Giant isopods are the most representative group of crustaceans living in the deep sea environment with a huge body size. In order to understand the genetic basis of these large animals to adapt the harsh oligotrophic environment of the deep-sea, the genome of a deep-sea (-898 m) giant isopod Bathynomus jamesi was sequenced and its genome characteristics were analyzed. The genome assembly of B. jamesi has a total length of 5.89 Gb with a contig N50 of 587.28 Kb, which is among the largest one with high continuity of the sequenced crustacean genomes. The large genome size of B. jamesi is mainly attributable to the proliferation of transposable elements, especially for DNA transposons and CR1-type LINEs, which account for more than 84% of the genome. A number of expanded gene families in the genome were enriched in thyroid and insulin hormone signaling pathways, which might have driven the evolution of its huge body size. Transcriptomic analysis showed that several expanded gene families related to glycolysis and vesicular transport were specifically expressed in its digestive organs, revealing the molecular mechanism of nutrient absorption and utilization in oligotrophic environment adaptation. Taken together, the giant isopod genome provides a valuable resource for understanding the body size evolution and adaptation mechanisms of macrobenthos to the deep-sea environment.

Ark shells are commercially important clam species that inhabit in muddy sediments of shallow coasts in East Asia. For a long time, the lack of genome resources has hindered scientific research of ark shells. Here, we reported a high-quality chromosome-level genome assembly of Scapharca kagoshimensis, with an aim to unravel the molecular basis of heme biosynthesis, and develop genomic resources for genetic breeding and population genetics in ark shells. Nineteen scaffolds corresponding to 19 chromosomes were constructed from 938 contigs (contig N50=2.01 Mb) to produce a final high-quality assembly with a total length of 1.11 Gb and scaffold N50 around 60.64 Mb. The genome assembly represents 93.4% completeness via matching 303 eukaryota core conserved genes. A total of 24,908 protein-coding genes were predicted and 24,551 genes (98.56%) of which were functionally annotated. The enrichment analyses suggested that genes in heme biosynthesis pathways were expanded and positive selection of the hemoglobin genes was also found in the genome of S. kagoshimensis, which gives important insights into the molecular mechanisms and evolution of the heme biosynthesis in mollusca. The valuable genome assembly of S. kagoshimensis would provide a solid foundation for investigating the molecular mechanisms that underlie the diverse biological functions and evolutionary adaptations of S. kagoshimensis.