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

The long and short of doubling down: polyploidy, epigenetics, and the temporal dynamics of genome fractionation

(2018) Jonathan F Wendel et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The genome of Chenopodium quinoa

(2017) David E. Jarvis et al.   NATURE

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families

(2017) Ioanna Kalvari et al.   NUCLEIC ACIDS RESEARCH

Advances in the MYB–bHLH–WD Repeat (MBW) Pigment Regulatory Model: Addition of a WRKY Factor and Co-option of an Anthocyanin MYB for Betalain Regulation

(2017) Alan Lloyd et al.   PLANT AND CELL PHYSIOLOGY

QTL-seq approach identified genomic regions and diagnostic markers for rust and late leaf spot resistance in groundnut (Arachis hypogaea L.)

(2017) Manish K. Pandey et al.   PLANT BIOTECHNOLOGY JOURNAL

Molecular Mapping of Oil Content and Fatty Acids Using Dense Genetic Maps in Groundnut (Arachis hypogaea L.)

(2017) Yaduru Shasidhar et al.   Frontiers in Plant Science

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

(2017) Ze Peng et al.   Scientific Reports

Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules

(2016) Baptiste Mayjonade et al.   BIOTECHNIQUES

Signaling pathways of seed size control in plants

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

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

(2016) David John Bertioli et al.   NATURE GENETICS

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

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams

(2015) Henry Heberle et al.   BMC BIOINFORMATICS

First insight into divergence, representation and chromosome distribution of reverse transcriptase fragments from L1 retrotransposons in peanut and wild relative species

(2015) Sergio Sebastián Samoluk et al.   GENETICA

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

ALLMAPS: robust scaffold ordering based on multiple maps

(2015) Haibao Tang et al.   GENOME BIOLOGY

Genetic Mapping of QTLs Controlling Fatty Acids Provided Insights into the Genetic Control of Fatty Acid Synthesis Pathway in Peanut (Arachis hypogaea L.)

(2015) Ming Li Wang et al.   PLoS One

Identification of QTLs associated with oil content and mapping FAD2 genes and their relative contribution to oil quality in peanut (Arachis hypogaeaL.)

(2014) Manish K Pandey et al.   BMC GENETICS

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

(2014) Jeremy Schmutz et al.   NATURE GENETICS

Construction and Analysis of High-Density Linkage Map Using High-Throughput Sequencing Data

(2014) Dongyuan Liu et al.   PLoS One

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

(2014) B. Chalhoub et al.   SCIENCE

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations

(2013) Hiroki Takagi et al.   PLANT JOURNAL

SLAF-seq: An Efficient Method of Large-Scale De Novo SNP Discovery and Genotyping Using High-Throughput Sequencing

(2013) Xiaowen Sun et al.   PLoS One

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

Hi–C: A comprehensive technique to capture the conformation of genomes

(2012) Jon-Matthew Belton et al.   METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A beginner's guide to eukaryotic genome annotation

(2012) Mark Yandell et al.   NATURE REVIEWS GENETICS

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

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

Seed size: a priority trait in cereal crops

(2012) Markkandan Kesavan et al.   PHYSIOLOGIA PLANTARUM

Maternal control of seed size by EOD3/CYP78A6 in Arabidopsis thaliana

(2012) Wenjuan Fang et al.   PLANT JOURNAL

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

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Matita, a new retroelement from peanut: characterization and evolutionary context in the light of the Arachis A–B genome divergence

(2011) Stephan Nielen et al.   MOLECULAR GENETICS AND GENOMICS

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

The Medicago genome provides insight into the evolution of rhizobial symbioses

(2011) Nevin D. Young et al.   NATURE

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling

(2011) Reza Kalhor et al.   NATURE BIOTECHNOLOGY

Comparative analysis of peanut NBS-LRR gene clusters suggests evolutionary innovation among duplicated domains and erosion of gene microsynteny

(2011) Milind B. Ratnaparkhe et al.   NEW PHYTOLOGIST

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

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

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

How close are we to nitrogen-fixing cereals?

(2010) Myriam Charpentier et al.   CURRENT OPINION IN PLANT BIOLOGY

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Genome Annotation in Plants and Fungi: EuGene as a Model Platform

(2008) Sylvain Foissac et al.   Current Bioinformatics