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. 2025 Mar 24;12:496. doi: 10.1038/s41597-025-04824-0

A complete telomere-to-telomere chromosome-level genome assembly of X-ray tetra (Pristella maxillaris)

Chao Bian 1,#, Changxing Hu 1,2,#, Zhe He 1, Zigang Li 2,✉, Qiong Shi 1,✉
PMCID: PMC11933249  PMID: 40128533

Abstract

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.

Subject terms: Agricultural genetics, Genome

Background & Summary

X-ray tetra (Pristella maxillaris, Ulrey 1894) has attracted considerable attention for its nearly transparent body since its initial description in 1894. Native to the lower Amazon River basin in Brazil, Venezuela, and Guyana, it is widely distributed across the coastal river systems of northern South America, east of the Andes1. It is classified under the phylum Chordata, class Actinopterygii, order Characiformes, family Characidae, and genus Pristella. This specie spotlights an albino variant with full-body transparency at the adult stage, permitting skeletal and internal structures to be visible, particularly in abdominal regions2. This distinct transparency has made it highly popular in the world ornamental fish market, especially after its introduction to China in the 1990s3.

Adapted to both freshwater and brackish environments, the X-ray tetra can tolerate water temperatures from 22 and 30 °C and survives in cold conditions up to 12 °C3. It presents a silvery-white body with yellow tinged, black-spotted dorsal and anal fins bordered by white, and a deeply forked caudal fin with red markings. Its adipose fin lacks bony support, positioned between the dorsal and caudal fins1. Due to its remarkable transparency, the X-ray tetra is widely used as a model organism for extensive studies on chromatophore development, transparency mechanism, and molecular basis of adaptive coloration.

Despite its popularity for research and trade, international investigations on the X-ray tetra have focused primarily on its ecological adaptability4, morphological features5,6, and behavioral traits7,8. The transparent phenotype of X-ray tetra is attributed to the absence or reduction of melanophores, iridophores, and xanthophores, coupled with a thin and translucent dermal layer. 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. However, the molecular basis of its unique transparency remains largely unexplored, with availability of limited genomic resources. To date, only mitochondrial genome9 and transcriptome data3 have been reported, while no complete genome assembly exists. 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.

Recent advancements in high-throughput sequencing technologies have permitted molecular research in evolutionary analysis, functional gene discovery, and genomics-based breeding10. 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. This haplotypic assembly spans approximately 1.1 Gb and is anchored to 25 chromosomes. These genomics data lay the foundation for in-depth investigations on genomic architecture, functional genes, and genetic traits of this economically important fish.

Methods

Sample collection and DNA extraction

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). Muscle tissue was immediately flash-frozen in liquid nitrogen and stored at −80 °C for further use. Genomic DNA (gDNA) was extracted using a TIANamp Genomic DNA Extraction Kit (Tiangen, Beijing, China), following the manufacturer’s protocol to obtain high-molecular-weight DNA for subsequent whole genome sequencing13.

DNA concentration and purity were measured on a Qubit 3.0 Fluorometer (Thermo Fisher Scientific, Waltham, MA, USA) and a Nanodrop spectrophotometer (Thermo Fisher Scientific)14 respectively, and integrity was verified on a 1.0% agarose gel. Animal experiments complied with the Ministry of Science and Technology of China’s humane treatment guidelines and were approved by Shenzhen University’s Animal Care and Use Committee.

Library preparation for genome and transcriptome sequencing

PacBio HiFi long-read sequencing

DNA libraries were prepared using the SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences, Menlo Park, CA, USA) following the PacBio’s standard protocol, and then sequenced on a PacBio Sequel II platform15. High-accuracy consensus reads were generated using the Circular Consensus Sequencing (CCS, SMRT Link v11.0) software16, yielding ~70.2 Gb of HiFi data with an N50 length of 21.3 kb (Table 1).

Table 1.

Statistics of the T2T genome assembly and annotation.

Parameter Value
HiFi reads (Gb) 70.2
Hi-C reads (Gb) 117.3
ONT reads (Gb) 30.0
RNA-seq data (Gb) 11.7
Genome size (Gb) 1.1
Contig N50 (Mb) 42.8
BUSCO 98.0%
Protein BUSCO 96.5%
Repeat ratio 46.4%
Gene number 28,456
Average gene length (bp) 21311.9
Functional gene number 27,991
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ONT ultra-long sequencing

A ultra-long library was prepared using an SQK-ULK001 kit according to the guidance from the manufacturer (Oxford Nanopore Technologies, UK). Sequencing on a PromethION flow cell (Oxford Nanopore Technologies) yielded 30.0 Gb of ultra-long reads after being processed with NECAT v200221 with default parameters17.

Hi-C Sequencing

Hi-C libraries were prepared from the fresh muscle sample using a GrandOmics Hi-C kit and DpnII restriction enzyme according to the manufacturer’s protocol (GrandOmics, Wuhan, China). In brief, gDNA was cross-linked, digested, biotin-labeled, ligated, and fragmented to 500 bp, followed by purification with streptavidin magnetic beads. Library quality and insert size were assessed using a Qubit 3.0 Fluorometer and an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), respectively. Libraries were sequenced on an Illumina NovaSeq. 6000 platform (Illumina, San Diego, CA, USA), generating ~117.3 Gb of high-quality 150 bp paired-end reads after being processed with Fastp v0.20.0 (https://github.com/OpenGene/fastp)18.

RNA sequencing

Total RNA was extracted from muscle tissue by using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) in accordance with the manufacturer’s instructions. RNA integrity was verified using an Agilent 2100 Bioanalyzer, and only those samples with an RNA Integrity Number (RIN) above 7.0 were selected for subsequent library preparation. Libraries were constructed using the DNA nanoball (DNB) technology on a DNBSEQ T7 platform (MGI, BGI Shenzhen, China), and sequencing was performed on a MGISEQ-2000 platform (MGI) to generate 11.7 Gb of 150-bp paired-end reads.

Genome assembly and quality evaluation

A genome assembly of X-ray tetra was initially completed using NextDenovo19 (v2.2-beta.0, https://github.com/Nextomics/NextDenovo) with the following parameters: -rerun 3 -read_cutoff 1k -pa_correction 2, resulting in primary contigs with a total size of ~1.1 Gb and a contig N50 of 14.9 Mb. Subsequently, Hi-C sequencing data were mapped to these assembled contigs using Bowtie2 v2.2.5 (parameters: --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end –reorder)20, and then effective linkage products were detected using HiC-Pro v2.8.121 under default settings, retaining only valid contact pairs to support the anchoring of contigs to chromosomes. To orient, order, and cluster contigs into chromosome-level scaffolds, we applied Juicer v1.5 (parameter: chr num 25)22 and 3D-DNA v170123 (parameters: -m haploid -r 2)23. Visualization and manual corrections were performed with Juicebox v1.11.0824 to adjust mis-assemblies and eliminate redundant contigs.

However, the primary chromosome-level genome assembly contained 188 gaps. To achieve a gap-free and T2T level assembly, LR_GapCloser v1.0 (parameters: -t 35 -m 1000000 -v 10000)25 and TGS-GapCloser v1.0.1 (parameter: -min_match 2000)26 were sequentially employed to fill these gaps. Centromere and telomere sequences were identified by using the QuarTeT software27. The final haplotypic genome assembly anchored 25 chromosomes (Figs. 1 and 2) with a total length of 1.1 Gb (Fig. 1, Table 2), which represents ~97.8% of the assembled contigs. The N50 value of these anchored chromosomes was increased to 43.9 Mb.

Fig. 1.

Fig. 1

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A Circos image of the 25 anchored chromosomes within the haplotypic genome. Data from the outside to the inside include the length and number of each chromosome, gene density distribution (bin = 1 Mb), repetitive sequence density (bin = 1 Mb), GC content (bin = 1 Mb), and a fish photo (in the center).

Fig. 2.

Fig. 2

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Chromosome heatmap of the Hi-C data. A total of 25 chromosomes were anchored for the hyplotypic genome.

Table 2.

Summary of the complete T2T chromosomes (Chr) in the assembled P. maxillaris genome.

Chr ID Chr Length (bp) Gap number Telomere number GC (%) Centromere start Centromere end Left number of telomere motifs Right number of telomere motifs
Chr1 103,378,760 0 2 38.32 75,632,438 75,762,961 68 35
Chr2 68,543,615 0 2 38.65 218,964 586,362 159 34
Chr3 51,255,812 0 2 38.68 48,013,427 48,171,079 313 36
Chr4 50,169,974 0 2 38.39 46,583,736 46,777,535 191 100
Chr5 49,437,457 0 2 38.65 13,894,232 14,284,261 146 65
Chr6 49,378,772 0 2 38.59 12,605,947 13,780,125 285 69
Chr7 46,097,283 0 2 38.82 20,127,014 20,261,987 144 319
Chr8 46,052,650 0 2 38.66 19,846,217 20,120,613 213 49
Chr9 44,084,817 0 2 38.72 9,379,270 10,726,203 80 101
Chr10 43,935,422 0 2 38.61 31,390,091 31,734,292 270 117
Chr11 42,828,344 0 2 39.02 21,401,988 21,656,115 136 307
Chr12 42,365,502 0 2 38.74 28,490,231 28,685,355 43 32
Chr13 41,184,826 0 2 38.61 31,295,681 31,493,960 48 43
Chr14 39,148,021 0 2 38.91 13,501,201 13,612,152 68 29
Chr15 38,797,547 0 2 38.77 34,806,423 34,917,167 31 111
Chr16 38,869,987 0 2 38.71 17,895,531 18,044,413 89 90
Chr17 37,822,013 0 2 38.99 5,199,257 5,351,441 60 166
Chr18 37,229,363 0 2 38.90 18,676,837 18,814,355 496 102
Chr19 36,416,246 0 2 39.12 15,114,627 15,252,090 433 39
Chr20 31,634,620 0 2 38.87 7,930,687 8,214,206 27 195
Chr21 30,622,564 0 2 38.96 26,468,809 26,761,178 48 56
Chr22 29,995,524 0 2 38.99 13,270,294 13,394,048 64 96
Chr23 30,150,453 0 2 39.20 17,301,026 17,510,512 25 251
Chr24 28,239,184 0 2 39.19 18,636,580 19,320,411 103 37
Chr25 27,287,464 0 2 38.67 16,643,226 17,036,456 98 46
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To evaluate genome completeness and accuracy, Benchmarking Universal Single-Copy Orthologs v5.2.2 (BUSCO)28 was utilized, employing the Actinopterygii odb10 dataset as the reference. Moreover, genome quality was assessed using the K-mer-based tool Merqury v1.3 (https://github.com/marbl/merqury)29 with a K-mer size of 19. This analysis compared K-mer frequency distributions between the genome assembly and whole-genome HIFI sequencing data, producing good metrics for genome completeness and quality values (QV). Our results demonstrated that 98.0% of complete BUSCO genes were discovered (Table 1), with 97.1% as single-copy genes. The assembly’s QV score was 41.8, indicating that the assembled X-ray tetra genome exhibits high continuity, reliability, and overall high quality.

Repeat element annotation

In the chromosome-scale genome assembly of X-ray tetra, repeat elements (REs) were characterized by using a combination of de novo and homology-based approaches. For the de novo prediction, RepeatModeler v2.0.130 and LTR-FINDER v1.0.631 were applied to develop a custom repeat library. Subsequently, RepeatMasker v4.1.032 was employed with default parameters to annotate REs in the genome based on the Repbase TE library v21.0133. For the homology-based approach, Tandem Repeats Finder v4.07 with optimized parameters (2 7 7 80 10 50 2000 -d -h)34 was utilized to identify tandem repeat sequences, while RepeatMasker v4.1.032 and RepeatProteinMask v4.1.032 were applied to annotate transposable elements (TEs) in the assembled genome with default settings. Centromere and telomere sequences were identified by using the quarTeT27 software.

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 (Table 1). A complete set of 50 telomeres (at both ends of each chromosome with telomeric sequences) were identified, and centromeres were present on the all 25 chromosomes (see more details in Fig. 3). This comprehensive repeat annotation provides a solid foundation for subsequent gene prediction and functional analysis.

Fig. 3.

Fig. 3

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Repeat distribution, telomere and centromere locations in the P. maxillaris genome. Arrows mark the complete set of 50 telomeres.

Gene prediction and functional annotation

To construct a comprehensive gene set for X-ray tetra, we utilized a combination of ab initio prediction, homology-based annotation, and transcriptome-based annotation to predict protein-coding genes14. For the homology-based annotation, protein sequences from four representative teleost species, including Danio rerio (zebrafish; GCF_000002035.6), Oryzias latipes (medaka; GCF_002234675.1), Takifugu rubripes (Japanese puffer; GCF_901000725.2), and Tetraodon nigroviridis (green spotted puffer; GCA_000180735.1) were downloaded from the NCBI database. These sequences were aligned to the assembled X-ray tetra genome using tBLASTn (with an e-value of 10−5)35, followed by further gene structure refinement with GeneWise v2.2.036 (parameters: –blast_eval 1e-5 –align_rate 0.5–extend_len 500). The transcriptome-based annotation utilized ~13.91 Gb of RNA-seq data to map the assembled genome with HISAT37. These RNA-seq alignments were then analyzed using Cufflinks v2.2.1 (http://cole-trapnell-lab.github.io/cufflinks/) to identify gene structures. These results from the three methods were then integrated by using MAKER (parameters: max_dna_len = 300000, min_contig = 500, pred_flank = 500, AED_threshold = 1, split_hit = 30000, single_exon = 1, single_length = 250, tries = 2)38 to create a non-redundant gene set.

For subsequent functional annotation, predicted protein sequences were compared against six public databases, including NCBI NR39, Swiss-Prot40, GO41, TrEMBL39, KOG42, and KEGG43, using BLASTP (e-value < 1e-5). Gene Ontology (GO) terms were also assigned using InterProScan44. Finally, a total of 28,456 protein-coding genes were annotated, with an average mRNA length of 21,311.9 bp. Each gene had an average of 9.7 exons, and the average exon length was 191.4 bp. Approximately 98.4% (27,991 genes) of the predicted genes were annotated with at least one database, highlighting the high completeness and reliability of the X-ray tetra gene annotation (Table 1, Fig. 3).

Data Records

The final genome assembly, gene set, and raw sequencing reads for P. maxillaris are publicly accessible on the NCBI and GenBank under accession numbers PRJNA1190323 and GCA_045781885.145. Annotated coding sequences and protein sequences have been archived on Figshare (10.6084/m9.figshare.27901167)46. Additionally, raw reads obtained by PacBio, ONT and Illumina sequencing are available on the NCBI under accession number SRP55270847.

Technical Validation

We constructed the 25 chromosomes for P. maxillaris with a high-quality Hi-C assembly. PacBio HiFi reads aligned to the genome assembly using Minimap2 achieved a mapping rate of 100.0%. Completeness was further evaluated with BUSCO v.5.2.2, using the Actinopterygii database (3,640 single-copy orthologs; OrthoDB v.10) as the reference. In short, our results indicated that 98.0% (3,567) of BUSCO genes were complete, with 97.1% (3,536) identified as single-copy, 0.9% (31) as duplicated, and 0.6% (22) as fragmented. A protein-level BUSCO assessment using the Actinopterygii dataset revealed 96.5% (3,512) completeness, with 95.2% (3,466) single-copy, 1.3% (46) duplicated, and 1.3% (48) fragmented orthologs, confirming high-quality gene annotation. The Merqury QV score of 41.8 further validated the high quality and reliability of our genome assembly and annotation.

Acknowledgements

This study was supported by Shenzhen Special Fund for Sustainable Development (no. KCXFZ20211020164013021), Guangxi Major Program for Science and Technology (no. GuikeAA24263042), and the Engineering Laboratory Support Program from Development and Reform Commission of Shenzhen Municipality (no. XMHT20220104019).

Author contributions

Q.S. and C.B. conceived this project; C.H and C.B. collected samples; C.B., C.H, Z.H., and Q.S assembled the genome and performed annotation; C.B., C.H and Z.L analyzed the data. C.B., C.H, Z.H. and Q.S wrote the manuscript; Q.S. and Z.L revised the manuscript. All authors have read and approved the final manuscript for publication.

Code availability

All scripts and pipelines used for the genome assembly and gene annotation followed the standard manuals and protocols of the applied bioinformatics software. No specific code was developed for this study.

Competing interests

The authors declare no competing interests.

Footnotes

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

These authors contributed equally: Chao Bian, Changxing Hu.

Contributor Information

Zigang Li, Email: lizg@pkusz.edu.cn.

Qiong Shi, Email: shiqiong@genomics.cn, Email: shiqiong@szu.edu.cn.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Citations

  1. Bian, C. et al. The genome and annotation of Pristella maxillaris. Figshare10.6084/m9.figshare.27901167 (2024).
  2. NCBI Sequence Read Archivehttps://identifiers.org/ncbi/insdc.sra:SRP552708 (2025).

Data Availability Statement

All scripts and pipelines used for the genome assembly and gene annotation followed the standard manuals and protocols of the applied bioinformatics software. No specific code was developed for this study.

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