The genome sequence of the Dracula fish, Danionella dracula (Britz, Conway & Rüber, 2009)
Open accessAbstract
We present a genome assembly from an individual Danionella dracula (the Dracula fish; Chordata; Actinopterygii; Cypriniformes; Danionidae; Danioninae). The genome sequence is 665.21 megabases in span. This is a scaffold-level assembly, with a scaffold N50 of 10.29 Mb.
AI snapshot
Written from the paper’s full text.
TL;DR
This genome note reports a scaffold-level genome assembly (fDanDra1.1) for the Dracula fish Danionella dracula, spanning 665.21 Mb with a scaffold N50 of 10.29 Mb. The assembly has QV 34.6, 98.97% k-mer completeness, and 90.3% BUSCO completeness.
Key findings
- The final assembly fDanDra1.1 is 665.21 Mb in 996 scaffolds, with scaffold N50 10.29 Mb, contig N50 2.3 Mb, 1,611 contigs, and longest scaffold 40 Mb (39,982,851 bp).
- Assembly quality metrics: QV 34.6; k-mer completeness 98.97%; BUSCO v5.3.2 actinopterygii_odb10 completeness 90.3% (single 87.9%, duplicated 2.4%, fragmented 0.7%, missing 9.0%, n=3,640).
- Sequencing coverage was 41-fold PacBio CLR and 104-fold 10X Genomics read clouds.
- Background: D. dracula is a miniature, transparent freshwater fish with a maximum recorded size of 16.7 mm standard length, sister to four other Danionella species, diverged from closest relatives about 29.5 mya, and used in neurophysiological research.
Methods
- Sample fDanDra1 (BioSample SAMEA104026433) was obtained through the aquarium trade/laboratory of Ralf Britz; specimens were euthanised with MS222, and DNA was extracted from head tissue, with HMW DNA sheared to 12–20 kb.
- Libraries were sequenced as Pacific Biosciences CLR on SEQUEL and 10X Genomics read clouds on HiSeqX.
- Assembly used Falcon-unzip, wtdbg as a synteny guide, scaff10x, PBJelly gap filling, Arrow and FreeBayes polishing, purge_haplotigs, and manual gEVAL assessment; metrics used Merqury, BlobToolKit, and BUSCO.
Limitations
- The paper states no limitations section. Evident from the text: the assembly is scaffold-level (996 scaffolds; scaffold N50 10.29 Mb; longest scaffold 40 Mb), not chromosome-level.
- Evident from the text: BUSCO completeness is 90.3%, with 9.0% missing and 0.7% fragmented, and no gene annotation is reported in this genome note.
- Evident from the text: the specimen was obtained through the aquarium trade, so wild provenance is not directly documented for the sequenced individual.
Model-written summary. Check it against the paper before relying on it.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
7 of 7 cited sources checked · 4 supported · 0 flagged · accuracy not yet measured
- Premisecitation
The Danioninae are an emerging model clade in the field of evo-devo, favoured for analyses of anatomy, pigmentation, gene family expansion and phylogeography.
“The Danioninae are an emerging model clade in the field of evo-devo, favoured for analyses of anatomy (especially bone morphology and growth), pigmentation, gene family expansion and phylogeography ( Braasch et al., 2015; Parichy, 2015).”
Quote in the paperSubstantial claim2 of 2 sources checked- cites Braasch et al., 2015 source
Section 3.3 describes danionins as an Evo-Devo model species complex and identifies variation in craniofacial anatomy, size, mineralization, and pigmentation as reasons to study them. It does not identify gene-family expansion or phylogeography as particular strengths of danionins; its discussion of genome duplication concerns another cyprinid subfamily, Cyprininae. Page numbers are unavailable in our copy. (LLM, conf=0.87)
Experimental — accuracy not yet measured - cites Parichy, 2015 source
The “Zebrafish relatives and their phylogeny” section (page unavailable) discusses Danioninae diversity in size and form, comparative development, Danio pigmentation, and phylogenetic relationships alongside geographic ranges. It does not support the more specific attribution that Danioninae are favoured for analyses of bone morphology and growth or gene family expansion. (LLM, conf=0.85)
Experimental — accuracy not yet measured
- Premisecitation
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.”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites Kadobianskyi et al., 2019 source
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
- Premiseown data
The genome assembly is from an individual Danionella dracula.
“We present a genome assembly from an individual Danionella dracula (the Dracula fish; Chordata; Actinopterygii; Cypriniformes; Danionidae; Danioninae).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites Britz et al., 2009 source
- Rests on an assumption: The specimen obtained through the aquarium trade is Danionella dracula.
- Findingown data
The BUSCO duplicated completeness is 2.4%.
“The estimated Quality Value (QV) of the final assembly is 34.6 with k-mer completeness of 98.97%, and the assembly has a BUSCO v5.3.2 completeness of 90.3% (single = 87.9%, duplicated = 2.4%), using the actinopterygii_odb10 reference set ( n = 3,640).”
- Also stated in: § Genome sequence report · plain
“BUSCO * | C:90.3%[S:87.9%,D:2.4%],F:0.7%,M:9.0%,n:3,640”
Quote in the paperNot a substantial claim - Also stated in: § Genome sequence report · plain
- Findingown data
The k-mer completeness of the final assembly is 98.97%.
“The estimated Quality Value (QV) of the final assembly is 34.6 with k-mer completeness of 98.97%, and the assembly has a BUSCO v5.3.2 completeness of 90.3% (single = 87.9%, duplicated = 2.4%), using the actinopterygii_odb10 reference set ( n = 3,640).”
- Also stated in: § Genome sequence report · plain
“k-mer completeness | 98.97%”
Quote in the paperNot a substantial claim - Also stated in: § Genome sequence report · plain
- Findingown data
The final assembly has 996 sequence scaffolds.
“The final assembly has a total length of 665.21 Mb in 996 sequence scaffolds with a scaffold N50 of 10.29 Mb ( Table 1, Figure 2, Figure 3 and Figure 4).”
- Also stated in: § Genome sequence report · plain
“Number of scaffolds | 996”
Quote in the paperNot a substantial claim - Also stated in: § Genome sequence report · plain
- Findingown data
The BUSCO single-copy completeness is 87.9%.
“The estimated Quality Value (QV) of the final assembly is 34.6 with k-mer completeness of 98.97%, and the assembly has a BUSCO v5.3.2 completeness of 90.3% (single = 87.9%, duplicated = 2.4%), using the actinopterygii_odb10 reference set ( n = 3,640).”
- Also stated in: § Genome sequence report · plain
“BUSCO * | C:90.3%[S:87.9%,D:2.4%],F:0.7%,M:9.0%,n:3,640”
Quote in the paperNot a substantial claim - Also stated in: § Genome sequence report · plain
- Findingown data
The assembly has a contig N50 of 2.3 Mb.
“Contig N50 length (Mb) | 2.3”
Quote in the paperNot a substantial claim - Findingown data
A total of 104-fold coverage in 10X Genomics read clouds was generated.
“A total of 41-fold coverage in Pacific Biosciences single-molecule continuous long reads (CLR) and 104-fold coverage in 10X Genomics read clouds were generated.”
Quote in the paperNot a substantial claim - Findingown data
The assembly has a scaffold N50 of 10.29 Mb.
“This is a scaffold-level assembly, with a scaffold N50 of 10.29 Mb.”
- Also stated in: § Genome sequence report · plain
“The final assembly has a total length of 665.21 Mb in 996 sequence scaffolds with a scaffold N50 of 10.29 Mb ( Table 1, Figure 2, Figure 3 and Figure 4).”
Quote in the paperNot a substantial claim - Also stated in: § Genome sequence report · plain
- Findingown data
The assembly has a BUSCO v5.3.2 completeness of 90.3%.
“The estimated Quality Value (QV) of the final assembly is 34.6 with k-mer completeness of 98.97%, and the assembly has a BUSCO v5.3.2 completeness of 90.3% (single = 87.9%, duplicated = 2.4%), using the actinopterygii_odb10 reference set ( n = 3,640).”
- Also stated in: § Genome sequence report · plain
“BUSCO * | C:90.3%[S:87.9%,D:2.4%],F:0.7%,M:9.0%,n:3,640”
Quote in the paperNot a substantial claim - Also stated in: § Genome sequence report · plain
- Findingown data
The genome sequence is 665.21 megabases in span.
“The genome sequence is 665.21 megabases in span.”
- Also stated in: § Genome sequence report · plain
“The final assembly has a total length of 665.21 Mb in 996 sequence scaffolds with a scaffold N50 of 10.29 Mb ( Table 1, Figure 2, Figure 3 and Figure 4).”
- Also stated in: § Genome sequence report · plain
“Span (Mb) | 665.21”
Quote in the paperNot a substantial claim - Also stated in: § Genome sequence report · plain
- Findingown data
The estimated Quality Value (QV) of the final assembly is 34.6.
“The estimated Quality Value (QV) of the final assembly is 34.6 with k-mer completeness of 98.97%, and the assembly has a BUSCO v5.3.2 completeness of 90.3% (single = 87.9%, duplicated = 2.4%), using the actinopterygii_odb10 reference set ( n = 3,640).”
- Also stated in: § Genome sequence report · plain
“Consensus quality (QV) | 34.6”
Quote in the paperNot a substantial claim - Also stated in: § Genome sequence report · plain
- Findingown data
A total of 41-fold coverage in Pacific Biosciences single-molecule continuous long reads (CLR) was generated.
“A total of 41-fold coverage in Pacific Biosciences single-molecule continuous long reads (CLR) and 104-fold coverage in 10X Genomics read clouds were generated.”
Quote in the paperNot a substantial claim - Findingown data
The assembly is a scaffold-level assembly.
“This is a scaffold-level assembly, with a scaffold N50 of 10.29 Mb.”
Quote in the paperNot a substantial claim
- Classified as probably not a substantial claim. 5
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationDanionella dracula has recently emerged as a model organism for neurophysiological research.
“Danionella dracula has recently emerged as a model organism for neurophysiological research ( Tatarsky et al., 2022), along with D. cerebrum ( Schulze et al., 2018), previously misidentified as D. translucida ( Britz et al., 2021).”
Quote in the paperNot a substantial claim3 of 3 sources checkedProbably not a substantial claim: may not pass S3 (load-bearing).
Findingown dataThe assembly has 1,611 contigs.
“Number of contigs | 1,611”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Findingown dataThe longest scaffold is 40 Mb.
“Longest scaffold (Mb) | 40”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Findingown dataThe BUSCO missing score is 9.0%.
“BUSCO * | C:90.3%[S:87.9%,D:2.4%],F:0.7%,M:9.0%,n:3,640”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Findingown dataThe BUSCO fragmented score is 0.7%.
“BUSCO * | C:90.3%[S:87.9%,D:2.4%],F:0.7%,M:9.0%,n:3,640”
Quote in the paperNot a substantial claim
The paper relies on this without support.
The specimen obtained through the aquarium trade is Danionella dracula.
“The specimen used for the study was obtained through the aquarium trade.”
The paper relies on this without support.
Danionella dracula is a member of the Danioninae and a close relative of the zebrafish Danio rerio.
“Danionella dracula is a member of the Danioninae and a close relative of the zebrafish Danio rerio.”
Cites
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Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
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BlobToolKit – Interactive Quality Assessment of Genome Assemblies
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Fast and accurate long-read assembly with wtdbg2
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Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies
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Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology
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sanger-tol/genomenote v1.0.dev
Muffato, M., Baby, C. S., & Surana, P. (2023) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.6785934 · Cited by 693 · see citing works
sanger-tol/readmapping v1.3.1 - Antipodean Opaleye (patch 1)
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Flagged first, then by citations
Research works printed but not linked: 1
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Cited by
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- Authors
- Rüber, L., Britz, R., Conway, K., Bista, I., McCarthy, S., Wood, J., Smith, M., Oliver, K., Howe, K., & Durbin, R.
- Affiliations
- University of Bern (CH)
- Senckenberg Natural History Collections Dresden (DE)
- Texas A&M University (US)
- Senckenberg Research Institute and Natural History Museum Frankfurt/M (DE)
- Wellcome Sanger Institute (GB)
- University of Cambridge (GB)
- Corresponding author
- Howe, Kerstin
- ORCID
- Venue
- Wellcome Open Research
- Publisher
- F1000 Research Ltd
- Published
- 2024-04-12
- Volume
- 9
- Pages
- 194
- ISSN
- 2398-502X (ISSN-L)
- PMC
- PMC11367074
- OpenAlex
- W4394743524
- Cited by
- 3
- References
- 24
- Citations by year
- 2026: 1 · 2025: 1 · 2024: 1
- FWCI
- 0.41
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Wellcome Open Research (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- Wellcome Trust (207492)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Agricultural and Biological Sciences › Aquatic Science › Fish Biology and Ecology Studies
- Keywords
- genome assembly, Danionidae, Cypriniformes, Actinopterygii, Chordata, fish genomics
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