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Genome-Wide Analysis of Family I84 Protease Inhibitor Genes in Three Bivalves Reveals Important Information About the Protein Family’s Evolution

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Abstract

Family I84 serine protease inhibitors are believed to be mollusk specific proteins involved in host defense. The molecular evolution of the family, however, remains to be understood. In this study, the genes of Family I84 protease inhibitors in 3 bivalves, Crassostrea gigas, Crassostrea virginica and Tegillarca granosa, were analyzed at the genomic level. A total of 66 Family I84 genes (22 in C. gigas, 28 in C. virginica and 16 in T. granosa) were identified from the 3 species. They distributed unevenly in the genomes involving 4 chromosomes in C. gigas and 5 chromosomes in C. virginica and T. granosa and some genes were tandemly duplicated. Most genes had 3 exons with 12 genes having 4 exons and 1 gene having 2 exons. All genes but 1 from C. gigas and 1 from T. granosa encoded peptides with a signal sequence at the N-terminus, and the properties of the predicted mature molecules were similar. Four conserved motifs were identified in the 66 amino acid sequences. Collinear analysis revealed higher collinearity between the 2 oyster species in general genes and in Family I84 genes. Phylogenetic analysis of the 66 genes with those previously reported from 3 other bivalves and 1 gastropod showed that Family I84 protease inhibitor genes from the same species tended to be grouped together in terminal branches of the constructed Maximum likelihood tree, but most internal nodes were poorly supported by the bootstrap values. In addition, differences in expression patterns between the genes of a same species were observed in the developmental stages and tissues of C. gigas and T. granosa. Moreover, the co-expression of genes within Family I84 and Family I84 genes with non-Family I84 were also detected in C. gigas and T. granosa. These results suggested that Family I84 protease inhibitor genes evolved by active duplications and structural and functional diversifications after the speciation of related mollusks, and the diversified protease inhibitor family was likely multifunctional.

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Data Availability

Both sequences from public database as indicated in the Materials and Methods section and home-generated data were used in this research. The home-generated sequence data used in the present research have been submitted to NCBI GenBank with the accession numbers of PRJNA852380 and PRJNA823812. All data information is provided in the Supplementary Tables 1 and 2.

Availability of Data

Both sequences from public database as indicated in the Materials and Methods section and home-generated data were used in this research. The home-generated sequence data used in the present research have been submitted to NCBI GenBank with the accession numbers of PRJNA852380 and PRJNA823812. All data information is provided in the Supplementary Tables 1 and 2.

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Acknowledgements

The authors express their sincere gratitude to members of Professor Yongbo Bao group from Zhejiang Wanli University, for their help on providing Tegillarca granosa transcriptomes analysis.

Funding

This work was financially supported by National Natural Science Foundation of China (32073010, 32002428), “3315” Innovative Team of Ningbo City, the Fundamental Research Funds for Zhejiang Province Universities and China Agriculture Research System supported by MOF and MARA.

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Authors and Affiliations

  1. Zhejiang Key Laboratory of Aquatic Germplasm Resource, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang Province, 315100, China

    Jinxia Mao, Jiali Lu, Sheng Liu, Youli Liu, Zhihua Lin & Qinggang Xue

  2. Ninghai Institute of Mariculture Breeding and Seed Industry , Zhejiang Wanli University, Ninghai, Zhejiang Province, 315604, China

    Jinxia Mao, Sheng Liu, Youli Liu, Zhihua Lin & Qinggang Xue

  3. National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China

    Jiali Lu

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  1. Jinxia Mao
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Contributions

Qinggang Xue designed and supervised the execution of the experiment. Jinxia Mao and Jiali Lu performed the experiments. Jinxia Mao, Jiali Lu and Sheng Liu analyzed the data. Jinxia Mao and Jiali Lu wrote the manuscript. Qinggang Xue, Sheng Liu and Youli Liu revised the manuscript. Zhihua Lin were involved in experiment design and manuscript discussion. All authors read and approved the final manuscript.

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Correspondence to Qinggang Xue.

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Ethics Approval

The S. constricta used in this work were collected from the Genetic Breeding Research Center (GBRC) of Zhejiang Wanli University, China. And all experimental procedures were approved by the Institutional Animal Care and Use Committee (IACUC) of Zhejiang Wanli University, China.

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Jinxia Mao and Jiali Lu both contributed equally.

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Mao, J., Lu, J., Liu, S. et al. Genome-Wide Analysis of Family I84 Protease Inhibitor Genes in Three Bivalves Reveals Important Information About the Protein Family’s Evolution. Mar Biotechnol 25, 729–748 (2023). https://doi.org/10.1007/s10126-023-10236-1

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