CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research

Comparative genome analyses highlight transposon-mediated genome expansion and the evolutionary architecture of 3D genomic folding in cotton

(2021) Maojun Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Gossypium stocksii genome as a novel resource for cotton improvement

(2021) Corrinne E Grover et al.   G3-Genes Genomes Genetics

Cotton D genome assemblies built with long-read data unveil mechanisms of centromere evolution and stress tolerance divergence

(2021) Zhaoen Yang et al.   BMC BIOLOGY

Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases

(2021) Margaret Staton et al.   BRIEFINGS IN BIOINFORMATICS

The Gossypium anomalum genome as a resource for cotton improvement and evolutionary analysis of hybrid incompatibility

(2021) Corrinne E Grover et al.   G3-Genes Genomes Genetics

The Gossypium longicalyx Genome as a Resource for Cotton Breeding and Evolution

(2020) Corrinne E. Grover et al.   G3-Genes Genomes Genetics

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

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

(2019) Yan Hu et al.   NATURE GENETICS

Extensive intraspecific gene order and gene structural variations in upland cotton cultivars

(2019) Zhaoen Yang et al.   Nature Communications

Genome sequencing of the Australian wild diploid species Gossypium australe highlights disease resistance and delayed gland morphogenesis

(2019) Yingfan Cai et al.   PLANT BIOTECHNOLOGY JOURNAL

De Novo Genome Sequence Assemblies of Gossypium raimondii and Gossypium turneri

(2019) Joshua A. Udall et al.   G3-Genes Genomes Genetics

The Genome Sequence of Gossypioides kirkii Illustrates a Descending Dysploidy in Plants

(2019) Joshua A. Udall et al.   Frontiers in Plant Science

Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits

(2018) Xiongming Du et al.   NATURE GENETICS

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

(2018) Lisa Harper et al.   Database-The Journal of Biological Databases and Curation

Insights into the Evolution of the New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing

(2018) Corrinne E Grover et al.   Genome Biology and Evolution

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

(2018) Maojun Wang et al.   NATURE GENETICS

GenBank

(2018) Eric W Sayers et al.   NUCLEIC ACIDS RESEARCH

The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics

(2017) Laurel Cooper et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants

(2017) Pascal Schläpfer et al.   PLANT PHYSIOLOGY

New extension software modules to enhance searching and display of transcriptome data in Tripal databases

(2017) Ming Chen et al.   Database-The Journal of Biological Databases and Curation

Genetic Analysis and QTL Detection on Fiber Traits Using Two Recombinant Inbred Lines and Their Backcross Populations in Upland Cotton

(2016) Lianguang Shang et al.   G3-Genes Genomes Genetics

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

(2015) Fuguang Li 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

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp.

(2015) A. M. Hulse-Kemp et al.   G3-Genes Genomes Genetics

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Field Book: An Open-Source Application for Field Data Collection on Android

(2014) Trevor W. Rife et al.   CROP SCIENCE

Genome sequence of the cultivated cotton Gossypium arboreum

(2014) Fuguang Li et al.   NATURE GENETICS

Linkage Map Construction and Quantitative Trait Locus Analysis of Agronomic and Fiber Quality Traits in Cotton

(2014) Michael A. Gore et al.   Plant Genome

The challenge of constructing, classifying, and representing metabolic pathways

(2013) Ron Caspi et al.   FEMS MICROBIOLOGY LETTERS

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

(2013) Jing Yu et al.   NUCLEIC ACIDS RESEARCH

Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases

(2013) Lacey-Anne Sanderson et al.   Database-The Journal of Biological Databases and Curation

Insights into the Evolution of Cotton Diploids and Polyploids from Whole-Genome Re-sequencing

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

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

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

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres

(2012) Andrew H. Paterson et al.   NATURE

The draft genome of a diploid cotton Gossypium raimondii

(2012) Kunbo Wang et al.   NATURE GENETICS

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

InterPro in 2011: new developments in the family and domain prediction database

(2011) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

Tripal: a construction toolkit for online genome databases

(2011) S. P. Ficklin et al.   Database-The Journal of Biological Databases and Curation

Evolution of the Sequence Ontology terms and relationships

(2010) Christopher J. Mungall et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature

(2010) Rosemary Shrestha et al.   AoB Plants

CMap 1.01: a comparative mapping application for the Internet

(2009) K. Youens-Clark et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program

(2008) Michel Schneider et al.   Journal of Proteomics