The DOI matches its Crossref record.
A chromosome-level reference genome assembly of the Reeve’s moray eel (Gymnothorax reevesii)
Abstract
Due to potentially hostile behaviors and elusive habitats, moray eels (Muraenidae) as one group of apex predators in coral reefs all across the globe have not been well investigated. Here, we constructed a chromosome-level genome assembly for the representative Reeve’s moray eel (Gymnothorax reevesii). This haplotype genome assembly is 2.17 Gb in length, and 97.87% of the sequences are anchored into 21 chromosomes. It contains 56.34% repetitive sequences and 23,812 protein-coding genes, of which 96.77% are functionally annotated. This sequenced marine species in Anguilliformes makes a good complement to the genetic resource of eel genomes. It not only provides a genetic resource for in-depth studies of the Reeve’s moray eel, but also enables deep-going genomic comparisons among various eels.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
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?
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.”
From A complete telomere-to-telomere chromosome-level genome assembly of X-ray tetra (Pristella maxillaris) (2025) · cites this paper as [12]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
No references could be resolved yet.
Research works printed but not linked: 65
- Böhlke, E. B. & Smith, D. G. Type catalogue of Indo-Pacific Muraenidae. Proc. Acad. Nat. Sci. Phila. 152, 89–172 (2002). · DOI
- Smith, D. G., Bogorodsky, S. V., Mal, A. O. & Alpermann, T. J. Review of the moray eels (Anguilliformes: Muraenidae) of the Red Sea, with description of a new species. Zootaxa 4704, 1–87 (2019). · DOI
- Smith, D. G. A checklist of the moray eels of the world (Teleostei: Anguilliformes: Muraenidae). Zootaxa 3474, 1–64 (2012). · DOI
- Nelson, J. S., Grande, T. C. & Wilson, M. V. H. Fishes of the World. (John Wiley & Sons, 2016). · DOI
- Mohapatra, A., Mohanty, S. R., Smith, D. G., Mishra, S. S. & Roy, S. Gymnothorax odishi sp. nov. (Muraenidae: Muraeninae), a short brown unpatterned moray eel from Bay of Bengal, India. Zootaxa 4420, 123–130 (2018). · DOI
- Reece, J. S., Bowen, B. W., Smith, D. G. & Larson, A. Molecular phylogenetics of moray eels (Muraenidae) demonstrates multiple origins of a shell-crushing jaw (Gymnomuraena, Echidna) and multiple colonizations of the Atlantic Ocean. Mol. Phylogenet. Evol. 57, 829–835 (2010). · DOI
- Ramos-Castro, M., Loh, K. H. & Chen, H. M. A descriptive and comparative neurocranium morphology of Anguilliformes fishes in Taiwan waters. Zootaxa 5023, 509–536 (2021). · DOI
- Arai, T. Ecology and evolution of migration in the freshwater eels of the genus Anguilla Schrank, 1798. Heliyon 6, e05176 (2020). · DOI
- López, J. A., Westneat, M. W. & Hanel, R. The phylogenetic affinities of the mysterious Anguilliform genera Coloconger and Thalassenchelys as supported by mtDNA sequences. Copeia 2007, 959–966 (2007). · DOI
- Reece, J. S. & Mehta, R. S. Evolutionary history of elongation and maximum body length in moray eels (Anguilliformes: Muraenidae). Biol. J. Linn. Soc. 109, 861–875 (2013). · DOI
- Brown, J. H. & Lasiewski, R. C. Metabolism of weasels: the cost of being long and thin. Ecology 53, 939–943 (1972). · DOI
- Schmidt-Nielsen, K. & Knut, S.N. Scaling: why is animal size so important? (Cambridge university press, 1984). · DOI · Paper page
- Damas, J., Corbo, M. & Lewin, H. A. Vertebrate chromosome evolution. Annu. Rev. Anim. Biosci. 9, 1–27 (2021). · DOI
- Wang, H. et al. A Chromosome-level assembly of the Japanese eel genome, insights into gene duplication and chromosomal reorganization. Gigascience 11, giac120 (2022). · DOI
- Ronchetti, E., Salvadori, S. & Deiana, A. M. Genome size and AT content in Anguilliformes. Eur. J. Histochem. 39, 259–264 (1995).
- Prokofiev, A. M. Additions to the species composition of morays of the Bay of Nha Trang (South China Sea, central Vietnam)(Anguilliformes: Muraenidae). J. Ichthyol. 50, 38–43 (2010). · DOI
- Chen, H. M., Shao, K. T. & Chen, C. T. A review of the muraenid eels (Family Muraenidae) from Taiwan with descriptions of twelve new records. Zool. Stud. 33, 44–64 (1994).
- Ramos-Castro, M., Chen, H. M. & Mao, B. S. Descriptions of neurocranium morphology in 34 species of moray eels (Muraenidae) found in Taiwan. Zootaxa 4810, 081–109 (2020). · DOI
- Blake, J. A., Bult, C. J., Kadin, J. A., Richardson, J. E. & Eppig, J. T. The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics. Nucleic Acids Res. 39, D842–D848 (2011). · DOI
- Luo, R. et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1, 18 (2012). · DOI
- Rhoads, A. & Au, K. F. PacBio Sequencing and Its Applications. Genom. Proteom. Bioinform. 13, 278–289 (2015). · DOI
- Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018). · DOI · Paper page
- Vurture, G. W. et al. GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics 33, 2202–2204 (2017). · DOI
- Deorowicz, S., Kokot, M., Grabowski, S. & Debudaj-Grabysz, A. KMC 2: fast and resource-frugal k-mer counting. Bioinformatics 31, 1569–1576 (2015). · DOI
- Sun, H., Ding, J., Piednoël, M. & Schneeberger, K. findGSE: estimating genome size variation within human and Arabidopsis using k-mer frequencies. Bioinformatics 34, 550–557 (2018). · DOI
- Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods 18, 170–175 (2021). · DOI · Paper page
- Hu, J., Fan, J., Sun, Z. & Liu, S. NextPolish: a fast and efficient genome polishing tool for long-read assembly. Bioinformatics 36, 2253–2255 (2020). · DOI
- Rhie, A., Walenz, B. P., Koren, S. & Phillippy, A. M. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 21, 245 (2020). · DOI · Paper page
- Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015). · DOI · Paper page
- Parra, G., Bradnam, K. & Korf, I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23, 1061–1067 (2007). · DOI
- Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018). · DOI · Paper page
- Formenti, G. et al. Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs. Bioinformatics 38, 4214–4216 (2022). · DOI
- Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012). · DOI · Paper page
- Servant, N. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 16, 259 (2015). · DOI · Paper page
- Burton, J. N. et al. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat. Biotechnol. 31, 1119–1125 (2013). · DOI · Paper page
- Durand, N. C. et al. Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom. Cell Syst. 3, 99–101 (2016). · DOI
- Chen, N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinformatics 5, 4.10.1–4.10.14 (2004). · DOI
- Han, Y. & Wessler, S. R. MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences. Nucleic Acids Res. 38, e199 (2010). · DOI
- Jurka, J. et al. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110, 462–467 (2005). · DOI
- Abrusán, G., Grundmann, N., DeMester, L. & Makalowski, W. TEclass—a tool for automated classification of unknown eukaryotic transposable elements. Bioinformatics 25, 1329–1330 (2009). · DOI
- Shao, F., Han, M. & Peng, Z. Evolution and diversity of transposable elements in fish genomes. Sci. Rep. 9, 15399 (2019). · DOI
- Hao, Z. et al. RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms. PeerJ Comput. Sci. 6, e251 (2020). · DOI
- Keilwagen, J. et al. Using intron position conservation for homology-based gene prediction. Nucleic Acids Res. 44, e89 (2016). · DOI
- Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013). · DOI · Paper page
- Haas, B. J. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol. 9, R7 (2008). · DOI
- Kovaka, S. et al. Transcriptome assembly from long-read RNA-seq alignments with StringTie2. Genome Biol. 20, 278 (2019). · DOI
- Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644–652 (2011). · DOI
- Stanke, M., Diekhans, M., Baertsch, R. & Haussler, D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24, 637–644 (2008). · DOI · Paper page
- Bairoch, A. et al. The universal protein resource (UniProt). Nucleic Acids Res. 33, D154–D159 (2005). · DOI · Paper page
- Ogata, H. et al. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 27, 29–34 (1999). · DOI · Paper page
- Galperin, M. Y., Makarova, K. S., Wolf, Y. I. & Koonin, E. V. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res. 43, D261–D269 (2015). · DOI
- The Gene Ontology Consortium. The Gene Ontology resource: 20 years and still GOing strong. Nucleic Acids Res. 47, D330–D338 (2019). · DOI · Paper page
- Wang, Y. et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 40, e49 (2012). · DOI · Paper page
- Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639–1645 (2009). · DOI
- Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307–321 (2010). · DOI · Paper page
- Ronquist, F. et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539–542 (2012). · DOI
- Yang, Z. H. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007). · DOI · Paper page
- Tang, K. L. & Fielitz, C. Phylogeny of moray eels (Anguilliformes: Muraenidae), with a revised classification of true eels (Teleostei: Elopomorpha: Anguilliformes). Mitochondrial DNA 24, 55–66 (2013). · DOI
- Barth, J. M. I. et al. Stable species boundaries despite ten million years of hybridization in tropical eels. Nat. Commun. 11, 1433 (2020). · DOI
- Rabosky, D. L. et al. Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nat. Commun. 4, 1958 (2013). · DOI
- NCBI Bioproject https://www.ncbi.nlm.nih.gov/bioproject/PRJNA934055 (2023).
- Park, E. H. & Kang, Y. S. Karyotype conservation and difference in DNA amount in Anguilloid fishes. Science 193, 64–66 (1976). · DOI
- Vasconcelos, A. J. M. & Molina, W. F. Cytogenetical studies in five Atlantic Anguilliformes fishes. Genet. Mol. Biol. 32, 83–90 (2009). · DOI
- Kai, W. et al. A ddRAD-based genetic map and its integration with the genome assembly of Japanese eel (Anguilla japonica) provides insights into genome evolution after the teleost-specific genome duplication. BMC Genomics 15, 233 (2014). · DOI
- Tang, H. et al. Synteny and collinearity in plant genomes. Science 320, 486–488 (2008). · DOI
Cited by
Sorted by citations
Bian, C., Hu, C., He, Z., Li, Z., & Shi, Q. (2025) · Scientific Data · doi:10.1038/s41597-025-04824-0 · Cited by 2
Self-citation
Metadata
- Authors
- Zhang, K., Huang, Y., Zhang, Y., Liang, R., Li, Q., Li, R., Zhao, X., Bian, C., Chen, Y., Wu, J., Shi, Q., & Lin, L.
- Venue
- Scientific Data
- Published
- 2023-07-29
- Volume
- 10
- Issue
- 1
- ISSN
- 2052-4463
- PMC
- PMC10387071
- Cited by
- 8
- References
- 0
- Language
- en
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.
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 ›
Are you an author, or do you see a problem with this page? Request a review