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References from A near-complete quail genome identifies heterochromatin expansion and chromosome architecture remodeling. Local targets link to admitted publications; unresolved targets remain external evidence.
Remarkably High Repeat Content in the Genomes of Sparrows: The Importance of Genome Assembly Completeness for Transposable Element Discovery
10.1093/gbe/evae067 · 2024 · External reference
Comparative genomics reveals insights into avian genome evolution and adaptation
10.1126/science.1251385 · 2014 · External reference
Evolution of bird genomes—a transposon’s-eye view
10.1111/nyas.13295 · 2017 · External reference
Introducing the Bird Chromosome Database: An Overview of Cytogenetic Studies in Birds
10.1159/000507768 · 2020 · External reference
MicroFinder: conserved gene-set mapping and assembly ordering for manual curation of bird dot microchromosomes
10.1093/gigascience/giag036 · 2026 · External reference
Unresolved reference
External reference
Evolutionary analysis of a complete chicken genome
2023 · External reference
Transposable elements shape the landscape of heterozygous structural variation in a bird genome
10.24272/j.issn.2095-8137.2024.237 · 2025 · External reference
Evolution and expression patterns of the neo-sex chromosomes of the crested ibis
10.1038/s41467-024-46052-x · 2024 · External reference
The evolutionary implications of chromosome banding pattern homologies in the bird order Galliformes
2008 · External reference
Further Resolution of the Quail Karyotype and Characterization of Microchromosomes by Counterstain-Enhanced Fluorescence
10.1093/oxfordjournals.jhered.a110815 · 1989 · External reference
Chromosome-level genome assembly and methylome profile yield insights for the conservation of endangered loggerhead sea turtles
10.1093/gigascience/giaf054 · 2025 · External reference
Comparative genomics illuminates karyotype and sex chromosome evolution of sharks
2024 · External reference
Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization
10.1101/gr.276840.122 · 2023 · External reference
Stable genome structures in living fossil fishes
2026 · External reference
Origin and evolution of avian microchromosomes
10.1159/000063018 · 2002 · External reference
Recurrent chromosome reshuffling and the evolution of neo-sex chromosomes in parrots
10.1038/s41467-022-28585-1 · 2022 · External reference
Three amphioxus reference genomes reveal gene and chromosome evolution of chordates
2023 · External reference
Microchromosomes are building blocks of bird, reptile, and mammal chromosomes
10.1073/pnas.2112494118 · 2021 · External reference
Evolution of chromosomes and nuclear architectures of amniotes
10.1038/s41467-025-67427-8 · 2025 · External reference
The Centromere: Chromatin Foundation for the Kinetochore Machinery
10.1016/j.devcel.2014.08.016 · 2014 · External reference
Highly repeated DNA sequences in birds: The structure and evolution of an abundant, tandemly repeated 190-bp DNA fragment in parrots
10.1016/s0888-7543(05)80242-3 · 1992 · External reference
Transcription on lampbrush chromosomes of a centromerically localized highly repeated DNA in pigeon (Columba) relates to sequence arrangement
10.1007/bf02261722 · 1996 · External reference
Centromeric tandem repeat from the chaffinch genome: Isolation and molecular characterization
10.1139/g00-098 · 2001 · External reference
A new family of satellite DNA sequences as a major component of centromeric heterochromatin in owls (Strigiformes)
10.1007/s00412-003-0267-z · 2004 · External reference
Dynamic Chromosome Reorganization in the Osprey (Pandion haliaetus, Pandionidae, Falconiformes): Relationship between Chromosome Size and the Chromosomal Distribution of Centromeric Repetitive DNA Sequences
10.1159/000358407 · 2014 · External reference
Molecular cytogenetic characterization of repetitive sequences comprising centromeric heterochromatin in three Anseriformes species
10.1371/journal.pone.0214028 · 2019 · External reference
A 41–42 bp tandemly repeated sequence isolated from nuclear envelopes of chicken erythrocytes is located predominantly on microchromosomes
10.1007/bf01735329 · 1990 · External reference
Characterization of a new repetitive sequence that is enriched on microchromosomes of turkey
10.1007/bf00352284 · 1992 · External reference
Molecular cloning and characterization of novel centromeric repetitive DNA sequences in the blue-breasted quail (Coturnix chinensis, Galliformes)
10.1159/000071044 · 2002 · External reference
Chromosome size-correlated and chromosome size-uncorrelated homogenization of centromeric repetitive sequences in New World quails
10.1007/s10577-014-9402-3 · 2014 · External reference
Genome organization of major tandem repeats and their specificity for heterochromatin of macro- and microchromosomes in Japanese quail
10.1139/gen-2022-0012 · 2022 · External reference
Japanese quail (Coturnix japonica) as a laboratory animal model
10.1038/laban1108-513 · 2008 · External reference
The quail genome: insights into social behaviour, seasonal biology and infectious disease response
10.1186/s12915-020-0743-4 · 2020 · External reference
Unresolved reference
2013 · External reference
Large Inversions Shape Diversification and Genome Evolution in Common Quails
10.1111/mec.17740 · 2025 · External reference
Polymorphic Heterochromatic Segments in Japanese Quail Microchromosomes
10.1159/000245914 · 2009 · External reference
Heterochromatic regions in Japanese quail chromosomes: comprehensive molecular-cytogenetic characterization and 3D mapping in interphase nucleus
10.1007/s10577-018-9597-9 · 2019 · External reference
Centromere positions in chicken and Japanese quail chromosomes: de novo centromere formation versus pericentric inversions
10.1007/s10577-012-9319-7 · 2012 · External reference
Tandem 41-bp repeats in chicken and Japanese quail genomes: FISH mapping and transcription analysis on lampbrush chromosomes
10.1007/s00412-007-0117-5 · 2007 · External reference
Towards complete and error-free genome assemblies of all vertebrate species
10.1038/s41586-021-03451-0 · 2021 · External reference
Spatio-temporal transcriptome dynamics coordinate rapid transition of core crop functions in ‘lactating’ pigeon
10.1371/journal.pgen.1010746 · 2023 · External reference
A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals
10.1093/gigascience/giaa142 · 2021 · External reference
Chickens possess centromeres with both extended tandem repeats and short non-tandem-repetitive sequences
10.1101/gr.106245.110 · 2010 · External reference
Chromosome Engineering Allows the Efficient Isolation of Vertebrate Neocentromeres
10.1016/j.devcel.2013.02.009 · 2013 · External reference
Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds
10.1038/s41559-019-0850-1 · 2019 · External reference
An atlas of regulatory elements in chicken: A resource for chicken genetics and genomics
10.1126/sciadv.ade1204 · 2023 · External reference
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
10.1038/nature03154 · 2004 · External reference
Dynamics of genome size evolution in birds and mammals
10.1073/pnas.1616702114 · 2017 · External reference
A high-quality reference genome for the Ural Owl ( Strix uralensis ) enables investigations of cell cultures as a genomic resource for endangered species
10.1093/gigascience/giaf106 · 2025 · External reference
Chromosome-level genome assembly of the European green woodpecker Picus viridis
10.1093/g3journal/jkae042 · 2024 · External reference
The complete genome of a songbird
10.1016/j.cell.2026.07.018 · 2026 · External reference
A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes
10.1101/gr.271569.120 · 2021 · External reference
Near telomere-to-telomere genome assemblies of Silkie Gallus and Mallard Anas platyrhynchos restored the structure of chromosomes and “missing” genes in birds
10.1186/s40104-024-01141-1 · 2025 · External reference
Establishment of H3K9-methylated heterochromatin and its functions in tissue differentiation and maintenance
10.1038/s41580-022-00483-w · 2022 · External reference
Differential enrichment of H3K9me3 at annotated satellite DNA repeats in human cell lines and during fetal development in mouse
10.1186/s13072-021-00423-6 · 2021 · External reference
H1 linker histones silence repetitive elements by promoting both histone H3K9 methylation and chromatin compaction
10.1073/pnas.1920725117 · 2020 · External reference
Heterochromatin: did H3K9 methylation evolve to tame transposons?
10.1186/s13059-021-02550-5 · 2021 · External reference
Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
10.1016/j.cels.2016.07.002 · 2016 · External reference
Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom
10.1016/j.cels.2015.07.012 · 2016 · External reference
Fast and accurate de novo genome assembly from long uncorrected reads
10.1101/gr.214270.116 · 2017 · External reference
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
10.1371/journal.pone.0112963 · 2014 · External reference
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
10.1093/bioinformatics/btv351 · 2015 · External reference
RepeatModeler2 for automated genomic discovery of transposable element families
10.1073/pnas.1921046117 · 2020 · External reference
De novo reconstruction of satellite repeat units from sequence data
10.1101/gr.278005.123 · 2023 · External reference
Full-length transcriptome assembly from RNA-Seq data without a reference genome
10.1038/nbt.1883 · 2011 · External reference
Genome Annotation and Curation Using MAKER and MAKER-P
10.1002/0471250953.bi0411s48 · 2014 · External reference
Using native and syntenically mapped cDNA alignments to improve de novo gene finding
10.1093/bioinformatics/btn013 · 2008 · External reference
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
10.1186/gb-2008-9-1-r7 · 2008 · External reference
Chorus2: design of genome-scale oligonucleotide-based probes for fluorescence in situ hybridization
10.1111/pbi.13610 · 2021 · External reference
Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes
10.1038/s41467-024-45385-x · 2024 · External reference
Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM
2013 · External reference
Sambamba: fast processing of NGS alignment formats
10.1093/bioinformatics/btv098 · 2015 · External reference
BEDTools: a flexible suite of utilities for comparing genomic features
10.1093/bioinformatics/btq033 · 2010 · External reference
Model-based Analysis of ChIP-Seq (MACS)
10.1186/gb-2008-9-9-r137 · 2008 · External reference
New strategies to improve minimap2 alignment accuracy
10.1093/bioinformatics/btab705 · 2021 · External reference
A complete bacterial genome assembled de novo using only nanopore sequencing data
10.1038/nmeth.3444 · 2015 · External reference
GFF Utilities: GffRead and GffCompare
10.12688/f1000research.23297.1 · 2020 · External reference
Synteny and Collinearity in Plant Genomes
10.1126/science.1153917 · 2008 · External reference
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
10.1038/s41587-019-0201-4 · 2019 · External reference
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
10.1093/bioinformatics/btt656 · 2014 · External reference
Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization
10.1093/nar/gky504 · 2018 · External reference
Unresolved reference
2007 · External reference
ChromHMM: automating chromatin-state discovery and characterization
10.1038/nmeth.1906 · 2012 · External reference
The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities
10.1098/rstb.2020.0186 · 2021 · External reference
HISAT: a fast spliced aligner with low memory requirements
10.1038/nmeth.3317 · 2015 · External reference
Indexing Graphs for Path Queries with Applications in Genome Research
10.1109/tcbb.2013.2297101 · 2014 · External reference
FISH—in Fish Chromosomes
2022 · External reference
Efficient chromatin profiling of H3K4me3 modification in cotton using CUT&Tag
10.1186/s13007-020-00664-8 · 2020 · External reference
ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide
10.1002/0471142727.mb2129s109 · 2015 · External reference
Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations
10.1186/s12915-019-0687-8 · 2019 · External reference
Integrative analysis of 111 reference human epigenomes
10.1038/nature14248 · 2015 · External reference