Differential gene expression in the intestines of Chinese mitten crabs with three carapace colors

Qi Zhu; Maolei Wei; Xinxin Chen; Zhichao Rong; Dongran Yang; Xiaowu Chen; Xugan Wu

doi:10.1007/s11033-025-10808-5

Differential gene expression in the intestines of Chinese mitten crabs with three carapace colors

Mol Biol Rep. 2025 Jul 15;52(1):712. doi: 10.1007/s11033-025-10808-5.

Authors

Qi Zhu^#¹, Maolei Wei^#¹, Xinxin Chen¹, Zhichao Rong¹, Dongran Yang¹, Xiaowu Chen^{2

3

4}, Xugan Wu^{5

6

7}

Affiliations

¹ Centre for Research on Environmental Ecology and Fish Nutrition of the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China.
² Centre for Research on Environmental Ecology and Fish Nutrition of the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China. xwchen@shou.edu.cn.
³ Key Laboratory of Freshwater Aquatic Genetic Resources Certified by the Ministry of Agriculture and Rural Affairs of China, Shanghai Ocean University, Shanghai, 201306, China. xwchen@shou.edu.cn.
⁴ College of Fisheries and Life Science, Shanghai Ocean University, No. 999, Huchenghuan Rd, Shanghai, 201306, China. xwchen@shou.edu.cn.
⁵ Centre for Research on Environmental Ecology and Fish Nutrition of the Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China. xgwu@shou.edu.cn.
⁶ Key Laboratory of Freshwater Aquatic Genetic Resources Certified by the Ministry of Agriculture and Rural Affairs of China, Shanghai Ocean University, Shanghai, 201306, China. xgwu@shou.edu.cn.
⁷ College of Fisheries and Life Science, Shanghai Ocean University, No. 999, Huchenghuan Rd, Shanghai, 201306, China. xgwu@shou.edu.cn.

^# Contributed equally.

PMID: 40663185
DOI: 10.1007/s11033-025-10808-5

Abstract

Background: Carapace color in Chinese mitten crab (Eriocheir sinensis) influences both commercial value and physiological traits, yet its molecular basis remains unclear. The intestine plays a key role in pigment absorption and metabolism, but its involvement in pigmentation has been understudied. This study aimed to investigate intestinal gene expression differences among red, white, and green carapace strains.

Methods and results: We sequenced intestinal RNA from red, white, and green morphs (n = 3 per group) on an Illumina NovaSeq platform. Following fastp quality control and Salmon quantification, 6,214 genes were identified as differentially expressed (|log2FC| ≥ 1, FDR < 0.05). Functional enrichment linked these genes to pigment transport and biosynthesis pathways, including ABC transporters, SLC carriers, carotenoid binding, and tyrosine metabolism. Seven representative DEGs (CRCN‑A1, CRCN-A2, ABCC4, ABCF1, slc23a1, slc49a4, TYROB) were validated by qRT‑PCR, with expression trends congruent to RNA‑seq results.

Conclusion: Intestinal gene expression contributes to carapace pigmentation through distinct carotenoid‑transport and melanin pathways. These insights offer molecular targets for selective breeding and functional validation.

Keywords: Eriocheir sinensis; Carapace pigmentation; Carotenoids; Melanin; Transcriptome.

MeSH terms

Animal Shells / metabolism
Animals
Brachyura* / genetics
Brachyura* / metabolism
Color
Gene Expression Profiling / methods
Gene Expression Regulation
Intestines / physiology
Pigmentation* / genetics
Transcriptome / genetics

Abstract

MeSH terms

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