LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes

Whole-Genome Analysis of Individual Meiotic Events in Drosophila melanogaster Reveals That Noncrossover Gene Conversions Are Insensitive to Interference and the Centromere Effect

(2016) Danny E. Miller et al.   GENETICS

Sequence of the Sugar Pine Megagenome

(2016) Kristian A. Stevens et al.   GENETICS

DNA methylome of the 20-gigabase Norway spruce genome

(2016) Israel Ausin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evidence of extensive non-allelic gene conversion among LTR elements in the human genome

(2016) Beniamino Trombetta et al.   Scientific Reports

Whole-Genome Analysis of Individual Meiotic Events in Drosophila melanogaster Reveals That Noncrossover Gene Conversions Are Insensitive to Interference and the Centromere Effect

(2016) Danny E. Miller et al.   GENETICS

Sequence of the Sugar Pine Megagenome

(2016) Kristian A. Stevens et al.   GENETICS

The Ty1-copia LTR retroelement family PARTC is highly conserved in conifers over 200MY of evolution

(2015) Andrea Zuccolo et al.   GENE

Determination of epigenetic inheritance, genetic inheritance, and estimation of genome DNA methylation in a full-sib family of Cupressus sempervirens L.

(2015) Evangelia V. Avramidou et al.   GENE

DNA methylation epigenetically silences crossover hot spots and controls chromosomal domains of meiotic recombination inArabidopsis

(2015) Nataliya E. Yelina et al.   GENES & DEVELOPMENT

DNA methylation restrains transposons from adopting a chromatin signature permissive for meiotic recombination

(2015) Natasha Zamudio et al.   GENES & DEVELOPMENT

Low Levels of LTR Retrotransposon Deletion by Ectopic Recombination in the Gigantic Genomes of Salamanders

(2015) Matthew Blake Frahry et al.   JOURNAL OF MOLECULAR EVOLUTION

The Plant Genome Integrative Explorer Resource: PlantGenIE.org

(2015) David Sundell et al.   NEW PHYTOLOGIST

A survey of Gypsy and Copia LTR-retrotransposon superfamilies and lineages and their distinct dynamics in the Populus trichocarpa (L.) genome

(2015) Lucia Natali et al.   Tree Genetics & Genomes

Extreme Recombination Frequencies Shape Genome Variation and Evolution in the Honeybee, Apis mellifera

(2015) Andreas Wallberg et al.   PLoS Genetics

In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae

(2015) Jiří Macas et al.   PLoS One

Extensive and Biased Intergenomic Nonreciprocal DNA Exchanges Shaped a Nascent Polyploid Genome, Gossypium (Cotton)

(2014) Hui Guo et al.   GENETICS

Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation

(2014) J. L. Wegrzyn et al.   GENETICS

Epigenetic Variability in the Genetically Uniform Forest Tree Species Pinus pinea L

(2014) Enrique Sáez-Laguna et al.   PLoS One

Phylogeny and Divergence Times of Gymnosperms Inferred from Single-Copy Nuclear Genes

(2014) Ying Lu et al.   PLoS One

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

(2014) David B Neale et al.   GENOME BIOLOGY

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data

(2013) Inanc Birol et al.   BIOINFORMATICS

Tandem repeats derived from centromeric retrotransposons

(2013) Anupma Sharma et al.   BMC GENOMICS

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

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

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

Multilocus estimation of divergence times and ancestral effective population sizes ofOryzaspecies and implications for the rapid diversification of the genus

(2013) Xin-Hui Zou et al.   NEW PHYTOLOGIST

The Amborella Genome and the Evolution of Flowering Plants

(2013) et al.   SCIENCE

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Slow but not low: genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms

(2012) Emmanuel Buschiazzo et al.   BMC EVOLUTIONARY BIOLOGY

Epigenetic control of transposon transcription and mobility in Arabidopsis

(2012) Etienne Bucher et al.   CURRENT OPINION IN PLANT BIOLOGY

Very Low Rate of Gene Conversion in the Yeast Genome

(2012) Claudio Casola et al.   MOLECULAR BIOLOGY AND EVOLUTION

Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation

(2012) M. Colome-Tatche et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Loss of DNA methylation affects the recombination landscape in Arabidopsis

(2012) M. Mirouze et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transposable Elements, Epigenetics, and Genome Evolution

(2012) N. V. Fedoroff   SCIENCE

Double-Strand Breaks in Heterochromatin Move Outside of a Dynamic HP1a Domain to Complete Recombinational Repair

(2011) Irene Chiolo et al.   CELL

The Ins and Outs of Heterochromatic DNA Repair

(2011) Craig L. Peterson   DEVELOPMENTAL CELL

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences

(2010) Allen Kovach et al.   BMC GENOMICS

Nonallelic Gene Conversion in the Genus Drosophila

(2010) C. Casola et al.   GENETICS

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

Centromeres Convert but Don't Cross

(2010) Paul B. Talbert et al.   PLOS BIOLOGY

Widespread Gene Conversion in Centromere Cores

(2010) Jinghua Shi et al.   PLOS BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization

(2009) X. Wang et al.   GENOME RESEARCH

Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants

(2009) J. S. Hawkins 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

LTR retrotransposon landscape in Medicago truncatula: more rapid removal than in rice

(2008) Hao Wang et al.   BMC GENOMICS

Gene conversion in the rice genome

(2008) Shuqing Xu et al.   BMC GENOMICS