Assembly and annotation of a draft genome sequence for Glycine latifolia , a perennial wild relative of soybean

Accessions of Perennial Glycine Species With Resistance to Multiple Types of Soybean Cyst Nematode (Heterodera glycines)

(2017) L. Wen et al.   PLANT DISEASE

Characterizing the allopolyploid species among the wild relatives of soybean: Utility of reduced representation genotyping methodologies

(2017) Sue Sherman-Broyles et al.   Journal of Systematics and Evolution

Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce

(2017) Sebastian Reyes-Chin-Wo et al.   Nature Communications

Distinct Patterns of Gene Gain and Loss: Diverse Evolutionary Modes of NBS-Encoding Genes in Three Solanaceae Crop Species

(2017) Lan-Hua Qian et al.   G3-Genes Genomes Genetics

The Diversification of PlantNBS-LRRDefense Genes Directs the Evolution of MicroRNAs That Target Them

(2016) Yu Zhang et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2016) David John Bertioli et al.   NATURE GENETICS

A hybrid approach for de novo human genome sequence assembly and phasing

(2016) Yulia Mostovoy et al.   NATURE METHODS

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

CDD/SPARCLE: functional classification of proteins via subfamily domain architectures

(2016) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Draft genome assembly and annotation of Glycyrrhiza uralensis , a medicinal legume

(2016) Keiichi Mochida et al.   PLANT JOURNAL

Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics’ GemCode Sequencing Data

(2016) Lauren Coombe et al.   PLoS One

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.

(2015) Katharina J. Hoff et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Identification and distribution of the NBS-LRR gene family in the Cassava genome

(2015) Roberto Lozano et al.   BMC GENOMICS

Satellite DNA in Plants: More than Just Rubbish

(2015) Manuel A. Garrido-Ramos   CYTOGENETIC AND GENOME RESEARCH

CNL Disease Resistance Genes in Soybean and Their Evolutionary Divergence

(2015) Madhav P. Nepal et al.   Evolutionary Bioinformatics

Uncovering the dynamic evolution of nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes in Brassicaceae

(2015) Yan-Mei Zhang et al.   Journal of Integrative Plant Biology

HMMER web server: 2015 update

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

TheSolanum commersoniiGenome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives

(2015) Riccardo Aversano et al.   PLANT CELL

Evolutionary Patterns and Coevolutionary Consequences ofMIRNAGenes and MicroRNA Targets Triggered by Multiple Mechanisms of Genomic Duplications in Soybean

(2015) Meixia Zhao et al.   PLANT CELL

Intersubgeneric hybridization between Glycine max and G. tomentella: production of F1, amphidiploid, BC1, BC2, BC3, and fertile soybean plants

(2015) R. J. Singh et al.   THEORETICAL AND APPLIED GENETICS

Understanding crop genetic diversity under modern plant breeding

(2015) Yong-Bi Fu   THEORETICAL AND APPLIED GENETICS

Targeted mutagenesis in soybean using the CRISPR-Cas9 system

(2015) Xianjun Sun et al.   Scientific Reports

ALLMAPS: robust scaffold ordering based on multiple maps

(2015) Haibao Tang et al.   GENOME BIOLOGY

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

The wild side of a major crop: Soybean's perennial cousins from Down Under

(2014) Sue Sherman-Broyles et al.   AMERICAN JOURNAL OF BOTANY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Legume Crops Phylogeny and Genetic Diversity for Science and Breeding

(2014) Petr Smýkal et al.   CRITICAL REVIEWS IN PLANT SCIENCES

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

(2014) Ying-hui Li et al.   NATURE BIOTECHNOLOGY

A reference genome for common bean and genome-wide analysis of dual domestications

(2014) Jeremy Schmutz et al.   NATURE GENETICS

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Methodology for creating alloplasmic soybean lines by usingGlycine tomentellaas a maternal parent

(2014) R. J. Singh et al.   PLANT BREEDING

Long-Term Evolution of Nucleotide-Binding Site-Leucine-Rich Repeat Genes: Understanding Gained from and beyond the Legume Family

(2014) Zhu-Qing Shao et al.   PLANT PHYSIOLOGY

Comparative Mapping of the Wild Perennial Glycine latifolia and Soybean (G. max) Reveals Extensive Chromosome Rearrangements in the Genus Glycine

(2014) Sungyul Chang et al.   PLoS One

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

(2014) W. Xiong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fine mapping of the Asian soybean rust resistance gene Rpp2 from soybean PI 230970

(2014) Neil Yu et al.   THEORETICAL AND APPLIED GENETICS

Deep Evolutionary Comparison of Gene Expression Identifies Parallel Recruitment of Trans-Factors in Two Independent Origins of C4 Photosynthesis

(2014) Sylvain Aubry et al.   PLoS Genetics

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

(2013) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

The CentO satellite confers translational and rotational phasing on cenH3 nucleosomes in rice centromeres

(2013) T. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of high-quality single-nucleotide polymorphisms in Glycine latifolia using a heterologous reference genome sequence

(2013) Sungyul Chang et al.   THEORETICAL AND APPLIED GENETICS

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

(2013) Daniël P Melters et al.   GENOME BIOLOGY

REAPR: a universal tool for genome assembly evaluation

(2013) Martin Hunt et al.   GENOME BIOLOGY

Genome-wide mapping of NBS-LRR genes and their association with disease resistance in soybean

(2012) Yang Kang et al.   BMC PLANT BIOLOGY

A High Resolution Genetic Map Anchoring Scaffolds of the Sequenced Watermelon Genome

(2012) Yi Ren et al.   PLoS One

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

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

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

SoyTEdb: a comprehensive database of transposable elements in the soybean genome

(2010) Jianchang Du et al.   BMC GENOMICS

Functional centromeres in soybean include two distinct tandem repeats and a retrotransposon

(2010) Ahmet L. Tek et al.   CHROMOSOME RESEARCH

Erratum: Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Comparison of Global, Gene-Specific, and Relaxed Clock Methods in a Comparative Genomics Framework: Dating the Polyploid History of Soybean (Glycine max)

(2010) Ashley N. Egan et al.   SYSTEMATIC BIOLOGY

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Molecular and Chromosomal Evidence for Allopolyploidy in Soybean

(2009) N. Gill et al.   PLANT PHYSIOLOGY

Three Sequenced Legume Genomes and Many Crop Species: Rich Opportunities for Translational Genomics

(2009) S. B. Cannon et al.   PLANT PHYSIOLOGY

Structure-based discovery and description of plant and animal Helitrons

(2009) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs

(2009) W. Muchero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps

(2008) H. Tang et al.   GENOME RESEARCH

Fractionation of Synteny in a Genomic Region Containing Tandemly Duplicated Genes across Glycine max, Medicago truncatula, and Arabidopsis thaliana

(2008) J. A. Schlueter et al.   JOURNAL OF HEREDITY

Plant Receptor-Like Serine Threonine Kinases: Roles in Signaling and Plant Defense

(2008) Ahmed J. Afzal et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Differential Accumulation of Retroelements and Diversification of NB-LRR Disease Resistance Genes in Duplicated Regions following Polyploidy in the Ancestor of Soybean

(2008) R. W. Innes et al.   PLANT PHYSIOLOGY

Identification of an Apoplastic Protein Involved in the Initial Phase of Salt Stress Response in Rice Root by Two-Dimensional Electrophoresis

(2008) L. Zhang et al.   PLANT PHYSIOLOGY

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

(2008) Brian J Haas et al.   GENOME BIOLOGY