ArticleBMC genomics2022
Long-read sequencing of the zebrafish genome reorganizes genomic architecture.
Article in BMC genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
17 citing papers in PubMed, 21 citations in OpenAlex.
- Article
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- Seaside to Bedside: Assembly in Research for Emerging Human Fungal Pathogen Candida auris.Methods in molecular biology (Clifton, N.J.) · 2025Article
- The dynamics and functional impact of tRNA repertoires during early embryogenesis in zebrafish.The EMBO journal · 2024Article
- Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery.G3 (Bethesda, Md.) · 2024Article
- High Diversity of Long Terminal Repeat Retrotransposons in Compact Vertebrate Genomes: Insights from Genomes ofAnimals : an open access journal from MDPI · 2024Article
- Recent insights into crosstalk between genetic parasites and their host genome.Briefings in functional genomics · 2024Review
- Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery.bioRxiv : the preprint server for biology · 2023Article
- The revised reference genome of the leopard gecko (Eublepharis macularius) provides insight into the considerations of genome phasing and assembly.The Journal of heredity · 2023Article
- Zebrafish regulatory genomic resources for disease modelling and regeneration.Disease models & mechanisms · 2023Article
- The revised reference genome of the leopard gecko (bioRxiv : the preprint server for biology · 2023Article
- Sequencing and assembling bear genomes: the bare necessities.Frontiers in zoology · 2022Review
- ONT-Based Alternative Assemblies Impact on the Annotations of Unique versus Repetitive Features in the Genome of a Romanian Strain ofInternational journal of molecular sciences · 2022Article
- Ongoing endeavors to detect mobilization of transposable elements.BMB reports · 2022Review
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundNanopore sequencing technology has revolutionized the field of genome biology with its ability to generate extra-long reads that can resolve regions of the genome that were previously inaccessible to short-read sequencing platforms. Over 50% of the zebrafish genome consists of difficult to map, highly repetitive, low complexity elements that pose inherent problems for short-read sequencers and assemblers.
resultsWe used long-read nanopore sequencing to generate a de novo assembly of the zebrafish genome and compared our assembly to the current reference genome, GRCz11. The new assembly identified 1697 novel insertions and deletions over one kilobase in length and placed 106 previously unlocalized scaffolds. We also discovered additional sites of retrotransposon integration previously unreported in GRCz11 and observed the expression of these transposable elements in adult zebrafish under physiologic conditions, implying they have active mobility in the zebrafish genome and contribute to the ever-changing genomic landscape.
conclusionsWe used nanopore sequencing to improve upon and resolve the issues plaguing the current zebrafish reference assembly, GRCz11. Zebrafish is a prominent model of human disease, and our corrected assembly will be useful for studies relying on interspecies comparisons and precise linkage of genetic events to disease phenotypes.
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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.