biostudies-arrayexpressDustin SokolowskiBathyergus suillushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17420One ONT-ULK sequencing run from the kidney of a single male CDMR (Bathyergus suillus) sample used to make the mBatSui1.1.primary genome assembly as an evolutionary comparator to our telomere-to-telomere naked mole-rat genome assembly. Specifically, we assembled a CDMR from a wild-derived sample in South African cape and sequenced in Toronto, Canada, using PacBio HiFi (89 Gb, read N50 = 18 Kb) and ONT-ULK (55 Gb, read N50 = 43 Kb) reads (contig N50 = 33 Mb, Compleasm S = 99%, QV = 71.0). This accession stores the ONT-ULK data for this assembly.biostudies-arrayexpressSequencing - For ultra-long sequencing, libraries were prepared starting with 80 µg of high molecular weight genomic DNA using the Ultra-Long DNA Sequencing Kit (SQK-ULK114, Oxford Nanopore Technologies, Oxford, UK) according to the manufacturer's protocol. Briefly, DNA diluted in EEB was incubated with a buffer containing fragmentation mix (FRA + FDB). Incubation was carried out at room temperature for 10 mins before being heat inactivated at 75C for 10mins. Following a brief incubation on ice, the fragmented and tagged DNA was incubated with rapid adapter (RA) for 30 mins at room temperature. The resulting fragmented and adapted library was then precipitated using precipitation buffer (PTB). The precipitate was pelleted and resuspended in elution buffer (EB) and allowed to redisolve overnight at 4C. The resulting library was then mixed with Sequencing buffer (SBU) and loading solution (LSU) prior to loading on a PromethION Flow Cell (R10.4.1, FLO-PRO114M). Runs were typically carried out for 72 hours while carrying flowcell flush and reloads every 24hrs (or as needed).Nucleic Acid Extraction - Ultra-high molecular weight DNA was extracted from the kidney tissue of a male using a modified phenol/chloroform DNA extraction method.Library Construction - DNA was extracted using the Monarch HMW tissue extraction kit according to manufacturers recommendations (New England Biolabs).Sample Collection - Adult Bathyergus suillus were wild-captured in Darling, Western Cape, South Africa using Hickman live traps baited with small pieces of sweet potato. Traps were monitored every 2–3 hours throughout the day and checked again early each morning after being left overnight. Permission to capture animals was obtained from all relevant landowners, and collection permits were issued by the appropriate conservation authorities (Western Cape permit no. CN44-87-13780). All procedures were approved by the University of Pretoria Animal Use and Care Committee (ethics clearance no. NAS022/2021) and conducted under DAFF Section 20 approval (SDAH-Epi-21051907211). Captured animals were transported to the University of Pretoria and housed individually at approximately 23°C, 21% O₂, and 50% relative humidity under a 12 h light:12 h dark photoperiod. Animals were maintained in large polyurethane crates (1 × 0.5 × 0.5 m) containing wood shavings and paper towelling as nesting material in temperature-controlled rooms. All wild-caught African mole-rat species were acclimated to captivity for a minimum of one year prior to tissue collection. Animals were euthanized by cervical dislocation and decapitation. Immediately after death, biological tissues were rapidly dissected within 60 s and flash-frozen in liquid nitrogen. Samples were subsequently stored at −80 °C until further analysis.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesMetabolomicsUnknownTranscriptomicsGenomicsProteomicsPromethIONThe naked mole-rat (NMR; Heterocephalus glaber) is a eusocial subterranean rodent with a highly unusual set of physiological traits that has attracted great interest amongst the scientific community. However, the genetic basis of most of these traits has not been elucidated. To facilitate our understanding of the molecular mechanisms underlying NMR physiology and behaviour, we generated a long-read chromosomal-level genome assembly of the NMR. This genome was subsequently annotated and incorporated into multiple whole genome alignments in the Ensembl database. Our long-read assembly identified thousands of repeats and genes that were previously unassembled in the NMR and improved the results of routinely used short-read sequencing-based experiments such as RNA-seq, snRNA-seq, and ATAC-seq. We identified several spermatozoa related gene losses that may underlie the unique degenerative sperm phenotype in NMRs (IRGC, FSCB, AKAP3, MROH2B, CATSPER1, DCDC2C, ATP1A4, TEKT5, and ZAN), and an additional gene loss related to the established NK-cell absence in NMRs (PILRB). We resolved several tandem duplications in genes related to pathways underlying unique NMR adaptations including hypoxia tolerance, oxidative stress, and nervous system protection (TINF2, TCP1, KYAT1). Lastly, we describe our ongoing efforts to generate a reference telomere-to-telomere assembly in the NMR which includes the resolution of complex gene families. This new reference genome should accelerate the discovery of the genetic underpinnings of NMR physiology and adaptation.DNA-seqBathyergus suillusAn updated reference genome sequence and annotation reveals gene losses and gains underlying naked mole-rat biologyDaniel HartPhillip ZuzarteNigel BennettMihai MiclausDustin SokolowskiMichael WilsonJared SimpsonDustin J Sokolowski, Mihai Miclăuș, Alexander Nater, Daniel Hart, Nigel Bennett, Mariela Faykoo-Martinez, Kendra Hoekzema, Philip Zuzarte, Simon Monis, Sana Akhtar Alvi, Jason Erdmann, Archana Lal Erdmann, Rathnakumar Kumaragurubaran, Jonathan Bayerl, DongAhn Yoo, Nadia Karimpour, Kyra Ungerleider, Huayun Hou, Fergal J Martin, Thibaut Hourlier, Zoe Clarke, Heidi E L Lischer, Dragos V Leordean, Yiyue Jiang, Trevor J Pugh, Ewan St J Smith, Leanne Haggerty, Diana J Laird, Jingtao Lilue, Melissa M Holmes, Evan E Eichler, Rémy Bruggmann, Jared T Simpson, Gabriel Balmus, Michael D WilsonfalseONT ULK sequencing of a male cape dune mole-rat kidney sampleOne ONT-ULK sequencing run from the kidney of a single male CDMR (Bathyergus suillus) sample used to make the mBatSui1.1.primary genome assembly as an evolutionary comparator to our telomere-to-telomere naked mole-rat genome assembly. Specifically, we assembled a CDMR from a wild-derived sample in South African cape and sequenced in Toronto, Canada, using PacBio HiFi (89 Gb, read N50 = 18 Kb) and ONT-ULK (55 Gb, read N50 = 43 Kb) reads (contig N50 = 33 Mb, Compleasm S = 99%, QV = 71.0). This accession stores the ONT-ULK data for this assembly.2026-08-05T00:00:00Z2026-08-05T01:00:47.067Z2026-07-29T12:09:55.468ZE-MTAB-1742039651266ERP203003EFO_0002944EFO_0004170EFO_0002693EFO_0005518EFO_000418410.1101/2024.11.26.625329