The DOI matches its Crossref record; 41 of the 41 references it cites were found in a registry or an index; 1 of the 5 sources its claims cite were checked for support.
A telomere-to-telomere chromosome-scale genome assembly of glass catfish (Kryptopterus vitreolus)
Open accessAbstract
Glass catfish (Kryptopterus vitreolus) is commonly distributed in several Asian countries, such as Thailand, Malaysia, and Indonesia. It is renowned for its near-transparent appearance, which has drawn considerable attention for biomedical research and the tropical ornamental fish industry. Here, we successfully constructed the first telomere-to-telomere (T2T) chromosome-scale genome assembly for glass catfish, by integration of PacBio HiFi, Nanopore ONT ultra-long, and Hi-C sequencing technologies. The haplotypic assembly covers approximately 687.7 Mb in length, featuring a high contig N50 of 21.3 Mb. This assembly was then anchored into 32 chromosomes, presenting a complete set of 64 telomeres and 32 centromeres. It was predicted with 252.4 Mb of repetitive sequences and annotated with a total of 24,696 protein-coding genes. Subsequent BUSCO analysis revealed high genome completeness (up to 96.4%). This high-quality T2T genome assembly not only provides a valuable genetic resource for investigating the molecular mechanisms underlying transparency, but also supports in-depth studies on functional genomics, genetic diversity, and selective breeding for this economically important fish species.
Overview
AI snapshot
Written from the paper’s full text.
TL;DR
The paper reports the first telomere-to-telomere, chromosome-scale genome assembly for glass catfish (*Kryptopterus vitreolus*), built from PacBio HiFi, Nanopore ONT ultra-long, and Hi-C data. The ~687.7 Mb haplotypic assembly is anchored into 32 chromosomes with 64 telomeres, 32 centromeres, 24,696 protein-coding genes, and 96.4% BUSCO completeness.
Key findings
- The final haplotypic assembly is ~687.7 Mb with a contig N50 of 21.3 Mb, anchored into 32 chromosomes and representing ~98.5% of assembled contigs; it contains a complete set of 64 telomeres and 32 centromeres.
- Repetitive sequences total ~252.4 Mb, or 36.7% of the genome; 24,696 protein-coding genes were annotated, with 24,307 genes (98.4%) annotated in at least one database.
- BUSCO completeness reached 96.4% (3,510/3,640 Actinopterygii orthologs), with 95.1% single-copy, 1.3% duplicated, and 0.6% fragmented; protein-level BUSCO was 92.5%, and Merqury QV was 39.7.
- Compared with the previous assembly, contig N50 increased from 1.2 Mb to 21.3 Mb, BUSCO from 90.3% to 96.4%, and gene number from 23,344 to 24,696.
Methods
- Three glass catfish individuals (1.0 g) were obtained from a local aquarium fish market in Guangzhou, Guangdong, China; gDNA was extracted from muscle tissue. Sequencing generated 75.0 Gb PacBio HiFi reads (N50 19.9 kb), 18.5 Gb ONT ultra-long reads (N50 56.2 kb), ~101.7 Gb Hi-C 150 bp paired-end reads, and 11.7 Gb transcriptome 150 bp paired-end reads from muscle.
- Assembly used NextDenovo for primary contigs (~698.3 Mb, contig N50 5.1 Mb), Hi-C data processed with Bowtie2 and HiC-Pro, then Juicer, 3D-DNA, and Juicebox to anchor 32 chromosomes; LR_GapCloser and TGS-GapCloser were used to fill 421 gaps.
- Repeat annotation combined de novo and homology-based methods (RepeatModeler, LTR-FINDER, RepeatMasker, Tandem Repeats Finder, RepeatProteinMask, quarTeT). Gene prediction combined homology-based annotation against five teleost species (tBLASTn/GeneWise) and transcriptome-derived annotation (Trinity/PASA) via MAKER, followed by functional annotation against SwissProt, TrEMBL, KEGG, and GO; quality was assessed with BUSCO and Merqury.
Limitations
- The paper does not include a dedicated limitations section and states no explicit limitations.
- Evident from the text: transcriptome data were derived only from muscle tissue, which may limit annotation of genes with tissue-specific expression.
- Evident from the text: the sample consisted of three individuals from a local aquarium fish market, so the assembly does not represent wild or population-level genetic diversity.
- Evident from the text: the assembly is described as haplotypic, not a phased diploid assembly.
Model-written summary. Check it against the paper before relying on it.
Integrity signals
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Cites
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Claims the paper makes
1 of 5 cited sources checked · 1 supported · 0 flagged
- Findingown data
The assembly has a contig N50 of 21.3 Mb.
“featuring a high contig N50 of 21.3 Mb.”
- Also stated in: § Genome assembly and quality evaluation · plain
“The contig N50 value of these anchored chromosomes was increased to 21.3 Mb, which is much higher than our previous report8 (1.2 Mb; Table 1).”
Quote in the paperSubstantial claim- Rests on an assumption: The three glass catfish individuals obtained from the local aquarium fish market were Kryptopterus vitreolus.
- Rests on an assumption: The sequenced individuals are representative of the Kryptopterus vitreolus species.
- Also stated in: § Genome assembly and quality evaluation · plain
- Findingown data
The Merqury QV score of the constructed genome assembly is 39.7.
“A Merqury QV score of 39.7 further validated the high quality and reliability of our constructed genome assembly.”
Quote in the paperSubstantial claim- Rests on an assumption: The three glass catfish individuals obtained from the local aquarium fish market were Kryptopterus vitreolus.
- Rests on an assumption: The sequenced individuals are representative of the Kryptopterus vitreolus species.
- Findingown data
The assembly was annotated with a total of 24,696 protein-coding genes.
“annotated with a total of 24,696 protein-coding genes.”
- Also stated in: § Gene prediction and functional annotation · plain
“Finally, a total of 24,696 protein-coding genes were annotated, with an average mRNA length of 15,135.6 bp.”
Quote in the paperNot a substantial claim- Rests on an assumption: The three glass catfish individuals obtained from the local aquarium fish market were Kryptopterus vitreolus.
- Rests on an assumption: The sequenced individuals are representative of the Kryptopterus vitreolus species.
- Also stated in: § Gene prediction and functional annotation · plain
- Findingown data
The haplotypic genome assembly has a total length of approximately 687.7 Mb.
“The haplotypic assembly covers approximately 687.7 Mb in length, featuring a high contig N50 of 21.3 Mb.”
- Also stated in: § Genome assembly and quality evaluation · plain
“The final haplotypic genome assembly anchored 32 chromosomes (Figs. 1 and 2) with a total length of 687.7 Mb (Fig. 1, Table 2), which represents ~98.5% of the assembled contigs.”
Quote in the paperSubstantial claim- Rests on an assumption: The three glass catfish individuals obtained from the local aquarium fish market were Kryptopterus vitreolus.
- Rests on an assumption: The sequenced individuals are representative of the Kryptopterus vitreolus species.
- Also stated in: § Genome assembly and quality evaluation · plain
- Findingown data
The final haplotypic genome assembly represents approximately 98.5% of the assembled contigs.
“which represents ~98.5% of the assembled contigs.”
Quote in the paperNot a substantial claim- Rests on an assumption: The three glass catfish individuals obtained from the local aquarium fish market were Kryptopterus vitreolus.
- Rests on an assumption: The sequenced individuals are representative of the Kryptopterus vitreolus species.
- Findingown data
The assembly was anchored into 32 chromosomes.
“This assembly was then anchored into 32 chromosomes, presenting a complete set of 64 telomeres and 32 centromeres.”
- Also stated in: § Genome assembly and quality evaluation · plain
“The final haplotypic genome assembly anchored 32 chromosomes (Figs. 1 and 2) with a total length of 687.7 Mb”
Quote in the paperSubstantial claim- Rests on an assumption: The three glass catfish individuals obtained from the local aquarium fish market were Kryptopterus vitreolus.
- Rests on an assumption: The sequenced individuals are representative of the Kryptopterus vitreolus species.
- Also stated in: § Genome assembly and quality evaluation · plain
- Findingown data
Approximately 98.4% (24,307) of the predicted genes were annotated with at least one database.
“Approximately 98.4% (24,307 genes) of the predicted genes were annotated with at least one database, highlighting the high completeness and reliability of the glass catfish gene annotation (Table 1).”
Quote in the paperNot a substantial claim- Rests on an assumption: The three glass catfish individuals obtained from the local aquarium fish market were Kryptopterus vitreolus.
- Rests on an assumption: The sequenced individuals are representative of the Kryptopterus vitreolus species.
- Findingown data
The new assembly has a much higher contig N50 (21.3 Mb) than the previous assembly (1.2 Mb).
“The contig N50 value of these anchored chromosomes was increased to 21.3 Mb, which is much higher than our previous report8 (1.2 Mb; Table 1).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [8] Bian, C. et al. Chromosome-level genome assembly of the glass catfish (Kryptopterus vitreolus) reveals molecular clues to its transparent phenotype. Zool Res 45, 1027–1036 (2024). source
A check is scheduled.
- Rests on an assumption: The three glass catfish individuals obtained from the local aquarium fish market were Kryptopterus vitreolus.
- Rests on an assumption: The sequenced individuals are representative of the Kryptopterus vitreolus species.
- Findingown data
The new assembly has a better BUSCO completeness (96.4%) than the previous assembly (90.3%).
“| BUSCO | 96.4% | 90.3% |”
- Also stated in: § Background & Summary · plain
“with much higher scaffold N50 and better BUSCO”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [8] Bian, C. et al. Chromosome-level genome assembly of the glass catfish (Kryptopterus vitreolus) reveals molecular clues to its transparent phenotype. Zool Res 45, 1027–1036 (2024). source
A check is scheduled.
- Rests on an assumption: The three glass catfish individuals obtained from the local aquarium fish market were Kryptopterus vitreolus.
- Rests on an assumption: The sequenced individuals are representative of the Kryptopterus vitreolus species.
- Also stated in: § Background & Summary · plain
- Findingown data
Protein-level BUSCO assessment with the Actinopterygii dataset revealed 92.5% completeness (3,367 orthologs).
“Protein-level BUSCO assessment with the Actinopterygii dataset revealed 92.5% (3,367) completeness, with 90.8% (3,306) single-copy, 1.7% (61) duplicated, and 2.4% (88) fragmented orthologs, confirming a high-quality gene annotation.”
Quote in the paperSubstantial claim- Rests on an assumption: The three glass catfish individuals obtained from the local aquarium fish market were Kryptopterus vitreolus.
- Rests on an assumption: The sequenced individuals are representative of the Kryptopterus vitreolus species.
- Findingown data
BUSCO analysis revealed genome completeness of 96.4% (3,510 of 3,640 BUSCO genes complete).
“Subsequent BUSCO analysis revealed high genome completeness (up to 96.4%).”
- Also stated in: § Technical Validation · plain
“In summary, 96.4% (3,510) of BUSCO genes were complete, with 95.1% (3,462) being identified as single-copy, 1.3% (48) as duplicated, and a mere 0.6% (21) as fragmented.”
Quote in the paperSubstantial claim- Rests on an assumption: The three glass catfish individuals obtained from the local aquarium fish market were Kryptopterus vitreolus.
- Rests on an assumption: The sequenced individuals are representative of the Kryptopterus vitreolus species.
- Also stated in: § Technical Validation · plain
- Study design and conductown data
PacBio HiFi reads aligned to the genome assembly achieved a 100.0% mapping rate.
“The PacBio HiFi reads, aligned to the genome assembly utilizing Minimap2, achieved an impeccable mapping rate of 100.0%, and the HIC reads also gained a 100% mapping rate.”
Quote in the paperNot a substantial claim- Rests on an assumption: The three glass catfish individuals obtained from the local aquarium fish market were Kryptopterus vitreolus.
- Rests on an assumption: The sequenced individuals are representative of the Kryptopterus vitreolus species.
- Study design and conductown data
Hi-C reads aligned to the genome assembly achieved a 100% mapping rate.
“The PacBio HiFi reads, aligned to the genome assembly utilizing Minimap2, achieved an impeccable mapping rate of 100.0%, and the HIC reads also gained a 100% mapping rate.”
Quote in the paperNot a substantial claim- Rests on an assumption: The three glass catfish individuals obtained from the local aquarium fish market were Kryptopterus vitreolus.
- Rests on an assumption: The sequenced individuals are representative of the Kryptopterus vitreolus species.
- It may state two separate claims as one. 7
- Probably not a substantial claim. 3
It may state two separate claims as one.
PremisecitationIn a previous glass catfish genome study, the authors reported a draft chromosome-level genome assembly and identified key genes such as tyrp1 and edn3 that play potential roles in pigmentation formation.
“In our previous glass catfish genome study8, we reported a draft chromosome-level genome assembly with identification of some key genes, such as tyrp1 and edn3, which play potential roles in pigmentation formation.”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [8] Bian, C. et al. Chromosome-level genome assembly of the glass catfish (Kryptopterus vitreolus) reveals molecular clues to its transparent phenotype. Zool Res 45, 1027–1036 (2024). source
It may state two separate claims as one.
Findingown dataThe authors constructed the first telomere-to-telomere (T2T) chromosome-scale genome assembly for glass catfish (Kryptopterus vitreolus), using PacBio HiFi, Nanopore ONT ultra-long, and Hi-C sequencing technologies.
“Here, we successfully constructed the first telomere-to-telomere (T2T) chromosome-scale genome assembly for glass catfish, by integration of PacBio HiFi, Nanopore ONT ultra-long, and Hi-C sequencing technologies.”
- Also stated in: § Background & Summary · plain
“we constructed a highly improved telomere-to-telomere (T2T) chromosome-scale genome assembly (with much higher scaffold N50 and better BUSCO) for glass catfish”
Quote in the paperSubstantial claim- Rests on an assumption: The three glass catfish individuals obtained from the local aquarium fish market were Kryptopterus vitreolus.
- Rests on an assumption: The sequenced individuals are representative of the Kryptopterus vitreolus species.
- Also stated in: § Background & Summary · plain
It may state two separate claims as one.
Findingown dataThe assembly contains a complete set of 64 telomeres and 32 centromeres.
“presenting a complete set of 64 telomeres and 32 centromeres.”
- Also stated in: § Repeat element annotation · plain
“including a complete set of 64 telomeres and 32 centromeres (see more details in Fig. 3).”
Quote in the paperSubstantial claim- Rests on an assumption: The three glass catfish individuals obtained from the local aquarium fish market were Kryptopterus vitreolus.
- Rests on an assumption: The sequenced individuals are representative of the Kryptopterus vitreolus species.
- Also stated in: § Repeat element annotation · plain
Probably not a substantial claim. The paper’s conclusions may not depend on it.
Findingown dataHi-C sequencing generated approximately 101.7 Gb of 150 bp paired-end reads.
“generating ~101.7 Gb of 150 bp paired-end reads.”
Quote in the paperNot a substantial claim- Rests on an assumption: The three glass catfish individuals obtained from the local aquarium fish market were Kryptopterus vitreolus.
- Rests on an assumption: The sequenced individuals are representative of the Kryptopterus vitreolus species.
It may state two separate claims as one.
Findingown dataPacBio HiFi sequencing yielded 75.0 Gb of HiFi data with an N50 length of 19.9 kb.
“yielding 75.0 Gb of HiFi data (Table 1) with an N50 length of 19.9 kb.”
Quote in the paperNot a substantial claim- Rests on an assumption: The three glass catfish individuals obtained from the local aquarium fish market were Kryptopterus vitreolus.
- Rests on an assumption: The sequenced individuals are representative of the Kryptopterus vitreolus species.
It may state two separate claims as one.
Findingown dataThe assembly was predicted to contain approximately 252.4 Mb of repetitive sequences, constituting 36.7% of the total genome length.
“It was predicted with 252.4 Mb of repetitive sequences and annotated with a total of 24,696 protein-coding genes.”
- Also stated in: § Repeat element annotation · plain
“The final analysis revealed that approximately 252.4 Mb of the glass catfish genome consisted of repetitive sequences (Fig. 3), constituting 36.7% of the total genome length (Table 1).”
Quote in the paperNot a substantial claim- Rests on an assumption: The three glass catfish individuals obtained from the local aquarium fish market were Kryptopterus vitreolus.
- Rests on an assumption: The sequenced individuals are representative of the Kryptopterus vitreolus species.
- Also stated in: § Repeat element annotation · plain
It may state two separate claims as one.
Findingown dataONT ultra-long sequencing yielded about 18.5 Gb of ultra-long reads with an N50 length of 56.2 kb.
“about 18.5 Gb of ultra-long reads (Table 1) with an N50 length of 56.2 kb were yielded.”
Quote in the paperSubstantial claim- Rests on an assumption: The three glass catfish individuals obtained from the local aquarium fish market were Kryptopterus vitreolus.
- Rests on an assumption: The sequenced individuals are representative of the Kryptopterus vitreolus species.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
Findingown dataTranscriptome sequencing generated 11.7 Gb of 150-bp paired-end reads.
“to generate 11.7 Gb of 150-bp paired-end reads.”
Quote in the paperNot a substantial claim- Rests on an assumption: The three glass catfish individuals obtained from the local aquarium fish market were Kryptopterus vitreolus.
- Rests on an assumption: The sequenced individuals are representative of the Kryptopterus vitreolus species.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
PremisecitationNg & Kottelat's study resolved the long-standing misidentification by classifying the glass catfish as a distinct species, K. vitreolus.
“Previous Ng & Kottelat’s study1 resolved this long-standing issue by classifying the glass catfish as a distinct species, named as K. vitreolus.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [1] Ng, H. H. & Kottelat, M. After eighty years of misidentification, a name for the glass catfish (Teleostei: Siluridae). Zootaxa 3630, 308–316 (2013). source
It may state two separate claims as one.
PremisecitationThe previous glass catfish genome assembly contained too many gaps with low BUSCO values, leading to many missing fragments and shortcomings in genome completeness and details.
“However, this assembly contains too many gaps with low BUSCO values that led to a lot of missing fragments for shortcoming in genome completeness and details.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [8] Bian, C. et al. Chromosome-level genome assembly of the glass catfish (Kryptopterus vitreolus) reveals molecular clues to its transparent phenotype. Zool Res 45, 1027–1036 (2024). source
The paper relies on this without support.
The three glass catfish individuals obtained from the local aquarium fish market were Kryptopterus vitreolus.
“Three glass catfish individuals (1.0 g) were obtained from a local aquarium fish market in Guangzhou, Guangdong, China.”
The paper relies on this without support.
The sequenced individuals are representative of the Kryptopterus vitreolus species.
“Three glass catfish individuals (1.0 g) were obtained from a local aquarium fish market in Guangzhou, Guangdong, China.”
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Self-citationBian, C., 深圳大学生命与海洋科学学院水产基因组学实验室, 广. 深. 5., Laboratory of Aquatic Genomics, C. O. L. S. A. O., Li, R.-H., Ruan, Z.-Q., Chen, W.-T., Huang, Y., Liu, L.-Y., Zhou, H.-L., Chong, C.-M., et al. (2024) · Zoological Research · doi:10.24272/j.issn.2095-8137.2023.396 · Cited by 4
Self-citationA telomere-to-telomere chromosome-level genome of glass catfish, Kryptopterus vitreolus
Bian, C. (2025) · Figshare · doi:10.6084/m9.figshare.28333385 · Cited by 1
Self-citation
Flagged first, then by citations
Research works printed but not linked: 3
- Han, J. et al. Establishment of glass catfish (Kryptopterus bicirrhis) fin-derived cells. Cell Biol Int 18, e00008 (2011).
- Lin, Y. et al. quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification. Hortic Res-England 10, uhad127 (2023).
- NCBI Bioproject https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1169629 (2024).
Cited by
Sorted by citations
A near telomere-to-telomere genome assembly of Pterocryptis cochinchinensis
Chen, W., Ouyang, Y., Fan, Y., Huang, F., & Bian, C. (2026) · Scientific Data · doi:10.1038/s41597-026-07135-0
Self-citationKashyap, S., Patil, A. Y., Choudhury, M. R., Yeshwanth, H. M., Kumar, N., Nune, M., & Vasanthan, K. S. (2026) · Journal of Bionic Engineering · doi:10.1007/s42235-026-00913-x
Metadata
- Authors
- Bian, C., Li, D., Wang, Y., He, Z., Chen, W.-T., Chong, C.-M., Zhou, H., & Shi, Q.
- Affiliations
- Shenzhen University (CN)
- Jiaying University (CN)
- University of Macau (MO)
- Agricultural Genomics Institute at Shenzhen (CN)
- BGI Group (China) (CN)
- Corresponding author
- Bian, Chao
- Shi, Qiong
- Venue
- Scientific Data
- Published
- 2025-03-23
- Volume
- 12
- Issue
- 1
- Pages
- 483-483
- ISSN
- 2052-4463 (ISSN-L)
- PMC
- PMC11930924
- OpenAlex
- W4408764225
- Semantic Scholar
- 7bc0757a1b3336c1e944500f5891833bc1175b7d
- Cited by
- 2
- References
- 41
- Citations by year
- 2026: 2
- Type
- data paper
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Scientific Data (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Life Sciences › Agricultural and Biological Sciences › Aquatic Science › Fish Biology and Ecology Studies
- Keywords
- telomere-to-telomere genome assembly, chromosome-scale genome, haplotype-resolved genome assembly, repetitive DNA, protein-coding genes, transparency, ornamental fish, selective breeding
- MeSH terms
- Animals, Catfishes, Chromosomes, Telomere, Genome
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.
A language model drew the claims from the paper on 2026-11-10, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-11-10 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Cited sources are checked with a language model’s help (gpt-6-sol).
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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