The genomic basis of geographic differentiation and fiber improvement in cultivated cotton

Parallel and Intertwining Threads of Domestication in Allopolyploid Cotton

(2021) Daojun Yuan et al.   Advanced Science

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

Massive haplotypes underlie ecotypic differentiation in sunflowers

(2020) Marco Todesco et al.   NATURE

Introgression Leads to Genomic Divergence and Responsible for Important Traits in Upland Cotton

(2020) Shoupu He et al.   Frontiers in Plant Science

Extensive haplotypes are associated with population differentiation and environmental adaptability in Upland cotton (Gossypium hirsutum)

(2020) Panhong Dai et al.   THEORETICAL AND APPLIED GENETICS

Alien genomic introgressions enhanced fiber strength in upland cotton (Gossypium hirsutum L.)

(2020) Liyuan Wang et al.   INDUSTRIAL CROPS AND PRODUCTS

Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome

(2019) Fei He et al.   NATURE GENETICS

Genebank genomics bridges the gap between the conservation of crop diversity and plant breeding

(2019) Martin Mascher et al.   NATURE GENETICS

A comprehensive genome variation map of melon identifies multiple domestication events and loci influencing agronomic traits

(2019) Guangwei Zhao et al.   NATURE GENETICS

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

(2018) Zhiying Ma et al.   NATURE GENETICS

Eco-Evolutionary Genomics of Chromosomal Inversions

(2018) Maren Wellenreuther et al.   TRENDS IN ECOLOGY & EVOLUTION

Genomic variation in 3,010 diverse accessions of Asian cultivated rice

(2018) Wensheng Wang et al.   NATURE

Whole genome sequencing of a MAGIC population identified genomic loci and candidate genes for major fiber quality traits in upland cotton (Gossypium hirsutum L.)

(2018) Gregory N. Thyssen et al.   THEORETICAL AND APPLIED GENETICS

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions

(2017) P R Berg et al.   HEREDITY

WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas

(2017) Stephen E. Fick et al.   INTERNATIONAL JOURNAL OF CLIMATOLOGY

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

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Young inversion with multiple linked QTLs under selection in a hybrid zone

(2017) Cheng-Ruei Lee et al.   Nature Ecology & Evolution

Two adjacent inversions maintain genomic differentiation between migratory and stationary ecotypes of Atlantic cod

(2016) Tina Graceline Kirubakaran et al.   MOLECULAR ECOLOGY

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

(2015) Zhengkui Zhou et al.   NATURE BIOTECHNOLOGY

A supergene determines highly divergent male reproductive morphs in the ruff

(2015) Clemens Küpper et al.   NATURE GENETICS

A Y-like social chromosome causes alternative colony organization in fire ants

(2013) John Wang et al.   NATURE

A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica)

(2013) Guanqing Jia et al.   NATURE GENETICS

Megabase-Scale Inversion Polymorphism in the Wild Ancestor of Maize

(2012) Zhou Fang et al.   GENETICS

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Ecological Genomics of Anopheles gambiae Along a Latitudinal Cline: A Population-Resequencing Approach

(2011) C. Cheng et al.   GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Variance component model to account for sample structure in genome-wide association studies

(2010) Hyun Min Kang et al.   NATURE GENETICS

A Widespread Chromosomal Inversion Polymorphism Contributes to a Major Life-History Transition, Local Adaptation, and Reproductive Isolation

(2010) David B. Lowry et al.   PLOS BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Revisiting the Impact of Inversions in Evolution: From Population Genetic Markers to Drivers of Adaptive Shifts and Speciation?

(2008) Ary A. Hoffmann et al.   Annual Review of Ecology Evolution and Systematics