Watermelon (97103) v2 Genome

The version 2 of watermelon ‘97103’ was de novo assembled using PacBio long reads, combined with BioNano optical and Hi-C chromatin interaction maps. A total of 20.3 Gb PacBio sequences were generated with an N50 length of 10.8 kb, covering ~47.2× of the watermelon genome. The PacBio assembly had a total size of 359.8 Mb, containing 367 contigs with an N50 size of 2.3 Mb. A total of 410.7 Gb cleaned BioNano optical map data were generated and de novo assembled into BioNano genome maps, which were used to connect PacBio assembled contigs, resulting in 149 scaffolds with an N50 size of 21.9 Mb and a cumulative length of 365.1 Mb. Furthermore, a total of ~135.2 million cleaned Hi-C reads were generated, of which ~92.1 million (68.1%) were uniquely mapped to the assembly, which resulted in a final of ~69.5 million valid read pairs. The Hi-C data, combined with previously published genetic maps were used to order and orient the scaffolds into chromosome-scale pseudomolecules. Finally, 31 scaffolds with a total size of 362.7 Mb (99.3% of the assembly) were clustered into 11 chromosomes ranging from 27.1 to 37.9 Mb in length. Approximately 202.8 Mb (55.55%) of the assembly were annotated as repeat sequences and a total of 22,596 genes were predicted in the assembly.