Data from: De novo genome assembly of Ansell's mole-rat (Fukomys anselli)

This repository contains the genome assembly, gene structure annotation, and repeat annotation files for the Ansell’s mole-rat genome (DKFZ_Fans_1.0; GenBank: JBPETH000000000) as well as its mitochondrial genome (GenBank: PV670003). Genome assembly The genome was de novo assembled and polished using Flye v2.9.5 from ONT long reads basecalled by Dorado v0.9.0. Base errors were corrected with Illumina short reads using NextPolish v1.4.1. Haplotigs and overlaps were removed with purge_dups v1.2.6. Contamination was screened with BLAST+ v2.16.0 and BlobToolkit v4.4.0. Cleaned contigs were scaffolded with YaHS v1.2.2 using Hi-C data processed via a modified Arima Genomics mapping pipeline. The assembly was manually curated using Juicebox with Assembly Tools v2.17.0. DKFZ_Fans_1.0.fa.gz: Final curated assembly (FASTA). DKFZ_Fans_1.0.agp: Final curated assembly scaffold structure (AGP). Annotation of gene structures Gene structures were predicted with BRAKER v3.0.8 using Ansell’s mole-rat RNA-seq data from nine tissues, OrthoDB v12 vertebrate proteins, and NCBI RefSeq-annotated proteins from 41 rodent species. Genes predicted by AUGUSTUS and GeneMark-ETP that were combined and filtered by TSEBRA, guided by glires_odb10 via compleasm to enhance BUSCO completeness. DKFZ_Fans_1.0.braker.{gtf,gff3}.gz: Final gene set (GTF/GFF3). DKFZ_Fans_1.0.braker.codingseq.gz: Final gene set coding sequences (FASTA). DKFZ_Fans_1.0.braker.aa.gz: Final gene set protein sequences (FASTA). Annotation of repetitive elements Repeats and transposable elements were identified using Earl Grey v5.1.1 based on a de novo repeat library and known Fukomys damarensis repeats from the Dfam v3.7. DKFZ_Fans_1.0.filteredRepeats.{gff,bed}.gz: Repeat and transposable element annotations (GFF3/BED). Mitochondrial genome assembly and annotation The mitogenome was assembled from Illumina short reads using GetOrganelle v1.7.7.1 with the Fukomys damarensis (NC_027742.1) and Heterocephalus glaber (NC_015112.1) mitogenomes as seeds. Mitochondrial features were annotated with MitoAnnotator v4.0.9, visually inspected, and start and end positions were adjusted when necessary based on comparisons with the mitochondrial gene sequences and annotations of F. damarensis and H. glaber. DKFZ_Fans_1.0.mtdna.fa.gz: Mitochondrial genome sequence (FASTA). DKFZ_Fans_1.0.mtdna.gb: Mitochondrial genome features (GenBank flat file). UPDATES: Version 1.1.0 added the mitochondrial genome assembly and annotation files to the repository.