Discovery of Novel Genes Derived from Transposable Elements Using Integrative Genomic Analysis

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

(2015) Irina Makarevitch et al.   PLoS Genetics

Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

(2014) G Albert Wu et al.   NATURE BIOTECHNOLOGY

A reference genome for common bean and genome-wide analysis of dual domestications

(2014) Jeremy Schmutz et al.   NATURE GENETICS

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity

(2014) Marjori A. Matzke et al.   NATURE REVIEWS GENETICS

Cassava genome from a wild ancestor to cultivated varieties

(2014) Wenquan Wang et al.   Nature Communications

DAYSLEEPER: a nuclear and vesicular-localized protein that is expressed in proliferating tissues

(2013) Marijn Knip et al.   BMC PLANT BIOLOGY

Small RNAs, big impact: small RNA pathways in transposon control and their effect on the host stress response

(2013) Bayly S. Wheeler   CHROMOSOME RESEARCH

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

(2013) Juliane C. Dohm et al.   NATURE

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds

(2013) Rajinder Singh et al.   NATURE

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution

(2013) Ignazio Verde et al.   NATURE GENETICS

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

(2013) Annabelle Haudry et al.   NATURE GENETICS

The Capsella rubella genome and the genomic consequences of rapid mating system evolution

(2013) Tanja Slotte et al.   NATURE GENETICS

ZBED Evolution: Repeated Utilization of DNA Transposons as Regulators of Diverse Host Functions

(2013) Alexander Hayward et al.   PLoS One

Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing

(2013) U. Hellsten et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Amborella Genome and the Evolution of Flowering Plants

(2013) et al.   SCIENCE

Genome sequence of the date palm Phoenix dactylifera L

(2013) Ibrahim S. Al-Mssallem et al.   Nature Communications

Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

(2013) Aurélie Kapusta et al.   PLoS Genetics

The Reference Genome of the Halophytic Plant Eutrema salsugineum

(2013) Ruolin Yang et al.   Frontiers in Plant Science

Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.)

(2013) Ray Ming et al.   GENOME BIOLOGY

Transposable Elements: An Abundant and Natural Source of Regulatory Sequences for Host Genes

(2012) Rita Rebollo et al.   Annual Review of Genetics

ALOG domains: provenance of plant homeotic and developmental regulators from the DNA-binding domain of a novel class of DIRS1-type retroposons

(2012) Lakshminarayan M Iyer et al.   Biology Direct

The SLEEPER genes: a transposase-derived angiosperm-specific gene family

(2012) Marijn Knip et al.   BMC PLANT BIOLOGY

The impact of transposable elements on eukaryotic genomes: From genome size increase to genetic adaptation to stressful environments

(2012) Benoît Chénais et al.   GENE

Diversification of hAT transposase paralogues in the sugarcane genome

(2012) Erika M. de Jesus et al.   MOLECULAR GENETICS AND GENOMICS

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

(2012) Angélique D’Hont et al.   NATURE

Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres

(2012) Andrew H. Paterson et al.   NATURE

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Reference genome sequence of the model plant Setaria

(2012) Jeffrey L Bennetzen et al.   NATURE BIOTECHNOLOGY

How important are transposons for plant evolution?

(2012) Damon Lisch   NATURE REVIEWS GENETICS

Genomicus: five genome browsers for comparative genomics in eukaryota

(2012) Alexandra Louis et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2012)   NUCLEIC ACIDS RESEARCH

The genome of flax (Linum usitatissimum) assembledde novofrom short shotgun sequence reads

(2012) Zhiwen Wang et al.   PLANT JOURNAL

29 Mammalian Genomes Reveal Novel Exaptations of Mobile Elements for Likely Regulatory Functions in the Human Genome

(2012) Craig B. Lowe et al.   PLoS One

Transposable Elements, Epigenetics, and Genome Evolution

(2012) N. V. Fedoroff   SCIENCE

Transposable element small RNAs as regulators of gene expression

(2012) Andrea D. McCue et al.   TRENDS IN GENETICS

DNA-binding domains of plant-specific transcription factors: structure, function, and evolution

(2012) Kazuhiko Yamasaki et al.   TRENDS IN PLANT SCIENCE

A Gene Family Derived from Transposable Elements during Early Angiosperm Evolution Has Reproductive Fitness Benefits in Arabidopsis thaliana

(2012) Zoé Joly-Lopez et al.   PLoS Genetics

The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation

(2012) Guillaume Blanc et al.   GENOME BIOLOGY

Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana

(2011) Mark TA Donoghue et al.   BMC EVOLUTIONARY BIOLOGY

RNA-directed DNA methylation

(2011) Huiming Zhang et al.   CURRENT OPINION IN PLANT BIOLOGY

The cutting crew - ribonucleases are key players in the control of plastid gene expression

(2011) R. Stoppel et al.   JOURNAL OF EXPERIMENTAL BOTANY

Gypsy and the Birth of the SCAN Domain

(2011) R. O. Emerson et al.   JOURNAL OF VIROLOGY

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

The genome of the mesopolyploid crop species Brassica rapa

(2011) Xiaowu Wang et al.   NATURE GENETICS

The genome of the extremophile crucifer Thellungiella parvula

(2011) Maheshi Dassanayake et al.   NATURE GENETICS

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

(2011) Tina T Hu et al.   NATURE GENETICS

GenBank

(2011) D. A. Benson et al.   NUCLEIC ACIDS RESEARCH

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Binding Site Analysis of FAR-RED ELONGATED HYPOCOTYL3 Reveals Its Novel Function in Arabidopsis Development

(2011) X. Ouyang et al.   PLANT CELL

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

The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants

(2011) J. A. Banks et al.   SCIENCE

A Brief History of the Status of Transposable Elements: From Junk DNA to Major Players in Evolution

(2010) C. Biemont   GENETICS

A Domesticated piggyBac Transposase Plays Key Roles in Heterochromatin Dynamics and DNA Cleavage during Programmed DNA Deletion in Tetrahymena thermophila

(2010) Chao-Yin Cheng et al.   MOLECULAR BIOLOGY OF THE CELL

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

Draft genome sequence of the oilseed species Ricinus communis

(2010) Agnes P Chan et al.   NATURE BIOTECHNOLOGY

The genome of woodland strawberry (Fragaria vesca)

(2010) Vladimir Shulaev et al.   NATURE GENETICS

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

(2010) Riccardo Velasco et al.   NATURE GENETICS

Alternative splicing and evolution: diversification, exon definition and function

(2010) Hadas Keren et al.   NATURE REVIEWS GENETICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Genomic Analysis of Organismal Complexity in the Multicellular Green Alga Volvox carteri

(2010) S. E. Prochnik et al.   SCIENCE

Molecular domestication of transposable elements: From detrimental parasites to useful host genes

(2009) L. Sinzelle et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

PiggyMac, a domesticated piggyBac transposase involved in programmed genome rearrangements in the ciliate Paramecium tetraurelia

(2009) C. Baudry et al.   GENES & DEVELOPMENT

The Contribution of Transposable Elements to Expressed Coding Sequence in Arabidopsis thaliana

(2009) Steven Lockton et al.   JOURNAL OF MOLECULAR EVOLUTION

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

The genome of the cucumber, Cucumis sativus L.

(2009) Sanwen Huang et al.   NATURE GENETICS

Gene duplication and evolutionary novelty in plants

(2009) Lex E. Flagel et al.   NEW PHYTOLOGIST

TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences

(2009) Yujun Han et al.   NUCLEIC ACIDS RESEARCH

PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update

(2009) Pawel Durek et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

AtnMat2, a nuclear-encoded maturase required for splicing of group-II introns in Arabidopsis mitochondria

(2009) I. Keren et al.   RNA

Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas

(2009) A. Z. Worden et al.   SCIENCE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

ZBED6, a Novel Transcription Factor Derived from a Domesticated DNA Transposon Regulates IGF2 Expression and Muscle Growth

(2009) Ellen Markljung et al.   PLOS BIOLOGY

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

A Link between RNA Metabolism and Silencing Affecting Arabidopsis Development

(2008) Brian D. Gregory et al.   DEVELOPMENTAL CELL

Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets

(2008) Nicolas Buisine et al.   GENOMICS

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

(2008) Ray Ming et al.   NATURE

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS

Genome-Wide Analysis of the “Cut-and-Paste” Transposons of Grapevine

(2008) Andrej Benjak et al.   PLoS One

Synteny and Collinearity in Plant Genomes

(2008) H. Tang et al.   SCIENCE