*Article* **Effects of Long-Term High Carbonate Alkalinity Stress on the Ovarian Development in** *Exopalaemon carinicauda*

**Xiuhong Zhang 1,2,†, Jiajia Wang 1,2,†, Chengwei Wang 1,2, Wenyang Li 1,2, Qianqian Ge 3, Zhen Qin 1,2, Jian Li 1,2 and Jitao Li 1,2,\***


**Abstract:** Saline–alkaline water limits the growth and survival of aquatic animals due to its high carbonate alkalinity, high pH, and various ion imbalances. The ridgetail white prawn *Exopalaemon carinicauda* is strongly adaptable to the saline–alkaline water, making it an excellent candidate species for large-scale aquaculture in saline–alkaline areas. To explore the effect of long-term high carbonate alkalinity stress on ovarian development in *E. carinicauda* for assisting the development of saline–alkaline aquaculture, we performed ovary histology analysis and RNA–sequencing of the eyestalk and ovary in order to compare the transcriptomic responses of individuals in high carbonate alkalinity (8 mmol/L) with a control group (2 mmol/L) for 60 days. It was found that high carbonate alkalinity stress resulted in a loose arrangement of oogonia and a small number of surrounding follicular cells. A total of 1102 differentially expressed genes (DEGs) in ovary tissue were identified under high carbonate alkalinity stress, and the 18 important DEGs were associated with ovarian development. The majority of the DEGs were enriched in ECM–receptor interaction, Folate biosynthesis, the FoxO signaling pathway, insect hormone biosynthesis, and lysosome, which were involved in the ovarian development of *E. carinicauda*. A total of 468 DEGs were identified in eyestalk tissue under high carbonate alkalinity stress, and the 13 important DEGs were associated with ovarian development. KEGG enrichment analysis found that ECM–receptor interaction, folate biosynthesis, lysosome, metabolic pathways, and retinol metabolism may be involved in the ovarian development under high carbonate alkalinity stress. Our results provide new insights and reveal the genes and pathways involved in the ovarian development of *E. carinicauda* under long-term high carbonate alkalinity stress.

**Keywords:** carbonate alkalinity stress; *Exopalaemon carinicauda*; reproduction; ovary; eyestalk; transcriptome
