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.

Phylogeographic studies based on molecular information have been attracting attention because they have come to play a significant role in the elucidation of the population structure and phylogenetic relationships of species. Furthermore, molecular tools have helped to reveal evidence for cryptic biodiversity, including in many cases the discovery of new species. We focused on the phylogeography of stenopsychid caddisflies. The family Stenopsychidae has a distribution area mainly within the Southern Hemisphere, and only the Stenopsyche caddisflies have spread into parts of the Asian region of the Northern Hemisphere. They inhabit most of the major rivers/streams in Japan at relatively high density and are large and voluminous-bodied species among the benthic animals of Japanese rivers. Therefore, they are considered to be the most important species in the river ecosystem. We conducted phylogenetic analyses for 21 species of the genus Stenopsyche. The results of our genetic analyses inferred from the mitochondrial cytochrome c oxidase subunit I (COI) and nuclear elongation factor (EF)-1a strongly supported the previous morphologically based classification. Stenopsyche species inhabiting southern areas of the Asian region also have been evaluated as being lineages that diverged at a relatively earlier period than the species inhabiting northern areas of Asia. Therefore, a gradual trend has suggested an evolutionary history in which distributional expansion occurred from southern Asia toward northeastern Asia and was accompanied by corresponding species differentiation. Furthermore, newly observed genetically cryptic lineages not yet known to exist were found among the previously described species.

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ABSTRACT:The freshwater amphipod Crangonyx floridanus (Amphipoda: Crangonyctidae) has considered to be recently introduced from North America to Japan, and now the recorded sites of collection cover nearly all over Japan excluding the northern part. In this study, we surveyed further areas outside the known distribution ranges and also examined the population genetic structure and the phylogenetic relationships between Japanese and North American populations based on nuclear (18S rRNA) and mitochondrial (COI) DNA sequences. We found that this amphipod already reached to Hokkaido, the northernmost Japan, and suggested the rapid expansion in a pattern of concentric circles from the central part of Japan. The genetic analysis showed the genetic homogeneity of Japanese population in contrast to the genetic diversification in North American Crangonyx populations. The process of introduction, establishment, and expansion of this amphipod in Japan may be explained as follows. A limited number of individuals from a North American native population were probably inadvertently introduced and established somewhere within the Kanto region. After that the local population size increased and the range of its distribution was rapidly expanded over Japan.