Different Modes of Gene Duplication Show Divergent Evolutionary Patterns and Contribute Differently to the Expansion of Gene Families Involved in Important Fruit Traits in Pear (Pyrus bretschneideri)

The evolutionary significance of polyploidy

(2017) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome

(2017) Tianying Lan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene duplication can impart fragility, not robustness, in the yeast protein interaction network

(2017) Guillaume Diss et al.   SCIENCE

Evidence for the fixation of gene duplications by positive selection inDrosophila

(2016) Margarida Cardoso-Moreira et al.   GENOME RESEARCH

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

The developmental transcriptome atlas of the biofuel cropCamelina sativa

(2016) Sateesh Kagale et al.   PLANT JOURNAL

Evolution of gene duplication in plants

(2016) Nicholas Panchy et al.   PLANT PHYSIOLOGY

Large-Scale Gene Relocations following an Ancient Genome Triplication Associated with the Diversification of Core Eudicots

(2016) Yupeng Wang et al.   PLoS One

Expansion and Function of Repeat Domain Proteins During Stress and Development in Plants

(2016) Manisha Sharma et al.   Frontiers in Plant Science

The wondrous cycles of polyploidy in plants

(2015) Jonathan F. Wendel   AMERICAN JOURNAL OF BOTANY

Is post-polyploidization diploidization the key to the evolutionary success of angiosperms?

(2015) Steven Dodsworth et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Progress, challenges and the future of crop genomes

(2015) Todd P Michael et al.   CURRENT OPINION IN PLANT BIOLOGY

Compensatory Drift and the Evolutionary Dynamics of Dosage-Sensitive Duplicate Genes

(2015) A. Thompson et al.   GENETICS

Maintenance and Loss of Duplicated Genes by Dosage Subfunctionalization

(2015) Jean-Francois Gout et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of cis-regulatory elements and regulatory networks in duplicated genes of Arabidopsis thaliana

(2015) Andrej A Arsovski et al.   PLANT PHYSIOLOGY

Genome identification and analysis of genes encoding the key enzymes involved in organic acid biosynthesis pathway in apple, grape, and sweet orange

(2015) Lingfei Shangguan et al.   SCIENTIA HORTICULTURAE

The causes and molecular consequences of polyploidy in flowering plants

(2014) Gaurav D. Moghe et al.   Annals of the New York Academy of Sciences

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time

(2014) Gavin C Conant et al.   CURRENT OPINION IN PLANT BIOLOGY

Ancient Gene Duplicates in Gossypium (Cotton) Exhibit Near-Complete Expression Divergence

(2014) Simon Renny-Byfield et al.   Genome Biology and Evolution

Gene length and expression level shape genomic novelties

(2014) Vladislav Grishkevich et al.   GENOME RESEARCH

Differential retention and divergent resolution of duplicate genes following whole-genome duplication

(2014) Casey L. McGrath et al.   GENOME RESEARCH

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

(2014) Kevin Vanneste et al.   GENOME RESEARCH

Subcellular Relocalization and Positive Selection Play Key Roles in the Retention of Duplicate Genes of Populus Class III Peroxidase Family

(2014) L.-L. Ren et al.   PLANT CELL

The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes

(2014) Shengyi Liu et al.   Nature Communications

Different patterns of gene structure divergence following gene duplication in Arabidopsis

(2013) Yupeng Wang et al.   BMC GENOMICS

Gene body methylation shows distinct patterns associated with different gene origins and duplication modes and has a heterogeneous relationship with gene expression inOryza sativa(rice)

(2013) Yupeng Wang et al.   NEW PHYTOLOGIST

The Genome Database for Rosaceae (GDR): year 10 update

(2013) Sook Jung et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Patterns of Gene Duplication and Their Contribution to Expansion of Gene Families in Grapevine

(2013) Nian Wang et al.   PLANT MOLECULAR BIOLOGY REPORTER

Prevalent Role of Gene Features in Determining Evolutionary Fates of Whole-Genome Duplication Duplicated Genes in Flowering Plants

(2013) W.-k. Jiang et al.   PLANT PHYSIOLOGY

Mining and comparison of the genes encoding the key enzymes involved in sugar biosynthesis in apple, grape, and sweet orange

(2013) Lingfei Shangguan et al.   SCIENTIA HORTICULTURAE

The genome of the pear (Pyrus bretschneideri Rehd.)

(2012) J. Wu et al.   GENOME RESEARCH

Pervasive Indels and Their Evolutionary Dynamics after the Fish-Specific Genome Duplication

(2012) Baocheng Guo et al.   MOLECULAR BIOLOGY AND EVOLUTION

PGDD: a database of gene and genome duplication in plants

(2012) Tae-Ho Lee et al.   NUCLEIC ACIDS RESEARCH

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Pericentromeric Effects Shape the Patterns of Divergence, Retention, and Expression of Duplicated Genes in the Paleopolyploid Soybean

(2012) J. Du et al.   PLANT CELL

Gene balance hypothesis: Connecting issues of dosage sensitivity across biological disciplines

(2012) J. A. Birchler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genome of Prunus mume

(2012) Qixiang Zhang et al.   Nature Communications

Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication

(2011) J. Huerta-Cepas et al.   BRIEFINGS IN BIOINFORMATICS

Selection for Higher Gene Copy Number after Different Types of Plant Gene Duplications

(2011) Corey M. Hudson et al.   Genome Biology and Evolution

Genome duplication in amphibians and fish: an extended synthesis

(2011) B. K. Mable et al.   JOURNAL OF ZOOLOGY

The genome of the extremophile crucifer Thellungiella parvula

(2011) Maheshi Dassanayake et al.   NATURE GENETICS

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

Seventy Million Years of Concerted Evolution of a Homoeologous Chromosome Pair, in Parallel, in Major Poaceae Lineages

(2011) Xiyin Wang et al.   PLANT CELL

Two-Phase Resolution of Polyploidy in theArabidopsisMetabolic Network Gives Rise to Relative and Absolute Dosage Constraints

(2011) Michaël Bekaert et al.   PLANT CELL

Modes of Gene Duplication Contribute Differently to Genetic Novelty and Redundancy, but Show Parallels across Divergent Angiosperms

(2011) Yupeng Wang et al.   PLoS One

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

ANK6, a mitochondrial ankyrin repeat protein, is required for male-female gamete recognition in Arabidopsis thaliana

(2010) F. Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies

(2010) Dapeng Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Bias in Plant Gene Content Following Different Sorts of Duplication: Tandem, Whole-Genome, Segmental, or by Transposition

(2009) Michael Freeling   Annual Review of Plant Biology

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

(2009) X. Wang et al.   GENOME RESEARCH

Distinguishing Among Evolutionary Models for the Maintenance of Gene Duplicates

(2009) M. W. Hahn   JOURNAL OF HEREDITY

Heterogeneous Patterns of Gene-Expression Diversification in Mammalian Gene Duplicates

(2009) D. Farre et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene duplication and evolutionary novelty in plants

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

Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event

(2009) J. A. Fawcett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps

(2008) H. Tang et al.   GENOME RESEARCH

Many or most genes in Arabidopsis transposed after the origin of the order Brassicales

(2008) M. Freeling et al.   GENOME RESEARCH

On the Expansion of the Pentatricopeptide Repeat Gene Family in Plants

(2008) N. O'Toole et al.   MOLECULAR BIOLOGY AND EVOLUTION

Importance of Lineage-Specific Expansion of Plant Tandem Duplicates in the Adaptive Response to Environmental Stimuli

(2008) K. Hanada et al.   PLANT PHYSIOLOGY

Genomic Plasticity and the Diversity of Polyploid Plants

(2008) A. R. Leitch et al.   SCIENCE

Synteny and Collinearity in Plant Genomes

(2008) H. Tang et al.   SCIENCE