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

Genetic and Evolution Analysis of Extrafloral Nectary in Cotton

(2020) Wei Hu et al.   PLANT BIOTECHNOLOGY JOURNAL

Gossypium Genomics: Trends, Scope, and Utilization for Cotton Improvement

(2020) Zuoren Yang et al.   TRENDS IN PLANT SCIENCE

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

DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning

(2019) Peng Ni et al.   BIOINFORMATICS

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

(2019) Alexey M Kozlov et al.   BIOINFORMATICS

Centromere Satellite Repeats Have Undergone Rapid Changes in Polyploid Wheat Subgenomes

(2019) Handong Su et al.   PLANT CELL

Long-range interactions between proximal and distal regulatory regions in maize

(2019) En Li et al.   Nature Communications

Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data

(2019) Qian Liu et al.   Nature Communications

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

(2019) Zhaoen Yang et al.   Nature Communications

Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells

(2019) Yanxiao Zhang et al.   NATURE GENETICS

The Impact of Centromeres on Spatial Genome Architecture

(2019) Héloïse Muller et al.   TRENDS IN GENETICS

De Novo Genome Sequence Assemblies of Gossypium raimondii and Gossypium turneri

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

Mechanismal analysis of resistance to Verticillium dahliae in upland cotton conferred by overexpression of RPL18A-6 (Ribosomal Protein L18A-6)

(2019) Yihao Zhang et al.   INDUSTRIAL CROPS AND PRODUCTS

Parallelization of MAFFT for large-scale multiple sequence alignments

(2018) Tsukasa Nakamura et al.   BIOINFORMATICS

RNA-seq analysis reveals alternative splicing under salt stress in cotton, Gossypium davidsonii

(2018) Guozhong Zhu et al.   BMC GENOMICS

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

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

N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development, and Stress Responses

(2018) Qian Zhang et al.   Molecular Plant

Transcriptional regulation of nitrogen-associated metabolism and growth

(2018) Allison Gaudinier et al.   NATURE

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

(2018) Maojun Wang et al.   NATURE GENETICS

The dark side of centromeres: types, causes and consequences of structural abnormalities implicating centromeric DNA

(2018) V. Barra et al.   Nature Communications

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

(2017) Sergey Koren et al.   GENOME RESEARCH

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Rapid proliferation and nucleolar organizer targeting centromeric retrotransposons in cotton

(2016) Jinlei Han et al.   PLANT JOURNAL

Genome-wide annotation and characterization of CLAVATA/ESR (CLE) peptide hormones of soybean (Glycine max) and common bean (Phaseolus vulgaris), and their orthologues ofArabidopsis thaliana

(2015) April H. Hastwell et al.   JOURNAL OF EXPERIMENTAL BOTANY

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

(2015) Tianzhen Zhang et al.   NATURE BIOTECHNOLOGY

The molecular basis for centromere identity and function

(2015) Kara L. McKinley et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Accurate identification of centromere locations in yeast genomes using Hi-C

(2015) N. Varoquaux et al.   NUCLEIC ACIDS RESEARCH

Structural heterogeneity and functional diversity of topologically associating domains in mammalian genomes

(2015) Xiao-Tao Wang et al.   NUCLEIC ACIDS RESEARCH

InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic

(2014) Erik L.L. Sonnhammer et al.   NUCLEIC ACIDS RESEARCH

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

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

The Cotton Centromere Contains a Ty3-gypsy-like LTR Retroelement

(2012) Song Luo et al.   PLoS One

FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads

(2012) Haibin Xu et al.   PLoS One

Cotton genetic resources. A review

(2011) Mehboob-ur-Rahman et al.   Agronomy for Sustainable Development

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

Proteomic identification of differentially expressed proteins in Gossypium thurberi inoculated with cotton Verticillium dahliae

(2011) Fu’an Zhao et al.   PLANT SCIENCE

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Major Evolutionary Transitions in Centromere Complexity

(2009) Harmit S. Malik et al.   CELL

SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap

(2008) A. D. Johnson et al.   BIOINFORMATICS

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

(2008) Brian J Haas et al.   GENOME BIOLOGY