As an important freshwater aquaculture species in China, the Chinese mitten crab (Eriocheir japonica sinensis) has high economic and nutritional value. However, limited genomic information is currently available for studying of basic development and genetic diversity. Here, we performed whole-genome sequencing, assembly, and annotation based on third-generation genome sequencing technology. The size of the E. j. sinensis assembled genome was approximately 1.27 Gb, close to the estimated size (1.19 Gb), with a contig N50 length of 3.19 Mb. Furthermore, based on assessment using Benchmarking Universal Single-Copy Orthologs (BUSCO), 94.00% of the expected eukaryotic genes were completely present in the genome assembly. In addition, repetitive sequences accounted for ~61.42% of the assembled genome, and 22,619 protein-coding genes were annotated. Comparative genomics analysis demonstrated that the Chinese mitten crab diverged from Penaeus vannamei ~373.6 million years ago, with a faster evolution rate than shrimp. We anticipate that the annotated high-quality genome of E. j. sinensis will promote research on its basic development and evolution and make substantial contributions to comparative genomic analyses of crustaceans.

The blue king crab, Paralithodes platypus, which belongs to the family Lithodidae, is a commercially and ecologically important species. However, a high‐quality reference genome for the king crab has not yet been reported. Here, we assembled the first chromosome‐level blue king crab genome, which contains 104 chromosomes and an N50 length of 51.15 Mb. Furthermore, we determined that the large genome size can be attributed to the insertion of long interspersed nuclear elements and long tandem repeats. Genome assembly assessment showed that 96.54% of the assembled transcripts could be aligned to the assembled genome. Phylogenetic analysis showed the blue king crab to have a close relationship with the Eubrachyura crabs, from which it diverged 272.5 million years ago. Population history analyses indicated that the effective population of the blue king crab declined sharply and then gradually increased from the Cretaceous and Neogene periods, respectively. Furthermore, gene families related to developmental pathways, steroid and thyroid hormone synthesis, and inflammatory regulation were expanded in the genome, suggesting that these genes contributed substantially to the environmental adaptation and unique body plan evolution of the blue king crab. The high‐quality reference genome reported here provides a solid molecular basis for further study of the blue king crab's development and environmental adaptation.

Bellamya aeruginosa belongs to the family Viviparidae and is widely distributed in freshwater ecosystems in Asia. This species is resilient to thermal stress and can survive in polluted waters and consequently has been widely studied as a sentinel species for assessing ecosystem risk. To gain resources to study how B. aeruginosa adapts to harsh environments at the molecular level, we assembled a high-quality genome of this species and compared responses in transcriptome sequencing following exposure to wastewater, heat stress, and cold stress. We assembled a pseudo-chromosome genome for B. aeruginosa (1.2 Gb, 8 chromosomes) through the integration of multiple sequencing strategies. Comparative genomic analyses demonstrated that genes for the expansion of the Viviparidae branch comprising Cipangopaludina cathayensis, Bellamya purificata, and B. aeruginosa were enriched in GO terms such as developmental growth involved in morphogenesis, regulation of animal organ morphogenesis, and regulation of embryonic development. This may be related to the pattern of viviparous reproduction in viviparids. Transcriptomic analyses revealed that this organism relies on lipid metabolism regulation and antioxidant systems to adapt to hypoxic stresses imposed by wastewater. Additionally, we identified multiple genes encoding heat shock proteins (Hsps) among differentially expressed genes resulting from temperature stress treatments, suggesting that the heat shock response plays a crucial role in enabling B. aeruginosa to cope with environmental stress. In light of these observations, we conducted a comprehensive identification and analysis of the Hsp gene family within B. aeruginosa, discovering that the number of Hsp20 family members was significantly higher in this species compared to other closely related organisms—corresponding with our previous analyses regarding gene family expansion and contraction. This study has yielded a high-quality genome of B. aeruginosa and provided insights into the potential molecular mechanisms that underpin the organism’s environmental resilience, and that Hsps in this species are sensitive to environmental stresses and play a key role in its stress mechanisms.

Heat shock proteins (HSPs) play a crucial role in the survival of organisms by facilitating their response to various stress conditions. Cipangopaludina chinensis is an important aquaculture species in China that is highly resistant to temperature changes. To better understand the adaptation mechanisms of C. chinensis to temperature fluctuations, we identified and analyzed the HSPs in C. chinensis (CchHSPs). The 36 identified CchHSPs are distributed on nine chromosomes, and the proteins they encode predominantly exhibit alpha-helix structures. In phylogenetic analyses, each HSP subfamily formed a monophyletic clade. Different CchHSPs showed specific high expression in different tissues. In addition, CchHPS70-09, CchHPS70-12, and CchHPS90-02 were identified as hub genes in the protein-protein interaction network, and the significant elevation of the expression of these genes in foot muscle under heat stress further validated their importance for the adaptation of C. chinensis to environmental stress. This study advances our understanding of the mechanisms underlying the adaptability and stress resistance conferred by the HSP gene family in C. chinensis. These insights will facilitate future efforts aimed at designing molecular markers and conducting molecular breeding programs for this economically valuable species.