DOI: 10.5061/dryad.m37pvmdf4
title: Genome sequencing/assembly and genetic diversity of Heterocephalus glaber

description: Naked mole-rats (Heterocephalus glaber) are a species of rodent endemic to
 the horn of Africa, notable among mammals for their long lifespans,
 resistance to a variety of stresses, and eusocial mating
 behavior.  Though their natural species range extends across
 large portions of Kenya, Ethiopia, Somalia, and Djibouti, the vast
 majority of genetic and genomic analyses focus on Kenyan
 specimens.  Here, we constructed a chromosome-scale reference
 genome assembly for H.glaber, then leveraged it, along with modern
 whole-genome sequencing, to characterize the genetic diversity of
 specimens deriving from Kenya, southern Ethiopia, and eastern
 Ethiopia.  We found the Kenyan and southern Ethiopian specimens
 to be closely related to each other and highly diverged from eastern
 Ethiopian specimens.  We also found specimens collected from
 nearby locations in southern Ethiopia to be more closely related to Kenyan
 specimens than to each other, emphasizing the importance of local
 migration barriers to gene flow in wild H.glaber populations.
description: # Genome sequencing/assembly and genetic diversity of Heterocephalus
 glaber Dataset DOI: [10.5061/dryad.m37pvmdf4](10.5061/dryad.m37pvmdf4) ##
 Description of the data and file structure This study presents an assembly
 of the genome for *H.glaber*, along with gene annotations and alignment to
 other mammalian genomes. It also provides polymorphism data from animals
 collected from multiple geographic regions. ### Files and variables ####
 File: SuppTables1-8.xlsx **Description:** An Excel file with all
 Supplemental Tables: Supplemental Table 1: Genome assembly statistics
 across assembly steps. This table provides a detailed breakdown of
 assembly metrics at each stage of the genome assembly pipeline.
 Supplemental Table 2: Groups of super-scaffolds, compiled using
 chromosome-sorted sequencing (as depicted in Figure 1A). This table lists
 the organization of scaffolds into chromosome-scale groupings, based on
 chromosome sorting and sequencing. Supplemental Table 3: Statistics for
 the 10-species whole genome alignment. Supplemental Figure 1 depicts the
 phylogenetic tree, which is provided in Newick format in Supplemental Text
 File 1. Supplemental Table 4: Metadata for genome-sequenced animals. See
 preprint for details. includes species, sample identifiers, Supplemental
 Table 5: For genome-sequenced animals, information about tissue/cell
 sample type, coverage statistics, and polymorphism counts. Each
 animal's SRA experiment ID is also listed. Supplemental Table 6:
 Contains exact pairwise kinship values used to generate the kinship matrix
 displayed in Figure 2B. Useful for replicating or extending kinship
 analysis. Supplemental Table 7: Provides the raw intersection counts
 between alleles that were used to generate the Venn diagrams in Figure 3,
 enabling precise comparison of overlapping features. Supplemental Table 8:
 This table maps each RNA-seq slice (based on size selection) to its
 corresponding experiment ID in the SRA database. Further methodological
 details are available in the preprint. #### File: SuppTextFile1.txt
 **Description:** Phylogenetic trees in Newick text, for genome-aligned
 species and *H.glaber* individuals from Kenya and Ethiopia. #### File:
 SuppDataFile1.json **Description:** A JSON-formatted pandas data frame of
 the enrichment scores, from flow-sorted chromosome sequencing.  These
 scores estimate the likelihood of each pair of scaffolds deriving from the
 same chromosome. #### File: SuppDataFile2.Geno.tgz
 **Description:** Polymorphisms discovered through whole-genome
 sequencing.  This file unzips into 63 *.geno_score.csv files, organized
 into files by super-scaffold.  This file pairs with coverage data provided
 in SuppDataFile2.Depth.tgz. #### File: SuppDataFile2.Depth.tgz
 **Description:** Per-animal, per-polymorphism information on the
 sequencing coverage used to call genotypes.  This file unzips into 63
 *.depth.csv files, organized like SuppDataFile2.Geno.tgz. #### File:
 SuppDataFile3.Maf.tgz **Description:** Whole-genome alignments, generated
 by Cactus, of the genome assemblies produced here (*H.glaber*,
 *F.damarensis*, and *C.porcellus*) plus relevant mammals' published
 genome assemblies (see preprint for details).  This Gnu-zipped tar file
 includes the .maf-format whole-genome alignment.  Support files can be
 found in SuppDataFile3.Sup.tgz. #### File: SuppDataFile3.Sup.tgz
 **Description:** Support files for the whole-genome alignments provided in
 SuppDataFile3.Maf.tgz (multiple files packaged into this GNU-zipped tar
 file). #### File: SuppDataFile4.tgz **Description:** Gene annotation
 files, in. .gff3 and .gp formats, bundled into a GNU-zipped tar file. ###
 Genome assemblies:
 Naked_mole_rat_genome.tgz, Damara_mole_rat_genome.tgz, Guinea_pig_genome.tgz Gnu-zipped tar files: each contains a fasta-format text file with the genome assembly. For the Damaraland mole-rat and guinea pig genomes, contig names had to be changed from the output of the assembler in order to make them NCBI-compliant. Original names are used in the multiple sequence alignments, so a table is also provided mapping updated names to original names (note that original names are also provided as extra information on the sequence header lines of the fasta files).