The bright side of transposons in crop evolution

The repetitive component of the sunflower genome as shown by different procedures for assembling next generation sequencing reads

(2013) Lucia Natali et al.   BMC GENOMICS

Testing for Associations between Loci and Environmental Gradients Using Latent Factor Mixed Models

(2013) Eric Frichot et al.   MOLECULAR BIOLOGY AND EVOLUTION

Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations

(2013) Stéphane De Mita et al.   MOLECULAR ECOLOGY

The impact of transposable elements in environmental adaptation

(2013) Elena Casacuberta et al.   MOLECULAR ECOLOGY

Allopolyploidy has a moderate impact on restructuring at three contrasting transposable element insertion sites in resynthesizedBrassica napusallotetraploids

(2013) Véronique Sarilar et al.   NEW PHYTOLOGIST

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

The Use of RelocaTE and Unassembled Short Reads to Produce High-Resolution Snapshots of Transposable Element Generated Diversity in Rice

(2013) Sofia M. C. Robb et al.   G3-Genes Genomes Genetics

Active Transposition in Genomes

(2012) Cheng Ran Lisa Huang et al.   Annual Review of Genetics

Statistical challenges associated with detecting copy number variations with next-generation sequencing

(2012) Shu Mei Teo et al.   BIOINFORMATICS

Association mapping in sunflower for sclerotinia head rot resistance

(2012) Corina M Fusari et al.   BMC PLANT BIOLOGY

The genome of the pear (Pyrus bretschneideri Rehd.)

(2012) J. Wu et al.   GENOME RESEARCH

The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

(2012) Angélique D’Hont et al.   NATURE

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential

(2012) Gengyun Zhang et al.   NATURE BIOTECHNOLOGY

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

(2012) E. Butelli et al.   PLANT CELL

A mutation in the rice chalcone isomerase gene causes the golden hull and internode 1 phenotype

(2012) Lilan Hong et al.   PLANTA

A Large Insertion in bHLH Transcription Factor BrTT8 Resulting in Yellow Seed Coat in Brassica rapa

(2012) Xia Li et al.   PLoS One

ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize

(2012) H.-Y. Hung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genome of melon (Cucumis melo L.)

(2012) J. Garcia-Mas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A transposable element insertion within ZmGE2 gene is associated with increase in embryo to endosperm ratio in maize

(2012) Pan Zhang et al.   THEORETICAL AND APPLIED GENETICS

Maize genetic diversity and association mapping using transposable element insertion polymorphisms

(2012) Tatiana Zerjal et al.   THEORETICAL AND APPLIED GENETICS

New Insight into the History of Domesticated Apple: Secondary Contribution of the European Wild Apple to the Genome of Cultivated Varieties

(2012) Amandine Cornille et al.   PLoS Genetics

The Structure of Genealogies in the Presence of Purifying Selection: A Fitness-Class Coalescent

(2011) Aleksandra M. Walczak et al.   GENETICS

Modulation of AUXIN-BINDING PROTEIN 1 gene expression in maize and the teosintes by transposon insertions in its promoter

(2011) Nabil Elrouby et al.   MOLECULAR GENETICS AND GENOMICS

Multi-gene analysis provides a well-supported phylogeny of Rosales

(2011) Shu-dong Zhang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

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

(2011) Anthony Studer et al.   NATURE GENETICS

inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data

(2011) Ji Qi et al.   NUCLEIC ACIDS RESEARCH

Transpositional landscape of the rice genome revealed by paired-end mapping of high-throughput re-sequencing data

(2011) François Sabot et al.   PLANT JOURNAL

BraSto, a Stowaway MITE from Brassica: recently active copies preferentially accumulate in the gene space

(2011) Véronique Sarilar et al.   PLANT MOLECULAR BIOLOGY

Molecular evidence for a single evolutionary origin of domesticated rice

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

Staying afloat in the sensor data deluge

(2011) John H. Porter et al.   TRENDS IN ECOLOGY & EVOLUTION

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

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

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

(2010) Masaki Momose et al.   GENETICS

Using Environmental Correlations to Identify Loci Underlying Local Adaptation

(2010) G. Coop et al.   GENETICS

Validation of Rearrangement Break Points Identified by Paired-End Sequencing in Natural Populations of Drosophila melanogaster

(2010) Julie M. Cridland et al.   Genome Biology and Evolution

Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor

(2010) R. A. Swanson-Wagner et al.   GENOME RESEARCH

Population Genomics of Transposable Elements in Drosophila melanogaster

(2010) D. A. Petrov et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genome of woodland strawberry (Fragaria vesca)

(2010) Vladimir Shulaev et al.   NATURE GENETICS

Genome-wide association studies of 14 agronomic traits in rice landraces

(2010) Xuehui Huang et al.   NATURE GENETICS

The genome of the domesticated apple (Malus × domestica Borkh.)

(2010) Riccardo Velasco et al.   NATURE GENETICS

Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana

(2010) Joy Bergelson et al.   NATURE REVIEWS GENETICS

Mobilization of retrotransposons in synthetic allotetraploid tobacco

(2010) M. Petit et al.   NEW PHYTOLOGIST

T-lex: a program for fast and accurate assessment of transposable element presence using next-generation sequencing data

(2010) Anna-Sophie Fiston-Lavier et al.   NUCLEIC ACIDS RESEARCH

Megabase Level Sequencing Reveals Contrasted Organization and Evolution Patterns of the Wheat Gene and Transposable Element Spaces

(2010) Frédéric Choulet et al.   PLANT CELL

Bs1, a New Chimeric Gene Formed by Retrotransposon-Mediated Exon Shuffling in Maize

(2010) N. Elrouby et al.   PLANT PHYSIOLOGY

The Purple Cauliflower Arises from Activation of a MYB Transcription Factor

(2010) L.-W. Chiu et al.   PLANT PHYSIOLOGY

Association and Linkage Analysis of Aluminum Tolerance Genes in Maize

(2010) Allison M. Krill et al.   PLoS One

Genome-Wide Patterns of Adaptation to Temperate Environments Associated with Transposable Elements in Drosophila

(2010) Josefa González et al.   PLoS Genetics

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

Excision of an Active CACTA-Like Transposable Element From DFR2 Causes Variegated Flowers in Soybean [Glycine max (L.) Merr.]

(2009) M. Xu et al.   GENETICS

Association Studies Identify Natural Variation at PHYC Linked to Flowering Time and Morphological Variation in Pearl Millet

(2009) A.-A. Saidou et al.   GENETICS

Single Nucleotide Polymorphisms in the Allene Oxide Synthase 2 Gene Are Associated With Field Resistance to Late Blight in Populations of Tetraploid Potato Cultivars

(2009) K. Pajerowska-Mukhtar et al.   GENETICS

Recent amplification and impact of MITEs on the genome of grapevine (Vitis vinifera L.)

(2009) Andrej Benjak et al.   Genome Biology and Evolution

Detecting loci under selection in a hierarchically structured population

(2009) L Excoffier et al.   HEREDITY

Adaptive Evolution Involving Gene Duplication and Insertion of a Novel Ty1/copia-Like Retrotransposon in Soybean

(2009) Akira Kanazawa et al.   JOURNAL OF MOLECULAR EVOLUTION

A Recent Adaptive Transposable Element Insertion Near Highly Conserved Developmental Loci in Drosophila melanogaster

(2009) J. Gonzalez et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

Unexpected consequences of a sudden and massive transposon amplification on rice gene expression

(2009) Ken Naito et al.   NATURE

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

(2009) Antoine Martin et al.   NATURE

Selective epigenetic control of retrotransposition in Arabidopsis

(2009) Marie Mirouze et al.   NATURE

Computational methods for discovering structural variation with next-generation sequencing

(2009) Paul Medvedev et al.   NATURE METHODS

A comparative view of the evolution of grasses under domestication

(2009) Sylvain Glémin et al.   NEW PHYTOLOGIST

Impact of transposable elements on the organization and function of allopolyploid genomes

(2009) Christian Parisod et al.   NEW PHYTOLOGIST

Genome-wide scans for footprints of natural selection

(2009) T. K. Oleksyk et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

(2009) Lucie Fernandez et al.   PLANT JOURNAL

Mu Transposon Insertion Sites and Meiotic Recombination Events Co-Localize with Epigenetic Marks for Open Chromatin across the Maize Genome

(2009) Sanzhen Liu et al.   PLoS Genetics

The quest for adaptive evolution: a theoretical challenge in a maze of data

(2008) Maud I Tenaillon et al.   CURRENT OPINION IN PLANT BIOLOGY

MOLECULAR DEMOGRAPHIC HISTORY OF THE ANNUAL SUNFLOWERSHELIANTHUS ANNUUSANDH. PETIOLARIS-LARGE EFFECTIVE POPULATION SIZES AND RATES OF LONG-TERM GENE FLOW

(2008) Jared L. Strasburg et al.   EVOLUTION

Genetic Redundancy in Soybean Photoresponses Associated With Duplication of the Phytochrome A Gene

(2008) B. Liu et al.   GENETICS

Inferring the Strength of Selection in Drosophila under Complex Demographic Models

(2008) J. Gonzalez et al.   MOLECULAR BIOLOGY AND EVOLUTION

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

(2008) Ray Ming et al.   NATURE

Mapping and sequencing of structural variation from eight human genomes

(2008) Jeffrey M. Kidd et al.   NATURE

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing

(2008) Peter J Campbell et al.   NATURE GENETICS

High-resolution mapping of copy-number alterations with massively parallel sequencing

(2008) Derek Y Chiang et al.   NATURE METHODS

Refunctionalization of the ancient rice blast disease resistance genePitby the recruitment of a retrotransposon as a promoter

(2008) Keiko Hayashi et al.   PLANT JOURNAL

Helitron mediated amplification of cytochrome P450 monooxygenase gene in maize

(2008) Natalie Jameson et al.   PLANT MOLECULAR BIOLOGY

Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata

(2008) S. Lockton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2008) H. Xiao et al.   SCIENCE