Genome assembly of a giant isopod Bathynomus jamesi provides insights into the body size evolution and adaptation to deep-sea environment

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.