Parallel and Intertwining Threads of Domestication in Allopolyploid Cotton

Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution

(2020) Gai Huang et al.   NATURE GENETICS

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

(2020) Z. Jeffrey Chen et al.   NATURE GENETICS

Genomic analyses reveal the genetic basis of early maturity and identification of loci and candidate genes in upland cotton ( Gossypium hirsutum L.)

(2020) Libei Li et al.   PLANT BIOTECHNOLOGY JOURNAL

Genomic Insight into Differentiation and Selection Sweeps in the Improvement of Upland Cotton

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Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton

(2019) Yan Hu et al.   NATURE GENETICS

Population genomics reveals a fine‐scale recombination landscape for genetic improvement of cotton

(2019) Chao Shen et al.   PLANT JOURNAL

Evolutionary Insights into the Nature of Plant Domestication

(2019) Michael D. Purugganan   CURRENT BIOLOGY

Unraveling cis and trans regulatory evolution during cotton domestication

(2019) Ying Bao et al.   Nature Communications

Genomic Evidence for Complex Domestication History of the Cultivated Tomato in Latin America

(2019) Hamid Razifard et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetic Analysis of the Transition from Wild to Domesticated Cotton (Gossypium hirsutum L.)

(2019) Corrinne E. Grover et al.   G3-Genes Genomes Genetics

Comparison of village dog and wolf genomes highlights the role of the neural crest in dog domestication

(2018) Amanda L. Pendleton et al.   BMC BIOLOGY

Resequencing a core collection of upland cotton identifies genomic variation and loci influencing fiber quality and yield

(2018) Zhiying Ma et al.   NATURE GENETICS

Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice

(2018) Qiang Zhao et al.   NATURE GENETICS

TissueEnrich: Tissue-specific gene enrichment analysis

(2018) Ashish Jain et al.   BIOINFORMATICS

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

(2018) Maojun Wang et al.   NATURE GENETICS

Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits

(2017) Lei Fang et al.   NATURE GENETICS

Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication

(2017) Maojun Wang et al.   NATURE GENETICS

Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids

(2017) Christopher A. Saski et al.   Scientific Reports

SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data

(2017) Yuxin Chen et al.   GigaScience

Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia

(2016) Kevin J. Galinsky et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

(2016) Massimo Iorizzo et al.   NATURE GENETICS

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton

(2016) Justin T. Page et al.   PLoS Genetics

Early pre-Hispanic use of indigo blue in Peru

(2016) J. C. Splitstoser et al.   Science Advances

Evolution Is an Experiment: Assessing Parallelism in Crop Domestication and Experimental Evolution

(2015) Brandon S. Gaut   MOLECULAR BIOLOGY AND EVOLUTION

Re-evaluating the phylogeny of allopolyploid Gossypium L.

(2015) Corrinne E. Grover et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution

(2015) Fuguang Li et al.   NATURE BIOTECHNOLOGY

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

(2015) Zhengkui Zhou 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

ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap

(2015) Tauno Metsalu et al.   NUCLEIC ACIDS RESEARCH

Genomics of crop wild relatives: expanding the gene pool for crop improvement

(2015) Marta Brozynska et al.   PLANT BIOTECHNOLOGY JOURNAL

Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites

(2015) Xia Liu et al.   Scientific Reports

The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres

(2015) Daojun Yuan et al.   Scientific Reports

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Molecular confirmation of species status for the allopolyploid cotton species, Gossypium ekmanianum Wittmack

(2014) C. E. Grover et al.   GENETIC RESOURCES AND CROP EVOLUTION

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

(2014) Jeremy Schmutz et al.   NATURE GENETICS

Distribution and Differentiation of Wild, Feral, and Cultivated Populations of Perennial Upland Cotton (Gossypium hirsutum L.) in Mesoamerica and the Caribbean

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Molecular characterization of the Gossypium Diversity Reference Set of the US National Cotton Germplasm Collection

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A Bountiful Harvest: Genomic Insights into Crop Domestication Phenotypes

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

A comprehensive meta QTL analysis for fiber quality, yield, yield related and morphological traits, drought tolerance, and disease resistance in tetraploid cotton

(2013) Joseph I Said et al.   BMC GENOMICS

Evolution of crop species: genetics of domestication and diversification

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

CottonGen: a genomics, genetics and breeding database for cotton research

(2013) Jing Yu et al.   NUCLEIC ACIDS RESEARCH

Genetic diversity and population structure in the US Upland cotton (Gossypium hirsutum L.)

(2013) Priyanka Tyagi et al.   THEORETICAL AND APPLIED GENETICS

PolyCat: A Resource for Genome Categorization of Sequencing Reads From Allopolyploid Organisms

(2013) Justin T. Page et al.   G3-Genes Genomes Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

(2012) Pablo Cingolani et al.   FLY

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

(2012) Xuehui Huang et al.   NATURE

Comparative population genomics of maize domestication and improvement

(2012) Matthew B Hufford et al.   NATURE GENETICS

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

(2012) Cole Trapnell et al.   Nature Protocols

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs

(2011) H. E. L. Lischer et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Recent long-distance transgene flow into wild populations conforms to historical patterns of gene flow in cotton (Gossypium hirsutum) at its centre of origin

(2011) A. WEGIER et al.   MOLECULAR ECOLOGY

STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method

(2011) Dent A. Earl et al.   Conservation Genetics Resources

Cotton domestication: dramatic changes in a single cell

(2010) Briana L Gross et al.   BMC BIOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

Genome-wide association studies of 14 agronomic traits in rice landraces

(2010) Xuehui Huang et al.   NATURE GENETICS

Genetic perspectives on crop domestication

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

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

Inferring weak population structure with the assistance of sample group information

(2009) MELISSA J. HUBISZ et al.   Molecular Ecology Resources