Convergent adaptive evolution in marginal environments: unloading transposable elements as a common strategy among mangrove genomes

The origin, diversification and adaptation of a major mangrove clade (Rhizophoreae) revealed by whole genome sequencing

(2017) Shaohua Xu et al.   National Science Review

No Genome-Wide Protein Sequence Convergence for Echolocation

(2015) Z. Zou et al.   MOLECULAR BIOLOGY AND EVOLUTION

Determining the Null Model for Detecting Adaptive Convergence from Genomic Data: A Case Study using Echolocating Mammals

(2015) G. W. C. Thomas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Convergent evolution of the genomes of marine mammals

(2015) Andrew D Foote et al.   NATURE GENETICS

Population Genomics of Transposable Elements inDrosophila

(2014) Maite G. Barrón et al.   Annual Review of Genetics

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

Plant genome size variation: bloating and purging DNA

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

Widespread and frequent horizontal transfers of transposable elements in plants

(2014) M. El Baidouri et al.   GENOME RESEARCH

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

(2014) Jeremy Schmutz et al.   NATURE GENETICS

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

(2014) F. Denoeud et al.   SCIENCE

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

Compact genome of the Antarctic midge is likely an adaptation to an extreme environment

(2014) Joanna L. Kelley et al.   Nature Communications

Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis

(2014) Linhai Wang et al.   GENOME BIOLOGY

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

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

Genome-wide signatures of convergent evolution in echolocating mammals

(2013) Joe Parker et al.   NATURE

Architecture and evolution of a minute plant genome

(2013) Enrique Ibarra-Laclette 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

Genome size variation in wild and cultivated maize along altitudinal gradients

(2013) Concepción M. Díez et al.   NEW PHYTOLOGIST

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

Assembly and Validation of the Genome of the Nonmodel Basal Angiosperm Amborella

(2013) S. Chamala et al.   SCIENCE

Draft genome of the kiwifruit Actinidia chinensis

(2013) Shengxiong Huang et al.   Nature Communications

Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution

(2013) Jinfeng Chen et al.   Nature Communications

Transposon Variants and Their Effects on Gene Expression in Arabidopsis

(2013) Xi Wang et al.   PLoS Genetics

Co-evolution of plant LTR-retrotransposons and their host genomes

(2013) Meixia Zhao et al.   Protein & Cell

Nonallelic homologous recombination between retrotransposable elements is a driver of de novo unbalanced translocations

(2012) C. Robberecht et al.   GENOME RESEARCH

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

The draft genome of a diploid cotton Gossypium raimondii

(2012) Kunbo Wang et al.   NATURE GENETICS

The draft genome of sweet orange (Citrus sinensis)

(2012) Qiang Xu et al.   NATURE GENETICS

How important are transposons for plant evolution?

(2012) Damon Lisch   NATURE REVIEWS GENETICS

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

(2012) Zhiwen Wang et al.   PLANT JOURNAL

Transcriptional Homeostasis of a Mangrove Species, Ceriops tagal, in Saline Environments, as Revealed by Microarray Analysis

(2012) Shan Liang et al.   PLoS One

Insights into salt tolerance from the genome ofThellungiella salsuginea

(2012) Hua-Jun Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Community-wide convergent evolution in insect adaptation to toxic cardenolides by substitutions in the Na,K-ATPase

(2012) S. Dobler 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

Parallel Molecular Evolution in an Herbivore Community

(2012) Y. Zhen et al.   SCIENCE

The Cassava Genome: Current Progress, Future Directions

(2012) Simon Prochnik et al.   Tropical Plant Biology

Ultra-fast sequence clustering from similarity networks with SiLiX

(2011) Vincent Miele et al.   BMC BIOINFORMATICS

CONVERGENCE, ADAPTATION, AND CONSTRAINT

(2011) Jonathan B. Losos   EVOLUTION

Higher Intron Loss Rate in Arabidopsis thaliana Than A. lyrata Is Consistent with Stronger Selection for a Smaller Genome

(2011) J. A. Fawcett et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Dynamic interactions between transposable elements and their hosts

(2011) Henry L. Levin et al.   NATURE REVIEWS GENETICS

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

A Genetic and Structural Study of Genome Rearrangements Mediated by High Copy Repeat Ty1 Elements

(2011) Jason E. Chan et al.   PLoS Genetics

Status and distribution of mangrove forests of the world using earth observation satellite data

(2010) C. Giri et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Population Genomics of Transposable Elements in Drosophila melanogaster

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

Draft genome sequence of the oilseed species Ricinus communis

(2010) Agnes P Chan et al.   NATURE BIOTECHNOLOGY

The genome of Theobroma cacao

(2010) Xavier Argout et al.   NATURE GENETICS

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

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

(2010) Julie A. Law et al.   NATURE REVIEWS GENETICS

The Gypsy Database (GyDB) of mobile genetic elements: release 2.0

(2010) C. Llorens et al.   NUCLEIC ACIDS RESEARCH

Gene Expression Profiles in Response to Salt Stress in Hibiscus Tiliaceus

(2010) Guili Yang et al.   PLANT MOLECULAR BIOLOGY REPORTER

Salt tolerance mechanisms in mangroves: a review

(2010) Asish Kumar Parida et al.   TREES-STRUCTURE AND FUNCTION

Evolutionary dynamics of transposable elements in a small RNA world

(2010) Justin P. Blumenstiel   TRENDS IN GENETICS

A triptych of the evolution of plant transposable elements

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

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III

(2009)   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression

(2009) J. D. Hollister et al.   GENOME RESEARCH

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

(2009) Ken Naito et al.   NATURE

The genome of the cucumber, Cucumis sativus L.

(2009) Sanwen Huang et al.   NATURE GENETICS

Fine-grained annotation and classification of de novo predicted LTR retrotransposons

(2009) Sascha Steinbiss et al.   NUCLEIC ACIDS RESEARCH

Distinct Gene Number-Genome Size Relationships for Eukaryotes and Non-Eukaryotes: Gene Content Estimation for Dinoflagellate Genomes

(2009) Yubo Hou et al.   PLoS One

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

Hear, hear: the convergent evolution of echolocation in bats?

(2009) Emma C. Teeling   TRENDS IN ECOLOGY & EVOLUTION

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

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

(2008) Ray Ming et al.   NATURE

Double-strand breaks associated with repetitive DNA can reshape the genome

(2008) J. L. Argueso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA