AbstractSpangled emperor, Lethrinus nebulosus (Forsskål 1775), is a tropical marine fish of economic and cultural importance throughout the Indo-West Pacific. It is one of the most targeted recreational fishes in the Gascoyne Coast Bioregion of Western Australia where it serves as an indicator species for recreational fishing. Here, we present a highly accurate, near-gapless, chromosome-level, haplotype-phased reference genome assembly of L. nebulosus (Lethrinus nebulosus (Spangled Emperor) genome, fLetNeb1.1; PRJNA1074345), the first for the species and the first high-quality genome representative of the family Lethrinidae. The 1.09 Gb genome was assembled from PacBio HiFi and Dovetail Omni-C proximity ligation sequencing data. The contig N50 is 21–24 Mbp and BUSCO completeness greater than 99%. A preliminary gene annotation identified 24,583 genes with the predicted transcriptome achieving a BUSCO completeness score of 99.1% This resource will facilitate genomic studies to inform the sustainable management of L. nebulosus and other Lethrinids.
Background & SummarySpangled emperor, Lethrinus nebulosus (Forsskål 1775) is a tropical marine fish that is distributed throughout the Indo-West Pacific1. Lethrinus nebulosus is common on reef habitat down to 150 m (Fig. 1) and is sought after by recreational, commercial, charter and customary fishers1. In Australia, there are eight L. nebulosus stocks (at a management or jurisdictional level) from Perth on the southwest coast, across northern Australia to Sydney on the east coast2. In the Ningaloo Marine Park of Western Australia, L. nebulosus is one of the most popular angling fish3. This species also plays important role in the management of the Gascoyne Demersal Scalefish Resource as it is an indicator species, where their stock status is used to infer that of other similar species in the multi-species fishery2,4.Fig. 1Voucher image, species distribution and sampling location (a) voucher image of Lethrinus nebulosus (Forsskål 1775) specimen (fLetNeb1) sequenced in this study (b) a polygon (blue) of Lethrinus nebulosus (Forsskål 1775) distribution range inferred from the Global Biodiversity Information Facility (GBIF)4 records and Ocean Biodiversity Information System (OBIS)35 sightings. (c) Map of the Gascoyne bioregion and voucher sampling location of fLetNeb1 marked with a red dot.Full size imageDispersal of L. nebulosus individuals primarily occurs during the planktonic egg and larval phase, with adults generally considered site-attached5. Previous work indicates that there is a single genetic stock of L. nebulosus in northwestern Australia (Kimberley to Shark Bay), with evidence of genetic connectivity between the east and west coasts5. While large, connected populations typically harbour high genetic diversity and resilience, they may still experience localised population pressures and even declines, particularly in the context of a changing climate6,7. For example, changes in environmental conditions and habitat could affect larval dispersal or mortality, leading to reduced juvenile recruitment or altered distributions. Furthermore, the relatively site-attached nature of adult fish2,5 suggests that populations could be susceptible to localised disturbances, with limited opportunities to move to more suitable environments. Together, these factors could influence the stock sustainability of L. nebulosus.Here, we present a highly accurate, near-gapless, chromosome-level, haplotype-phased reference genome assembly of L. nebulosus. High-quality reference genome assemblies are increasingly considered foundational scientific resources that can facilitate a suite of molecular techniques to support sustainable management and biodiversity conservation. This high-quality genome assembly was generated using PacBio high fidelity (HiFi) long-read sequences (PacBio, CA, USA) scaffolded with Dovetail Genomics Omni-C (Cantata Bio, CA, USA) data and annotated with Illumina short-read (Illumina, CA, USA) transcriptomic data. It represents the first high-quality reference genome for the species and the family Lethrinidae (emperors).MethodsSample collectionAn adult L. nebulosus (356 mm fork length) was caught via fish trap, southwest of Barrow Island, Western Australia (within the Gascoyne Coast Bioregion) in July 2022. Gill and muscle tissue were rapidly aseptically dissected from the specimen to allow for immediate preservation by flash-freezing in liquid nitrogen. Sample collection from this non-model organism was conducted under marine field work conditions and this approach was determined to be the most expedient route to collect fresh flash frozen tissues that were likely to yield ultra-high molecular weight molecules amenable to long-read DNA and RNA sequencing (Department of Primary Industries and Regional Development exemption No. 251003922, see Ethics Declaration). The samples were stored at -80°C until further processing in the laboratory. Initial extraction and QC checks determined that the muscle sample yields insufficient to proceed with downstream workflows, so DNA and RNA extractions and sequencing were performed exclusively on gill tissue. In all cases, a margin was excised and the tissue rinsed thoroughly in deionised water prior to processing to minimise the chance of carryover contamination from parasites or other organisms.Genomic DNA extraction, library construction, and sequencingHigh molecular weight (HMW) genomic DNA was extracted from approximately 25 mg of gill tissue. Tissue was homogenised and pelleted as per the PacBio Nanobind tissue kit (PacBio, CA, USA) protocol using the TissueRuptor II (QIAGEN, Hilden, Germany). Cell lysis, and DNA isolation was performed following the PacBio “Extracting HMW DNA from skeletal muscle using Nanobind” procedure (102-579-200, Dec 2022). The quantity, and fragment length distribution of extracted gDNA were determined using a Qubit 3 Fluorometer with the Qubit dsDNA Broad-Range Assay Kit (Thermo Fisher Scientific, MA, USA), a NanoDrop One (Thermo Fisher Scientific, MA, USA) and a Femto Pulse with the Genomic DNA 165 kb kit (Agilent, CA, USA). A 12,500 bp PacBio HiFi SMRTbell® library was prepared using the PacBio SMRTbell® prep kit 3.0 according to manufacturer’s instructions. The library was sequenced across one and a half SMRT Cells on a PacBio Sequel IIe, producing 35 Gb of HiFi data with an average read length of 9,842 bp (Table 1).Table 1 Raw sequencing data of Lethrinus nebulosus (fLetNeb1).Full size tableChromatin conformation capture proximity ligation library construction and sequencingCryogenic grinding of flash-frozen L. nebulosus gill tissue in liquid nitrogen was used to facilitate the construction of a chromatin conformation capture proximity ligation library (Hi-C)8 using the Dovetail Omni-C proximity Ligation Assay kit, with the Dovetail Omni-C Module and Dovetail Library Module for Illumina kits (Cantata Bio, CA, USA) as per the manufacturer’s protocols. This method of acquiring Hi-C genome conformation data was chosen as it utilises a sequence-independent endonuclease, rather than restriction enzymes, to digest chromatin, providing more uniform sequencing coverage across the genome9,10. Shallow sequencing of the Omni-C libraries was performed on an Illumina iSeq. 100 platform using a 2 × 150 bp paired-end run, generating 725,338 paired reads to assess library complexity. Deep sequencing was then carried out on an Illumina NextSeq. 2000 platform with a 2 × 150 bp paired-end run configuration (Table 1) to generate chromosome conformation data.RNA extraction, library construction and sequencingFlash-frozen gill tissue from the same L. nebulosus specimen was used for an RNA extraction using the Monarch® Total RNA Miniprep Kit (New England Biolabs, MA, USA) following the manufacturers recommendations. The quantity and quality of extracted RNA was assessed using a NanoDrop One, Qubit HS RNA Kit and TapeStation 4150 system High Sensitivity RNA ScreenTape (Agilent, CA, USA). RNA was then concentrated and purified using the Monarch® RNA Cleanup Kit. Subsequently, an RNA-seq library was constructed using the Illumina Stranded mRNA Prep before sequencing on an Illumina NovaSeq. 6000 using 2 × 150 bp reads on a SP flow cell (Table 1).Genome assembly and quality assessmentA chromosome-level reference genome of L. nebulosus was assembled from the data11 following Vertebrate Genomes Project workflows12,13.Raw PacBio HiFi reads were assessed for quality and sequencing adapter contamination using HiFiAdapterFilt v2.014. Unassembled reads were passed through Meryl v1.3 (k = 31)15 and GenomeScope2 v2.016 to generate a genome profile and genome size estimate of 1.09 Gb (Supplementary Figure S1). HiFiasm v0.19.817 was used to produce phased haplotype contig-level assemblies based on filtered HiFi and Omni-C reads.Omni-C reads were aligned to contig-level assemblies using BWA v0.7.1718, followed by detection of ligation junctions and removal of PCR duplicates with pairtools v1.0.219. A final sorted bam file was generated for each haplotype using samtools v1.16.120. Sorted bam files containing alignment results of Omni-C reads to contig-level assemblies for each haplotype were produced following the Omni-C mapping pipeline21 and used to scaffold the assemblies with YAHS v1.2a.222. The scaffolded assemblies underwent decontamination using FCS-GX v0.5.423 and Tiara v1.0.324 to eliminate sequences originating from foreign organisms or mitochondria.PretextMap v0.1.9 (https://github.com/sanger-tol/PretextMap) generated Omni-C contact maps using Omni-C read alignments and decontaminated scaffold-level assemblies for each haplotype. Haplotype assemblies were then concatenated for dual manual curation using PretextView v0.2.5 (https://github.com/sanger-tol/PretextView). The quality of the final curated genome assemblies was assessed using gfastats v1.3.625, analysis of Benchmarking Universal Single-Copy Orthologs (BUSCO) v5.4.726 Actinopterygii genes (actinopterygii_odb10) and Merqury v1.315.The curated L. nebulosus genome assembly was 1,092,800,854 bp, with more than 98.9% of the Haplotype 1 and Haplotype 2 scaffolds assigned to chromosomes (Fig. 2, Table 2). BUSCO analysis indicated that an average of 99.35% complete genes were present in the final assemblies, of which 99.1% were single copy (Table 2). Merqury assessment of the base-level accuracy and completeness resulted in QV scores of 61.26 and 61.17 for Haplotype 1 and Haplotype 2, respectively, and a diploid completeness of 99.61% (Table 2). A chromSyn27 synteny plot based on BUSCO collinearity blocks (minregion = 0 minbusco = 1) showed a high degree of synteny between haplotypes (Supplementary Figure S2).Fig. 2Omni-C linked contact maps of the final curated genome assembly of Lethrinus nebulosus reference genome (fLetNeb1.1) (a) haplotype 1, and (b) haplotype 2. All chromosomes are ordered by length and the statistics detail how many scaffolds were not assigned to chromosomes, the maximum length of these scaffolds (Mb), followed by the percentage of the overall assembly they represent.Full size imageTable 2 Genome assembly statistics of Lethrinus nebulosus reference genome (fLetNeb1.1).Full size tableRepeat annotationA repeat library was generated with RepeatModeler v2.0.528 using the diploid L. nebulosus genome assembly, with the resulting library used to repeat mask the L. nebulosus haplotype 1 genome using RepeatMasker v4.1.528. The repeat annotation table was generated using the RepeatMasker buildSummary.pl script. Telomeres were predicted with Telociraptor (https://github.com/slimsuite/telociraptor) and TIDK (-s AACCCT)29 (Supplementary Figure S2). Overall, RepeatMasker identified 452,320,117 bp of repetitive elements, covering 39.91% of the genome (Table 3), these repetitive regions were enriched at the ends of the chromosomes (Fig. 3), as were the assembly gaps (Fig. 2, Supplementary Figure S2).Table 3 Repetitive elements of the Lethrinus nebulosus reference genome (fLetNeb1.1) haplotype 1 assembly.Full size tableFig. 3Features of the phased haplotype 1 chromosomes of Lethrinus nebulosus reference genome (fLetNeb1.1). Concentric tracks from the outside inward represent chromosomes (numbered by length), gaps (gaps of unknown length appear as 100 bp in the assembly), GC content calculated using BEDTools v2.31.136 using a sliding window of 10,000 bp, and repeat density calculated using RepeatMasker v4.1.5 with a 10,000 bp sliding window. Visualisation created using the R package circlize v0.4.1637,38. Fish graphic © Marinewise.com.au.Full size imageGene annotationThe assembled Lethrinus nebulosus reference genome (fLetNeb1.1) was preliminarily annotated using the Eukaryotic Genome Annotation Pipeline - External (EGAPx) (https://github.com/ncbi/egapx). In total, 24,583 genes (29,167 isoforms) were annotated. The average coding sequence length was 1,858.5 bp with 10.25 exons per gene. The predicted transcriptome was 99.1% complete according to BUSCO (actinopterygii_odb10 n = 3640), with only 23 genes missing. Ribosomal rRNA genes were predicted with Barrnap v0.9 (–kingdom euk) (https://github.com/tseemann/barrnap). Complete ribosomal gene clusters were predicted at the ends of four chromosomes: 17, 18, 20 and 24 (Supplementary Figure S2) in addition to 26 unplaced hap1 scaffolds.A final annotation of the Lethrinus nebulosus reference genome (fLetNeb1.1) will become available based on the NCBI RefSeq pipeline, accessible via umbrella BioProject PRJNA1074345 (https://www.ncbi.nlm.nih.gov/bioproject/1046164).Data RecordsAll data (sequencing and assemblies) for the Lethrinus nebulosus reference genome (fLetNeb1) are deposited in NCBI under the umbrella BioProject PRJNA1074345. The PacBio HiFi, Dovetail Omni-C and Illumina RNA-seq data is accessioned under BioProject PRJNA1107547 and can be found at https://identifiers.org/ncbi/insdc.sra:SRP505806 (2024)11. The assembled genome and assembly information is deposited in NCBI GenBank and is accessible at https://identifiers.org/ncbi/insdc.gca:GCA_045362495.130 (2024) and https://identifiers.org/ncbi/insdc.gca:GCA_045362485.1 (2024)31.Technical ValidationMolecular validation of nominal specimen identityAvailable genetic data indicates that L. nebulosus constitutes a single biological stock in Western Australia32. Nevertheless, cryptic diversity is recognised in other regions33 across the species distribution range (Fig. 1). With this in mind, we performed a molecular validation of the nominal identity of our samples and voucher specimen, to confirm they represent L. nebulosus as opposed to cryptic diversity in the lineage. This step also served to confirm that the datasets contributing to the assembly (Omni-C and PacBio HiFi) matched the nominal species identity (i.e. internal quality control check to confirm that no tube or data swaps had occurred during sample processing). Complete mitochondrial genomes were assembled from both the PacBio HiFi and Omni-C data. The Cytochrome Oxidase I (COI) barcoding gene was mined from the mitochondrial genomes and placed in a phylogeny including all representatives of L. nebulosus that were available on The Barcode of Life Data Systems (BOLD; v4.boldsystems.org) database that included sampling location information. Sequences (n = 70) were trimmed to a consistent 472 bp region and aligned across all taxa, plus representatives of Lethrinus obsoletus, Lethrinus harak and Lethrinus laticaudis as outgroups, using Geneious Prime® 2024.0.7. Phylogenetic analyses were performed in PAUP* v4.0c. Internal model test options identified the Tamura–Nei (TrN) + þ gamma distribution (0.311) as the best model of sequence evolution. A neighbour-joining tree was estimated and bootstrapped with 1000 replicates (Fig. 4).Fig. 4Neighbour-joining tree (TrN + þ) showing clustering of Lethrinus nebulosus COI haplotypes sampled throughout the species distribution range. Major nodes were supported with >50% bootstrap replicates. The barcodes recovered from data generated for the reference genome and specimen reported herein are shown in red.Full size imageThe analysis clustered L. nebulosus diversity into three major clades; the western Indian Ocean and Red Sea, the northern Indian Ocean, and the central Indo-Pacific (Fig. 4). Identical COI haplotypes were recovered from both the PacBio HiFi and Omni-C datasets, these clustered with other representatives nominally identified as L. nebulosus from Australia and the Indo-Pacific. We therefore feel comfortable that this reference genome represents L. nebulosus from Western Australia.Quality control of nucleic acids and extractsThe quality and quantity of extracted DNA was assessed using a Qubit 3 Fluorometer, a NanoDrop One Spectrophotometer and an Agilent Femto Pulse. The DNA extract was determined to be of high molecular weight, with a concentration 326 ng/µl, a Qubit:NanoDrop ratio of 0.84 and an average length of 21,681 bp. The quality of the Omni-C lysate was assessed using a Qubit 3 Fluorometer and 4150 TapeStation system. The Omni-C lysate had a yield of 938 ng and a 91% Chromatin Digestion Efficiency (CDE) metric between the recommended range of 100–2500 bp. RNA quality and quantity was determined using a Qubit 3 Fluorometer and a 4150 TapeStation system. The RNA extract had a concentration of 162 ng/µl and an RNA integrity number (RIN) value of 7.4.Evaluation of the genome assemblyThe quality of the haplotype phased Lethrinus nebulosus reference genome (fLetNeb1.1) assembly was calculated using gfastats v1.3.625, Merqury v1.315 and BUSCO v 5.4.726 using the Actinopterygii lineage database (actinopterygii_odb10). Gfastats v1.3.6 indicated that the N50 (a measure of contiguity) of each haplotype was greater than 20 Mb, with more than 98% of the sequences assigned to chromosomes (Table 2). In addition, both Merqury and BUSCO determined that the Lethrinus nebulosus reference genome (fLetNeb1.1) is more than 99% complete (Table 2). DepthKopy v1.5.134 was used to establish predicted copy numbers for genes, scaffolds, and 100 kb windows based on the single-copy read depth (33.0×) calculated from Complete BUSCO genes. DepthKopy profiles for Complete and Duplicated BUSCO genes are very similar (Supplementary Figure S3) with 27/29 (93.1%) Duplicated BUSCO genes predicted to be genuine biological gene duplications. Profiles for annotated genes and sliding 100 kb windows both confirm that the majority of the genome has been assembled without duplication or collapse (Supplementary Figure S3). Together these metrics indicate that the haplotype phased assembly obtained for Lethrinus nebulosus reference genome (fLetNeb1) is high-quality and meets standards, and quality metrics of the Earth BioGenome Project35 and the Vertebrate Genomes Project13.Ethics declarationIn Western Australia, the Animal Welfare Act 2002 does not require the Department of Primary Industries and Regional Development (DPIRD) to obtain a permit to use animals for scientific purposes unless the species are outside the provisions of the Fish Resources Management Act 1994 and Fish Resources Management Regulations 1995. Nonetheless, sampling was undertaken in strict adherence to the DPIRD Policy for the handling, use and care of marine fauna for research purposes.
Code availability
No custom scripts or code was used in the validation of the dataset. The data analyses used standard bioinformatic tools specified in the methods. The data and code used to generate the figures is available on GitHub: https://github.com/MinderooFoundation/Data_desc_fLetNeb1.
ReferencesFroese, R. & Pauly, D. Fishbase. World Wide Web electronic publication. Version (02/2024), www.fishbase.org (2024).Wakefield, C. et al. Spangled Emperor (2023). (Fisheries Research and Development Corporation, 2023).Cresswell, A. K. et al. Disentangling the response of fishes to recreational fishing over 30 years within a fringing coral reef reserve network. Biol Conserv 237, 514–524, https://doi.org/10.1016/j.biocon.2019.06.023 (2019).Article
MATH
Google Scholar
Secretariat, G. GBIF: GBIF Backbone Taxonomy. https://doi.org/10.15468/39omei. Accessed via https://www.gbif.org/species/2374885 (2024).Berry, O., England, P., Marriott, R. J., Burridge, C. P. & Newman, S. J. Understanding age-specific dispersal in fishes through hydrodynamic modelling, genetic simulations and microsatellite DNA analysis. Molecular Ecology 21, 2145–2159, https://doi.org/10.1111/j.1365-294X.2012.05520.x (2012).Article
PubMed
Google Scholar
Taylor, R. S. et al. High genetic load without purging in caribou, a diverse species at risk. Curr Biol 34 https://doi.org/10.1016/j.cub.2024.02.002 (2024).Vandewoestijne, S., Schtickzelle, N. & Baguette, M. Positive correlation between genetic diversity and fitness in a large, well-connected metapopulation. Bmc Biol 6 https://doi.org/10.1186/1741-7007-6-46 (2008).Belton, J. M. et al. Hi-C: a comprehensive technique to capture the conformation of genomes. Methods 58, 268–276, https://doi.org/10.1016/j.ymeth.2012.05.001 (2012).Article
CAS
PubMed
MATH
Google Scholar
Liu, N. et al. Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C. Epigenet Chromatin 14 https://doi.org/10.1186/s13072-021-00417-4 (2021).Yamaguchi, K. et al. Technical considerations in Hi-C scaffolding and evaluation of chromosome-scale genome assemblies. Molecular Ecology 30, 5923–5934, https://doi.org/10.1111/mec.16146 (2021).Article
CAS
PubMed
PubMed Central
MATH
Google Scholar
Parata, L. et al. Lethrinus nebulosus (Spangled Emperor), fLetNeb1, sequence data, https://identifiers.org/ncbi/insdc.sra:SRP505806 (2024).Larivière, D. et al. Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Nature Biotechnology 42, 367–370, https://doi.org/10.1038/s41587-023-02100-3 (2024).Article
CAS
PubMed
PubMed Central
MATH
Google Scholar
Rhie, A. et al. Towards complete and error-free genome assemblies of all vertebrate species. Nature 592, 737–746 (2021).Article
ADS
CAS
PubMed
PubMed Central
MATH
Google Scholar
Sim, S. B., Corpuz, R. L., Simmonds, T. J. & Geib, S. M. HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly. BMC Genomics 23, 157, https://doi.org/10.1186/s12864-022-08375-1 (2022).Article
PubMed
PubMed Central
Google Scholar
Rhie, A., Walenz, B. P., Koren, S. & Phillippy, A. M. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome biology 21, 1–27 (2020).Article
Google Scholar
Ranallo-Benavidez, T. R., Jaron, K. S. & Schatz, M. C. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nature Communications 11, 1432, https://doi.org/10.1038/s41467-020-14998-3 (2020).Article
ADS
CAS
PubMed
PubMed Central
Google Scholar
Cheng, H. et al. Haplotype-resolved assembly of diploid genomes without parental data. Nature Biotechnology 40, 1332–1335, https://doi.org/10.1038/s41587-022-01261-x (2022).Article
CAS
PubMed
MATH
Google Scholar
Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589–595, https://doi.org/10.1093/bioinformatics/btp698 (2010).Article
CAS
PubMed
PubMed Central
MATH
Google Scholar
Abdennur, N. et al. Pairtools: From sequencing data to chromosome contacts. Plos Comput Biol 20 https://doi.org/10.1371/journal.pcbi.1012164 (2024).Danecek, P. et al. Twelve years of SAMtools and BCFtools. Gigascience 10 https://doi.org/10.1093/gigascience/giab008 (2021).D Genomics. Omni-C: From fastq to final valid pairs bam file, (2021).Zhou, C., McCarthy, S. A. & Durbin, R. YaHS: yet another Hi-C scaffolding tool. Bioinformatics 39, btac808, https://doi.org/10.1093/bioinformatics/btac808 (2023).Article
CAS
PubMed
Google Scholar
Astashyn, A. et al. Rapid and sensitive detection of genome contamination at scale with FCS-GX. Genome Biology 25 https://doi.org/10.1186/s13059-024-03198-7 (2024).Karlicki, M., Antonowicz, S. & Karnkowska, A. Tiara: deep learning-based classification system for eukaryotic sequences. Bioinformatics 38, 344–350, https://doi.org/10.1093/bioinformatics/btab672 (2022).Article
CAS
PubMed
MATH
Google Scholar
Formenti, G. et al. Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs. Bioinformatics 38, 4214–4216, https://doi.org/10.1093/bioinformatics/btac460 (2022).Article
CAS
PubMed
PubMed Central
MATH
Google Scholar
Manni, M., Berkeley, M. R., Seppey, M., Simao, F. A. & Zdobnov, E. M. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Molecular Biology and Evolution 38, 4647–4654, https://doi.org/10.1093/molbev/msab199 (2021).Article
CAS
PubMed
PubMed Central
Google Scholar
Edwards, R. J., Dong, C., Park, R. F. & Tobias, P. A. A phased chromosome-level genome and full mitochondrial sequence for the dikaryotic myrtle rust pathogen, Austropuccinia psidii. BioRxiv, 2022.2004. 2022.489119 (2022).Flynn, J. M. et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proceedings of the National Academy of Sciences 117, 9451–9457 (2020).Article
ADS
CAS
MATH
Google Scholar
A Telomere Identification Toolkit. Zenodo. https://doi.org/10.5281/zenodo.10091385 (2023).Parata, L. et al. Lethrinus nebulosus (Spangled Emperor). Genbank https://identifiers.org/ncbi/insdc.gca:GCA_045362495.1 (2024).Parata, L. et al. Lethrinus nebulosus (Spangled Emperor). Genbank https://identifiers.org/ncbi/insdc.gca:GCA_045362485.1 (2024).Johnson, M., Hebbert, D. & Moran, M. Genetic analysis of populations of north-western Australian fish species. Marine and Freshwater Research 44, 673–685, https://doi.org/10.1071/MF9930673 (1993).Article
MATH
Google Scholar
Healey, A. J. E. et al. Genetic analysis reveals harvested Lethrinus nebulosus in the Southwest Indian Ocean comprise two cryptic species. ICES Journal of Marine Science 75, 1465–1472, https://doi.org/10.1093/icesjms/fsx245 (2018).Article
MATH
Google Scholar
Chen, S. H. et al. Chromosome-level de novo genome assembly of (New South Wales waratah) using long-reads, linked-reads and Hi-C. Molecular Ecology Resources 22, 1836–1854, https://doi.org/10.1111/1755-0998.13574 (2022).Article
CAS
PubMed
MATH
Google Scholar
Lewin, H. A. et al. Earth BioGenome Project: Sequencing life for the future of life. P Natl Acad Sci USA 115, 4325–4333, https://doi.org/10.1073/pnas.1720115115 (2018).Article
ADS
CAS
MATH
Google Scholar
OBIS. Ocean Biodiversity Information System. Intergovernmental Oceanographic Commission of UNESCO, https://obis.org/ (2024).Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842, https://doi.org/10.1093/bioinformatics/btq033 (2010).Article
CAS
PubMed
PubMed Central
MATH
Google Scholar
Gu, Z., Gu, L., Eils, R., Schlesner, M. & Brors, B. circlize Implements and enhances circular visualization in R. Bioinformatics 30, 2811–2812, https://doi.org/10.1093/bioinformatics/btu393 (2014).Article
CAS
PubMed
Google Scholar
Download referencesAcknowledgementsWe acknowledge traditional owners throughout Western Australia, and their continuing connection to the land, sea, and community, including those with connections to Barrow Island from where this specimen was collected. We pay our respects to all Aboriginal people and communities and their cultures, and to Elders both past and present. Logistical support for this project was provided by the Department of Primary Industries and Regional Development (DPIRD), Government of Western Australia. We gratefully acknowledge the crew of RV Naturaliste (DPIRD) for their contributions to sample acquisition. Data described herein was generated via generous support of Minderoo Foundation and resources provided by the Pawsey Supercomputing Research Centre with funding from the Australian Government and the Government of Western Australia.Author informationAuthors and AffiliationsMinderoo OceanOmics Centre at UWA, Oceans Institute, University of Western Australia, Crawley, WA, AustraliaLara Parata, Liam Anstiss, Emma de Jong, Adrianne Doran, Richard J. Edwards, Anna Depiazzi, Ibrahim Faseeh, Lauren Huet, Sang Huynh, Laura Missen, Tyler Peirce, Philipp E. Bayer, Adam J. Bennett, Stephen J. Burnell, Matthew W. Fraser, Priscila Goncalves, Anya Kardailsky, Georgia M. Nester, Jessica Pearce, Eric J. Raes, Sebastian Rauschert, Julie C. Robidart, Ebony M. Thorpe & Shannon CorriganWestern Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, 39 Northside Drive, Hillarys, 6025, WA, AustraliaStephen J. Newman, Samuel D. Payet, Craig L. Skepper & Corey B. WakefieldMinderoo Foundation, Perth, WA, AustraliaMarcelle E. Ayad, Philipp E. Bayer, Adam J. Bennett, Stephen J. Burnell, Madalyn K. Cooper, Matthew W. Fraser, Priscila Goncalves, Anya Kardailsky, Georgia M. Nester, Jessica Pearce, Eric J. Raes, Sebastian Rauschert, Julie C. Robidart, Ebony M. Thorpe & Shannon CorriganAuthorsLara ParataView author publicationsYou can also search for this author in
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PubMed Google ScholarConsortiaOceanOmics CentreAnna Depiazzi, Ibrahim Faseeh, Lauren Huet, Sang Huynh, Laura Missen & Tyler PeirceOceanOmics DivisionMarcelle E. Ayad, Philipp E. Bayer, Adam J. Bennett, Stephen J. Burnell, Madalyn K. Cooper, Matthew W. Fraser, Priscila Goncalves, Anya Kardailsky, Georgia M. Nester, Jessica Pearce, Eric J. Raes, Sebastian Rauschert, Julie C. Robidart & Ebony M. ThorpeContributionsL.P. contributed to data acquisition, genome assembly and curation, data interpretation, drafting and critical review of the manuscript. E.D.J. contributed to genome assembly and curation, and critical review of the manuscript. A.D. and L.A. contributed to data acquisition and critical review of the manuscript. R.J.E. contributed to genome assembly and curation, data interpretation and critical review of the manuscript. S.C. contributed to project administration, sample acquisition, data interpretation and critical review of the manuscript. C.L.S., C.B.W. and S.J.N. contributed sample acquisition, specimen identification and preservation, and critical review of the manuscript. S.D.P. contributed data interpretation and critical review of the manuscript. All authors read and approved the final manuscript. OceanOmics Division and OceanOmics Centre are a consortium of authors contributing to infrastructure, program administration, and delivery that facilitated the production of this dataset.Corresponding authorCorrespondence to
Lara Parata.Ethics declarations
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The authors declare no competing interests.
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Reprints and permissionsAbout this articleCite this articleParata, L., Anstiss, L., de Jong, E. et al. Chromosome-level genome assembly of the spangled emperor, Lethrinus nebulosus (Forsskål 1775).
Sci Data 12, 435 (2025). https://doi.org/10.1038/s41597-025-04690-wDownload citationReceived: 15 October 2024Accepted: 20 February 2025Published: 13 March 2025DOI: https://doi.org/10.1038/s41597-025-04690-wShare this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy to clipboard
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