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

Are orphan genes protein-coding, prediction artifacts, or non-coding RNAs?

(2016) Neel Prabh et al.   BMC BIOINFORMATICS

Comparative analysis of plant immune receptor architectures uncovers host proteins likely targeted by pathogens

(2016) Panagiotis F. Sarris et al.   BMC BIOLOGY

Domestication history and geographical adaptation inferred from a SNP map of African rice

(2016) Rachel S Meyer et al.   NATURE GENETICS

Integration of decoy domains derived from protein targets of pathogen effectors into plant immune receptors is widespread

(2016) Thomas Kroj et al.   NEW PHYTOLOGIST

Extensive sequence divergence between the reference genomes of two eliteindicarice varieties Zhenshan 97 and Minghui 63

(2016) Jianwei Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation

(2016) James B. Pease et al.   PLOS BIOLOGY

Genome and Comparative Transcriptomics of African Wild Rice Oryza longistaminata Provide Insights into Molecular Mechanism of Rhizomatousness and Self-Incompatibility

(2015) Yesheng Zhang et al.   Molecular Plant

Genome Alignment Spanning Major Poaceae Lineages Reveals Heterogeneous Evolutionary Rates and Alters Inferred Dates for Key Evolutionary Events

(2015) Xiyin Wang et al.   Molecular Plant

Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm

(2015) Meilina Ong-Abdullah et al.   NATURE

The EMBL-EBI bioinformatics web and programmatic tools framework

(2015) Weizhong Li et al.   NUCLEIC ACIDS RESEARCH

Genes from scratch – the evolutionary fate of de novo genes

(2015) Christian Schlötterer   TRENDS IN GENETICS

“Out of Pollen” Hypothesis for Origin of New Genes in Flowering Plants: Study from Arabidopsis thaliana

(2014) Dong-Dong Wu et al.   Genome Biology and Evolution

The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication

(2014) Muhua Wang et al.   NATURE GENETICS

Rapid diversification of fiveOryzaAA genomes associated with rice adaptation

(2014) Qun-Jie Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive introgression in a malaria vector species complex revealed by phylogenomics

(2014) M. C. Fontaine et al.   SCIENCE

Disentangling Methodological and Biological Sources of Gene Tree Discordance on Oryza (Poaceae) Chromosome 3

(2014) Derrick J. Zwickl et al.   SYSTEMATIC BIOLOGY

Coming of age: orphan genes in plants

(2014) Zebulun W. Arendsee et al.   TRENDS IN PLANT SCIENCE

The life cycle of Drosophila orphan genes

(2014) Nicola Palmieri et al.   eLife

A novel conserved mechanism for plant NLR protein pairs: the “integrated decoy” hypothesis

(2014) Stella Cesari et al.   Frontiers in Plant Science

New Gene Evolution: Little Did We Know

(2013) Manyuan Long et al.   Annual Review of Genetics

Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution

(2013) Rafik Neme et al.   BMC GENOMICS

The International Oryza Map Alignment Project: development of a genus-wide comparative genomics platform to help solve the 9 billion-people question

(2013) Julie Jacquemin et al.   CURRENT OPINION IN PLANT BIOLOGY

Deep Transcriptome Sequencing of Wild Halophyte Rice, Porteresia coarctata, Provides Novel Insights into the Salinity and Submergence Tolerance Factors

(2013) R. Garg et al.   DNA RESEARCH

Shared Subgenome Dominance Following Polyploidization Explains Grass Genome Evolutionary Plasticity from a Seven Protochromosome Ancestor with 16K Protogenes

(2013) Florent Murat et al.   Genome Biology and Evolution

High Occurrence of Functional New Chimeric Genes in Survey of Rice Chromosome 3 Short Arm Genome Sequences

(2013) Chengjun Zhang et al.   Genome Biology and Evolution

Phylogenetic relationships and genome divergence among the AA- genome species of the genus Oryza as revealed by 53 nuclear genes and 16 intergenic regions

(2013) Ting Zhu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Fifteen Million Years of Evolution in the Oryza Genus Shows Extensive Gene Family Expansion

(2013) Julie Jacquemin et al.   Molecular Plant

Gramene 2013: comparative plant genomics resources

(2013) Marcela K. Monaco et al.   NUCLEIC ACIDS RESEARCH

The Rice Resistance Protein Pair RGA4/RGA5 Recognizes the Magnaporthe oryzae Effectors AVR-Pia and AVR1-CO39 by Direct Binding

(2013) S. Cesari et al.   PLANT CELL

Selective Acquisition and Retention of Genomic Sequences by Pack-Mutator-Like Elements Based on Guanine-Cytosine Content and the Breadth of Expression

(2013) A. A. Ferguson et al.   PLANT PHYSIOLOGY

Coordination of Leaf Photosynthesis, Transpiration, and Structural Traits in Rice and Wild Relatives (Genus Oryza)

(2013) R. Giuliani et al.   PLANT PHYSIOLOGY

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

(2013) M. S. Campbell et al.   PLANT PHYSIOLOGY

Could abiotic stress tolerance in wild relatives of rice be used to improve Oryza sativa?

(2013) Brian J. Atwell et al.   PLANT SCIENCE

Plant F-Box Protein Evolution Is Determined by Lineage-Specific Timing of Major Gene Family Expansion Waves

(2013) Aura Navarro-Quezada et al.   PLoS One

Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

(2013) Aurélie Kapusta et al.   PLoS Genetics

Páramo is the world's fastest evolving and coolest biodiversity hotspot

(2013) Santiago Madriñán et al.   Frontiers in Genetics

LEA proteins: IDPs with versatile functions in cellular dehydration tolerance: Figure 1

(2012) Dirk K. Hincha et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Proto-genes and de novo gene birth

(2012) Anne-Ruxandra Carvunis et al.   NATURE

Retrotransposons Control Fruit-Specific, Cold-Dependent Accumulation of Anthocyanins in Blood Oranges

(2012) E. Butelli et al.   PLANT CELL

Gene family evolution in green plants with emphasis on the origination and evolution ofArabidopsis thalianagenes

(2012) Ya-Long Guo   PLANT JOURNAL

Transposable elements reveal a stem cell-specific class of long noncoding RNAs

(2012) David Kelley et al.   GENOME BIOLOGY

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana

(2011) Mark TA Donoghue et al.   BMC EVOLUTIONARY BIOLOGY

The Oryza BAC resource: a genus-wide and genome scale tool for exploring rice genome evolution and leveraging useful genetic diversity from wild relatives

(2011) Jetty S.S. Ammiraju et al.   BREEDING SCIENCE

The species of the genus Oryza and transfer of useful genes from wild species into cultivated rice, O. sativa

(2011) Kshirod K. Jena   BREEDING SCIENCE

Factors that Contribute to Variation in Evolutionary Rate among Arabidopsis Genes

(2011) L. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Long-Range and Targeted Ectopic Recombination between the Two Homeologous Chromosomes 11 and 12 in Oryza Species

(2011) J. Jacquemin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Testing for Ancient Admixture between Closely Related Populations

(2011) Eric Y. Durand et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Novel Protein RLS1 with NB–ARM Domains Is Involved in Chloroplast Degradation during Leaf Senescence in Rice

(2011) Bin-Bin Jiao et al.   Molecular Plant

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

Semi-dominant mutations in the CC-NB-LRR-type R gene, NLS1, lead to constitutive activation of defense responses in rice

(2011) Jiuyou Tang et al.   PLANT JOURNAL

A multifaceted genomics approach allows the isolation of the rice Pia-blast resistance gene consisting of two adjacent NBS-LRR protein genes

(2011) Yudai Okuyama et al.   PLANT JOURNAL

Reference-guided assembly of four diverse Arabidopsis thaliana genomes

(2011) K. Schneeberger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular evidence for a single evolutionary origin of domesticated rice

(2011) J. Molina et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mugsy: fast multiple alignment of closely related whole genomes

(2010) Samuel V. Angiuoli et al.   BIOINFORMATICS

genoPlotR: comparative gene and genome visualization in R

(2010) L. Guy et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution

(2010) F. Murat et al.   GENOME RESEARCH

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 sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Gramene database in 2010: updates and extensions

(2010) K. Youens-Clark et al.   NUCLEIC ACIDS RESEARCH

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

Durable panicle blast-resistance gene Pb1 encodes an atypical CC-NBS-LRR protein and was generated by acquiring a promoter through local genome duplication

(2010) Nagao Hayashi et al.   PLANT JOURNAL

Spatio-temporal patterns of genome evolution in allotetraploid species of the genus Oryza

(2010) Jetty S. S. Ammiraju et al.   PLANT JOURNAL

Rice pollen hybrid incompatibility caused by reciprocal gene loss of duplicated genes

(2010) Y. Mizuta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Armed and Dangerous

(2010)   SCIENCE

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Phylogenomic Analysis of BAC-end Sequence Libraries in Oryza (Poaceae)

(2010) Karen A. Cranston et al.   SYSTEMATIC BOTANY

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

A recent duplication revisited: phylogenetic analysis reveals an ancestral duplication highly-conserved throughout the Oryza genus and beyond

(2009) Julie Jacquemin et al.   BMC PLANT BIOLOGY

Rice Pi5-Mediated Resistance to Magnaporthe oryzae Requires the Presence of Two Coiled-Coil-Nucleotide-Binding-Leucine-Rich Repeat Genes

(2009) S.-K. Lee et al.   GENETICS

Identification of a New Rice Blast Resistance Gene, Pid3 , by Genomewide Comparison of Paired Nucleotide-Binding Site–Leucine-Rich Repeat Genes and Their Pseudogene Alleles Between the Two Sequenced Rice Genomes

(2009) Junjun Shang et al.   GENETICS

Phylogeny and biogeography of the rice tribe (Oryzeae): Evidence from combined analysis of 20 chloroplast fragments

(2009) Liang Tang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

The Functional Role of Pack-MULEs in Rice Inferred from Purifying Selection and Expression Profile

(2009) K. Hanada et al.   PLANT CELL

A Rice Gene of De Novo Origin Negatively Regulates Pathogen-Induced Defense Response

(2009) Wenfei Xiao et al.   PLoS One

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

The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages

(2009) Y. I. Wolf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

De Novo Next Generation Sequencing of Plant Genomes

(2009) Steve Rounsley et al.   Rice

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

Two Adjacent Nucleotide-Binding Site-Leucine-Rich Repeat Class Genes Are Required to Confer Pikm-Specific Rice Blast Resistance

(2008) I. Ashikawa et al.   GENETICS

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH

Database resources of the National Center for Biotechnology Information

(2008) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH

UVB sensitivity and cyclobutane pyrimidine dimer (CPD) photolyase genotypes in cultivated and wild rice species

(2008) Yutaka Iwamatsu et al.   PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES

Dynamic Evolution of Oryza Genomes Is Revealed by Comparative Genomic Analysis of a Genus-Wide Vertical Data Set

(2008) J. S.S. Ammiraju et al.   PLANT CELL

Refunctionalization of the ancient rice blast disease resistance genePitby the recruitment of a retrotransposon as a promoter

(2008) Keiko Hayashi et al.   PLANT JOURNAL