Comparison of Arachis monticola with Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of Peanut

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

(2019) Xiaoping Chen et al.   Molecular Plant

Identification of genomic regions and diagnostic markers for resistance to aflatoxin contamination in peanut (Arachis hypogaea L.)

(2019) Bolun Yu et al.   BMC GENETICS

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

Epigenetic perspectives on the evolution and domestication of polyploid plant and crops

(2018) Mingquan Ding et al.   CURRENT OPINION IN PLANT BIOLOGY

Structural variation in the 3D genome

(2018) Malte Spielmann et al.   NATURE REVIEWS GENETICS

Development of a High-Density Genetic Map Based on Specific Length Amplified Fragment Sequencing and Its Application in Quantitative Trait Loci Analysis for Yield-Related Traits in Cultivated Peanut

(2018) Zhihui Wang et al.   Frontiers in Plant Science

Control of grain size in rice

(2018) Na Li et al.   Plant Reproduction

Comparative root transcriptome of wild Arachis reveals NBS-LRR genes related to nematode resistance

(2018) Ana Paula Zotta Mota et al.   BMC PLANT BIOLOGY

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

(2018) et al.   SCIENCE

Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica

(2018) Timothy Paape et al.   Nature Communications

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

(2018) Maojun Wang et al.   NATURE GENETICS

Hidden genetic variation shapes the structure of functional elements in Drosophila

(2017) Mahul Chakraborty et al.   NATURE GENETICS

Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication

(2017) Maojun Wang et al.   NATURE GENETICS

Vacuolar processing enzyme 4 contributes to maternal control of grain size in barley by executing programmed cell death in the pericarp

(2017) Volodymyr Radchuk et al.   NEW PHYTOLOGIST

Chromosomes A07 and A05 associated with stable and major QTLs for pod weight and size in cultivated peanut (Arachis hypogaea L.)

(2017) Huaiyong Luo et al.   THEORETICAL AND APPLIED GENETICS

Gene expression profiling describes the genetic regulation of Meloidogyne arenaria resistance in Arachis hypogaea and reveals a candidate gene for resistance

(2017) Josh Clevenger et al.   Scientific Reports

How diploidization turned a tetraploid into a pseudotriploid

(2016) Terezie Mandáková et al.   AMERICAN JOURNAL OF BOTANY

Signaling pathways of seed size control in plants

(2016) Na Li et al.   CURRENT OPINION IN PLANT BIOLOGY

OsSPL13 controls grain size in cultivated rice

(2016) Lizhen Si et al.   NATURE GENETICS

The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

(2016) Jinghua Yang et al.   NATURE GENETICS

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

(2016) David John Bertioli et al.   NATURE GENETICS

Mechanisms underlying structural variant formation in genomic disorders

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

Using intron position conservation for homology-based gene prediction

(2016) Jens Keilwagen et al.   NUCLEIC ACIDS RESEARCH

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

(2016) Todd M. Lowe et al.   NUCLEIC ACIDS RESEARCH

Draft genome of the peanut A-genome progenitor (Arachis duranensis) provides insights into geocarpy, oil biosynthesis, and allergens

(2016) Xiaoping Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Is post-polyploidization diploidization the key to the evolutionary success of angiosperms?

(2015) Steven Dodsworth et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Maternal control of seed size in plants

(2015) Na Li et al.   JOURNAL OF EXPERIMENTAL BOTANY

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea 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

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Identification of QTLs for Rust Resistance in the Peanut Wild Species Arachis magna and the Development of KASP Markers for Marker-Assisted Selection

(2015) Soraya C. M. Leal-Bertioli et al.   G3-Genes Genomes Genetics

Genetic Mapping of Resistance to Meloidogyne arenaria in Arachis stenosperma : A New Source of Nematode Resistance for Peanut

(2015) Soraya C. M. Leal-Bertioli et al.   G3-Genes Genomes Genetics

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Networks controlling seed size in Arabidopsis

(2015) Gregorio Orozco-Arroyo et al.   Plant Reproduction

Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing

(2015) Sean P. Gordon et al.   PLoS One

The polyploidy revolution then...and now: Stebbins revisited

(2014) D. E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

PASTEC: An Automatic Transposable Element Classification Tool

(2014) Claire Hoede et al.   PLoS One

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

(2014) et al.   SCIENCE

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

(2014) B. Chalhoub et al.   SCIENCE

Infernal 1.1: 100-fold faster RNA homology searches

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

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

The F-Box Protein OsFBK12 Targets OsSAMS1 for Degradation and Affects Pleiotropic Phenotypes, Including Leaf Senescence, in Rice

(2013) Y. Chen et al.   PLANT PHYSIOLOGY

Brassinosteroid Regulates Seed Size and Shape in Arabidopsis

(2013) W.-B. Jiang et al.   PLANT PHYSIOLOGY

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

A study of the relationships of cultivated peanut (Arachis hypogaea) and its most closely related wild species using intron sequences and microsatellite markers

(2012) Márcio C. Moretzsohn et al.   ANNALS OF BOTANY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

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

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Genetic and geographic origin of domesticated peanut as evidenced by 5S rDNA and chloroplast DNA sequences

(2012) Marina Grabiele et al.   PLANT SYSTEMATICS AND EVOLUTION

Copy Number Variation of Multiple Genes at Rhg1 Mediates Nematode Resistance in Soybean

(2012) D. E. Cook et al.   SCIENCE

Quantitative trait locus analysis and construction of consensus genetic map for foliar disease resistance based on two recombinant inbred line populations in cultivated groundnut (Arachis hypogaea L.)

(2011) V. Sujay et al.   MOLECULAR BREEDING

The Medicago genome provides insight into the evolution of rhizobial symbioses

(2011) Nevin D. Young et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades

(2011) Marc R. Friedländer et al.   NUCLEIC ACIDS RESEARCH

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Genetic relationships among seven sections of genus Arachis studied by using SSR markers

(2010) Ravi Koppolu et al.   BMC PLANT BIOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

Recombination is suppressed in an alien introgression in peanut harboring Rma, a dominant root-knot nematode resistance gene

(2010) Ervin D. Nagy et al.   MOLECULAR BREEDING

Missing heritability and strategies for finding the underlying causes of complex disease

(2010) Evan E. Eichler et al.   NATURE REVIEWS GENETICS

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

(2010) Y. Han et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell 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

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

Venturing Beyond Beans and Peas: What Can We Learn from Chamaecrista?

(2009) S. R. Singer et al.   PLANT PHYSIOLOGY

NB-LRRs work a “bait and switch” on pathogens

(2009) Sarah M. Collier et al.   TRENDS IN PLANT SCIENCE

Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea)

(2008) Luu M Cuc et al.   BMC PLANT BIOLOGY

genBlastA: Enabling BLAST to identify homologous gene sequences

(2008) R. She et al.   GENOME RESEARCH

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

Resistance in Peanut Cultivars and Breeding Lines to Three Root-Knot Nematode Species

(2008) W. B. Dong et al.   PLANT DISEASE

TheSolanum lycopersicumauxin response factor 7 (SlARF7) regulates auxin signaling during tomato fruit set and development

(2008) Maaike de Jong et al.   PLANT JOURNAL

Genomic Plasticity and the Diversity of Polyploid Plants

(2008) A. R. Leitch et al.   SCIENCE

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

(2008) Brian J Haas et al.   GENOME BIOLOGY