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

Tracking the origin of two genetic components associated with transposable element bursts in domesticated rice

(2019) Jinfeng Chen et al.   Nature Communications

Structural variants in 3000 rice genomes

(2019) Roven Rommel Fuentes et al.   GENOME RESEARCH

A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour

(2019) Liyi Zhang et al.   Nature Communications

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

(2018) Joshua C. Stein et al.   NATURE GENETICS

The Sequenced Angiosperm Genomes and Genome Databases

(2018) Fei Chen et al.   Frontiers in Plant Science

Retrotranspositional landscape of Asian rice revealed by 3000 genomes

(2018) Marie-Christine Carpentier et al.   Nature Communications

Rapid and Recent Evolution of LTR Retrotransposons Drives Rice Genome Evolution During the Speciation of AA- Genome Oryza Species

(2017) Qun-Jie Zhang et al.   G3-Genes Genomes Genetics

Genetic control of the root system in rice under normal and drought stress conditions by genome-wide association study

(2017) Xiaokai Li et al.   PLoS Genetics

RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing

(2017) Jinfeng Chen et al.   PeerJ

Genome wide association analysis of cold tolerance at germination in temperate japonica rice (Oryza sativa L.) varieties

(2017) Ester Sales et al.   PLoS One

OsSPL13 controls grain size in cultivated rice

(2016) Lizhen Si et al.   NATURE GENETICS

Regulatory evolution of innate immunity through co-option of endogenous retroviruses

(2016) E. B. Chuong et al.   SCIENCE

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

(2015) Dario Copetti et al.   BMC GENOMICS

The Contributions of Transposable Elements to the Structure, Function, and Evolution of Plant Genomes

(2014) Jeffrey L. Bennetzen et al.   Annual Review of Plant Biology

Transposable elements, a treasure trove to decipher epigenetic variation: insights from Arabidopsis and crop epigenomes

(2014) M. Mirouze et al.   JOURNAL OF EXPERIMENTAL BOTANY

The 3,000 rice genomes project

(2014)   GigaScience

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

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

Activation and Epigenetic Regulation of DNA Transposon nDart1 in Rice

(2012) Chang-Ho Eun et al.   PLANT AND CELL PHYSIOLOGY

Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals

(2011) Vincent J Lynch et al.   NATURE GENETICS

Orthologous Comparisons of the Hd1 Region across Genera Reveal Hd1 Gene Lability within Diploid Oryza Species and Disruptions to Microsynteny in Sorghum

(2010) A. Sanyal et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

(2010) Susanna Atwell et al.   NATURE

Identification of an active LTR retrotransposon in rice

(2009) Nathalie Picault et al.   PLANT JOURNAL

Comparative sequence analysis ofMONOCULM1-orthologous regions in 14Oryzagenomes

(2009) Fei Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight

(2008) Jianfeng Weng et al.   CELL RESEARCH

New SINE families from rice, OsSN, with poly(A) at the 3’ ends

(2008) Suguru Tsuchimoto et al.   GENES & GENETIC SYSTEMS

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

(2008) H. Xiao et al.   SCIENCE