Hybrid genome assembly and annotation of Danionella translucida
Open accessPublished version of a preprint
Abstract
Studying neuronal circuits at cellular resolution is very challenging in vertebrates due to the size and optical turbidity of their brains. Danionella translucida , a close relative of zebrafish, was recently introduced as a model organism for investigating neural network interactions in adult individuals. Danionella remains transparent throughout its life, has the smallest known vertebrate brain and possesses a rich repertoire of complex behaviours. Here we sequenced, assembled and annotated the Danionella translucida genome employing a hybrid Illumina/Nanopore read library as well as RNA-seq of embryonic, larval and adult mRNA. We achieved high assembly continuity using low-coverage long-read data and annotated a large fraction of the transcriptome. This dataset will pave the way for molecular research and targeted genetic manipulation of this novel model organism.
AI snapshot
Written from the paper’s full text.
TL;DR
The authors generated a hybrid Illumina/Nanopore genome assembly and transcriptome annotation for the transparent fish *Danionella translucida*, a emerging vertebrate neuroscience model. The 735 Mb assembly has a scaffold N50 of 340.819 kb and 91.5% BUSCO genome completeness, while the annotation contains 24,097 protein-coding gene models with 86.3% BUSCO transcriptome completeness.
Key findings
- The hybrid assembly totaled 735.303 Mb across 27,639 scaffolds, with scaffold N50 340.819 kb, contig N50 133.131 kb, longest scaffold 3.085 Mb, and 88.3% of the genome in scaffolds >50 kb.
- BUSCO genome completeness was 91.5% complete (87.0% single, 4.5% duplicated), 3.6% fragmented, and 4.9% missing against 4,584 Actinopterygii orthologs.
- The MAKER annotation produced 24,097 protein-coding gene models, 21,491 functionally annotated, mean AED 0.18, and 95% of gene models with AED <0.5; BUSCO transcriptome completeness was 86.3% complete (80.6% single, 5.7% duplicated), 7.1% fragmented, and 6.6% missing.
- DT introns were shorter than zebrafish introns: median intron length was 462 bp in DT versus 1,119 bp in zebrafish, based on 19,192 unique orthologous protein pairs, with 16,751 used for average intron-length comparison.
Methods
- Genomic DNA was sequenced with Illumina paired-end (500 bp insert; 1.347 billion reads; 186×), Illumina mate-pair (~10 kb insert; 554 million reads; 77×), and one Nanopore MinION run (4.288 Gb; 824,880 reads; read N50 11.653 kb; 5.8×).
- Assembly used MaSuRCA v3.2.6 with raw paired-end and mate-pair libraries, followed by one round of Pilon v1.22 polishing; completeness was assessed with BUSCO v3 against Actinopterygii orthologs.
- Annotation used MAKER v2.31.10 with Trinity-assembled short-read RNA-seq, Nanopore cDNA reads, and proteomes from 11 fish species; SNAP and Augustus were trained, and tRNAscan-SE annotated tRNAs. Validation compared DT and zebrafish intron size distributions using CRB-BLAST orthologs.
Limitations
- The paper does not state a limitations section.
- Evident from the reported metrics: the assembly remains fragmented, with 27,639 scaffolds, 36,005 contigs, 1.306% gap sequences, and BUSCO missing/fragmented fractions of 4.9%/3.6% for the genome and 6.6%/7.1% for the annotation.
- Evident from the text: Nanopore genomic coverage was low at 5.8×, and the annotation relied on transcript evidence from limited stages (1–2 dpf embryos, 3 dpf larvae, and adult fish), which may not capture all transcripts.
Model-written summary. Check it against the paper before relying on it.
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Cites
Statistics
Claims the paper makes
7 of 15 cited sources checked · 4 supported · 0 flagged · accuracy not yet measured
- Premisecitation
The predicted genome size of Danionella translucida is around one half of the zebrafish reference genome.
“The predicted genome size of DT is around one half of the zebrafish reference genome33.”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [33] Howe, K. et al. The zebrafish reference genome sequence and its relationship to the human genome. Nat. Commun. 496, 498–503 (2013). source
- Premisecitation
Danionella translucida was recently developed as a model organism for optical investigation of neuronal circuit activity in vertebrates.
“Danionella translucida (DT), a transparent cyprinid fish1,2 with the smallest known vertebrate brain, was recently developed as a novel model organism for the optical investigation of neuronal circuit activity in vertebrates3,4.”
Quote in the paperSubstantial claim1 of 2 sources checked- cites [3] Schulze, L. et al. Transparent danionella translucida as a genetically tractable vertebrate brain model. Nat. Methods 15, 977–983 (2018). source
The indexed passages show a repository abstract and metadata, but no passage from the paper’s full text. Searches for optical investigation of neuronal circuits and for the reported genome-editing and transgenesis methods did not retrieve full-text evidence; the abstract alone cannot establish the verdict under this rubric. (LLM, conf=0.70)
Experimental — accuracy not yet measured - cites [4] Penalva, A. et al. Establishment of the miniature fish species Danionella translucida as a genetically and optically tractable neuroscience model. Preprint at https://doi.org/10.1101/444026v1.full (2018). source
Not checked in the free run.
- Findingown data
The final annotation set consists of 24,097 protein-coding gene models.
“The final set of annotations consisted of 24,097 protein-coding gene models with an average length of 13.4 kb and an average AED of 0.18 (Table 3).”
Quote in the paperNot a substantial claim - Findingown data
Short- and long-read RNA sequencing data used together with other fish species annotated proteomes produced an annotation dataset with BUSCO transcriptome completeness score of 86%.
“Short- and long-read RNA sequencing data used together with other fish species annotated proteomes produced an annotation dataset with BUSCO transcriptome completeness score of 86%.”
- Also stated in: § Transcriptome sequencing and annotation · plain
“The BUSCO transcriptome completeness search found 86% of complete Actinopterygii orthologs in the annotation set.”
Quote in the paperSubstantial claim - Also stated in: § Transcriptome sequencing and annotation · plain
- Findingown data
The average length of the final protein-coding gene models is 13.4 kb.
“The final set of annotations consisted of 24,097 protein-coding gene models with an average length of 13.4 kb and an average AED of 0.18 (Table 3).”
Quote in the paperNot a substantial claim
- Findingown data
A combination of deep-coverage Illumina sequencing with a single Nanopore sequencing run produced an assembly with scaffold N50 of approximately 340-341 kb.
“A combination of deep-coverage Illumina sequencing with a single Nanopore sequencing run produced an assembly with scaffold N50 of 340 kb and Benchmarking Universal Single-Copy Orthologs (BUSCO) genome completeness score of 92%.”
- Also stated in: § Genome assembly · plain
“The resulting 735 Mb assembly had a scaffold N50 of 341 kb, the longest scaffold being more than 3 Mb.”
Quote in the paperSubstantial claim - Also stated in: § Genome assembly · plain
- Findingown data
The longest scaffold in the assembly is more than 3 Mb.
“The resulting 735 Mb assembly had a scaffold N50 of 341 kb, the longest scaffold being more than 3 Mb.”
Quote in the paperNot a substantial claim - Findingown data
The Trinity assembly contigs were clustered into 146,103 genes.
“This produced 222448 contigs with an N50 length of 3586 bp, clustered into 146103 “genes”.”
Quote in the paperNot a substantial claim - Findingown data
For 16,751 orthologs with complete protein-coding transcript exon annotation in both fish, the distribution of average intron lengths was skewed towards long zebrafish introns in comparison to Danionella translucida.
“For 16,751 of those orthologs with complete protein-coding transcript exon annotation in both fish we calculated their respective average intron lengths (Fig. 4b). The distribution was again skewed towards long zebrafish introns in comparison to DT.”
Quote in the paperNot a substantial claim - Findingown data
In total, 19,192 unique orthologous protein pairs were identified between Danionella translucida and zebrafish.
“In total, we have identified 19,192 unique orthologous protein pairs.”
Quote in the paperNot a substantial claim - Findingown data
BUSCO transcriptome analysis revealed 96% of complete Actinopterygii orthologs in the Trinity assembly.
“BUSCO transcriptome analysis revealed 96% of complete Actinopterygii orthologs in the Trinity assembly.”
Quote in the paperNot a substantial claim - Findingown data
The majority of Danionella translucida tissues remain transparent throughout its life.
“The majority of DT tissues remain transparent throughout its life (Fig. 1).”
Quote in the paperSubstantial claim - Findingown data
The resulting genome assembly is 735 Mb.
“The resulting 735 Mb assembly had a scaffold N50 of 341 kb, the longest scaffold being more than 3 Mb.”
Quote in the paperNot a substantial claim - Findingown data
The average AED of the final annotation set is 0.18.
“The final set of annotations consisted of 24,097 protein-coding gene models with an average length of 13.4 kb and an average AED of 0.18 (Table 3).”
Quote in the paperNot a substantial claim - Premisecitation
Short-read-only assemblies often struggle with repetitive and intergenic regions, resulting in fragmented assembly and poor access to regulatory and promoter sequences.
“However, short-read-only assemblies often struggle with repetitive and intergenic regions, resulting in fragmented assembly and poor access to regulatory and promoter sequences5,6.”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [5] Shendure, J. & Ji, H. Next-generation DNA sequencing. Nat. Biotechnol. 26, 1135–1145 (2008). source
- cites [6] Watson, M. Mind the gaps - ignoring errors in long read assemblies critically affects protein prediction. Preprint at https://doi.org/10.1101/285049v1 (2018). source
Not checked in the free run.
- Classified as probably not a substantial claim. 4
- May combine two claims. 6
- The quote only partly states this claim. 1
Classified as probably not a substantial claim.
PremisecitationChanges in intron lengths have been shown to be a significant part of genomic truncations and expansions, such as severe intron shortening in Paedocypris or intron expansion in zebrafish.
“Changes in the intron lengths have been shown to be a significant part of genomic truncations and expansions, such as a severe intron shortening in another miniature fish species, Paedocypris35, or an intron expansion in zebrafish36.”
Quote in the paperSubstantial claim2 of 2 sources checked- cites [35] Malmstrøm, M. et al. The most developmentally truncated fishes show extensive hox gene loss and miniaturized genomes. Genome Biol. Evol. 10, 1088–1103 (2018). source
- cites [36] Moss, S. P., Joyce, D. A., Humphries, S., Tindall, K. J. & Lunt, D. H. Comparative analysis of teleost genome sequences reveals an ancient intron size expansion in the zebrafish lineage. Genome Biol. Evol. 3, 1187–1196 (2011). source
May combine two claims.
PremisecitationDanionella translucida is a transparent cyprinid fish with the smallest known vertebrate brain.
“Danionella translucida (DT), a transparent cyprinid fish1,2 with the smallest known vertebrate brain, was recently developed as a novel model organism for the optical investigation of neuronal circuit activity in vertebrates3,4.”
Quote in the paperSubstantial claim1 of 2 sources checked- cites [1] Roberts, T. R. Danionella translucida, a new genus and species of cyprinid fish from Burma, one of the smallest living vertebrates. Environ. Biol. Fishes 16, 231–241 (1986). source
- cites [2] Britz, R., Conway, K. W. & Rüber, L. Spectacular morphological novelty in a miniature cyprinid fish, danionella dracula n. sp. Proc. Biol. Sci. 276, 2179–2186 (2009). source
The paper identifies D. translucida as a Danionella species, and its title and opening summary identify Danionella as cyprinid fish. Its discussion of D. translucida in “Miniaturization, developmental truncation and evolutionary novelty” does not describe transparency or brain size; searches for those terms found no supporting passage. The paper therefore supports the cyprinid identification, but not the other attributes in the claim. (LLM, conf=0.84)
Experimental — accuracy not yet measured
Classified as probably not a substantial claim.
PremisecitationCombining short- and long-read sequencing technologies in hybrid assemblies recently produced high-quality genomes in fish.
“Combining short- and long-read sequencing technologies in hybrid assemblies recently produced high-quality genomes in fish8,9.”
Quote in the paperSubstantial claim2 of 2 sources checked- cites [8] Tan, M. H. et al. Finding Nemo: hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the Clownfish (Amphiprion ocellaris) genome assembly. GigaScience 7, 1–6 (2018). source
- cites [9] Tørrensen, O. K. et al. An improved genome assembly uncovers prolific tandem repeats in Atlantic cod. BMC Genomics 18, 1–23 (2017). source
The Methods (Genotyping by sequencing) describe Illumina sequencing of tomato samples, and the Results (GBS) describe aligning sequence tags to a tomato genome assembly. Searches for hybrid short- and long-read assemblies and fish genomes found no passage addressing the cited claim. Page numbers were not provided in our copy. (LLM, conf=0.77)
Experimental — accuracy not yet measured
May combine two claims.
Findingown dataThe Trinity de novo assembly of 100 bp paired-end RNA-seq reads produced 222,448 contigs with an N50 length of 3,586 bp.
“This produced 222448 contigs with an N50 length of 3586 bp, clustered into 146103 “genes”.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataMedian intron length is 462 bp in Danionella translucida and 1,119 bp in zebrafish.
“Median intron length values are in the range of the observed genome size difference (462 bp in DT as compared to 1,119 bp in zebrafish).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataThe Danionella translucida intron size distribution is similar to other fish species investigated in ref.35 and stands in stark contrast to the large tail of long introns in zebrafish.
“We found that the DT intron size distribution is similar to other fish species investigated in ref.35 which stands in stark contrast to the large tail of long introns in zebrafish.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites ref.35
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
May combine two claims. The quote only partly states this claim.
Findingown dataThe genome assembly has a BUSCO genome completeness score of 92% (91.5% of Actinopterygii orthologs found).
“A combination of deep-coverage Illumina sequencing with a single Nanopore sequencing run produced an assembly with scaffold N50 of 340 kb and Benchmarking Universal Single-Copy Orthologs (BUSCO) genome completeness score of 92%.”
- Also stated in: § Genome assembly · plain
“In total, 91.5% of the orthologs were found in the assembly.”
Quote in the paperSubstantial claim- Also stated in: § Genome assembly · plain
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationDanionella dracula, a close relative of Danionella translucida, has a genome of a similar size to Danionella translucida.
“Danionella dracula, a close relative of DT, possesses a unique developmentally truncated morphology34 and has a genome of a similar size (ENA Accession Number GCA_900490495.1).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites ENA Accession Number GCA_900490495.1
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
May combine two claims.
PremisecitationLong-read techniques are prone to errors, including frequent indels, which can lead to artefacts in long-read-only assemblies.
“Long-read techniques, such as PacBio and Nanopore, can generate reads up to 2 Mb7, but they are prone to errors, including frequent indels, which can lead to artefacts in long-read-only assemblies6.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [6] Watson, M. Mind the gaps - ignoring errors in long read assemblies critically affects protein prediction. Preprint at https://doi.org/10.1101/285049v1 (2018). source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationLong-read techniques such as PacBio and Nanopore can generate reads up to 2 Mb.
“Long-read techniques, such as PacBio and Nanopore, can generate reads up to 2 Mb7, but they are prone to errors, including frequent indels, which can lead to artefacts in long-read-only assemblies6.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [7] Payne, A., Holmes, N., Rakyan, V. & Loose, M. Whale watching with BulkVis: A graphical viewer for Oxford Nanopore bulk fast 5 files. Preprint at https://doi.org/10.1101/312256v1.full (2018). source
Checked before — its earlier verdict is held back until a new check runs.
The paper relies on this without support.
The size and opacity of vertebrate tissues limit optical access to the brain and hinder investigations of intact neuronal networks in vivo.
“The size and opacity of vertebrate tissues limit optical access to the brain and hinder investigations of intact neuronal networks in vivo.”
The paper relies on this without support.
A continuous annotated genome reference is still needed to enable targeted genetic and transgenic studies and facilitate the adoption of Danionella translucida as a model organism.
“Yet, a continuous annotated genome reference is still needed to enable targeted genetic and transgenic studies and facilitate the adoption of DT as a model organism.”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
A hybrid genome assembly for D. cerebrum has previously been published.
“A hybrid genome assembly for D. cerebrum has previously been published ( Kadobianskyi et al., 2019), and we complement this with publication of the D. dracula genome here.”
From The genome sequence of the Dracula fish, Danionella dracula (Britz, Conway & Rüber, 2009) (2024) · cites this paper as Kadobianskyi et al., 2019
The Abstract and Background & Summary report a published hybrid genome assembly, but identify the species as Danionella translucida, not D. cerebrum. Our copy does not identify those names as referring to the same species, so it does not support the species named in the claim. (LLM, conf=0.88)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
Nanopore cDNA library size differs between text and table
MajorThe methods report 190 Mb of Nanopore cDNA sequence data, while Table 1 reports 279.584 Mb for the same library. The read counts agree to rounding, so they do not explain the difference in total sequence size.
“resulting in 190 Mb sequence data distributed over 209k reads”
“| Total library size | 279.584 Mb |”
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- Penalva, A. et al. Establishment of the miniature fish species Danionella translucida as a genetically and optically tractable neuroscience model. Preprint at https://doi.org/10.1101/444026v1.full (2018). · DOI
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Nanopore sequencing technology, bioinformatics and applications
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HASLR: Fast Hybrid Assembly of Long Reads
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Evolutionary divergence of locomotion in two related vertebrate species
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- Authors
- Kadobianskyi, M., Schulze, L., Schuelke, M., & Judkewitz, B.
- Affiliations
- Einstein Center for Neurosciences Berlin (DE)
- Corresponding author
- Schuelke, Markus
- Judkewitz, Benjamin
- Venue
- Scientific Data
- Published
- 2019-08-26
- Volume
- 6
- Issue
- 1
- Pages
- 156-156
- ISSN
- 2052-4463 (ISSN-L)
- PMC
- PMC6710283
- OpenAlex
- W2970719793
- Cited by
- 36
- References
- 41
- Citations by year
- 2026: 9 · 2025: 2 · 2024: 5 · 2023: 1 · 2022: 6 · 2021: 5 · 2020: 5 · 2019: 2 · 2018: 1
- Type
- data paper
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Scientific Data (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Refubium (Universitätsbibliothek der Freien Universität Berlin) (submittedVersion, cc-by)
- Universitätsbibliothek der FU Berlin Hochschulschriftenstelle u. Dokumentenserver (cc-by)
- Funders
- Alfried Krupp von Bohlen und Halbach-Stiftung
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Zebrafish Biomedical Research Applications
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- genome assembly, genome annotation, transcriptome, hybrid sequencing, Nanopore long reads, Illumina sequencing, neural circuits, model organisms, RNA-seq
- MeSH terms
- RNA-Seq, Animals, Brain, Cyprinidae, Neurons, Gene Library, Genome, Molecular Sequence Annotation, Transcriptome
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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