Dynamic turnover of centromeres drives karyotype evolution in Drosophila

The molecular characterization of fixed inversions breakpoints unveils the ancestral character of the Drosophila guanche chromosomal arrangements

(2019) Dorcas J. Orengo et al.   Scientific Reports

Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects

(2019) Charikleia Karageorgiou et al.   BMC GENOMICS

Islands of retroelements are major components of Drosophila centromeres

(2019) Ching-Ho Chang et al.   PLOS BIOLOGY

TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain

(2019) Yan Gao et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

What is behind “centromere repositioning”?

(2018) Ingo Schubert   CHROMOSOMA

Simple and Complex Centromeric Satellites inDrosophilaSibling Species

(2018) Paul B. Talbert et al.   GENETICS

The high-quality genome sequence of the oceanic island endemic species Drosophila guanche reveals signals of adaptive evolution in genes related to flight and genome stability

(2018) Eva Puerma et al.   Genome Biology and Evolution

Double insertion of transposable elements provides a substrate for the evolution of satellite DNA

(2018) Michael P. McGurk et al.   GENOME RESEARCH

Non-B-Form DNA Is Enriched at Centromeres

(2018) Sivakanthan Kasinathan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Variable Rates of Simple Satellite Gains across the Drosophila Phylogeny

(2018) Kevin H -C Wei et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transcribing Centromeres: Noncoding RNAs and Kinetochore Assembly

(2018) Paul B. Talbert et al.   TRENDS IN GENETICS

Simple and Complex Centromeric Satellites inDrosophilaSibling Species

(2018) Paul B. Talbert et al.   GENETICS

Extensive exchange of transposable elements in the Drosophila pseudoobscura group

(2018) Tom Hill et al.   Mobile DNA

De novo assembly of a young Drosophila Y chromosome using single-molecule sequencing and chromatin conformation capture

(2018) Shivani Mahajan et al.   PLOS BIOLOGY

Heterochromatin-Enriched Assemblies Reveal the Sequence and Organization of the Drosophila melanogaster Y Chromosome

(2018) Ching-Ho Chang et al.   GENETICS

3D genomic architecture reveals that neocentromeres associate with heterochromatin regions

(2018) Kohei Nishimura et al.   JOURNAL OF CELL BIOLOGY

Single-molecule sequencing resolves the detailed structure of complex satellite DNA loci inDrosophila melanogaster

(2017) Daniel E. Khost et al.   GENOME RESEARCH

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

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

(2017) Sergey Koren et al.   GENOME RESEARCH

Patterns of Genome-Wide Diversity and Population Structure in the Drosophila athabasca Species Complex

(2017) Karen M. Wong Miller et al.   MOLECULAR BIOLOGY AND EVOLUTION

A mitosis-specific and R loop–driven ATR pathway promotes faithful chromosome segregation

(2017) Lilian Kabeche et al.   SCIENCE

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

(2017) Olga Dudchenko et al.   SCIENCE

Epigenetic origin of evolutionary novel centromeres

(2017) Doron Tolomeo et al.   Scientific Reports

Centromere inactivation on a neo-Y fusion chromosome in threespine stickleback fish

(2016) Jennifer N. Cech et al.   CHROMOSOME RESEARCH

Mapping 3D genome architecture through in situ DNase Hi-C

(2016) Vijay Ramani et al.   Nature Protocols

Inbreeding drives maize centromere evolution

(2016) Kevin L. Schneider et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene expression clines reveal local adaptation and associated trade-offs at a continental scale

(2016) Damiano Porcelli et al.   Scientific Reports

Comparative Analysis of Satellite DNA in the Drosophila melanogaster Species Complex

(2016) Madhav Jagannathan et al.   G3-Genes Genomes Genetics

Neocentromeres Provide Chromosome Segregation Accuracy and Centromere Clustering to Multiple Loci along a Candida albicans Chromosome

(2016) Laura S. Burrack et al.   PLoS Genetics

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

REPdenovo: Inferring De Novo Repeat Motifs from Short Sequence Reads

(2016) Chong Chu et al.   PLoS One

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

(2015) Ryan R. Wick et al.   BIOINFORMATICS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Diversity in the organization of centromeric chromatin

(2015) Florian A Steiner et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Establishment of Centromeric Chromatin by the CENP-A Assembly Factor CAL1 Requires FACT-Mediated Transcription

(2015) Chin-Chi Chen et al.   DEVELOPMENTAL CELL

De Novo Assembly and Annotation of the Asian Tiger Mosquito (Aedes albopictus) Repeatome with dnaPipeTE from Raw Genomic Reads and Comparative Analysis with the Yellow Fever Mosquito (Aedes aegypti)

(2015) Clément Goubert et al.   Genome Biology and Evolution

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations

(2015) Julie Brind’Amour et al.   Nature Communications

The structure of an endogenous Drosophila centromere reveals the prevalence of tandemly repeated sequences able to form i-motifs

(2015) Miguel Garavís et al.   Scientific Reports

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Simple Method for Fluorescence DNA In Situ Hybridization to Squashed Chromosomes

(2015) Amanda M. Larracuente et al.   Jove-Journal of Visualized Experiments

NCBI BLAST+ integrated into Galaxy

(2015) Peter J. A. Cock et al.   GigaScience

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

De novo transcriptome assembly reveals sex-specific selection acting on evolving neo-sex chromosomes in Drosophila miranda

(2014) Vera B Kaiser et al.   BMC GENOMICS

Tetris Is a Foldback Transposon that Provided the Building Blocks for an Emerging Satellite DNA of Drosophila virilis

(2014) Guilherme B. Dias et al.   Genome Biology and Evolution

Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization

(2014) N. Bonhoure et al.   GENOME RESEARCH

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

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

Correlated variation and population differentiation in satellite DNA abundance among lines ofDrosophila melanogaster

(2014) Kevin H.-C. Wei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tree of Sex: A database of sexual systems

(2014) Tia-Lynn Ashman et al.   Scientific Data

Chromosome Engineering Allows the Efficient Isolation of Vertebrate Neocentromeres

(2013) Wei-Hao Shang et al.   DEVELOPMENTAL CELL

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

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

Neocentromeres: a place for everything and everything in its place

(2013) Kristin C. Scott et al.   TRENDS IN GENETICS

Position-Effect Variegation, Heterochromatin Formation, and Gene Silencing in Drosophila

(2013) S. C. R. Elgin et al.   Cold Spring Harbor Perspectives in Biology

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

(2013) Daniël P Melters et al.   GENOME BIOLOGY

Neocentromeres and epigenetically inherited features of centromeres

(2012) Laura S. Burrack et al.   CHROMOSOME RESEARCH

Epigenetic Inactivation and Subsequent Heterochromatinization of a Centromere Stabilize Dicentric Chromosomes

(2012) Hiroshi Sato et al.   CURRENT BIOLOGY

Chromosomal translocations and palindromic AT-rich repeats

(2012) Takema Kato et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Enrichment of HP1a on Drosophila Chromosome 4 Genes Creates an Alternate Chromatin Structure Critical for Regulation in this Heterochromatic Domain

(2012) Nicole C. Riddle et al.   PLoS Genetics

Formation of novel CENP-A domains on tandem repetitive DNA and across chromosome breakpoints on human chromosome 8q21 neocentromeres

(2011) Dan Hasson et al.   CHROMOSOMA

Centromere repositioning in mammals

(2011) M Rocchi et al.   HEREDITY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Chromosomes, Conflict, and Epigenetics: Chromosomal Speciation Revisited

(2010) Judith D. Brown et al.   Annual Review of Genomics and Human Genetics

genoPlotR: comparative gene and genome visualization in R

(2010) L. Guy et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

First Case of a Neocentromere Formation in an Otherwise Normal Chromosome 7

(2010) T. Liehr et al.   CYTOGENETIC AND GENOME RESEARCH

Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin

(2010) N. C. Riddle et al.   GENOME RESEARCH

Satellite DNA and speciation: A species specific satellite DNA of Drosophila guanchel

(2010) L. Bachmann et al.   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

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

Major Evolutionary Transitions in Centromere Complexity

(2009) Harmit S. Malik et al.   CELL

An overview of plant centromeres

(2009) Guixiang Wang et al.   Journal of Genetics and Genomics

Double-strand DNA breaks recruit the centromeric histone CENP-A

(2009) S. G. Zeitlin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Neocentromeres: New Insights into Centromere Structure, Disease Development, and Karyotype Evolution

(2008) Owen J. Marshall et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A tale of two centromeres—diversity of structure but conservation of function in plants and animals

(2008) James A. Birchler et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Chromosomal Rearrangement Inferred From Comparisons of 12 Drosophila Genomes

(2008) A. Bhutkar et al.   GENETICS

Polytene Chromosomal Maps of 11 Drosophila Species: The Order of Genomic Scaffolds Inferred From Genetic and Physical Maps

(2008) S. W. Schaeffer et al.   GENETICS

Epigenetic regulation of centromeric chromatin: old dogs, new tricks?

(2008) Robin C. Allshire et al.   NATURE REVIEWS GENETICS

Heterochromatin Integrity Affects Chromosome Reorganization After Centromere Dysfunction

(2008) K. Ishii et al.   SCIENCE

Evolutionary-new centromeres preferentially emerge within gene deserts

(2008) Mariana Lomiento et al.   GENOME BIOLOGY