ArticleGenome biology2022
Widespread false gene gains caused by duplication errors in genome assemblies.
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 44 papers.
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Who cites it
44 citing papers in PubMed, 62 citations in OpenAlex.
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- Brachiopod genome unveils the evolution of BMP signalling in bilaterian body patterning.Nature communications · 2026Article
- Arms races between selfish genetic elements and their host defence in termites.Nature communications · 2026Article
- Chromosomal rearrangements and segmental deletions contribute to gene loss in squamates.BMC biology · 2026Article
- Troubleshooting common errors in assemblies of long-read metagenomes.Nature biotechnology · 2026Article
- Evaluating NGS-generated contig accuracy for detection and assignment of PRRSV against a reference genome in experimentally mixed PRRSV infection samples.Frontiers in veterinary science · 2026Article
- Pan-genomics of polyploid crops: from complexity to breeding.Frontiers in plant science · 2026Review
- 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
- Comparative analysis of the mobilome yields new insights into its diversity, dynamics and evolution in parasites of the Trypanosomatidae family.Parasitology · 2025Article
- Evolutionary duplication of the leishmanial adaptor protein α-SNAP plays a role in its pathogenicity.The Journal of biological chemistry · 2025Article
- Genomic Insights into Post-Domestication Expansion and Selection of Body Size in Ponies.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 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
Corrections and comments
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Authors and funding
12 authors at 6 institutions in 4 countries.
Funding
Abstract
backgroundFalse duplications in genome assemblies lead to false biological conclusions. We quantified false duplications in popularly used previous genome assemblies for platypus, zebra finch, and Anna's Hummingbird, and their new counterparts of the same species generated by the Vertebrate Genomes Project, of which the Vertebrate Genomes Project pipeline attempted to eliminate false duplications through haplotype phasing and purging. These assemblies are among the first generated by the Vertebrate Genomes Project where there was a prior chromosomal level reference assembly to compare with.
resultsWhole genome alignments revealed that 4 to 16% of the sequences are falsely duplicated in the previous assemblies, impacting hundreds to thousands of genes. These lead to overestimated gene family expansions. The main source of the false duplications is heterotype duplications, where the haplotype sequences were relatively more divergent than other parts of the genome leading the assembly algorithms to classify them as separate genes or genomic regions. A minor source is sequencing errors. Ancient ATP nucleotide binding gene families have a higher prevalence of false duplications compared to other gene families. Although present in a smaller proportion, we observe false duplications remaining in the Vertebrate Genomes Project assemblies that can be identified and purged.
conclusionsThis study highlights the need for more advanced assembly methods that better separate haplotypes and sequence errors, and the need for cautious analyses on gene gains.
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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.