

Transposable Elements Re-Wire and Fine-Tune the Transcriptome

(2013) Michael Cowley et al.   PLoS Genetics

Transposon Variants and Their Effects on Gene Expression in Arabidopsis

(2013) Xi Wang et al.   PLoS Genetics

MIPS PlantsDB: a database framework for comparative plant genome research

(2012) Thomas Nussbaumer et al.   NUCLEIC ACIDS RESEARCH

Retrotransposons Control Fruit-Specific, Cold-Dependent Accumulation of Anthocyanins in Blood Oranges

(2012) E. Butelli et al.   PLANT CELL

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis

(2011) Ikhlak Ahmed et al.   NUCLEIC ACIDS RESEARCH

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

SoyTEdb: a comprehensive database of transposable elements in the soybean genome

(2010) Jianchang Du et al.   BMC GENOMICS

Miniature Inverted-Repeat Transposable Elements of Stowaway Are Active in Potato

(2010) Masaki Momose et al.   GENETICS

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

A transposon-induced epigenetic change leads to sex determination in melon

(2009) Antoine Martin et al.   NATURE

Distribution, diversity, evolution, and survival of Helitrons in the maize genome

(2009) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome

(2009) Regina S. Baucom et al.   PLoS Genetics

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: New functional implications for MITEs

(2008) H. Kuang et al.   GENOME RESEARCH

A Retrotransposon-Mediated Gene Duplication Underlies Morphological Variation of Tomato Fruit

(2008) H. Xiao et al.   SCIENCE