Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza
Published 2018 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza
Authors
Keywords
-
Journal
NATURE GENETICS
Volume 50, Issue 2, Pages 285-296
Publisher
Springer Nature
Online
2018-01-17
DOI
10.1038/s41588-018-0040-0
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- 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
Find the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
SearchBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started