The DOI matches its Crossref record; 47 of the 47 references it cites were found in a registry or an index; 5 of the 19 sources its claims cite were checked for support.
A complete telomere-to-telomere chromosome-level genome assembly of X-ray tetra (Pristella maxillaris)
Open accessAbstract
X-ray tetra (Pristella maxillaris) originates from the lower Amazon basin in South America. It is renowned for its strikingly transparent body, which has drawn significant interests in biomedical research and the world ornamental fish industry. Nevertheless, genomic resources for this interesting fish species remains scarce, hindering exploration of the molecular basis behind its unique transparency. To address this gap, we constructed the first complete telomere-to-telomere (T2T) chromosome-scale genome assembly of the X-ray tetra by integration of PacBio HiFi, ONT ultra-long, and Hi-C sequencing technologies. This haplotypic assembly spans approximately 1.1 Gb, with a contig N50 of 42.8 Mb. It is anchored onto 25 chromosomes, highlighting a complete set of 50 telomeres and 25 centromeres. We predicted 514.3 Mb of repetitive sequences and annotated 28,456 protein-coding genes in the assembled genome. Subsequent BUSCO analysis discovered high genome completeness (98.0%). This high-quality T2T genome assembly provides a valuable genetic resource for investigating the molecular mechanisms underlying transparency, and supporting in-depth studies on functional genomics, genetic diversity, and selective breeding for this economically important species.
Overview
AI snapshot
Written from the paper’s full text.
TL;DR
This paper reports the first complete telomere-to-telomere, chromosome-level genome assembly of the X-ray tetra (*Pristella maxillaris*), a transparent ornamental fish, built from PacBio HiFi, ONT ultra-long, and Hi-C data. The ~1.1 Gb haplotypic assembly is anchored to 25 chromosomes with 50 telomeres and 25 centromeres, and includes 28,456 annotated protein-coding genes.
Key findings
- The haplotypic assembly spans ~1.1 Gb with a contig N50 of 42.8 Mb; anchored chromosomes cover ~97.8% of assembled contigs and have an N50 of 43.9 Mb.
- All 25 chromosomes are gap-free (0 gaps each) and carry a complete set of 50 telomeres and 25 centromeres.
- Repeat annotation identified ~514.3 Mb of repetitive sequences, accounting for 46.4% of the genome.
- 28,456 protein-coding genes were predicted (average mRNA length 21,311.9 bp; average 9.7 exons; average exon length 191.4 bp), with 27,991 (98.4%) annotated in at least one database.
- Completeness: BUSCO 98.0% (3,567 of 3,640 Actinopterygii orthologs; 97.1% single-copy, 0.9% duplicated, 0.6% fragmented); protein-level BUSCO 96.5%; Merqury QV 41.8; PacBio HiFi mapping rate 100.0%.
Methods
- One individual collected from a local company in Pudong District, Shanghai, China; muscle tissue flash-frozen for DNA and RNA extraction.
- Sequencing: PacBio Sequel II HiFi (~70.2 Gb, N50 21.3 kb), ONT PromethION ultra-long (~30.0 Gb), Illumina NovaSeq 6000 Hi-C (~117.3 Gb of 150 bp paired-end reads), and MGI RNA-seq (~11.7 Gb of 150 bp paired-end reads).
- Assembly: NextDenovo primary contigs, Hi-C scaffolding with Bowtie2/HiC-Pro/Juicer/3D-DNA/Juicebox, gap filling with LR_GapCloser and TGS-GapCloser, and centromere/telomere identification with quarTeT. Annotation combined ab initio, homology-based (four teleost species), and transcriptome-based prediction integrated with MAKER, followed by functional annotation against NR, Swiss-Prot, GO, TrEMBL, KOG, and KEGG plus InterProScan.
Limitations
- The paper states that prior to this work only mitochondrial genome and transcriptome data existed and no complete genome assembly was available, which motivated the study; it does not present a dedicated limitations section.
- Evident from the text: the assembly is haplotypic and derived from a single individual, so it does not capture within-species variation or phased haplotypes.
- Evident from the text: RNA-seq for annotation came only from muscle tissue, which may limit detection of genes with tissue-restricted expression.
Model-written summary. Check it against the paper before relying on it.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
5 of 19 cited sources checked · 0 supported · 0 flagged · accuracy not yet measured
- Findingown data
BUSCO analysis found 98.0% genome completeness.
“Subsequent BUSCO analysis discovered high genome completeness (98.0%).”
- Also stated in: § Genome assembly and quality evaluation · boosted
“Our results demonstrated that 98.0% of complete BUSCO genes were discovered”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [28] Simao, F. A. et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015). source
The Introduction describes BUSCO as a method for assessing genome completeness, and Table 1 reports 98% completeness for the D. melanogaster and A. nidulans assemblies. Those results do not establish the 98.0% value for the genome analyzed in the citing paper. (LLM, conf=0.82)
Experimental — accuracy not yet measured
- Also stated in: § Genome assembly and quality evaluation · boosted
- Findingown data
1.3% of protein-level BUSCO genes were fragmented.
“1.3% (48) fragmented orthologs”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [28] Simao, F. A. et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015). source
The Introduction defines fragmented BUSCO genes, and the Species section reports fragmentation percentages for several example assemblies and gene sets. Neither section reports 1.3% or 48 fragmented orthologs. Searches for the exact figures and for protein-level BUSCO results found no passage supporting that numerical claim. (LLM, conf=0.78)
Experimental — accuracy not yet measured
- Findingown data
0.9% of BUSCO genes were duplicated.
“0.9% (31) as duplicated”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [28] Simao, F. A. et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015). source
The Introduction defines a duplicated BUSCO as a complete gene found in more than one copy. The paper’s assessment table reports duplication percentages for example datasets, but our copy does not report 0.9% (31) as duplicated; searches for that percentage and count found no matching result. (LLM, conf=0.75)
Experimental — accuracy not yet measured
- Findingown data
The authors constructed the first complete telomere-to-telomere (T2T) chromosome-scale genome assembly of X-ray tetra by integrating PacBio HiFi, ONT ultra-long, and Hi-C sequencing technologies.
“we constructed the first complete telomere-to-telomere (T2T) chromosome-scale genome assembly of the X-ray tetra by integration of PacBio HiFi, ONT ultra-long, and Hi-C sequencing technologies.”
- Also stated in: § Background & Summary · plain
“In this study, we constructed a solid T2T chromosome-level genome assembly at the first time for X-ray tetra by integrating PacBio, ONT, and high-throughput chromatin conformation capture (Hi-C) technologies11,12.”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [11] Bian, C. et al. A chromosome-level genome assembly for the astaxanthin-producing microalga Haematococcus pluvialis. Sci Data 10, 511 (2023). source
Checked before — its earlier verdict is held back until a new check runs.
- cites [12] Zhang, K. et al. A chromosome-level reference genome assembly of the Reeve’s moray eel (Gymnothorax reevesii). Sci Data 10, 501 (2023). source
Checked before — its earlier verdict is held back until a new check runs.
- Rests on an assumption: The single X-ray tetra individual collected from a local company in Shanghai is correctly identified as Pristella maxillaris.
- Rests on an assumption: The genome assembly from this single individual is representative of the Pristella maxillaris species.
- Also stated in: § Background & Summary · plain
- Findingown data
The haplotypic assembly spans approximately 1.1 Gb.
“This haplotypic assembly spans approximately 1.1 Gb”
- Also stated in: § Background & Summary · plain
“This haplotypic assembly spans approximately 1.1 Gb and is anchored to 25 chromosomes.”
Quote in the paperNot a substantial claim - Also stated in: § Background & Summary · plain
- Findingown data
1.3% of protein-level BUSCO genes were duplicated.
“1.3% (46) duplicated”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [28] Simao, F. A. et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015). source
A check is scheduled.
- Findingown data
The assembly contains a complete set of 50 telomeres.
“highlighting a complete set of 50 telomeres”
- Also stated in: § Repeat element annotation · plain
“A complete set of 50 telomeres (at both ends of each chromosome with telomeric sequences) were identified”
Quote in the paperSubstantial claim - Also stated in: § Repeat element annotation · plain
- Findingown data
The assembly's QV score was 41.8.
“The assembly’s QV score was 41.8”
- Also stated in: § Technical Validation · plain
“The Merqury QV score of 41.8”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [29] Rhie, A. et al. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol 21 (2020). source
A check is scheduled.
- Also stated in: § Technical Validation · plain
- Findingown data
Approximately 98.4% (27,991 genes) of predicted genes were annotated with at least one database.
“Approximately 98.4% (27,991 genes) of the predicted genes were annotated with at least one database”
Quote in the paperSubstantial claim - Findingown data
Protein-level BUSCO assessment revealed 96.5% completeness.
“A protein-level BUSCO assessment using the Actinopterygii dataset revealed 96.5% (3,512) completeness”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [28] Simao, F. A. et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015). source
A check is scheduled.
- Findingown data
The assembly is anchored onto 25 chromosomes.
“It is anchored onto 25 chromosomes”
- Also stated in: § Genome assembly and quality evaluation · plain
“The final haplotypic genome assembly anchored 25 chromosomes”
Quote in the paperSubstantial claim - Also stated in: § Genome assembly and quality evaluation · plain
- Findingown data
97.1% of BUSCO genes were single-copy.
“with 97.1% as single-copy genes”
- Also stated in: § Technical Validation · plain
“97.1% (3,536) identified as single-copy”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [28] Simao, F. A. et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015). source
- Also stated in: § Technical Validation · plain
- Findingown data
ONT ultra-long sequencing yielded 30.0 Gb of ultra-long reads.
“yielded 30.0 Gb of ultra-long reads”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [17] Chen, Y. et al. Efficient assembly of nanopore reads via highly accurate and intact error correction. Nat Commun 12, 60 (2021). source
Checked before — its earlier verdict is held back until a new check runs.
- Findingown data
PacBio HiFi reads aligned to the genome assembly using Minimap2 achieved a mapping rate of 100.0%.
“PacBio HiFi reads aligned to the genome assembly using Minimap2 achieved a mapping rate of 100.0%.”
Quote in the paperSubstantial claim - Findingown data
The final haplotypic genome assembly represents approximately 97.8% of the assembled contigs.
“which represents ~97.8% of the assembled contigs”
Quote in the paperNot a substantial claim - Findingown data
The assembly contains 25 centromeres.
“and 25 centromeres”
- Also stated in: § Repeat element annotation · plain
“centromeres were present on the all 25 chromosomes”
Quote in the paperNot a substantial claim - Also stated in: § Repeat element annotation · plain
- Findingown data
The N50 value of the anchored chromosomes was increased to 43.9 Mb.
“The N50 value of these anchored chromosomes was increased to 43.9 Mb.”
Quote in the paperNot a substantial claim - Findingown data
The assembly has a contig N50 of 42.8 Mb.
“with a contig N50 of 42.8 Mb”
Quote in the paperSubstantial claim - Findingown data
The authors annotated 28,456 protein-coding genes in the assembled genome.
“annotated 28,456 protein-coding genes”
- Also stated in: § Gene prediction and functional annotation · plain
“a total of 28,456 protein-coding genes were annotated”
Quote in the paperNot a substantial claim - Also stated in: § Gene prediction and functional annotation · plain
- Findingown data
The primary chromosome-level genome assembly contained 188 gaps.
“the primary chromosome-level genome assembly contained 188 gaps”
Quote in the paperSubstantial claim - Findingown data
0.6% of BUSCO genes were fragmented.
“0.6% (22) as fragmented”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [28] Simao, F. A. et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015). source
- Findingown data
95.2% of protein-level BUSCO genes were single-copy.
“with 95.2% (3,466) single-copy”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [28] Simao, F. A. et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015). source
- Premisereasoning
The molecular basis of X-ray tetra's unique transparency remains largely unexplored.
“However, the molecular basis of its unique transparency remains largely unexplored, with availability of limited genomic resources.”
Quote in the paperSubstantial claim - Interpretationown data
The Merqury QV score of 41.8 validates the high quality and reliability of the genome assembly and annotation.
“further validated the high quality and reliability of our genome assembly and annotation”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [29] Rhie, A. et al. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol 21 (2020). source
- Interpretationown data
The protein-level BUSCO assessment confirms high-quality gene annotation.
“confirming high-quality gene annotation”
Quote in the paperSubstantial claim
- Probably not a substantial claim. 6
- It may state two separate claims as one. 9
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
PremisecitationPrevious transcriptomic studies showed that some genes associated with melanin synthesis (tyr and tyrp1) are significantly down-regulated, and expression of purine metabolism pathway genes associated with iridescent cells (gart and hprt) is reduced.
“Previous transcriptomic studies showed that some genes associated with melanin synthesis (i.e., tyr and tyrp1) are significantly down-regulated, and the expression of purine metabolism pathway genes associated with iridescent cells (such as gart and hprt) is reduced3.”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [3] Bian, F. F. et al. Morphological characteristics and comparative transcriptome analysis of three different phenotypes of Pristella maxillaris. Front Genet 10, 698 (2019). source
Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measured
Probably not a substantial claim. The paper’s conclusions may not depend on it.
Findingown dataHi-C sequencing generated approximately 117.3 Gb of high-quality 150 bp paired-end reads.
“generating ~117.3 Gb of high-quality 150 bp paired-end reads”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [18] Chen, S. F. et al. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, 884–890 (2018). source
The Results section (3.2 Quality evaluation) describes a paired-end 150 bp test dataset, but does not report Hi-C sequencing or approximately 117.3 Gb of reads. Searches for “117.3 Gb” and “Hi-C sequencing” found no passage in our copy supporting the attributed yield. (LLM, conf=0.76)
Experimental — accuracy not yet measured
It may state two separate claims as one.
Findingown dataInitial genome assembly using NextDenovo resulted in primary contigs with a total size of approximately 1.1 Gb and a contig N50 of 14.9 Mb.
“resulting in primary contigs with a total size of ~1.1 Gb and a contig N50 of 14.9 Mb”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [19] Hu, J. et al. NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads. Genome Biol 25, 107 (2024). source
Checked before — its earlier verdict is held back until a new check runs.
It may state two separate claims as one.
Findingown dataThe genome contains approximately 514.3 Mb of repetitive sequences, accounting for 46.4% of the genome.
“We predicted 514.3 Mb of repetitive sequences”
- Also stated in: § Repeat element annotation · plain
“The final results discovered that ~514.3 Mb of the X-ray tetra genome comprised repetitive sequences, accounting for 46.4% of the entire genome”
Quote in the paperNot a substantial claim- Also stated in: § Repeat element annotation · plain
Probably not a substantial claim. The paper’s conclusions may not depend on it.
Findingown dataEach gene had an average of 9.7 exons.
“Each gene had an average of 9.7 exons”
Quote in the paperNot a substantial claimProbably not a substantial claim. The paper’s conclusions may not depend on it.
Findingown dataRNA 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 claimProbably not a substantial claim. The paper’s conclusions may not depend on it.
Findingown dataThe average exon length was 191.4 bp.
“and the average exon length was 191.4 bp”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
Findingown dataHiFi sequencing yielded approximately 70.2 Gb of HiFi data with an N50 length of 21.3 kb.
“yielding ~70.2 Gb of HiFi data with an N50 length of 21.3 kb”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [16] Chin, C. S. et al. Nonhybrid, fnished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10, 563–569 (2013). source
Probably not a substantial claim. The paper’s conclusions may not depend on it.
Findingown dataThe average mRNA length of annotated genes is 21,311.9 bp.
“with an average mRNA length of 21,311.9 bp”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
PremisecitationTo date, only mitochondrial genome and transcriptome data have been reported for X-ray tetra, while no complete genome assembly exists.
“To date, only mitochondrial genome9 and transcriptome data3 have been reported, while no complete genome assembly exists.”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [9] Tang, C. B. et al. First determination and analysis of the complete mitochondrial genome of X-ray tetra Pristella maxillaris (Ulrey, 1894) (Actinopteri, Characidae). Mitochondrial DNA B 7, 253–254 (2022). source
Checked before — its earlier verdict is held back until a new check runs.
- cites [3] Bian, F. F. et al. Morphological characteristics and comparative transcriptome analysis of three different phenotypes of Pristella maxillaris. Front Genet 10, 698 (2019). source
Checked before — its earlier verdict is held back until a new check runs.
It may state two separate claims as one.
InterpretationreasoningThe lack of genomics data limits understanding of X-ray tetra's genetic regulatory mechanisms, adaptive evolution, and genetic diversity, restricting its potential for conservation and aquaculture practices.
“This lack of genomics data limits our understanding of its genetic regulatory mechanisms, adaptive evolution, and genetic diversity, hereby restricting its potential for conservative and aquaculture practices.”
Quote in the paperSubstantial claimIt may state two separate claims as one.
Premisenone givenGenomic resources for X-ray tetra remain scarce, hindering exploration of the molecular basis behind its unique transparency.
“Nevertheless, genomic resources for this interesting fish species remains scarce, hindering exploration of the molecular basis behind its unique transparency.”
Quote in the paperSubstantial claimIt may state two separate claims as one.
Interpretationown dataThe X-ray tetra gene annotation is highly complete and reliable.
“highlighting the high completeness and reliability of the X-ray tetra gene annotation”
Quote in the paperSubstantial claimIt may state two separate claims as one.
Interpretationown dataThe assembled X-ray tetra genome exhibits high continuity, reliability, and overall high quality.
“indicating that the assembled X-ray tetra genome exhibits high continuity, reliability, and overall high quality.”
Quote in the paperSubstantial claim
The paper relies on this without support.
The single X-ray tetra individual collected from a local company in Shanghai is correctly identified as Pristella maxillaris.
“A single X-ray tetra individual was collected from a local company in Pudong District, Shanghai, China (121°46′28″E, 31°11′7″N).”
The paper relies on this without support.
The genome assembly from this single individual is representative of the Pristella maxillaris species.
“A single X-ray tetra individual was collected from a local company in Pudong District, Shanghai, China (121°46′28″E, 31°11′7″N).”
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.
Conflicting RNA-seq data volumes
MinorThe RNA-seq methods and Table 1 report 11.7 Gb of data, but the gene-annotation methods say they used approximately 13.91 Gb of RNA-seq data. The text does not explain the additional data.
“The transcriptome-based annotation utilized ~13.91 Gb of RNA-seq data to map the assembled genome with HISAT37.”
“sequencing was performed on a MGISEQ-2000 platform (MGI) to generate 11.7 Gb of 150-bp paired-end reads.”
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Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Cui, Y., Yuan, Y., Bi, W., Wu, B., Cai, M., Fang, M., Shen, W., Wu, X., Han, F., & Wang, Z. (2025) · Advanced Science · doi:10.1002/advs.202506374 · Cited by 7
Telomere-to-telomere-level genome assembly and annotation of the Zi goose Anser cygnoides
Jiang, K., Wang, H., Cong, K., Liu, Y., Yin, J., Ren, X., Chen, Z., Yang, K., Zhang, Y., Wang, Q., et al. (2026) · Scientific Data · doi:10.1038/s41597-026-07143-0 · Cited by 1
Metadata
- Authors
- Bian, C., Hu, C., He, Z., Li, Z., & Shi, Q.
- Affiliations
- Shenzhen University (CN)
- Peking University (CN)
- Corresponding author
- Li, Zigang
- Shi, Qiong
- Venue
- Scientific Data
- Published
- 2025-03-24
- Volume
- 12
- Issue
- 1
- Pages
- 496-496
- ISSN
- 2052-4463 (ISSN-L)
- PMC
- PMC11933249
- OpenAlex
- W4408782444
- Cited by
- 2
- References
- 47
- Citations by year
- 2026: 1 · 2025: 1
- 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-level genome, genome assembly, transparency, centromere, repetitive DNA, protein-coding genes, ornamental fish, selective breeding
- MeSH terms
- Animals, Chromosomes, Telomere, Genome, Characidae
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.
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