Annotation files for the naked mole-rat (Heterocephalus glaber) telomere-to-telomere genome

Abstract

Repo Summary: This repository contains the summary annotation files for the naked mole-rat (Heterocephalus glaber) telomere-to-telomere genome, mHetGla1.1, and the primary assembly for the Cape-dune mole-rat genome (Bathyergus suillus), mBatsui1.1-pri, resources. Materials and methods for all sequencing, assembly, annotation and downstream analyses are described in depth in our manuscript; however the most relevant steps are briefly summarized below. Briefly, we generated initial repeat family libraries with RepeatModeller, while manually curating the top 20 most common repeat families in the NMR. Tandem repeats were called with TideCluster and incorporated into the repeat library. Repeats were then annotated in each assembly with RepeatMasker. For genic annotations, we combined public (Bens et al. 2018) and in-lab generated RNA-seq data across 23 adult tissues, and generated Iso-seq data across 16 tissues. We also generated RNA-seq data across 12 adult tissues in the Cape-dune mole-rat. For the NMR, we integrated these transcriptomic data with homologous-derived gene transfer from the mouse and ab initio gene prediction using GenAnT to annotate mHetGla1.1-hap1 and mHetGla1.1-hap2. We used our transcriptomic data, homologous-derived gene transfer from mouse and mHetGla1.1-pri, and ab initio gene prediction using GenAnT to annotate mBatSui1.1-pri. Mitochrondrial annotations were generated with Mitofinder and the 5S and 45S rRNA units were also identified with barrnap. Lastly, segmental duplications were called with both Biser and SEDEF. Study Abstract: The naked mole-rat (Heterocephalus glaber) is the longest-lived rodent and exhibits a suite of unusual traits, among them cancer resistance and eusociality. We present a diploid, haplotype-resolved, telomere-to-telomere genome assembly annotated with transcriptomes from 23 adult tissues. The assembly resolves satellite-free centromeres, the Y chromosome and a structurally polymorphic 30 megabase region of chromosome 15. We paired it with a long-read primary assembly of the Cape dune mole-rat (Bathyergus suillus), a shorter-lived solitary relative. Comparative analyses identify gene losses that uncouple sperm motility from fertility and segmental duplications in hypoxia tolerance, behavior and genome stability, including six copies of the mismatch-repair gene Pms1. These resources and genetic discoveries will accelerate our understanding of the genetic basis of the naked mole-rat's longevity, cancer resistance and reproductive biology to direct study. Summary of Files · mHetGla1v_h1_vs_h2.chrXY: Pairwise genome assembly alignment between mHetGla1.1-hap1 and mHetGla1.1-hap2 using minimap · *centromere*.bed: mHetGla1.1-hap1 and mHetGla1.1-hap2 centromeric placements · mHetGla1.pri.MT.v020326.gff.gz: mHetGla1.1-hap1 genome annotation from GenAnT with manual edits identified from working with the assembly · edited_mHetGla1.pri.MT.v020326.gff.gz : the same annotation but with redundant fragmented genes and pseudogenes filtered to improve compatibility with single-cell ‘omic tools. Kindly provided by Liz Chamiec-Case · *edited.geneSymbol.gff: · *rrna.gff: 5S rRNA and 45S rRNA units annotated by barrnap · * annotation_metrics_with_pseudogenes*: text file aggregative Mikado gene model scores, gene symbol, ad PGRe pseudogene calling for each annotation · PcGName.bed: simplified genome annotation file, with protein coding genes in green, pseudogenes identified by PGRe in red, and ncRNA in purple/orange. Note PGRe calls pseudogenes on potential frameshifts/stops in the gene model. We found a handful of examples where this is caused by a homologous exon that is skipped in the transcriptomic data being included in the overall model. As such, don’t exclusively rely on PGRe calls for pseudogene analysis with this specific annotation set. · *biser.bedpe: segmental duplications called by BISER · *SD.bed: segmental duplications called by SEDEF · *broadPeak: H3K4me1, H3K4me3, H3K27Ac ChIP-seq peaks identified by macs2. Reads were aligned using bwa-mem parameters tuned for alignments of short-read data to repetitive regions: (from Arora, Sullivan, and Dumont (2023). Cell Rep.: k = 19, w = 100, d = 100, r = 1.5, c = 10000, A = 1, B = 4, O = 6, E = 1, L = 5, U = 9, T = 30, v = 3) · repeat.bed: output of repeat annotation files for each assembly · _repeat_library.fa: repeatmodeller + TRC + Dfam repeat library for each species. Manual curation was performed on the NMR repeat library. These same manual curations were included as repeat families in the B.suillus library.