ArticlePLoS biology2018
De novo assembly of a young Drosophila Y chromosome using single-molecule sequencing and chromatin conformation capture.
Article in PLoS biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
68 citing papers in PubMed, 113 citations in OpenAlex.
- Convergence and conflict among telomere-specialized transposons across 60 million years of Drosophilid evolution.Genome research · 2026Article
- Causes and consequences of sex-chromosome turnovers in Diptera.Evolution letters · 2026Article
- Comparative gene annotation and orthology assignments across 301 species of Drosophilidae.bioRxiv : the preprint server for biology · 2026Article
- Comparative gene annotation and orthology assignments across 301 species of Drosophilidae.PLoS biology · 2026Article
- The tortured past of young polymorphic sex chromosomes revealed through multiplebioRxiv : the preprint server for biology · 2026Article
- Recombination Suppression Drives Expansion of the Drosophila Dot Chromosome.Molecular biology and evolution · 2025Article
- Comparative Genomics of Sex-Determination-Related Genes Reveals Shared Evolutionary Patterns Between Bivalves and Mammals, but Not Fruit Flies.Molecular ecology · 2025Article
- Genetic variation in recalcitrant repetitive regions of theGenome research · 2025Article
- Genomic origins and evolution of neo-sex chromosomes in Pacific Island birds.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A model of Hill-Robertson interference caused by purifying selection in a nonrecombining genome.Genetics · 2025Article
- Diversification and recurrent adaptation of the synaptonemal complex in Drosophila.PLoS genetics · 2025Article
- 3D chromatin maps of a brown alga reveal U/V sex chromosome spatial organization.Nature communications · 2024Article
- Sex chromosome cycle as a mechanism of stable sex determination.Journal of biochemistry · 2024Review
- Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life.PLoS biology · 2024Article
- Single-cell RNA-seq of Drosophila miranda testis reveals the evolution and trajectory of germline sex chromosome regulation.PLoS biology · 2024Article
- The Complex Landscape of Structural Divergence Between the Drosophila pseudoobscura and D. persimilis Genomes.Genome biology and evolution · 2024Article
- Positive Selection Drives cis-regulatory Evolution Across the Threespine Stickleback Y Chromosome.Molecular biology and evolution · 2024Article
- The highly improved genome ofLife science alliance · 2023Article
- Genetic conflict and the origin of multigene families: implications for sex chromosome evolution.Proceedings. Biological sciences · 2023Review
- Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life.bioRxiv : the preprint server for biology · 2023Article
8 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
While short-read sequencing technology has resulted in a sharp increase in the number of species with genome assemblies, these assemblies are typically highly fragmented. Repeats pose the largest challenge for reference genome assembly, and pericentromeric regions and the repeat-rich Y chromosome are typically ignored from sequencing projects. Here, we assemble the genome of Drosophila miranda using long reads for contig formation, chromatin interaction maps for scaffolding and short reads, and optical mapping and bacterial artificial chromosome (BAC) clone sequencing for consensus validation. Our assembly recovers entire chromosomes and contains large fractions of repetitive DNA, including about 41.5 Mb of pericentromeric and telomeric regions, and >100 Mb of the recently formed highly repetitive neo-Y chromosome. While Y chromosome evolution is typically characterized by global sequence loss and shrinkage, the neo-Y increased in size by almost 3-fold because of the accumulation of repetitive sequences. Our high-quality assembly allows us to reconstruct the chromosomal events that have led to the unusual sex chromosome karyotype in D. miranda, including the independent de novo formation of a pair of sex chromosomes at two distinct time points, or the reversion of a former Y chromosome to an autosome.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.