Genome Assembly
Initial estimates of the genome size were conducted by flow cytometry using Vigna radiata for reference (Kang et al., 2014). Genome size was confirmed by K-mer analysis using Jellyfish v2.29 (Marçais & Kingsford, 2011) and Illumina reads. Low-quality reads were filtered prior to de novo assembly, as previously described (Wu et al., 2019), and the assembly was performed with Canu v1.7 (Koren et al., 2017). We corrected the assembled contigs with two iterations of Pilon v1.23 (Walker et al., 2014). Contigs were anchored to chromosomes by Hi-C. The Hi-C library was prepared from 3 g of freshly ground young leaves, using liquid nitrogen and a mortar and pestle. The chromatin extraction, digestion, DNA ligation, purification, and fragmentation were all performed as previously described (Louwers et al., 2009). A total of 114,431,960 Hi-C Illumina reads were generated using Illumina Hiseq X Ten system. The draft assembly was scaffolded with Hi-C data using the 3D-DNA pipeline v180922 run with default parameters (Dudchenko et al., 2017). Hi-C reads were aligned to the draft assembly using the Juicer pipeline v1.6.2 (Durand, Robinson, et al., 2016; Durand, Shamim, et al., 2016). Results were polished using the Juicebox Assembly Tools - an assembly-specific module in the Juicebox visualization system v1.11.08 (Dudchenko et al., 2018). The Hi-C scaffolding resulted in six chromosome-length super scaffolds, representing a total of 95.36% of the assembled sequence.