REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Bacterial and Virus Strains
Biological Samples
Dicerorhinus sumatrensis sumatrensis	Cincinnati Museum Center	CMC M4249
Chemicals, Peptides, and Recombinant Proteins
Critical Commercial Assays
TruSeq® DNA PCR-Free LT Library Preparation Kit (24 samples)	Illumina, Inc.	20015962
Nextera Mate Pair Library Prep Kit (12 indexes, 48 gel-free samples or 12 gel-plus samples)	Illumina, Inc.	FC-132-1001
HiSeq PE Rapid Cluster Kit v2	Illumina, Inc.	PE-402-4002
HiSeq Rapid SBS Kit v2	Illumina, Inc.	FC-402-4023
Deposited Data
Whole genome shotgun sequence assembly	This paper	NCBI: PEKH00000000
Raw whole genome sequencing reads	This paper	NCBI: PRJNA415733
Experimental Models: Cell Lines
Experimental Models: Organisms/Strains
Oligonucleotides
Recombinant DNA
Software and Algorithms
Trimmomatic 0.33	[57]	http://www.usadellab.org/cms/?page=trimmomatic
kmergenie	[58]	http://kmergenie.bx.psu.edu
Jellyfish 2.2.3	[18]	http://www.genome.umd.edu/jellyfish.html
DISCOVAR de novo	[59]	https://software.broadinstitute.org/software/discovar/blog/
SOAP de novo 2.04	[60]	http://soap.genomics.org.cn/soapdenovo.html
Extreme Science and Engineering Discovery Environment (XSEDE)	[61]	https://www.xsede.org
Google Earth	Google Inc.	https://www.google.com/earth/
Burrows Wheeler Aligner Program (BWA) 0.715	[69]	http://bio-bwa.sourceforge.net
Basic Local Alignment Search Tool (BLAST) 2.5.0	[70]	https://blast.ncbi.nlm.nih.gov/Blast.cgi
SAM Tools 1.3.1	[71]	http://www.htslib.org
PICARD 2.4.0	Broad Institute	https://github.com/broadinstitute/picard
BAM Tools 1.3.1	[72]	https://github.com/pezmaster31/bamtools
Genome Analysis Toolkit (GATK) 3.6	[81]	https://software.broadinstitute.org/gatk/
Pairwise Sequentially Markovian Coalescent (PSMC) 0.6.5	[13]	https://github.com/lh3/psmc
MAXENT 3.3.3	[75]	https://biodiversityinformatics.amnh.org/open_source/maxent/
Other