## 5 Materials and Methods
One set was iteratively corrected with the command canu -correct -p asm -d setl_round1 genomeSize = 2.5 g corMinCoverage = 0 corMhMapSensitivity = high corOutCoverage = 100 -pacbio-raw setl/*.subreads.fastq.gz with the output of each round being the input for the next round. The reads were trimmed after three rounds of correction with the command canu trim -p asm -d setl_round3_trim genomeSize = 2.5 g correctedErrorRate = 0.105 -pacbio-corrected setl_round3/asm.correctedReads.fastq.gz. The second set of reads was corrected with the command canu -correct -p asm -d set2_round1 genomeSize = 2.5 g corMinCoverage = 0 corMhMapSensitivity = normal corOutCoverage = 100 -pacbio-raw set2/*subreads.fastq.gz and trimmed as set1. Lastly, the combined corrected reads were assembled with the command canu -assemble -p asm -d setl+set2 'genomeSize = 2.5 g 'correctedErrorRate = 0.105 'batOptions = -dg 3 -db 3 -dr 1 -ca 500 -cp 50' -pacbio-corrected set2_round1_trim/asm.trimmedReads.fastq.gz -pacbio-corrected setl_round3_trim/asm.trimmedReads.fasta.gz. This final assembly was polished with long read data in Arrow (SMRT Link 3.1.1, PacBio). A Chicago library was prepared as described previously [89]. Briefly, \(\sim\)500 ng of HMW gDNA was reconstituted into chromatin in vitro and fixed with formaldehyde. Fixed chromatin was digested with DpnII, the 5\({}^{\prime}\) overhangs filled in with biotinylated nucleotides, and then, free blunt ends were ligated. After ligation, crosslinks were reversed and the DNA purified from protein. Purified DNA was treated to remove biotin that was not internal to ligated fragments. The DNA was then sheared to \(\sim\)350 bp mean fragment size and sequencing libraries were generated using NEBNext Ultra enzymes and Illumina-compatible adapters. Biotin-containing fragments were isolated using streptavidin beads before PCR enrichment of each library. The libraries were sequenced on an Illumina HiSeq X to produce 208 million 2 \(\times\) 150 bp paired end reads. A Dovetail HiC library was prepared in a similar manner as described previously [90]. Briefly, for each library, chromatin was fixed in place with formaldehyde in the nucleus and then extracted Fixed chromatin was digested with DpnII, the 5\({}^{\prime}\) overhangs filled in with biotinylated nucleotides, and then free blunt ends were ligated. After ligation, crosslinks were reversed, and the DNA was purified from protein. Purified DNA was treated to remove biotin that was not internal to ligated fragments. The DNA was then sheared to \(\sim\)350 bp mean fragment size and sequencing libraries were generated using NEBNext Ultra enzymes and Illumina-compatible adapters. Biotin-containing fragments were isolated using streptavidin beads before PCR enrichment of each library. The libraries were sequenced on an Illumina HiSeq X to produce 143 million 2 \(\times\) 150 bp paired end reads. The input de novo assembly, Chicago library reads, and Dovetail Hi-C library reads were used as input data for HiRise, a software pipeline designed specifically for using proximity ligation data to scaffold genome assemblies [89]. An iterative analysis was conducted. First, Chicago library sequences were aligned to the draft input assembly using a modified SNAP read mapper [91]. The separations of Chicago read pairs mapped within draft scaffolds were analyzed with HiRise to produce a likelihood model for genomic distance between read pairs, and the model was used to identify and break putative misjoins to score prospective joins and make joins above a threshold. After aligning and scaffolding Chicago data, Dovetail HiC library sequences were aligned and scaffolded following the same method. Scaffolds that were determined to be \"contaminants\" (mitochondrial, duplicate, vector, or microbial as described in the next section) were removed prior to submission, resulting in 9961 final scaffolds and a total length of 2,346,604,983 bp. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JAHLJT00000000.