Phascolosoma esculenta is an economically species inhabiting the intertidal zone and is farmed with high output. During artificial propagation, P. esculenta underwent mass death after torrential rain due to low salinity. In this paper, the effect of salinity on P. esculenta was studied for the first time. The results showed that P. esculenta died when exposed to water of 10‰ salinity, and their body lengths were about two times larger than when exposed to salinity of 25‰. The groups exposed to 10‰ salinity underwent severe necrosis. The activity of T-SOD and T-AOC in nephridial tissues increased between 3 and 12 h, but not at 9 h, T-SOD was highest in the control group and lowest in the death group, and T-AOC was highest in the death group and lowest in the survivor group. The concentration of MDA increased from 3 to 9 h and then decreased, and was highest in the death group and lowest in the control group. 35,053 unique genes, including 15,445 new genes, were acquired based on the 61.63 Gb Clean RNA-Seq Data. 27773 average alternative splicing (AS) events were found in the death group, which was 83.74% and 83.54% of that in the control and survivor group, respectively. Additionally, 1596 significantly differentially expressed genes (DEGs) were observed, which were classified into several functional categories, including genes involved in ion transporters, cation transport, RNA processing, immune response etc. The study had also found a significant number of genes involved in the pathways, including Mineral absorption, AMPK signaling pathway, Oxidative phosphorylation, and Phagosome pathways, such as Hsp70, Hsp20, Gst, solute carrier family genes, calcium channel regulatory activity genes, and pre-rRNA processing proteins. Overall, these results provide numerous candidate genes for future investigations and valuable insights into the mechanisms underlying the culture of P. esculenta in lower salinity.
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