We focused on the genetic structure and evolutionary divergence of a typical habitat generalist mayfly, Isonychia japonica, inhabiting rivers widely distributed across eastern Asia. In the Japanese Archipelago, they are distributed across a wide range of environments, including up- and downstream areas in 1 river basin. We analyzed DNA sequences of this mayfly from both the mitochondrial (cytochrome oxidase c subunit I [COI] and 16S ribosomal RNA) and nuclear genomes (Histone H3 and ITS2) of specimens from populations across the eastern Asian region, with emphasis on the Japanese Archipelago. Isonychia japonica is genetically differentiated into 2 major clades (C = continental clade, J = Japanese Archipelago clade). Furthermore, clade J is composed of 2 subclades (clades J-U and J-D). Clade J is separated by environment, with specimens constituting clade J-U occurring in small-scale rivers of the upstream regions and specimens constituting clade J-D occurring in large-scale rivers of downstream regions. Clade J-D further consists of 2 minor subclades that occupy different geographical regions (clades J-DN and J-DS).

Insect silk is a versatile biomaterial. Lepidoptera and Trichoptera display some of the most diverse uses of silk, with varying strength, adhesive qualities, and elastic properties. Silk fibroin genes are long (>20 Kbp), with many repetitive motifs that make them challenging to sequence. Most research thus far has focused on conserved N- and C-terminal regions of fibroin genes because a full comparison of repetitive regions across taxa has not been possible. Using the PacBio Sequel II system and SMRT sequencing, we generated high fidelity (HiFi) long-read genomic and transcriptomic sequences for the Indianmeal moth (Plodia interpunctella) and genomic sequences for the caddisfly Eubasilissa regina. Both genomes were highly contiguous (N50 = 9.7 Mbp/32.4 Mbp, L50 = 13/11) and complete (BUSCO complete = 99.3%/95.2%), with complete and contiguous recovery of silk heavy fibroin gene sequences. We show that HiFi long-read sequencing is helpful for understanding genes with long, repetitive regions.