A route to de novo domestication of wild allotetraploid rice

CRISPR-mediated accelerated domestication of African rice landraces

(2020) Elia Lacchini et al.   PLoS One

Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff

(2020) Robert VanBuren et al.   Nature Communications

Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution

(2020) Gai Huang et al.   NATURE GENETICS

A platinum standard pan-genome resource that represents the population structure of Asian rice

(2020) Yong Zhou et al.   Scientific Data

Gene and genome duplications in the evolution of chemodiversity: perspectives from studies of Lamiaceae

(2020) Benjamin R Lichman et al.   CURRENT OPINION IN PLANT BIOLOGY

Roadmap for Accelerated Domestication of an Emerging Perennial Grain Crop

(2020) Lee DeHaan et al.   TRENDS IN PLANT SCIENCE

Agrobacterium-Mediated Genetic Transformation of Wild Oryza Species Using Immature Embryos

(2020) Sae Shimizu-Sato et al.   Rice

New Food Crop Domestication in the Age of Gene Editing: Genetic, Agronomic and Cultural Change Remain Co-evolutionarily Entangled

(2020) David L. Van Tassel et al.   Frontiers in Plant Science

The Genomics of Oryza Species Provides Insights into Rice Domestication and Heterosis

(2019) Erwang Chen et al.   Annual Review of Plant Biology

Agrobacterium-Mediated Transformation of Rice: Constraints and Possible Solutions

(2019) Sulaiman Mohammed et al.   Rice Science

In vitro induction of auto-allotetraploid in a newly developed wild rice line from Oryza alta Swallen

(2019) Liusheng Zhang et al.   PLANT CELL TISSUE AND ORGAN CULTURE

Revolutions in agriculture chart a course for targeted breeding of old and new crops

(2019) Yuval Eshed et al.   SCIENCE

Genetic strategies for improving crop yields

(2019) Julia Bailey-Serres et al.   NATURE

Assembly of chromosome-scale contigs by efficiently resolving repetitive sequences with long reads

(2019) Huilong Du et al.   Nature Communications

Genetic Regulation of Shoot Architecture

(2018) Bing Wang et al.   Annual Review of Plant Biology

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

(2018) Joshua C. Stein et al.   NATURE GENETICS

Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice

(2018) Qiang Zhao et al.   NATURE GENETICS

The rice genome revolution: from an ancient grain to Green Super Rice

(2018) Rod A. Wing et al.   NATURE REVIEWS GENETICS

A defensin-like protein drives cadmium efflux and allocation in rice

(2018) Jin-Song Luo et al.   Nature Communications

Newly Identified Wild Rice Accessions Conferring High Salt Tolerance Might Use a Tissue Tolerance Mechanism in Leaf

(2018) Manas R. Prusty et al.   Frontiers in Plant Science

Shifting the limits in wheat research and breeding using a fully annotated reference genome

(2018) et al.   SCIENCE

A single transcription factor promotes both yield and immunity in rice

(2018) Jing Wang et al.   SCIENCE

Efficient C-to-T base editing in plants using a fusion of nCas9 and human APOBEC3A

(2018) Yuan Zong et al.   NATURE BIOTECHNOLOGY

Domestication of wild tomato is accelerated by genome editing

(2018) Tingdong Li et al.   NATURE BIOTECHNOLOGY

De novo domestication of wild tomato using genome editing

(2018) Agustin Zsögön et al.   NATURE BIOTECHNOLOGY

Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

(2018) Jisen Zhang et al.   NATURE GENETICS

Current Strategies of Polyploid Plant Genome Sequence Assembly

(2018) Maria Kyriakidou et al.   Frontiers in Plant Science

A walk on the wild side: Oryza species as source for rice abiotic stress tolerance

(2017) Paloma Koprovski Menguer et al.   GENETICS AND MOLECULAR BIOLOGY

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

CRISPR-GE: A Convenient Software Toolkit for CRISPR-Based Genome Editing

(2017) Xianrong Xie et al.   Molecular Plant

Construction of a Genome-Wide Mutant Library in Rice Using CRISPR/Cas9

(2017) Xiangbing Meng et al.   Molecular Plant

The evolutionary significance of polyploidy

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

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

Genome diversity of tuber-bearingSolanumuncovers complex evolutionary history and targets of domestication in the cultivated potato

(2017) Michael A. Hardigan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequencing and de novo assembly of a near complete indica rice genome

(2017) Huilong Du et al.   Nature Communications

RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants

(2016) Pingchuan Li et al.   BMC GENOMICS

iTAK: A Program for Genome-wide Prediction and Classification of Plant Transcription Factors, Transcriptional Regulators, and Protein Kinases

(2016) Yi Zheng et al.   Molecular Plant

Breeding high-yield superior quality hybrid super rice by rational design

(2016) Qian Qian et al.   National Science Review

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool

(2015) Jennifer M. Shelton et al.   BMC GENOMICS

COLD1 Confers Chilling Tolerance in Rice

(2015) Yun Ma et al.   CELL

Meeting the Global Food Demand of the Future by Engineering Crop Photosynthesis and Yield Potential

(2015) Stephen P. Long et al.   CELL

A Robust CRISPR/Cas9 System for Convenient, High-Efficiency Multiplex Genome Editing in Monocot and Dicot Plants

(2015) Xingliang Ma et al.   Molecular Plant

Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution

(2015) Fuguang Li et al.   NATURE BIOTECHNOLOGY

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

(2015) Tianzhen Zhang et al.   NATURE BIOTECHNOLOGY

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Genome-Wide Disruption of Gene Expression in Allopolyploids but Not Hybrids of Rice Subspecies

(2014) Chunming Xu et al.   MOLECULAR BIOLOGY AND EVOLUTION

The BEL1-type homeobox geneSH5induces seed shattering by enhancing abscission-zone development and inhibiting lignin biosynthesis

(2014) Jinmi Yoon et al.   PLANT JOURNAL

Grain Number, Plant Height, and Heading Date7 Is a Central Regulator of Growth, Development, and Stress Response

(2014) X. Weng et al.   PLANT PHYSIOLOGY

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

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

Days to heading 7, a major quantitative locus determining photoperiod sensitivity and regional adaptation in rice

(2014) He Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

(2014) B. Chalhoub et al.   SCIENCE

Comparative cytological and transcriptomic analysis of pollen development in autotetraploid and diploid rice

(2014) Jinwen Wu et al.   Plant Reproduction

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Natural variation in Ghd7.1 plays an important role in grain yield and adaptation in rice

(2013) Wenhao Yan et al.   CELL RESEARCH

Multilocus estimation of divergence times and ancestral effective population sizes ofOryzaspecies and implications for the rapid diversification of the genus

(2013) Xin-Hui Zou et al.   NEW PHYTOLOGIST

An-1 Encodes a Basic Helix-Loop-Helix Protein That Regulates Awn Development, Grain Size, and Grain Number in Rice

(2013) J. Luo et al.   PLANT CELL

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

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

Climate Change Impacts on Global Food Security

(2013) T. Wheeler et al.   SCIENCE

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

(2013) Jinfeng Chen et al.   Nature Communications

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

A map of rice genome variation reveals the origin of cultivated rice

(2012) Xuehui Huang et al.   NATURE

Analysis of the bread wheat genome using whole-genome shotgun sequencing

(2012) Rachel Brenchley et al.   NATURE

Reference genome sequence of the model plant Setaria

(2012) Jeffrey L Bennetzen et al.   NATURE BIOTECHNOLOGY

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

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

Improvement of bacterial blight resistance of hybrid rice in China using the Xa23 gene derived from wild rice (Oryza rufipogon)

(2011) Yong-Li Zhou et al.   CROP PROTECTION

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice

(2010) Yongqing Jiao et al.   NATURE GENETICS

OsSPL14 promotes panicle branching and higher grain productivity in rice

(2010) Kotaro Miura et al.   NATURE GENETICS

Genome-wide association studies of 14 agronomic traits in rice landraces

(2010) Xuehui Huang et al.   NATURE GENETICS

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

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

Linking differential domain functions of the GS3 protein to natural variation of grain size in rice

(2010) H. Mao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Food Security: The Challenge of Feeding 9 Billion People

(2010) H. C. J. Godfray et al.   SCIENCE

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

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

Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities

(2009) Z. Tian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Molecular Evolution of the Pi-ta Gene Resistant to Rice Blast in Wild Rice (Oryza rufipogon)

(2008) C.-L. Huang et al.   GENETICS

Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps

(2008) H. Tang et al.   GENOME RESEARCH

Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice

(2008) Weiya Xue et al.   NATURE GENETICS

Analysis of 142 genes resolves the rapid diversification of the rice genus

(2008) Xin-Hui Zou et al.   GENOME BIOLOGY

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY