Chromosome-level genome assembly of the spangled emperor, Lethrinus nebulosus (Forsskål 1775)

The first data note from the Ocean Genomes project is now out in Scientific Data - a first-in-family genome from the emperor breams.

Parata L, Anstiss L, de Jong E, Doran A, Edwards RJ, Newman SJ, Payet SD, Skepper CL, Wakefield CB, OceanOmics Centre, OceanOmics Division & Corrigan S (2025): Chromosome-level genome assembly of the spangled emperor, Lethrinus nebulosus (Forsskål 1775). Scientific Data 12:435. DOI: 10.1038/s41597-025-04690-w.

Abstract

Spangled 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.

So long, Ocean Genomes... and thanks for all the fish!

After a successful couple of years, today was my last day at UWA. I am proud of the team that I helped to build at the Minderoo Oceanomics Centre at UWA, and the things we have accomplished together. The UWA Oceans Institute has been a fantastic place to work, and I look forward to completing some exciting ongoing collaborations in my capacity as adjunct. It's been exciting to see Ocean Genomes grow from a concept with a largely empty lab to a fully-fledged genome factory capable of generating multiple high-quality genomes a week. The associated publications should hopefully be following soon, and I look forward to continued collaboration with the team as an Oceans Institute adjunct.

Developments in DNA sequencing technology over the past few years have been immense, but the most impressive part for me has been witnessing the laboratory technical team optimising the sample preparations for sequencing. Everything gets so much harder when you move from human samples (the focus of most methods development and testing) into non-model organisms, and I am convinced that the quality of genomes we’ve been producing is in large part due to the quality of the DNA going into the sequencers.

I am now looking for my next challenge and am officially Open For Work. We’ll be moving back to Dublin at the end of January. If you are based in Ireland and need an experienced interdisciplinary problem solver with broad expertise across bioinformatics and biomolecular science, please get in touch! Academic and non-academic opportunities are welcome.

#ABACBS2024 Poster 102: Improving phased Hifiasm assemblies with 20 kb ONT reads

After a great presentation this morning by Emma de Jong on our High-Quality Genomes for Australian Lutjanidae Species (abstract below), if you’re at ABACBS2024 then please drop by Poster #102 to find out about some of the work we’re doing with ONT data.

Abstracts

Improving phased Hifiasm assemblies with 20 kb ONT reads

Richard J Edwards, Adrianne Doran, Emma de Jong, Lara Parata, Shannon Corrigan

The quality and quantity of genome assembly has improved dramatically over recent years. Many large-scale genome projects combine assembly of HiFi and HiC reads using Hifiasm to produce contiguous phased assemblies, scaffolded to chromosome-level. Nevertheless, HiFi reads are typically under 25 kb and can still struggle to assemble long, low diversity repeat regions. Obtaining ultra-long (100 kb or longer) ONT reads to solve this problem remains a significant challenge due to technical constraints and DNA sample requirements. Here, we explore the utility of using standard ONT long reads (20 kb or more) as “ultra-long” input to improve phased Hifiasm assemblies for 22 species of bony fish (Genome Size, 627 Mb 1.54 Gb). We also explore whether the new --telo-m mode in Hifiasm v0.9.0 improves telomere prediction. Incorporating 20kb+ ONT reads (7.8X 93.5X) significantly increased assembly contiguity. BUSCO Completeness was not significantly altered, although there was some re-partitioning of BUSCO genes between phased haplotypes for some species. Improvement did not strongly correlate with read depth (either HiFi or ONT), suggesting that the underlying read length distributions and/or specific genome features are more important for determining the outcome. Hifiasm --telo-m mode significantly increased telomere recovery, assembling over six times the number of gapless telomere-to-telomere chromosomes when combined with 20kb+ ONT reads. Verification of how these results translate to the ease of curation and/or quality of final HiC-scaffolded chromosome-level assemblies is ongoing, with a goal to determine whether the additional sample preparation and sequencing in the lab is cost-effective.

High-Quality Genomes for Australian Lutjanidae Species

Emma de Jong, Lara Parata, Philipp E Bayer, Shannon Corrigan, Richard J Edwards

Lutjanidae (snappers) are highly valued in commercial and recreational fisheries worldwide and serve as indicator species of the health of marine environments and fishery bioregions in Western Australia. Comprehensive genomic mapping of immune gene families of Lutjanidae species are lacking, but this information is critical for understanding disease vulnerability, the impact of environmental stress, improving aquaculture efforts and to provide insights into the health of wild populations. Despite their importance, only 3 out of 113 Lutjanid species currently have available reference genomes, two of which are highly fragmented (>11,000 and >200,000 contigs), impacting studies on gene families relevant to aquaculture. In this study, we present high-quality chromosome-level reference genomes for 14 Australian Lutjanidae species across seven genera, generated using HiFi and HiC data. We present initial comparative genomic analyses, including immune gene content and chromosomal synteny analyses across species. These analyses provide insights into the genomic architecture and evolutionary relationships within Lutjanidae. Ongoing work aims to comprehensively map and compare the immune gene family repertoire across Lutjanidae genera, as well as Lethrinidae species as an outgroup, to determine genus-specific changes in genes (e.g. loss, selection, duplication) important for pathogen detection, antigen presentation, inflammation, and immune memory. These genome assemblies will serve as a foundational resource to the wider scientific community interested in Lutjanidae

Towards telomere-to-telomere fish genomes with Oxford Nanopore Technologies gap-filling

It was a pleasure to be invited to the “What You’re Missing Matters” tour at Perth, and present some ongoing work investigating the best way to incorporate Oxford Nanopore Technologies data into our high-quality HiFi+HiC fish genomes. The results are too preliminary to share here (and will soon be superseded) but do get in touch if it sounds interesting to you.

Toward genome assemblies for all marine vertebrates: current landscape and challenges

The first Ocean Genomes paper is now out! This one is a small commentary piece, but some high-quality genomes are on their way - watch this space. Well, actually, watch this space at Genomes on a Tree!

de Jong E, Parata L, Bayer PE, Corrigan S & Edwards RJ (2024): Toward genome assemblies for all marine vertebrates: current landscape and challenges. Gigascience 13:giad119. [Gigascience] [PubMed]

Marine vertebrate biodiversity is fundamental to ocean ecosystem health but is threatened by climate change, overharvesting, and habitat degradation. High-quality reference genomes are valuable foundational scientific resources that can inform conservation efforts. Consequently, global consortia are striving to produce reference genomes for representatives of all life. Here, we summarize the current landscape of available marine vertebrate reference genomes, including their phylogenetic diversity and geographic hotspots of production. We discuss key logistical and technical challenges that remain to be overcome if we are to realize the vision of a comprehensive reference genome library of all marine vertebrates.

The OceanOmics Centre is hiring! Research technician positions available

We are recruiting two new positions for the Minderoo OceanOmics Centre at UWA: a Marine Genomics Research Technician and an eDNA Research Technician / Scientific Officer. These are both full-time two-year positions (with likely opportunities for extension), and applications close 11:55 PM AWST on Sunday, 6 August 2023. Please see the link below to find out more. Informal enquiries are also welcome - please contact Rich Edwards.

We are seeking two new members of the technical support team for the OceanOmics Centre, particularly with respect to all aspects of DNA sequencing (sample extraction, library preparation and setting up sequencing runs). You’ll get to play with the latest sequencing technologies, including Illumina NovaSeq/NextSeq, PacBio Sequel/Revio, and ONT PromethION P24. One role will focus on marine vertebrate reference genomes, and associated techniques (e.g. high molecular weight DNA extract, and HiC proximity ligation). The other role has an environmental DNA (eDNA) focus, with more emphasis on Illumina sequencing and liquid handling robots.

About the team

The Minderoo OceanOmics Centre at UWA is a partnership between UWA and Minderoo Foundation to undertake research and development under the direction of Minderoo’s OceanOmics Program. Part of Minderoo’s Flourishing Oceans initiative, this ambitious program aims to revolutionise ocean conservation through application of novel environmental DNA technologies. This includes the development of innovative laboratory and computational approaches to optimise and scale collection, processing and analysis of environmental DNA (eDNA) from marine environments, as well as generate a comprehensive reference library of marine vertebrate genome data. All data produced as part of the OceanOmics program will be subject to rigorous QA/QC and released publicly through open access repositories.

Located in the Bayliss Building on the UWA Crawley Campus, the OceanOmics Centre combines a joint Ocean Genomes Laboratory, an OceanOmics/eDNA Laboratory, and Computational Biology Services. Equipped with the latest high-throughput sequencing technology, liquid handling robotics, flow cytometry, and computational infrastructure, the centre is staffed by a collaborative team of scientists (from both Minderoo and UWA) and UWA technical staff. Core centre operations support the Minderoo OceanOmics Program, under the direction of senior Minderoo employees.

UWA staff, including this postholder, are part of the UWA Oceans Institute, a multidisciplinary research institution with core offices in the nearby Indian Ocean Marine Research Centre building, and liaise closely with Minderoo employees for day-to-day operations.

For more details, and to apply, visit the UWA jobs site: https://external.jobs.uwa.edu.au/cw/en/job/512661 and https://external.jobs.uwa.edu.au/cw/en/job/514981.

We are also recruiting students for three Pawsey student internships.

The Minderoo OceanOmics Centre at UWA is hiring - lab manager position available

We are recruiting a new lab manager position for the Minderoo OceanOmics Centre at UWA. This is a full-time three-year position, available at Level 6 or 7, depending on experience. Applications close 11:55 PM AWST on Thursday, 13 July 2023. Please see the link below to find out more. Informal enquiries are also welcome - please contact Rich Edwards.

We are seeking a detail-oriented professional who possesses excellent organisational and managerial skills, ideally with a strong scientific background. Your operations experience will ensure smooth functioning of the laboratory, promoting a safe, productive and efficient working environment. As lab manager, you will work closely with the Lead Academic of the OceanOmics Centre to optimise operations to support the goals of Minderoo’s OceanOmics Program.

About the team

The Minderoo OceanOmics Centre at UWA is a partnership between UWA and Minderoo Foundation to undertake research and development under the direction of Minderoo’s OceanOmics Program. Part of Minderoo’s Flourishing Oceans initiative, this ambitious program aims to revolutionise ocean conservation through application of novel environmental DNA technologies. This includes the development of innovative laboratory and computational approaches to optimise and scale collection, processing and analysis of environmental DNA (eDNA) from marine environments, as well as generate a comprehensive reference library of marine vertebrate genome data. All data produced as part of the OceanOmics program will be subject to rigorous QA/QC and released publicly through open access repositories.

Located in the Bayliss Building on the UWA Crawley Campus, the OceanOmics Centre combines a joint Ocean Genomes Laboratory, an OceanOmics/eDNA Laboratory, and Computational Biology Services. Equipped with the latest high-throughput sequencing technology, liquid handling robotics, flow cytometry, and computational infrastructure, the centre is staffed by a collaborative team of scientists (from both Minderoo and UWA) and UWA technical staff. Core centre operations support the Minderoo OceanOmics Program, under the direction of senior Minderoo employees. UWA staff, including this postholder, are part of the UWA Oceans Institute, a multidisciplinary research institution with core offices in the nearby Indian Ocean Marine Research Centre building, and liaise closely with Minderoo employees for day-to-day operations.

For more details, and to apply, visit the UWA jobs site: https://external.jobs.uwa.edu.au/cw/en/job/514000.

Watch this space for some further opportunities coming soon: two laboratory research technicians, and three Pawsey student internships.