ArticleGenome biology2022
False gene and chromosome losses in genome assemblies caused by GC content variation and repeats.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
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- The Vertebrate Genomes Project Phase I: A global reference genome resource.bioRxiv : the preprint server for biology · 2026Article
- The Paipu framework enables creation of a large-scale mammalian cancer transcriptomics atlas.bioRxiv : the preprint server for biology · 2026Article
- Development and validation of a tetra-primer ARMS-PCR assay for genotyping the MTHFR (rs1801131) c.1286 A > C (p.Glu429Ala) polymorphism: a comparative study with KASP.Molecular biology reports · 2026Article
- Epigenomic methylome landscape of promoters in vertebrate genomes.bioRxiv : the preprint server for biology · 2026Article
- A new chromosome-level genome assembly for western painted turtle Chrysemys picta bellii, a model for extreme physiological adaptations.BMC genomics · 2026Article
- Decoding the Avian Missing Gene Mystery: Dot Chromosomes Unmask Extensive Gene Loss and Novel Genetic Instability.Genome biology and evolution · 2026Article
- Chromosomal rearrangements and segmental deletions contribute to gene loss in squamates.BMC biology · 2026Article
- Genomic and functional characterization of Pseudosulfitobacter pseudonitzschiae BPC-C4-2: a growth-promoting symbiont in Antarctic Ulva communities.BMC genomics · 2026Article
- Sex chromosome turnover and structural genome divergence shape meiotic outcomes in hybridizing Cobitis.GigaScience · 2026Article
- Unraveling forensic timelines using molecular markers in Phormia regina maggots.PLoS genetics · 2025Article
- Insights into Convergent Evolution From Studying Amino Acid Patterns in Independent Lineages of Birds.Genome biology and evolution · 2025Article
- The complete genome of a songbird.bioRxiv : the preprint server for biology · 2025Article
- Linking phenotype to genotype using comprehensive genomic comparisons.Current opinion in genetics & development · 2025Review
- Illuminating the mystery of thylacine extinction: a role for relaxed selection and gene loss.Proceedings. Biological sciences · 2025Article
- Chromosome-scale genome assembly and annotation of two geographically distinct strains of malaria vector Anopheles albimanus.Scientific reports · 2025Article
- Rampant Interkingdom Horizontal Gene Transfer in Pezizomycotina? An Updated Inspection of Anomalous Phylogenies.International journal of molecular sciences · 2025Article
- Chromosome-level reference genome assembly of the gyrfalcon (Falco rusticolus) and population genomics offer insights into the falcon population in Mongolia.Scientific reports · 2025Article
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19 authors.
Funding
Abstract
backgroundMany short-read genome assemblies have been found to be incomplete and contain mis-assemblies. The Vertebrate Genomes Project has been producing new reference genome assemblies with an emphasis on being as complete and error-free as possible, which requires utilizing long reads, long-range scaffolding data, new assembly algorithms, and manual curation. A more thorough evaluation of the recent references relative to prior assemblies can provide a detailed overview of the types and magnitude of improvements.
resultsHere we evaluate new vertebrate genome references relative to the previous assemblies for the same species and, in two cases, the same individuals, including a mammal (platypus), two birds (zebra finch, Anna's hummingbird), and a fish (climbing perch). We find that up to 11% of genomic sequence is entirely missing in the previous assemblies. In the Vertebrate Genomes Project zebra finch assembly, we identify eight new GC- and repeat-rich micro-chromosomes with high gene density. The impact of missing sequences is biased towards GC-rich 5'-proximal promoters and 5' exon regions of protein-coding genes and long non-coding RNAs. Between 26 and 60% of genes include structural or sequence errors that could lead to misunderstanding of their function when using the previous genome assemblies.
conclusionsOur findings reveal novel regulatory landscapes and protein coding sequences that have been greatly underestimated in previous assemblies and are now present in the Vertebrate Genomes Project reference genomes.
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