A reference-grade genome assembly for Gossypium bickii and insights into its genome evolution and formation of pigment glands and gossypol

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

Aromatization of natural products by a specialized detoxification enzyme

(2020) Jin-Quan Huang et al.   Nature Chemical Biology

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

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

(2019) Yan Hu et al.   NATURE GENETICS

Melatonin enhances cotton immunity to Verticillium wilt via manipulating lignin and gossypol biosynthesis

(2019) Cheng Li et al.   PLANT JOURNAL

Genome wide search to identify reference genes candidates for gene expression analysis in Gossypium hirsutum

(2019) P. K. Smitha et al.   BMC PLANT BIOLOGY

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

The gland localized CGP1 controls gland pigmentation and gossypol accumulation in cotton

(2019) Wei Gao et al.   PLANT BIOTECHNOLOGY JOURNAL

Characterization of gossypol biosynthetic pathway

(2018) Xiu Tian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten

(2018) Shalima S. Nair et al.   Epigenetics & Chromatin

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data

(2018) James T. Robinson et al.   Cell Systems

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

OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs

(2018) Evgenia V Kriventseva et al.   NUCLEIC ACIDS RESEARCH

Genes regulating gland development in the cotton plant

(2018) Madhusudhana R. Janga et al.   PLANT BIOTECHNOLOGY JOURNAL

Molecular evolution of the plastid genome during diversification of the cotton genus

(2017) Zhiwen Chen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The cotton (Gossypium hirsutum ) NAC transcription factor (FSN1) as a positive regulator participates in controlling secondary cell wall biosynthesis and modification of fibers

(2017) Jie Zhang et al.   NEW PHYTOLOGIST

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

(2017) Olga Dudchenko et al.   SCIENCE

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

Genetic basis for glandular trichome formation in cotton

(2016) Dan Ma et al.   Nature Communications

Monoterpenol Oxidative Metabolism: Role in Plant Adaptation and Potential Applications

(2016) Tina Ilc et al.   Frontiers in Plant Science

A Complete and Accurate Ab Initio Repeat Finding Algorithm

(2015) Shuaibin Lian et al.   Interdisciplinary Sciences-Computational Life Sciences

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

Genome sequence of the cultivated cotton Gossypium arboreum

(2014) Fuguang Li et al.   NATURE GENETICS

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

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

(2013) Jing Yu et al.   NUCLEIC ACIDS RESEARCH

A Genetic and Metabolic Analysis Revealed that Cotton Fiber Cell Development Was Retarded by Flavonoid Naringenin

(2013) J. Tan et al.   PLANT PHYSIOLOGY

Hi–C: A comprehensive technique to capture the conformation of genomes

(2012) Jon-Matthew Belton et al.   METHODS

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

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

(2009) Likun Wang et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The MYB transcription factor GhMYB25 regulates early fibre and trichome development

(2009) Adriane Machado et al.   PLANT JOURNAL

Synteny and Collinearity in Plant Genomes

(2008) H. Tang et al.   SCIENCE

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY