Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations

Genetic Dissection of Seed Dormancy using Chromosome Segment Substitution Lines in Rice (Oryza sativa L.)

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Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics

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High-quality genome sequence of white lupin provides insight into soil exploration and seed quality

(2020) Bárbara Hufnagel et al.   Nature Communications

Rice GERMIN-LIKE PROTEIN 2-1 Functions in Seed Dormancy under the Control of Abscisic Acid and Gibberellic Acid Signaling Pathways

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

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Pan-Genome of Wild and Cultivated Soybeans

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Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

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The barley pan-genome reveals the hidden legacy of mutation breeding

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Multiple wheat genomes reveal global variation in modern breeding

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Characterizing the Major Structural Variant Alleles of the Human Genome

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Fast and accurate genomic analyses using genome graphs

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TIR-Learner, a New Ensemble Method for TIR Transposable Element Annotation, Provides Evidence for Abundant New Transposable Elements in the Maize Genome

(2019) Weijia Su et al.   Molecular Plant

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

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Structural variants in 3000 rice genomes

(2019) Roven Rommel Fuentes et al.   GENOME RESEARCH

OsMADS18, a membrane-bound MADS-box transcription factor, modulates plant architecture and the abscisic acid response in rice

(2019) Xiaoming Yin et al.   JOURNAL OF EXPERIMENTAL BOTANY

Copy Number Variation in Domestication

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Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement

(2019) Ning Yang et al.   NATURE GENETICS

Generic Repeat Finder: A High-Sensitivity Tool for Genome-Wide De Novo Repeat Detection

(2019) Jieming Shi et al.   PLANT PHYSIOLOGY

Extensive intraspecific gene order and gene structural variations in upland cotton cultivars

(2019) Zhaoen Yang et al.   Nature Communications

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Structural variation in the sequencing era

(2019) Steve S. Ho et al.   NATURE REVIEWS GENETICS

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

(2019) Huilong Du et al.   Nature Communications

LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons

(2019) Shujun Ou et al.   Mobile DNA

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

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

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

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Genome-wide Hi-C analysis reveals extensive hierarchical chromatin interactions in rice

(2018) Qianli Dong et al.   PLANT JOURNAL

Koshihikari: a premium short-grain rice cultivar – its expansion and breeding in Japan

(2018) Asako Kobayashi et al.   Rice

MUMmer4: A fast and versatile genome alignment system

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Novel sequences, structural variations and gene presence variations of Asian cultivated rice

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Genomic variation in 3,010 diverse accessions of Asian cultivated rice

(2018) Wensheng Wang et al.   NATURE

Variation graph toolkit improves read mapping by representing genetic variation in the reference

(2018) Erik Garrison et al.   NATURE BIOTECHNOLOGY

Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes

(2018) Silong Sun et al.   NATURE GENETICS

Identification and characterization of rice blast resistance gene Pid4 by a combination of transcriptomic profiling and genome analysis

(2018) Zhixiong Chen et al.   Journal of Genetics and Genomics

N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development, and Stress Responses

(2018) Qian Zhang et al.   Molecular Plant

Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense

(2018) Maojun Wang et al.   NATURE GENETICS

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

(2017) Sergey Koren et al.   GENOME RESEARCH

Rice Expression Database (RED): An integrated RNA-Seq-derived gene expression database for rice

(2017) Lin Xia et al.   Journal of Genetics and Genomics

Natural Variation in the Promoter of GSE5 Contributes to Grain Size Diversity in Rice

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

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

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Genomic structural variation-mediated allelic suppression causes hybrid male sterility in rice

(2017) Rongxin Shen et al.   Nature Communications

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

(2017) Huilong Du et al.   Nature Communications

funRiceGenes dataset for comprehensive understanding and application of rice functional genes

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Several wall-associated kinases participate positively and negatively in basal defense against rice blast fungus

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Mechanisms underlying structural variant formation in genomic disorders

(2016) Claudia M. B. Carvalho et al.   NATURE REVIEWS GENETICS

OsVIL1 controls flowering time in rice by suppressing OsLF under short days and by inducing Ghd7 under long days

(2016) Hee Joong Jeong et al.   PLANT CELL REPORTS

Overexpression of OsDT11, which encodes a novel cysteine-rich peptide, enhances drought tolerance and increases ABA concentration in rice

(2016) Xiaoming Li et al.   PLANT MOLECULAR BIOLOGY

Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes

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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

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

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Copy number variation at the GL7 locus contributes to grain size diversity in rice

(2015) Yuexing Wang et al.   NATURE GENETICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

The Birth of a Black Rice Gene and Its Local Spread by Introgression

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A trehalose-6-phosphate phosphatase enhances anaerobic germination tolerance in rice

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SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

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InterProScan 5: genome-scale protein function classification

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Natural variation of rice strigolactone biosynthesis is associated with the deletion of twoMAX1orthologs

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HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes

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Genome-wide copy number variations in Oryza sativa L.

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Diverse Mechanisms of Somatic Structural Variations in Human Cancer Genomes

(2013) Lixing Yang et al.   CELL

Phenotypic impact of genomic structural variation: insights from and for human disease

(2013) Joachim Weischenfeldt et al.   NATURE REVIEWS GENETICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

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

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A framework for variation discovery and genotyping using next-generation DNA sequencing data

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The Strigolactone Story

(2010) Xiaonan Xie et al.   Annual Review of Phytopathology

A Human Genome Structural Variation Sequencing Resource Reveals Insights into Mutational Mechanisms

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Variance component model to account for sample structure in genome-wide association studies

(2010) Hyun Min Kang et al.   NATURE GENETICS

MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

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The Sequence Alignment/Map format and SAMtools

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Fast and accurate short read alignment with Burrows-Wheeler transform

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Evidence-based gene predictions in plant genomes

(2009) C. Liang et al.   GENOME RESEARCH

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

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

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Principal component analysis of genetic data

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