Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA sequencing of sperm extracted from the epididymis in naked mole-rat subordinates, naked mole-rat ex-subordinates, and mice

ABSTRACT: Naked mole-rat show a strong phenotype of sperm hypo-motility and abnormal morphology. Comparative genomic analyses in our study presenting the telomere-to-telomere genome for the naked mole-rat identified several sperm-gene relaxation and sperm-gene loss events in the NMR. To test the transcriptomic impacts of these gene-loss events, we performed RNA-seq between the sperm of NMR subordinates, ex-subordinates released from suppressive colony cues, and mice. Briefly, only 5-15% of NMR sperm have typical morphology, and only ~7% of those sperm were motile, whereas over 70% of M. musculus sperm are intact and motile There was insufficient motile sperm in the NMR to separate sperm based on motility before RNA-seq. This study was sequenced with sufficient depth to allow for improved sperm-gene annotation. As such, each sample contains over 50 million reads sequenced. In this study, we compared subordinate vs. ex-subordinates in the NMR, as well as all mice vs. all NMRs

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mus musculus

SUBMITTER: Dustin Sokolowski

PROVIDER: E-MTAB-17270 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

An updated reference genome sequence and annotation reveals gene losses and gains underlying naked mole-rat biology.

Sokolowski Dustin J DJ Miclăuș Mihai M Nater Alexander A Faykoo-Martinez Mariela M Hoekzema Kendra K Zuzarte Philip P Monis Simon S Alvi Sana Akhtar SA Erdmann Jason J Erdmann Archana Lal AL Kumaragurubaran Rathnakumar R Bayerl Jonathan J Yoo DongAhn D Karimpour Nadia N Ungerleider Kyra K Hou Huayun H J Martin Fergal F Hourlier Thibaut T Clarke Zoe Z Lischer Heidi E L HEL Leordean Dragos V DV Jiang Yiyue Y Pugh Trevor J TJ Smith Ewan St J ESJ Haggerty Leanne L Laird Diana J DJ Lilue Jingtao J Holmes Melissa M MM Eichler Evan E EE Bruggmann Rémy R Simpson Jared T JT Balmus Gabriel G Wilson Michael D MD

bioRxiv : the preprint server for biology 20241128

The naked mole-rat (NMR; <i>Heterocephalus glaber</i>) 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 in ...[more]

PMID: 39651266

Similar Datasets

Project description:The naked mole-rat (NMR; Heterocephalus glaber) has recently gained considerable attention in the scientific community for its unique potential to unveil novel insights in the fields of medicine, biochemistry, and evolution. NMRs exhibit unique adaptations that include protracted fertility, cancer resistance, eusociality, and anoxia. This suite of adaptations is not found in other rodent species, suggesting that interrogating conserved and accelerated regions in the NMR genome will find regions of the NMR genome fundamental to their unique adaptations. However, the current NMR genome assembly has limits that make studying structural variations, heterozygosity, and non-coding adaptations challenging. We present a complete diploid naked-mole rat genome assembly by integrating long-read and 10X-linked read genome sequencing of a male NMR and its parents, and Hi-C sequencing in the NMR hypothalamus (N=2). Reads were identified as maternal, paternal or ambiguous (TrioCanu). We then polished genomes with Flye, Racon and Medaka. Assemblies were then scaffolded using the following tools in order: Scaff10X, Salsa2, 3d-DNA, Minimap2-alignment between assemblies, and the Juicebox Assembly Tools. We then subjected the assemblies to another round of polishing, including short-read polishing with Freebayes. We assembled the NMR mitochondrial genome with mitoVGP. Y chromosome contigs were identified by aligning male and female 10X linked reads to the paternal genome and finding male-biased contigs not present in the maternal genome. Contigs were assembled with publicly available male NMR Fibroblast Hi-C-seq data (SRR820318). Both assemblies have their sex chromosome haplotypes merged so that both assemblies have a high-quality X and Y chromosome. Finally, assemblies were evaluated with Quast, BUSCO, and Merqury, which all reported the base-pair quality and contiguity of both assemblies as high-quality. The assembly will next be annotated by Ensembl using public RNA-seq data from multiple tissues (SRP061363). Together, this assembly will provide a high-quality resource to the NMR and comparative genomics communities.

Dataset Information

RNA sequencing of sperm extracted from the epididymis in naked mole-rat subordinates, naked mole-rat ex-subordinates, and mice

Publications

An updated reference genome sequence and annotation reveals gene losses and gains underlying naked mole-rat biology.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets