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

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

Tetrasomic Recombination Is Surprisingly Frequent in Allotetraploid Arachis

(2015) Soraya Leal-Bertioli et al.   GENETICS

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

Tetrasomic Recombination Is Surprisingly Frequent in Allotetraploid Arachis

(2015) Soraya Leal-Bertioli et al.   GENETICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Construction of a SNP-based genetic linkage map in cultivated peanut based on large scale marker development using next-generation double-digest restriction-site-associated DNA sequencing (ddRADseq)

(2014) Xiaojing Zhou et al.   BMC GENOMICS

Genome sizes in diploid and allopolyploid Arachis L. species (section Arachis)

(2014) Sergio Sebastián Samoluk et al.   GENETIC RESOURCES AND CROP EVOLUTION

Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements

(2014) Rajiv C. McCoy et al.   PLoS One

The repetitive component of the A genome of peanut (Arachis hypogaea) and its role in remodelling intergenic sequence space since its evolutionary divergence from the B genome

(2013) David J. Bertioli et al.   ANNALS OF BOTANY

Integrated Consensus Map of Cultivated Peanut and Wild Relatives Reveals Structures of the A and B Genomes of Arachis and Divergence of the Legume Genomes

(2013) K. Shirasawa et al.   DNA RESEARCH

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

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

(2013) M. S. Campbell et al.   PLANT PHYSIOLOGY

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

COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly

(2012) B. Liu et al.   BIOINFORMATICS

A high-density genetic map of Arachis duranensis, a diploid ancestor of cultivated peanut

(2012) Ervin D Nagy et al.   BMC GENOMICS

In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut

(2012) Kenta Shirasawa et al.   BMC PLANT BIOLOGY

Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential

(2012) Gengyun Zhang et al.   NATURE BIOTECHNOLOGY

Genome-wide genetic changes during modern breeding of maize

(2012) Yinping Jiao et al.   NATURE GENETICS

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

An International Reference Consensus Genetic Map with 897 Marker Loci Based on 11 Mapping Populations for Tetraploid Groundnut (Arachis hypogaea L.)

(2012) Bhimana Gautami et al.   PLoS One

‘Leveling’ the playing field for analyses of single-base resolution DNA methylomes

(2012) Matthew D. Schultz et al.   TRENDS IN GENETICS

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

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

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

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

An overview of peanut and its wild relatives

(2011) David J. Bertioli et al.   Plant Genetic Resources-Characterization and Utilization

An integrated genetic linkage map of cultivated peanut (Arachis hypogaea L.) constructed from two RIL populations

(2011) Hongde Qin et al.   THEORETICAL AND APPLIED GENETICS

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

A SSR-based composite genetic linkage map for the cultivated peanut (Arachis hypogaea L.) genome

(2010) Yanbin Hong et al.   BMC PLANT BIOLOGY

FIDEL—a retrovirus-like retrotransposon and its distinct evolutionary histories in the A- and B-genome components of cultivated peanut

(2010) Stephan Nielen et al.   CHROMOSOME 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

Conservation and divergence of methylation patterning in plants and animals

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

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

Species relationships among the wild B genome of Arachis species (section Arachis) based on FISH mapping of rDNA loci and heterochromatin detection: a new proposal for genome arrangement

(2010) Germán Robledo et al.   THEORETICAL AND APPLIED GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Genetic mapping of wild introgressions into cultivated peanut: a way toward enlarging the genetic basis of a recent allotetraploid

(2009) Daniel Foncéka et al.   BMC PLANT BIOLOGY

A linkage map for the B-genome of Arachis (Fabaceae) and its synteny to the A-genome

(2009) Márcio C Moretzsohn et al.   BMC PLANT BIOLOGY

Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

(2009) Z. Tian et al.   GENOME RESEARCH

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

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

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

Monte Verde: Seaweed, Food, Medicine, and the Peopling of South America

(2008) T. D. Dillehay et al.   SCIENCE