Dynamics and Adaptive Benefits of Protein Domain Emergence and Arrangements during Plant Genome Evolution

Natural diversity and adaptation in plant secondary metabolism

(2011) Juergen Kroymann   CURRENT OPINION IN PLANT BIOLOGY

Chimeric Genes as a Source of Rapid Evolution in Drosophila melanogaster

(2011) R. L. Rogers et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Dynamics and Evolutionary Potential of Domain Loss and Emergence

(2011) A. D. Moore et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)

(2011) Eman K Al-Dous et al.   NATURE BIOTECHNOLOGY

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

(2011) Tina T Hu et al.   NATURE GENETICS

Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes

(2011) Anna R. Reineke et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Michaël Bekaert et al.   PLANT CELL

Plant responses to insect herbivory: interactions between photosynthesis, reactive oxygen species and hormonal signalling pathways

(2011) PAVEL I. KERCHEV et al.   PLANT CELL AND ENVIRONMENT

Recently Formed Polyploid Plants Diversify at Lower Rates

(2011) I. Mayrose et al.   SCIENCE

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

(2011) J. A. Banks et al.   SCIENCE

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires

(2011) Christian M Zmasek et al.   GENOME BIOLOGY

Insights from the Comparison of Plant Genome Sequences

(2010) Andrew H. Paterson et al.   Annual Review of Plant Biology

Doomed Lovers: Mechanisms of Isolation and Incompatibility in Plants

(2010) Kirsten Bomblies   Annual Review of Plant Biology

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

WD-repeat instability and diversification of the Podospora anserina hnwd non-self recognition gene family

(2010) Damien Chevanne et al.   BMC EVOLUTIONARY BIOLOGY

Molecular and phylogenetic characterization of the sieve element occlusion gene family in Fabaceae and non-Fabaceae plants

(2010) Boris Rüping et al.   BMC PLANT BIOLOGY

Genome-Wide Phylogenetic Comparative Analysis of Plant Transcriptional Regulation: A Timeline of Loss, Gain, Expansion, and Correlation with Complexity

(2010) Daniel Lang et al.   Genome Biology and Evolution

Asymmetric Configurations and N-terminal Rearrangements in Connexin26 Gap Junction Channels

(2010) Atsunori Oshima et al.   JOURNAL OF MOLECULAR BIOLOGY

Evolution of domain promiscuity in eukaryotic genomes—a perspective from the inferred ancestral domain architectures

(2010) Inbar Cohen-Gihon et al.   Molecular BioSystems

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 Theobroma cacao

(2010) Xavier Argout et al.   NATURE GENETICS

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

(2010) Riccardo Velasco et al.   NATURE GENETICS

Stress and developmental responses of terpenoid biosynthetic genes in Cistus creticus subsp. creticus

(2010) Irene Pateraki et al.   PLANT CELL REPORTS

Rapid Diversification of Cell Signaling Phenotypes by Modular Domain Recombination

(2010) S. G. Peisajovich et al.   SCIENCE

Quantifying the mechanisms of domain gain in animal proteins

(2010) Marija Buljan et al.   GENOME BIOLOGY

The evolution of protein domain families

(2009) Marija Buljan et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

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

Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus

(2009) Xiaohan Yang et al.   GENOMICS

Evolution of Plant MADS Box Transcription Factors: Evidence for Shifts in Selection Associated with Early Angiosperm Diversification and Concerted Gene Duplications

(2009) H. Shan et al.   MOLECULAR BIOLOGY AND 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

The evolutionary significance of ancient genome duplications

(2009) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

The Pfam protein families database

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

PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants

(2009) S. Proost et al.   PLANT CELL

Nature of the protein universe

(2009) M. Levitt   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The frequency of polyploid speciation in vascular plants

(2009) T. E. Wood et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Triassic origin and early radiation of multicellular volvocine algae

(2009) M. D. Herron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

The Evolutionary Mechanics of Domain Organization in Proteomes and the Rise of Modularity in the Protein World

(2009) Minglei Wang et al.   STRUCTURE

Contrasting evolutionary dynamics between angiosperm and mammalian genomes

(2009) Eduard Kejnovsky et al.   TRENDS IN ECOLOGY & EVOLUTION

Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication

(2009) Li-Jun Ma et al.   PLoS Genetics

Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome

(2009) Regina S. Baucom et al.   PLoS Genetics

GENE LOSS UNDER NEIGHBORHOOD SELECTION FOLLOWING WHOLE GENOME DUPLICATION AND THE RECONSTRUCTION OF THE ANCESTRAL POPULUS GENOME

(2009) CHUNFANG ZHENG et al.   Journal of Bioinformatics and Computational Biology

Just how versatile are domains?

(2008) January Weiner et al.   BMC EVOLUTIONARY BIOLOGY

Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome

(2008) R. S. Baucom et al.   GENOME RESEARCH

Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps

(2008) H. Tang et al.   GENOME RESEARCH

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

(2008) Ray Ming et al.   NATURE

The Trichoplax genome and the nature of placozoans

(2008) Mansi Srivastava et al.   NATURE

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH

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

(2008) K. Hanada et al.   PLANT PHYSIOLOGY

Novelties of the flowering plant pollen tube underlie diversification of a key life history stage

(2008) J. H. Williams   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Repeated independent evolution of obligate pollination mutualism in the Phyllantheae-Epicephala association

(2008) A. Kawakita et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Arrangements in the modular evolution of proteins

(2008) Andrew D. Moore et al.   TRENDS IN BIOCHEMICAL SCIENCES

Domain Tree-Based Analysis of Protein Architecture Evolution

(2007) K. Forslund et al.   MOLECULAR BIOLOGY AND EVOLUTION

Investigation of Loss and Gain of Introns in the Compact Genomes of Pufferfishes (Fugu and Tetraodon)

(2007) Y.-H. Loh et al.   MOLECULAR BIOLOGY AND EVOLUTION