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.