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Background <p>Crustacyanins (CRCNs) are a pigment-protein widely distributed in crustaceans, and their main function is to bind to astaxanthin to achieve regulation of crustacean body color through protein-ligand interactions. The CRCN gene family forms a highly homologous gene cluster through duplication and subsequent mutations. Current research primarily focuses on characterizing specific subunits of the CRCN gene family in particular species, whereas systematic studies on the subunits of the CRCN gene family across multiple species at the genome level are still lacking.</p> Results <p>A total of 24, 44, 51, 17, 4, and 2 <i>CRCN</i> genes were identified in <i>Neocaridina denticulata sinensis</i>, <i>Penaeus chinensis</i>, <i>Macrobrachium rosenbergii</i>, <i>Procambarus clarkii</i>, <i>Eriocheir sinensis</i>, and <i>Portunus trituberculatus</i>, respectively. Chromosomal localization analysis revealed that the CRCN gene family is distributed in gene clusters on specific chromosomes in shrimp. Ka/Ks analysis showed that the tandem duplicated gene pairs of <i>CRCN</i> are under purifying selection. The expression of <i>CRCN</i> genes (<i>NdCRCNs</i>) in <i>N. denticulata sinensis</i> varies significantly in different tissues. The NdCRCN proteins were expressed in both muscle and epidermis, but their expression in the epidermis was substantially higher than in muscle tissue.</p> Conclusions <p>This study conducted a genome-wide identification and evolutionary analysis of the CRCN gene family, and the results showed that this gene cluster was significantly expanded in shrimp species. The obtained NdCRCN-specific binding antibody caused cross-reactivity in <i>P. chinensis</i>, <i>M. rosenbergii</i>, and <i>P. clarkii</i>. In addition, we determined the cellular localization of CRCN in the epidermis and muscle at the protein level. This study systematically analyzed the CRCN gene family in crustaceans, providing important references for subsequent research.</p>

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Genome-wide identification of the crustacyanin gene family in Neocaridina denticulata sinensis based on comparative genomics and localization analysis

  • 期刊论文

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  • 发表日期：

    2025年11月27日

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  • Dandan Feng,
  • Hongrui Li,
  • Yijie Liu,
  • Shangpeng Wang,
  • Yingwen Li,
  • Yangcan Gao,
  • Yuying Sun,
  • Jiquan Zhang

摘要

Background

Crustacyanins (CRCNs) are a pigment-protein widely distributed in crustaceans, and their main function is to bind to astaxanthin to achieve regulation of crustacean body color through protein-ligand interactions. The CRCN gene family forms a highly homologous gene cluster through duplication and subsequent mutations. Current research primarily focuses on characterizing specific subunits of the CRCN gene family in particular species, whereas systematic studies on the subunits of the CRCN gene family across multiple species at the genome level are still lacking.

Results

A total of 24, 44, 51, 17, 4, and 2 CRCN genes were identified in Neocaridina denticulata sinensis, Penaeus chinensis, Macrobrachium rosenbergii, Procambarus clarkii, Eriocheir sinensis, and Portunus trituberculatus, respectively. Chromosomal localization analysis revealed that the CRCN gene family is distributed in gene clusters on specific chromosomes in shrimp. Ka/Ks analysis showed that the tandem duplicated gene pairs of CRCN are under purifying selection. The expression of CRCN genes (NdCRCNs) in N. denticulata sinensis varies significantly in different tissues. The NdCRCN proteins were expressed in both muscle and epidermis, but their expression in the epidermis was substantially higher than in muscle tissue.

Conclusions

This study conducted a genome-wide identification and evolutionary analysis of the CRCN gene family, and the results showed that this gene cluster was significantly expanded in shrimp species. The obtained NdCRCN-specific binding antibody caused cross-reactivity in P. chinensis, M. rosenbergii, and P. clarkii. In addition, we determined the cellular localization of CRCN in the epidermis and muscle at the protein level. This study systematically analyzed the CRCN gene family in crustaceans, providing important references for subsequent research.