Sea cucumbers are one of the most common large animals in the deep-sea benthic communities, and those of the genus Pannychia are particularly abundant in the bathyal North Pacific Ocean. In Japanese waters, three species of Pannychia have been reported, mainly from the northern and eastern parts of the country. Here, we describe two new species from the western part of Japan. These two new species were placed in Pannychia by the presence of dorsal papillae on the ventrolateral radii and the presence of large wheel ossicles with rim teeth. They are distinguished from all other nominal species of Pannychia on the basis of the morphological characteristics of their body wheel ossicles. Pannychia nagasakimaruae sp. nov. has a unique ossicle composition in its dorsal and ventral body walls: four forms of wheel ossicles. Pannychia rinkaimaruae sp. nov. differs from other congeners in its small wheel ossicles in the dorsal and ventral body walls, which have conical rim teeth. We barcoded partial COI gene sequences from holotypes and paratypes of two new Japanese species. Our molecular phylogenetic analysis showed that these two new morphologically recognized Japanese species form distinct clades separated from other Pacific Pannychia species, so that the two new Japanese species were also supported by genetic results. In addition, we describe and visualize the poorly calcified calcareous rings of the two new species using X-ray μCT system, a useful method for observing such structures, which are important structures in holothurian anatomy.

Recent advances in DNA research have increased the necessity for museums to preserve not only morphological specimens but also their DNA, leading us to maintain tissue samples linked to specimens at −80 °C. DNA analysis has become an essential tool for taxonomic research and biodiversity assessment; however, freezer storage for all samples is impractical due to space limitations and operational costs. This creates a pressing need to develop more widely applicable DNA preservation methods. We investigated the comparative effects of traditional preservation methods versus DESS (DMSO/EDTA/saturated NaCl solution) preservation on both morphology and DNA integrity using museum specimens from various taxonomic groups. Our results demonstrated that DESS preservation maintained high-quality DNA fragments exceeding >15 kb at room temperature across all examined species, with nematode samples maintaining DNA integrity even after 10 years of storage. When preserving whole organisms, the optimal preservation solution conditions for maintaining both morphological features and DNA integrity varied among species. Notably, DNA integrity was maintained even after complete evaporation of the DESS solution. These findings suggest that DESS utilization for specimen DNA preservation is effective across many species, not only for long-term storage in environments without freezer facilities but also for temporary preservation until freezing.

Two new species of fauveliopsid annelids, Fauveliopsis antri sp. nov. and Laubieriopsis soyoae sp. nov., are described based on specimens collected from Japanese waters. Fauveliopsis antri sp. nov. inhabits submarine caves and can be discriminated from the other congeners by the following features: i) 32 chaetigers, ii) chaetigers 1–3 with stout hooks, iii) minute body (about 1 mm in length), iv) all parapodia with same number of chaetae (2 notochaetae; 2 neurochaetae), and v) presence of dorsal and ventral papillae. Laubieriopsis soyoae sp. nov. inhabits deep water sediments and can be distinguished from the other congeners by: i) 24 chaetigers, ii) chaetigers 1–3 without annulations, and iii) acicular chaetae with tips entire, without denticles.

We determined the complete mitochondrial genome sequence of a holothurian Euapta godeffroyi belonging to the order Apodida. The complete mitogenome of E. godeffroyi was 16,410 bp in length and consisted of 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes. The orders of PCGs and rRNAs did not match those of any recorded holothurian mitogenomes. The maximum likelihood (ML) phylogenetic tree placed E. godeffroyi as the sister group to chiridotid species and supported the monophyly of the order Apodida.