About 1.5 g of 3‐week‐old seedlings were used for the Hi‐C library construction. Hi‐C libraries were created using a previously described method (Mascher et al., 2017 (link)). Libraries (based on HindIII) with fragments ranging from 300 to 700 bp size were constructed and sequenced on the Illumina X‐TEN platform (Illumina). Mapping of Hi‐C reads and assignment to restriction fragments were performed as described previously (Burton et al., 2013 (link)). We performed duplicate removal, sorting and quality evaluation using HiC‐Pro v2.10.0 (Servant et al., 2015 (link)) with the command of ‘mapped_2hic_fragments.py ‐v ‐S ‐s 100 ‐l 1000 ‐a ‐f ‐r ‐o’. The raw counts of the Hi‐C links were aggregated in 100‐kb bins and normalized separately for intra‐ and inter‐chromosomal contacts using HiC‐Pro. The corrected contigs were assembled into 12 chromosome‐level scaffolds by LACHESIS (Burton et al., 2013 (link)). Adjacent contigs were linked together by filling the gap with ‘N’. Finally, 12 high‐quality pseudochromosome‐level genomes were built for representative GJ accessions.