ArticleMolecular ecology resources2021
Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise.
Article in Molecular ecology resources, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers, 1 of them a synthesis that pooled it.
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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
100 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A lizard is never late: Squamate genomics as a recent catalyst for understanding sex chromosome and microchromosome evolution.The Journal of heredity · 2023Pooled it
- The rate and spectrum of germline mutations in chicken from a commercial pedigree line.Genetics, selection, evolution : GSE · 2026Article
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- Chromosome-level genome assembly of the sand martin (Riparia riparia).Scientific data · 2026Article
- Disentangled Assembly Graphs Reveal Hidden Eukaryotic Diversity in eDNA Metagenomic Data.Molecular ecology resources · 2026Article
- Multidirectional Chromosomal Painting in the Harpy Eagle (Animals : an open access journal from MDPI · 2026Article
- Silver chimaera genome highlights lineage-specific sex chromosome and opsin gene evolution in holocephalans.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- MicroFinder: conserved gene-set mapping and assembly ordering for manual curation of bird dot microchromosomes.GigaScience · 2026Article
- Genome misassembly detection using Stash: A data structure based on stochastic tile hashing.PloS one · 2026Article
- Genome sequence assembly and annotation ofNAR genomics and bioinformatics · 2025Article
- Neo-sex Chromosomes Track the Mitochondrial Phylogeny and Exhibit an Extensive Added Stratum of Recombination Suppression in Honeyeaters (Aves: Meliphagidae).Genome biology and evolution · 2025Article
- A complete reference genome assembly and annotation of the Black Redstart (Phoenicurus ochruros).Scientific data · 2025Article
- High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae.Genome research · 2025Article
- A Strategy for Single-Run Sequencing of the Water Buffalo Genome: (II) Fast One-Step Assembly of Highly Continuous Chromosome Sequences.Animals : an open access journal from MDPI · 2025Article
- Chromosomal Inversions Mediated by Tandem Insertions of Transposable Elements.Genome biology and evolution · 2025Article
- Variation of and associations with the depth and evenness of sequencing coverage in archived plastid genomes.Scientific reports · 2025Article
- Variation of and associations with the depth and evenness of sequencing coverage in archived plastid genomes.Research square · 2025Article
- Assembly of female and male hihi genomes (stitchbird; Notiomystis cincta) enables characterization of the W chromosome and resources for conservation genomics.Molecular ecology resources · 2025Article
- Museomics unravels cryptic diversity in an endemic group of New Guinean songbirds.Biology letters · 2025Article
40 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors.
Funding
Abstract
Genome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies now enable assembling genomes at unprecedented quality and contiguity. However, the difficulty in assembling repeat-rich and GC-rich regions (genomic "dark matter") limits insights into the evolution of genome structure and regulatory networks. Here, we compare the efficiency of currently available sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter. By adopting different de novo assembly strategies, we compare individual draft assemblies to a curated multiplatform reference assembly and identify the genomic features that cause gaps within each assembly. We show that a multiplatform assembly implementing long-read, linked-read and proximity sequencing technologies performs best at recovering transposable elements, multicopy MHC genes, GC-rich microchromosomes and the repeat-rich W chromosome. Telomere-to-telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is now possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects for optimized completeness of both the coding and noncoding parts of nonmodel genomes.
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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.