Genomic inferences of domestication events are corroborated by written records in Brassica rapa

SNP diversity within and among Brassica rapa accessions reveals no geographic differentiation

(2016) P. Tanhuanpää et al.   GENOME

Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea

(2016) Feng Cheng et al.   NATURE GENETICS

Turnip Time Travels: Age Estimates in Brassicaceae

(2016) Andreas Franzke et al.   TRENDS IN PLANT SCIENCE

Population Genomic Analysis Reveals Differential Evolutionary Histories and Patterns of Diversity across Subgenomes and Subpopulations of Brassica napus L.

(2016) Elodie Gazave et al.   Frontiers in Plant Science

Genetic divergence of turnip (Brassica rapa L. em. Metzg. subsp. rapa) inferred from simple sequence repeats in chloroplast and nuclear genomes and morphology

(2015) Yu Takahashi et al.   GENETIC RESOURCES AND CROP EVOLUTION

Computationally Efficient Composite Likelihood Statistics for Demographic Inference

(2015) Alec J. Coffman et al.   MOLECULAR BIOLOGY AND EVOLUTION

Development of a leafy Brassica rapa fixed line collection for genetic diversity and population structure analysis

(2015) Wenxing Pang et al.   MOLECULAR BREEDING

Clumpak : a program for identifying clustering modes and packaging population structure inferences across K

(2015) Naama M. Kopelman et al.   Molecular Ecology Resources

The butterfly plant arms-race escalated by gene and genome duplications

(2015) Patrick P. Edger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomics and the Contrasting Dynamics of Annual and Perennial Domestication

(2015) Brandon S. Gaut et al.   TRENDS IN GENETICS

Assessing and broadening genetic diversity of a rapeseed germplasm collection

(2015) Jinfeng Wu et al.   BREEDING SCIENCE

Diversification times among Brassica (Brassicaceae) crops suggest hybrid formation after 20 million years of divergence

(2014) T. Arias et al.   AMERICAN JOURNAL OF BOTANY

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

(2014) Y. Xie et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Sampling strategies for frequency spectrum-based population genomic inference

(2014) John D Robinson et al.   BMC EVOLUTIONARY BIOLOGY

Genome-Wide Association Study Dissects the Genetic Architecture of Seed Weight and Seed Quality in Rapeseed (Brassica napus L.)

(2014) F. Li et al.   DNA RESEARCH

fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets

(2014) Anil Raj et al.   GENETICS

Center of Origin and Centers of Diversity in an Ancient Crop, Brassica rapa (Turnip Rape)

(2014) Y. Guo et al.   JOURNAL OF HEREDITY

Polyploid Evolution of the Brassicaceae during the Cenozoic Era

(2014) Sateesh Kagale et al.   PLANT CELL

Archaeological and genetic insights into the origins of domesticated rice

(2014) B. L. Gross et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) B. Chalhoub et al.   SCIENCE

Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea

(2014) Isobel AP Parkin et al.   GENOME BIOLOGY

A Bountiful Harvest: Genomic Insights into Crop Domestication Phenotypes

(2013) Kenneth M. Olsen et al.   Annual Review of Plant Biology

Understanding rice domestication and implications for cultivar improvement

(2013) Tao Sang et al.   CURRENT OPINION IN PLANT BIOLOGY

Genomic inference accurately predicts the timing and severity of a recent bottleneck in a nonmodel insect population

(2013) Rajiv C. McCoy et al.   MOLECULAR ECOLOGY

Evolution of crop species: genetics of domestication and diversification

(2013) Rachel S. Meyer et al.   NATURE REVIEWS GENETICS

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

(2012) Pablo Cingolani et al.   FLY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Reproductive Isolation during Domestication

(2012) H. Dempewolf et al.   PLANT CELL

From forest to field: Perennial fruit crop domestication

(2011) Allison J. Miller et al.   AMERICAN JOURNAL OF BOTANY

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

The genome of the mesopolyploid crop species Brassica rapa

(2011) Xiaowu Wang et al.   NATURE GENETICS

Comparative Methods for Association Studies: A Case Study on Metabolite Variation in a Brassica rapa Core Collection

(2011) Dunia Pino Del Carpio et al.   PLoS One

Molecular evidence for a single evolutionary origin of domesticated rice

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

Origins of the amphiploid species Brassica napus L. investigated by chloroplast and nuclear molecular markers

(2010) Charlotte J Allender et al.   BMC PLANT BIOLOGY

Genetic diversity in domesticated soybean (Glycine max) and its wild progenitor (Glycine soja) for simple sequence repeat and single-nucleotide polymorphism loci

(2010) Ying-Hui Li et al.   NEW PHYTOLOGIST

Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana

(2010) M. A. Beilstein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The patterns of population differentiation in a Brassica rapa core collection

(2010) Dunia Pino Del Carpio et al.   THEORETICAL AND APPLIED GENETICS

Genetic perspectives on crop domestication

(2010) Briana L. Gross et al.   TRENDS IN PLANT SCIENCE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Paleopolyploidy in the Brassicales: Analyses of the Cleome Transcriptome Elucidate the History of Genome Duplications in Arabidopsis and Other Brassicales

(2009) Michael S. Barker et al.   Genome Biology and Evolution

The nature of selection during plant domestication

(2009) Michael D. Purugganan et al.   NATURE

Starch grain and phytolith evidence for early ninth millennium B.P. maize from the Central Balsas River Valley, Mexico

(2009) D. R. Piperno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Domestication Process and Domestication Rate in Rice: Spikelet Bases from the Lower Yangtze

(2009) D. Q Fuller et al.   SCIENCE

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics