The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding of the origin of domestic goat

The origin of domestication genes in goats

(2020) Zhuqing Zheng et al.   Science Advances

The evolutionary history of grey wolf Y chromosomes

(2019) Linnéa Smeds et al.   MOLECULAR ECOLOGY

Comparison of Y-chromosome-linked TSPY, TSPY2, and PRAMEY genes in Taurus cattle, yaks, and interspecific hybrid bulls

(2019) Gong-Wei Zhang et al.   JOURNAL OF DAIRY SCIENCE

Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus

(2018) Sofia A. Quinodoz et al.   CELL

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ancient goat genomes reveal mosaic domestication in the Fertile Crescent

(2018) Kevin G. Daly et al.   SCIENCE

Convergent genomic signatures of domestication in sheep and goats

(2018) Florian J. Alberto et al.   Nature Communications

Mitochondrial DNA variation reveals maternal origins and demographic dynamics of Ethiopian indigenous goats

(2018) Getinet Mekuriaw Tarekegn et al.   Ecology and Evolution

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

Population structure, genetic diversity and selection signatures within seven indigenous Pakistani goat populations

(2018) C. Kumar et al.   ANIMAL GENETICS

Genetic diversity and maternal lineages of south Indian goats

(2018) Ranganathan Kamalakkannan et al.   MOLECULAR BIOLOGY REPORTS

The Eurasian Steppe is an important goat propagation route: A phylogeographic analysis using mitochondrial DNA and Y-chromosome sequences of Kazakhstani goats

(2018) Risa Tabata et al.   ANIMAL SCIENCE JOURNAL

DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets

(2017) Julio Rozas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

(2017) Derek M Bickhart et al.   NATURE GENETICS

Differential distribution of Y-chromosome haplotypes in Swiss and Southern European goat breeds

(2017) Oriol Vidal et al.   Scientific Reports

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y

(2016) Marta Tomaszkiewicz et al.   GENOME RESEARCH

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

(2016) Mihaela Pertea et al.   Nature Protocols

Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes

(2016) Andrew Brantley Hall et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Paternal phylogeography and genetic diversity of East Asian goats

(2015) A. Waki et al.   ANIMAL GENETICS

Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication

(2015) Yang Dong et al.   BMC GENOMICS

Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability

(2015) Licia Colli et al.   BMC GENOMICS

Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses

(2015) Tobias Bidon et al.   Genome Biology and Evolution

A recent bottleneck of Y chromosome diversity coincides with a global change in culture

(2015) Monika Karmin et al.   GENOME RESEARCH

Y-chromosomal variation of local goat breeds of Turkey close to the domestication centre

(2015) B. Cinar Kul et al.   JOURNAL OF ANIMAL BREEDING AND GENETICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

popart: full-feature software for haplotype network construction

(2015) Jessica W. Leigh et al.   Methods in Ecology and Evolution

Y genetic variation and phenotypic diversity in health and disease

(2015) Laure K Case et al.   Biology of Sex Differences

BESST - Efficient scaffolding of large fragmented assemblies

(2014) Kristoffer Sahlin et al.   BMC BIOINFORMATICS

Copy number variations of the extensively amplified Y-linked genes, HSFY and ZNF280BY, in cattle and their association with male reproductive traits in Holstein bulls

(2014) Xiang-Peng Yue et al.   BMC GENOMICS

An update of the goat genome assembly using dense radiation hybrid maps allows detailed analysis of evolutionary rearrangements in Bovidae

(2014) Xiaoyong Du et al.   BMC GENOMICS

Sequencing the Mouse Y Chromosome Reveals Convergent Gene Acquisition and Amplification on Both Sex Chromosomes

(2014) Y.Q. Shirleen Soh et al.   CELL

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani et al.   GENOME RESEARCH

Origins and functional evolution of Y chromosomes across mammals

(2014) Diego Cortez et al.   NATURE

Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution

(2013) G. Li et al.   GENOME RESEARCH

Efficient identification of Y chromosome sequences in the human andDrosophilagenomes

(2013) Antonio Bernardo Carvalho et al.   GENOME RESEARCH

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

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Domestication Process of the Goat Revealed by an Analysis of the Nearly Complete Mitochondrial Protein-Encoding Genes

(2013) Koh Nomura et al.   PLoS One

High-resolution autosomal radiation hybrid maps of the pig genome and their contribution to the genome sequence assembly

(2012) Bertrand Servin et al.   BMC GENOMICS

Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes

(2012) Jennifer F. Hughes et al.   NATURE

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)

(2012) Yang Dong et al.   NATURE BIOTECHNOLOGY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Testis-Specific Protein Y-Encoded Copy Number Is Correlated to Its Expression and the Field Fertility of Canadian Holstein Bulls

(2012) C.K. Hamilton et al.   Sexual Development

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

ZNF280BY and ZNF280AY: autosome derived Y-chromosome gene families in Bovidae

(2011) Yang Yang et al.   BMC GENOMICS

The origin and evolution of vertebrate sex chromosomes and dosage compensation

(2011) A M Livernois et al.   HEREDITY

Increased Resolution of Y Chromosome Haplogroup T Defines Relationships among Populations of the Near East, Europe, and Africa

(2011) Fernando L. Mendez et al.   HUMAN BIOLOGY

A Large Expansion of the HSFY Gene Family in Cattle Shows Dispersion across Yq and Testis-Specific Expression

(2011) Christine K. Hamilton et al.   PLoS One

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content

(2010) Jennifer F. Hughes et al.   NATURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Molecular Cytogenetics and Comparative Mapping in Goats (Capra hircus, 2n = 60)

(2009) L. Schibler et al.   CYTOGENETIC AND GENOME RESEARCH

Fast model-based estimation of ancestry in unrelated individuals

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

Effects of heat stress on mammalian reproduction

(2009) P. J. Hansen   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Characterization and distribution of retrotransposons and simple sequence repeats in the bovine genome

(2009) D. L. Adelson 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

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Stochastic properties of generalised Yule models, with biodiversity applications

(2008) Tanja Gernhard et al.   JOURNAL OF MATHEMATICAL BIOLOGY

The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals

(2008) S. Naderi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2008) Brian J Haas et al.   GENOME BIOLOGY

Are cattle, sheep, and goats endangered species?

(2007) P. TABERLET et al.   MOLECULAR ECOLOGY