Chromosome-level genome assembly of the stonefly Indonemoura scalprata (Plecoptera: Nemouridae)

Plecoptera (stoneflies) are hemimetabolous insects of significant ecological importance in freshwater ecosystems and are key to understanding early insect diversification and aquatic adaptation. Here, we present a high-quality, chromosome-level reference genome assembly for Indonemoura scalprata (Li & Yang, 2007), a nemourid stonefly widely distributed in southern China (Fujian, Guangdong, and Guangxi), with the sequenced specimen originating from the Qianjiadong National Nature Reserve in Guangxi. The genome was assembled using PacBio HiFi reads and Hi-C chromatin interaction data. The final assembly spans 257.81 Mb, with 99.76% (257.18 Mb) successfully anchored into 11 pseudochromosomes. The scaffold N50 reaches 26.45 Mb, and BUSCO completeness using the insecta_odb12 dataset (n = 3,114) is 97.0%. Repetitive elements constitute 31.20% of the genome (80.44 Mb). We identified 1,491 non-coding RNAs and predicted 12,200 protein-coding genes, achieving 97.7% completeness in the BUSCO (insecta_odb12) assessment. This high-quality genome provides a valuable resource for comparative genomics in Polyneoptera and studies of adaptation to cold, fast-flowing streams and early winged insect evolution.