Methods for accurate quantification of LTR-retrotransposon copy number using short-read sequence data: a case study in Sorghum

Phylogenetic reconstruction using four low-copy nuclear loci strongly supports a polyphyletic origin of the genusSorghum

(2015) Jennifer S. Hawkins et al.   ANNALS OF BOTANY

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

(2015) Irina Makarevitch et al.   PLoS Genetics

Plant genome size variation: bloating and purging DNA

(2014) T. P. Michael   Briefings in Functional Genomics

How a Retrotransposon Exploits the Plant's Heat Stress Response for Its Activation

(2014) Vladimir V. Cavrak et al.   PLoS Genetics

RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads

(2013) P. Novak et al.   BIOINFORMATICS

Comparative Genomic Paleontology across Plant Kingdom Reveals the Dynamics of TE-Driven Genome Evolution

(2013) Moaine El Baidouri et al.   Genome Biology and Evolution

Evolutionary Dynamics of Retrotransposons Assessed by High-Throughput Sequencing in Wild Relatives of Wheat

(2013) Natacha Senerchia et al.   Genome Biology and Evolution

The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution

(2013) M C Estep et al.   HEREDITY

Seed shattering in a wild sorghum is conferred by a locus unrelated to domestication

(2013) H. Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CACTA-like transposable element in ZmCCT attenuated photoperiod sensitivity and accelerated the postdomestication spread of maize

(2013) Q. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reference genome sequence of the model plant Setaria

(2012) Jeffrey L Bennetzen et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

APCluster: an R package for affinity propagation clustering

(2011) U. Bodenhofer et al.   BIOINFORMATICS

Genome Size and Transposable Element Content as Determined by High-Throughput Sequencing in Maize and Zea luxurians

(2011) Maud I. Tenaillon et al.   Genome Biology and Evolution

An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress

(2011) Hidetaka Ito et al.   NATURE

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

(2011) Tina T Hu et al.   NATURE GENETICS

Identification of a functional transposon insertion in the maize domestication gene tb1

(2011) Anthony Studer et al.   NATURE GENETICS

Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata

(2011) J. D. Hollister et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Novel Retrotransposon Inserted in the Dominant Vrn-B1 Allele Confers Spring Growth Habit in Tetraploid Wheat ( Triticum turgidum L.)

(2011) C.-G. Chu et al.   G3-Genes Genomes Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data

(2010) Petr Novák et al.   BMC BIOINFORMATICS

The evolution of transposable elements in natural populations of self-fertilizing Arabidopsis thaliana and its outcrossing relative Arabidopsis lyrata

(2010) Steven Lockton et al.   BMC EVOLUTIONARY BIOLOGY

Epigenetic Regulation of Repetitive Elements Is Attenuated by Prolonged Heat Stress inArabidopsis

(2010) Ales Pecinka et al.   PLANT CELL

Temperature controls nuclear import of Tam3 transposase in Antirrhinum

(2010) Kaien Fujino et al.   PLANT JOURNAL

A triptych of the evolution of plant transposable elements

(2010) Maud I. Tenaillon et al.   TRENDS IN PLANT SCIENCE

Stress-Induced Activation of Heterochromatic Transcription

(2010) Mireille Tittel-Elmer et al.   PLoS Genetics

Proliferation of Ty3/gypsy-like retrotransposons in hybrid sunflower taxa inferred from phylogenetic data

(2009) Mark C Ungerer et al.   BMC BIOLOGY

The allotetraploid Arabidopsis thaliana–Arabidopsis lyrata subsp. petraea as an alternative model system for the study of polyploidy in plants

(2009) Julien Beaulieu et al.   MOLECULAR GENETICS AND GENOMICS

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

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

Rapid structural and epigenetic reorganization near transposable elements in hybrid and allopolyploid genomes in Spartina

(2009) Christian Parisod et al.   NEW PHYTOLOGIST

Transposon-induced gene activation as a mechanism generating cluster shape somatic variation in grapevine

(2009) Lucie Fernandez et al.   PLANT JOURNAL

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

Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome

(2008) R. S. Baucom et al.   GENOME RESEARCH

Genome-Wide Analysis of Transposon Insertion Polymorphisms Reveals Intraspecific Variation in Cultivated Rice

(2008) X. Huang et al.   PLANT PHYSIOLOGY

Rapid alterations of gene expression and cytosine methylation in newly synthesized Brassica napus allopolyploids

(2008) Yanhao Xu et al.   PLANTA

Genome assembly forensics: finding the elusive mis-assembly

(2008) Adam M Phillippy et al.   GENOME BIOLOGY