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Integrated Analysis of Coding Genes and Non-coding RNAs Associated with Shell Color in the Pacific Oyster (Crassostrea gigas)

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Abstract

Molluscan shell color polymorphism is important in genetic breeding, while the molecular information mechanism for shell coloring is unclear. Here, high-throughput RNA sequencing was used to compare expression profiles of coding and non-coding RNAs (ncRNAs) from Pacific oyster Crassostrea gigas with orange and black shell, which were from an F2 family constructed by crossing an orange shell male with a black shell female. First, 458, 13, and 8 differentially expressed genes (DEGs), lncRNAs (DELs), and miRNAs (DEMs) were identified, respectively. Functional analysis suggested that the DEGs were significantly enriched in 9 pathways including tyrosine metabolism and oxidative phosphorylation pathways. Several genes related to melanin synthesis and biomineralization expressed higher whereas genes associated with carotenoid pigmentation or metabolism expressed lower in orange shell oyster. Then, based on the ncRNA analysis, 163 and 20 genes were targeted by 13 and 8 differentially expressed lncRNAs (DELs) and miRNAs (DEMs), severally. Potential DELs-DEMs-DEGs interactions were also examined. Seven DEMs-DEGs pairs were detected, in which tyrosinase-like protein 1 was targeted by lgi-miR-133-3p and lgi-miR-252a and cytochrome P450 was targeted by dme-miRNA-1-3p. These results revealed that melanin synthesis-related genes and miRNAs-mRNA interactions functioned on orange shell coloration, which shed light on the molecular regulation of shell coloration in marine shellfish.

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Abbreviations

tyr1 :

Tyrosinase-like protein 1

sfrp3 :

Secreted frizzled-related protein 3

calm1 :

Neo-calmodulin-like

CYP450 :

Cytochrome P450

cox19 :

Cytochrome c oxidase assembly protein COX19-like

coa7 :

Cytochrome c oxidase assembly factor 7-like

timp3 :

Metalloproteinase inhibitor 3-like

fib :

Nacrein-like protein isoform X1

rpl24 :

60S ribosomal protein L24

RBP4 :

Retinol-binding protein 4

RAR :

Retinoic acid receptor

LDLR :

Low-density lipoprotein receptor

SLC :

Solute carrier

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Funding

This work was supported by the grants from National Natural Science Foundation of China (31972789 and 31772843), Weihai City (2018NS01), and Industrial Development Project of Qingdao City (20-3-4-16-nsh).

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Authors and Affiliations

  1. Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China

    Zhuanzhuan Li, Qi Li, Shikai Liu, Ziqiang Han, Lingfeng Kong & Hong Yu

  2. Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China

    Qi Li

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  1. Zhuanzhuan Li
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  2. Qi Li
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Correspondence to Qi Li.

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Li, Z., Li, Q., Liu, S. et al. Integrated Analysis of Coding Genes and Non-coding RNAs Associated with Shell Color in the Pacific Oyster (Crassostrea gigas). Mar Biotechnol 23, 417–429 (2021). https://doi.org/10.1007/s10126-021-10034-7

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