Genome Re-Sequencing of Semi-Wild Soybean Reveals a Complex Soja Population Structure and Deep Introgression

Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing

(2013) Ying-hui Li et al.   BMC GENOMICS

Genetic diversity and gene flow dynamics revealed in the rare mixed populations of wild soybean (Glycine soja) and semi-wild type (Glycine gracilis) in China

(2013) Ke-Jing Wang et al.   GENETIC RESOURCES AND CROP EVOLUTION

The genomic signature of dog domestication reveals adaptation to a starch-rich diet

(2013) Erik Axelsson et al.   NATURE

Diversity and population structure of black soybean landraces originating from Tanba and neighboring regions

(2012) Tomoko Hirota et al.   BREEDING SCIENCE

A map of rice genome variation reveals the origin of cultivated rice

(2012) Xuehui Huang et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Database resources of the National Center for Biotechnology Information

(2012)   NUCLEIC ACIDS RESEARCH

Toward almost closed genomes with GapFiller

(2012) Marten Boetzer et al.   GENOME BIOLOGY

Fine-Scale Phylogenetic Structure and Major Events in the History of the Current Wild Soybean (Glycine soja) and Taxonomic Assignment of Semi-Wild Type (Glycine gracilis Skvortz.) within the Chinese Subgenus Soja

(2011) Ke-Jing Wang et al.   JOURNAL OF HEREDITY

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

Identification of single nucleotide polymorphisms and haplotypes associated with yield and yield components in soybean (Glycine max) landraces across multiple environments

(2011) Derong Hao et al.   THEORETICAL AND APPLIED GENETICS

Natural introgression from cultivated soybean (Glycine max) into wild soybean (Glycine soja) with the implications for origin of populations of semi-wild type and for biosafety of wild species in China

(2010) Ke-Jing Wang et al.   GENETIC RESOURCES AND CROP EVOLUTION

Genetic Analysis of Genes Controlling Natural Variation of Seed Coat and Flower Colors in Soybean

(2010) Kiwoung Yang et al.   JOURNAL OF HEREDITY

The origin and fate of morphological intermediates between wild and cultivated soybeans in their natural habitats in Japan

(2010) Y. KURODA et al.   MOLECULAR ECOLOGY

Whole-genome resequencing reveals loci under selection during chicken domestication

(2010) Carl-Johan Rubin et al.   NATURE

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection

(2010) Hon-Ming Lam et al.   NATURE GENETICS

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

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

Interspecific gene flow and the origin of semi-wild soybean revealed by capturing the natural occurrence of introgression between wild and cultivated soybean populations

(2010) K-J. Wang et al.   PLANT BREEDING

Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome

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

Detection and correction of false segmental duplications caused by genome mis-assembly

(2010) David R Kelley et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) R. Li et al.   GENOME RESEARCH

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

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

(2009) Ken Chen et al.   NATURE METHODS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China

(2008) Yinghui Li et al.   THEORETICAL AND APPLIED GENETICS