Haplotype-resolved chromosomal-level genome assembly of Mastigias papua

Mastigias papua is a representative species of the Scyphozoa class. Its outer umbrella surface is covered with white spots and it is mainly distributed in the Pacific and Indian Ocean. In this study, we generated a haplotype-resolved, chromosome-scale genome assembly for M. papua using PacBio HiFi long reads and Hi-C technology. The resulting assembly contains two haplotypes (Hap A and Hap B) with sizes of 379.81 MB (contig N50 = 13.03 Mb) and 344.57 MB (contig N50 = 14.24 Mb), and both anchored to 21 chromosomes with anchor ratio of 94.35% and 97.59%, respectively. The sequencing depth, mapping coverage, contig continuity, and BUSCO assessment collectively indicate a high-quality haplotype-resolved genome assembly. This high-quality genome assembly provides a valuable resource for further genetic studies and genetic improvement of the group of M. papua. BUSCO assessment indicated that the completeness of the two haploid genomes was 93.3% (HapA) and 92.2% (HapB), respectively, demonstrating excellent assembly quality. Annotation results identified 27,401 protein-coding genes and 182.83 Mb of repetitive sequences (accounting for 48.14% of the genome) in HapA, while HapB contained 23,905 protein-coding genes and 158.00 Mb of repetitive sequences (representing 45.85% of the genome). Functional annotation revealed that over 88% of the genes could be matched to public databases such as NR, KEGG, and GO. These phased genome assemblies and gene annotations provide a quality-controlled genomic resource for Mastigias papua.