Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement

5Gs for crop genetic improvement

(2020) Rajeev K Varshney et al.   CURRENT OPINION IN PLANT BIOLOGY

Improved genome assembly provides new insights into genome evolution in a desert poplar ( Populus euphratica )

(2020) Zhiyang Zhang et al.   Molecular Ecology Resources

Trait associations in the pangenome of pigeon pea ( Cajanus cajan )

(2020) Junliang Zhao et al.   PLANT BIOTECHNOLOGY JOURNAL

Reply to: Evaluating two different models of peanut’s origin

(2020) Weijian Zhuang et al.   NATURE GENETICS

Evaluating two different models of peanut’s origin

(2020) David J. Bertioli et al.   NATURE GENETICS

Cotton Duplicated Genes Produced by Polyploidy Show Significantly Elevated and Unbalanced Evolutionary Rates, Overwhelmingly Perturbing Gene Tree Topology

(2020) Fanbo Meng et al.   Frontiers in Genetics

High resolution mapping of restoration of fertility (Rf) by combining large population and high density genetic map in pigeonpea [Cajanus cajan (L.) Millsp]

(2020) Rachit K. Saxena et al.   BMC GENOMICS

Sequencing of cultivated peanut, Arachis hypogaea, yields insights into genome evolution and oil improvement

(2019) Xiaoping Chen et al.   Molecular Plant

The genome sequence of segmental allotetraploid peanut Arachis hypogaea

(2019) David J. Bertioli et al.   NATURE GENETICS

The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication

(2019) Weijian Zhuang et al.   NATURE GENETICS

How can a high-quality genome assembly help plant breeders?

(2019) Juliana Benevenuto et al.   GigaScience

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

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Construction and comparison of three reference‐quality genome assemblies for soybean

(2019) Babu Valliyodan et al.   PLANT JOURNAL

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

The Rosa genome provides new insights into the domestication of modern roses

(2018) Olivier Raymond et al.   NATURE GENETICS

D-GENIES: dot plot large genomes in an interactive, efficient and simple way

(2018) Floréal Cabanettes et al.   PeerJ

A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome

(2018) Robert VanBuren et al.   GigaScience

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

(2018) Maojun Wang et al.   NATURE GENETICS

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data

(2017) Wen-Biao Jiao et al.   GENOME RESEARCH

An Overlooked Paleotetraploidization in Cucurbitaceae

(2017) Jinpeng Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Whole-genome resequencing of 292 pigeonpea accessions identifies genomic regions associated with domestication and agronomic traits

(2017) Rajeev K Varshney et al.   NATURE GENETICS

Hierarchically Aligning 10 Legume Genomes Establishes a Family-Level Genomics Platform

(2017) Jinpeng Wang et al.   PLANT PHYSIOLOGY

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

(2017) Olga Dudchenko et al.   SCIENCE

Transcriptome profiles reveal gene regulation of peanut (Arachis hypogaea L.) nodulation

(2017) Ze Peng et al.   Scientific Reports

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

(2016) Pingchuan Li et al.   BMC GENOMICS

The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut

(2016) David John Bertioli et al.   NATURE GENETICS

Iterative Usage of Fixed and Random Effect Models for Powerful and Efficient Genome-Wide Association Studies

(2016) Xiaolei Liu et al.   PLoS Genetics

Comprehensive Comparative Genomic and Transcriptomic Analyses of the Legume Genes Controlling the Nodulation Process

(2016) Zhenzhen Qiao et al.   Frontiers in Plant Science

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

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

Draft genome sequence of subterranean clover, a reference for genus Trifolium

(2016) Hideki Hirakawa et al.   Scientific Reports

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

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

De Novo Plant Genome Assembly Based on Chromatin Interactions: A Case Study of Arabidopsis thaliana

(2015) Ting Xie 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

Comparative genomic de-convolution of the cotton genome revealed a decaploid ancestor and widespread chromosomal fractionation

(2015) Xiyin Wang et al.   NEW PHYTOLOGIST

Draft genome sequence of adzuki bean, Vigna angularis

(2015) Yang Jae Kang et al.   Scientific Reports

Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement

(2015) Jose J. De Vega et al.   Scientific Reports

Prioritization of candidate genes in “QTL-hotspot” region for drought tolerance in chickpea (Cicer arietinum L.)

(2015) Sandip M Kale et al.   Scientific Reports

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

The Contributions of Transposable Elements to the Structure, Function, and Evolution of Plant Genomes

(2014) Jeffrey L. Bennetzen et al.   Annual Review of Plant Biology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

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

(2014) B. Chalhoub et al.   SCIENCE

Genome sequence of mungbean and insights into evolution within Vigna species

(2014) Yang Jae Kang et al.   Nature Communications

Genetic anchoring of whole-genome shotgun assemblies

(2014) Martin Mascher et al.   Frontiers in Genetics

Infernal 1.1: 100-fold faster RNA homology searches

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

Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

(2013) Mira V. Han et al.   MOLECULAR BIOLOGY AND EVOLUTION

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

(2013) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Genetic dissection of drought tolerance in chickpea (Cicer arietinum L.)

(2013) Rajeev K. Varshney et al.   THEORETICAL AND APPLIED GENETICS

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

(2012) Pablo Cingolani et al.   FLY

A genome triplication associated with early diversification of the core eudicots

(2012) Yuannian Jiao et al.   GENOME BIOLOGY

The Medicago genome provides insight into the evolution of rhizobial symbioses

(2011) Nevin D. Young et al.   NATURE

Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers

(2011) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

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

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

(2010) A. McKenna et al.   GENOME RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Evolutionary and Expression Signatures of Pseudogenes in Arabidopsis and Rice

(2009) C. Zou et al.   PLANT PHYSIOLOGY

Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses

(2009) Xiyin Wang et al.   GENOME BIOLOGY

Genome Structure of the Legume, Lotus japonicus

(2008) S. Sato et al.   DNA RESEARCH

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

(2008) Brian J Haas et al.   GENOME BIOLOGY