Comparative transcriptomic analysis provides insights into the molecular basis of brachyurization and adaptation to benthic lifestyle in Eriocheir sinensis

• 1016 DEGs were identified between megalopae and the first juvenile crab in Eriocheir sinensis.
• 169 genes were assigned to morphogenic pathways (Wnt, Hedgehog and hormone synthesis).
• In megalopae, 38 up-regulated genes were associated with cytoskeleton construction.
• In juvenile, 53 up-regulated genes were related to cuticle development and protein degradation.
• Sensory perception and immunity related genes were highly expressed in megalopae.

The development of Eriocheir sinensis from the megalopa to the first juvenile crab undergoes brachyurization and a habitat transition from pelagic to benthic lifestyle. However, the molecular mechanism of this process is poorly understood in crabs. Using next-generation RNA sequencing, we identified 22,622 annotated unigenes and 1016 differentially expressed genes especially involved in metamorphosis, sensory perception and immunity in the two stages. Among 22,622 unigenes, 169 unigenes were assigned to morphogenic pathways (i.e., Wnt, Hedgehog and hormone biosynthesis). For metamorphosis, 38 up-regulated genes in megalopae were associated with cytoskeleton construction, while, 52 up-regulated genes in juvenile were related to cuticle development and protein degradation. Several crucial genes involved in phototransduction and two olfactory-related genes were significantly up-regulated in megalopae. Moreover, 44 immunity-related genes were highly expressed in megalopae. This study provides a comprehensive view of brachyurization and benthic adaptation mechanisms in E. sinensis.