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Jiang K, Xu C, Yu H, Kong L, Liu S, Li Q. Transcriptomic and Physiological Analysis Reveal Melanin Synthesis-Related Genes and Pathways in Pacific Oysters (Crassostrea gigas). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:364-379. [PMID: 38483671 DOI: 10.1007/s10126-024-10302-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 03/06/2024] [Indexed: 04/25/2024]
Abstract
Shell color is one of the shell traits of molluscs, which has been regarded as an economic trait in some bivalves. Pacific oysters (Crassostrea gigas) are important aquaculture shellfish worldwide. In the past decade, several shell color strains of C. gigas were developed through selective breeding, which provides valuable materials for research on the inheritance pattern and regulation mechanisms of shell color. The inheritance patterns of different shell colors in C. gigas have been identified in certain research; however, the regulation mechanism of oyster pigmentation and shell color formation remains unclear. In this study, we performed transcriptomic and physiological analyses using black and white shell oysters to investigate the molecular mechanism of melanin synthesis in C. gigas. Several pigmentation-related pathways, such as cytochrome P450, melanogenesis, tyrosine metabolism, and the cAMP signaling pathway were found. The majority of differentially expressed genes and some signaling molecules from these pathways exhibited a higher level in the black shell oysters than in the white, especially after L-tyrosine feeding, suggesting that those differences may cause a variation of tyrosine metabolism and melanin synthesis. In addition, the in vitro assay using primary cells from mantle tissue showed that L-tyrosine incubation increased cAMP level, gene and protein expression, and melanin content. This study reveals the difference in tyrosine metabolism and melanin synthesis in black and white shell oysters and provides evidence for the potential regulatory mechanism of shell color in oysters.
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Affiliation(s)
- Kunyin Jiang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Chengxun Xu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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2
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Li M, Tang J, Yuan M, Huang B, Liu Y, Wei L, Han Y, Zhang X, Wang X, Yu G, Sang X, Fan N, Cai S, Zheng Y, Zhang M, Wang X. Outer fold is sole effective tissue among three mantle folds with regard to oyster shell colour. Int J Biol Macromol 2023; 241:124655. [PMID: 37121412 DOI: 10.1016/j.ijbiomac.2023.124655] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/02/2023]
Abstract
Molluscs constitute the second largest phylum of animals in the world, and shell colour is one of their most important phenotypic characteristics. In this study, we found among three folds on the mantle edge of oyster, only the outer fold had the same colour as the shell. Transcriptome and mantle cutting experiment indicated that the outer fold may be mainly reflected in chitin framework formation and biomineralisation. There were obvious differences in SEM structure and protein composition between the black and white shell periostraca. The black shell periostraca had more proteins related to melanin biosynthesis and chitin binding. Additionally, we identified an uncharacterized protein gene (named as CgCBP) ultra-highly expressed only in the black outer fold and confirmed its function of chitin-binding and CaCO3 precipitation promoting. RNAi also indicated that CgCBP knockdown could change the structure of shell periostracum and reduce shell pigmentation. All these results suggest that the mantle outer fold plays multiple key roles in shell periostraca bioprocessing, and shell periostracum structure affected by chitin-binding protein is functionally correlated with shell pigmentation. The investigation of oyster shell periostracum structure and shell colour will provide a better understanding in pigmentation during biological mineralisation in molluscs.
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Affiliation(s)
- Mai Li
- School of Agriculture, Ludong University, Yantai, China
| | - Juyan Tang
- School of Agriculture, Ludong University, Yantai, China
| | | | - Baoyu Huang
- School of Agriculture, Ludong University, Yantai, China
| | - Yaqiong Liu
- School of Agriculture, Ludong University, Yantai, China
| | - Lei Wei
- School of Agriculture, Ludong University, Yantai, China
| | - Yijing Han
- School of Agriculture, Ludong University, Yantai, China
| | - Xuekai Zhang
- School of Agriculture, Ludong University, Yantai, China
| | - Xiaona Wang
- School of Agriculture, Ludong University, Yantai, China
| | - Guoxu Yu
- Changdao National Marine Park Management Center, Yantai, China
| | - Xiuxiu Sang
- School of Agriculture, Ludong University, Yantai, China
| | - Nini Fan
- Changdao Enhancement and Experiment Station, Chinese Academy of Fishery Sciences, Yantai, China
| | - Shuai Cai
- Changdao Enhancement and Experiment Station, Chinese Academy of Fishery Sciences, Yantai, China
| | - Yanxin Zheng
- Changdao Enhancement and Experiment Station, Chinese Academy of Fishery Sciences, Yantai, China
| | - Meiwei Zhang
- School of Agriculture, Ludong University, Yantai, China.
| | - Xiaotong Wang
- School of Agriculture, Ludong University, Yantai, China.
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Yuan C, Mao J, Sun H, Wang Y, Guo M, Wang X, Tian Y, Hao Z, Ding J, Chang Y. Genome-wide DNA methylation profile changes associated with shell colouration in the Yesso scallop (Patinopecten yessoensis) as measured by whole-genome bisulfite sequencing. BMC Genomics 2021; 22:740. [PMID: 34649514 PMCID: PMC8515700 DOI: 10.1186/s12864-021-08055-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/05/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mollusca, a phylum of highly rich species, possess vivid shell colours, but the underlying molecular mechanism remains to be elucidated. DNA methylation, one of the most common epigenetic modifications in eukaryotes, is believed to play a vital role in various biological processes. However, analysis of the effects of DNA methylation on shell colouration has rarely been performed in molluscs, limiting the current knowledge of the molecular mechanism of shell colour formation. RESULTS In the present study, to reveal the role of epigenetic regulation in shell colouration, WGBS, the "gold standard" of DNA methylation analysis, was first performed on the mantle tissues of Yesso scallops (Patinopecten yessoensis) with different shell colours (brown and white), and DNA methylomes at single-base resolution were generated. About 3% of cytosines were methylated in the genome of the Yesso scallop. A slight increase in mCG percentage and methylation level was found in brown scallops. Sequence preference of nearby methylated cytosines differed between high and low methylation level sites and between the brown- and white-shelled scallops. DNA methylation levels varied among the different genomic regions; all the detected regions in the brown group exhibited higher methylation levels than the white group. A total of 41,175 DMRs (differentially methylated regions) were detected between brown and white scallops. GO functions and pathways associated with the biosynthesis of melanin and porphyrins were significantly enriched for DMRs, among which several key shell colour-related genes were identified. Further, different correlations between mRNA expression levels and DNA methylation status were found in these genes, suggesting that DNA methylation regulates shell colouration in the Yesso scallop. CONCLUSIONS This study provides genome-wide DNA methylation landscapes of Yesso scallops with different shell colours, offering new insights into the epigenetic regulatory mechanism underlying shell colour.
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Affiliation(s)
- Changzi Yuan
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Junxia Mao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China.
| | - Hongyan Sun
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Yiying Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Ming Guo
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Xubo Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Ying Tian
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Zhenlin Hao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Jun Ding
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China.
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Li Z, Li Q, Liu S, Han Z, Kong L, Yu H. Integrated Analysis of Coding Genes and Non-coding RNAs Associated with Shell Color in the Pacific Oyster (Crassostrea gigas). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2021; 23:417-429. [PMID: 33929611 DOI: 10.1007/s10126-021-10034-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/14/2021] [Indexed: 06/12/2023]
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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Affiliation(s)
- Zhuanzhuan Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Ziqiang Han
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
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Genome-wide identification, characterisation and expression analysis of the ALAS gene in the Yesso scallop (Patinopecten yessoensis) with different shell colours. Gene 2020; 757:144925. [PMID: 32622991 DOI: 10.1016/j.gene.2020.144925] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 06/13/2020] [Accepted: 06/27/2020] [Indexed: 12/19/2022]
Abstract
Porphyrins, one of the most common shell pigments, are by-products of the haem pathway. 5-Aminolaevulinate synthase (ALAS) is the first and rate-limiting enzyme in this pathway and has been well studied in vertebrate species. However, the function of ALAS in shell colouration has been poorly studied in molluscs, which are renowned for their colourful shells. In the present study, an ALAS gene, named PyALAS, was identified through whole-genome scanning in the Yesso scallop (Patinopecten yessoensis), an economically and evolutionarily important bivalve species in which the shell colour represents polymorphism. Two conserved domains were detected in the PyALAS protein sequence, including a Preseq-ALAS domain and a 5-ALAS domain, confirming the identification of PyALAS. Phylogenetic analysis of the ALAS proteins among various invertebrate and vertebrate species revealed a high consistency between the molecular evolution of ALAS and the species taxonomy. PyALAS was ubiquitously expressed in most adult tissues of the Yesso scallop. The left mantle expressed a significantly higher level of PyALAS than the right side in brown scallops, whereas there was no significant difference in white scallops. Significantly different expression levels of PyALAS was also detected between the two different shell colour strains. These data indicate that PyALAS plays an important role in shell colouration in Yesso scallops and the present study provides new insights into the molecular mechanism of shell colouration in molluscs.
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6
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Tettelbach ST, Furman BT, Hughes SWT, Carroll JM, Peterson BJ, Havelin J, Tettelbach CRH, Patricio RM. Attempted use of an uncommon bay scallop color morph for tracking the contribution of restoration efforts to population recovery. Restor Ecol 2020. [DOI: 10.1111/rec.13109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stephen T. Tettelbach
- Marine ProgramCornell Cooperative Extension 3690 Cedar Beach Road Southold NY 11971 U.S.A
- Professor Emeritus of BiologyLong Island University 720 Northern Boulevard Brookville New York 11548 U.S.A
| | - Bradley T. Furman
- Florida Fish Wildlife Conservation CommissionFlorida Fish and Wildlife Research Institute 100 Eighth Avenue SE St. Petersburg FL 33701 U.S.A
| | - Scott W. T. Hughes
- Marine ProgramCornell Cooperative Extension 3690 Cedar Beach Road Southold NY 11971 U.S.A
| | - John M. Carroll
- Department of BiologyGeorgia Southern University 1332 Southern Drive Statesboro GA 30458 U.S.A
| | - Bradley J. Peterson
- School of Marine and Atmospheric SciencesStony Brook‐Southampton 8 Little Neck Road Southampton NY 11968 U.S.A
| | - Jason Havelin
- Marine ProgramCornell Cooperative Extension 3690 Cedar Beach Road Southold NY 11971 U.S.A
| | - Christian R. H. Tettelbach
- Estuary & Ocean Science Center, Romberg Tiburon CampusSan Francisco State University 3150 Paradise Drive Tiburon CA 94920 U.S.A
| | - R. Michael Patricio
- Marine ProgramCornell Cooperative Extension 3690 Cedar Beach Road Southold NY 11971 U.S.A
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7
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Ren G, Chen C, Jin Y, Zhang G, Hu Y, Shen W. A Novel Tyrosinase Gene Plays a Potential Role in Modification the Shell Organic Matrix of the Triangle Mussel Hyriopsis cumingii. Front Physiol 2020; 11:100. [PMID: 32153421 PMCID: PMC7045039 DOI: 10.3389/fphys.2020.00100] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 01/27/2020] [Indexed: 12/17/2022] Open
Abstract
Although tyrosinases have been speculated to participate in the shell formation of mollusks, there is still a lack of experimental evidence to support this assumption. In this study, a novel tyrosinase designated HcTyr2 was isolated and characterized from the freshwater mussel Hyriopsis cumingii. The change in HcTyr2 mRNA expression during the process of embryonic development was detected by real-time quantitative PCR. The result showed that the expression of HcTyr2 mRNA was significantly upregulated at the stages of gastrulae and unmatured glochidia (P < 0.05), suggesting that this gene might fundamentally participate in the biogenesis and growth of the initial shell. Meanwhile, the upregulation of HcTyr2 mRNA at the stages of shell regeneration 24 h and 9 days after shell notching in the mantle edge (P < 0.05) implied that it might play an important role in shell periostracum and nacre formation by mediating the cross-linking of quinoproteins to promote the maturity of organic matrix. Additionally, the knockdown of HcTyr2 mRNA by RNA interference resulted in not only the suppression of periostracum growth but also structural disorder of nacre aragonite tablets, as detected by scanning electron microscopy. These results suggested that HcTyr2 might regulate the growth of shell by its oxidative ability to transform soluble matrix proteins into insoluble matrix proteins, then promoting the maturity of the shell organic framework in H. cumingii. In general, our results suggested the importance of HcTyr2 in the shell formation and regeneration of H. cumingii.
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Affiliation(s)
- Gang Ren
- School of Life Sciences, Shaoxing University, Shaoxing, China.,College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chao Chen
- School of Life Sciences, Shaoxing University, Shaoxing, China
| | - Yefei Jin
- School of Life Sciences, Shaoxing University, Shaoxing, China
| | - Genfang Zhang
- College of Agriculture and Bioengineering, Jinhua Polytechnic, Jinhua, China
| | - Yiwei Hu
- School of Life Sciences, Shaoxing University, Shaoxing, China
| | - Wenying Shen
- School of Life Sciences, Shaoxing University, Shaoxing, China
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Mao J, Zhang W, Wang X, Song J, Yin D, Tian Y, Hao Z, Han B, Chang Y. Histological and Expression Differences Among Different Mantle Regions of the Yesso Scallop (Patinopecten yessoensis) Provide Insights into the Molecular Mechanisms of Biomineralization and Pigmentation. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:683-696. [PMID: 31385168 DOI: 10.1007/s10126-019-09913-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 07/15/2019] [Indexed: 06/10/2023]
Abstract
The molecular mechanisms of shell formation and pigmentation are issues of great interest in molluscan studies due to the unique physical and biological properties of shells. The Yesso scallop, Patinopecten yessoensis, is one of the most important maricultural bivalves in Asian countries, and its shell color shows polymorphism. To gain more information about the underlying mechanisms of shell formation and pigmentation, this study presents the first analyses of histological and transcriptional differences between different mantle regions of the Yesso scallop, which are thought to be responsible for the formation of different shell layers. The results showed major microstructural differences between the edge and central mantles, which were closely associated with their functions. Different biomineralization-related GO functions, which might participate in the formation of different shell layers, were significantly enriched in the different mantle regions, indicating the different molecular functions of the two mantle regions in shell formation. The melanogenesis pathway, which controls melanin biosynthesis, was the most significantly enriched pathway in the DEGs between the two mantle regions, indicating its important role in shell pigmentation. Tyr, the key and rate-limiting gene in melanogenesis, was expressed at a remarkably high level in the central mantle, while the upstream regulatory genes included in melanogenesis were mainly upregulated in the edge mantle, suggesting the different molecular functions of the two mantle regions in shell pigmentation.
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Affiliation(s)
- Junxia Mao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Wenjing Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Xubo Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Jian Song
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Donghong Yin
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Ying Tian
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Zhenlin Hao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Bing Han
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China.
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Mao J, Zhang X, Zhang W, Tian Y, Wang X, Hao Z, Chang Y. Genome-wide identification, characterization and expression analysis of the MITF gene in Yesso scallops (Patinopecten yessoensis) with different shell colors. Gene 2018; 688:155-162. [PMID: 30552980 DOI: 10.1016/j.gene.2018.11.096] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/25/2018] [Accepted: 11/28/2018] [Indexed: 01/03/2023]
Abstract
The microphthalmia-associated transcription factor (MITF) is the center of the regulator network of melanin synthesis in vertebrates. However, the role of MITF in shell color formation is poorly studied in mollusks. In the present study, an MITF gene, PyMITF, was first identified at the whole-genome level in Yesso scallop (Patinopecten yessoensis), an evolutionarily and economically important species, the shell color of which shows polymorphism. The PyMITF is a large gene spanning ~37 kb in the genome with 7 introns and 8 exons. A basic helix-loop-helix leucine zipper (bHLH-LZ) domain was detected in the PyMITF protein sequence, which can bind the canonical E-box sequence in the promoter region of the downstream genes. Phylogenetic analysis of the MITFs among vertebrates and invertebrates revealed that the molecular evolution of MITFs was consistent with the species taxonomy. Different expression levels of PyMITF were detected among different shell color strains, indicating the important role of PyMITF involved in shell pigmentation. Besides, PyMITF was expressed at a significantly higher level in the central mantle than that in the edge mantle, proving the participation of the central mantle in shell color formation in molecular level for the first time. The work provides valuable information for the molecular mechanism study of shell color formation.
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Affiliation(s)
- Junxia Mao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Xiaosen Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Wenjing Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Ying Tian
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Xubo Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Zhenlin Hao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China.
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10
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Cloning of a microphthalmia-associated transcription factor gene and its functional analysis in nacre formation and melanin synthesis in Hyriopsis cumingii. AQUACULTURE AND FISHERIES 2018. [DOI: 10.1016/j.aaf.2018.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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11
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The ultrastructural features of embryonic and early larval development in Yesso scallop, Mizuhopecten yessoensis. Tissue Cell 2018; 53:76-86. [DOI: 10.1016/j.tice.2018.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 06/01/2018] [Accepted: 06/11/2018] [Indexed: 11/23/2022]
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12
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Sun X, Liu Z, Wu B, Zhou L, Wang Q, Wu W, Yang A. Differences between fast and slow muscles in scallops revealed through proteomics and transcriptomics. BMC Genomics 2018; 19:377. [PMID: 29783952 PMCID: PMC5963113 DOI: 10.1186/s12864-018-4770-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 05/09/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Scallops possess striated and catch adductor muscles, which have different structure and contractile properties. The striated muscle contracts very quickly for swimming, whereas the smooth catch muscle can keep the shells closed for long periods with little expenditure of energy. In this study, we performed proteomic and transcriptomic analyses of differences between the striated (fast) and catch (slow) adductor muscles in Yesso scallop Patinopecten yessoensis. RESULTS Transcriptomic analysis reveals 1316 upregulated and 8239 downregulated genes in slow compared to fast adductor muscle. For the same comparison, iTRAQ-based proteomics reveals 474 differentially expressed proteins (DEPs), 198 up- and 276 downregulated. These DEPs mainly comprise muscle-specific proteins of the sarcoplasmic reticulum, extracellular matrix, and metabolic pathways. A group of conventional muscle proteins-myosin heavy chain, myosin regulatory light chain, myosin essential light chain, and troponin-are enriched in fast muscle. In contrast, paramyosin, twitchin, and catchin are preferentially expressed in slow muscle. The association analysis of proteomic and transcriptomic data provides the evidences of regulatory events at the transcriptional and posttranscriptional levels in fast and slow muscles. Among 1236 differentially expressed unigenes, 22.7% show a similar regulation of mRNA levels and protein abundances. In contrast, more unigenes (53.2%) exhibit striking differences between gene expression and protein abundances in the two muscles, which indicates the existence of fiber-type specific, posttranscriptional regulatory events in most of myofibrillar proteins, such as myosin heavy chain, titin, troponin, and twitchin. CONCLUSIONS This first, global view of protein and mRNA expression levels in scallop fast and slow muscles reveal that regulatory mechanisms at the transcriptional and posttranscriptional levels are essential in the maintenance of muscle structure and function. The existence of fiber-type specific, posttranscriptional regulatory mechanisms in myofibrillar proteins will greatly improve our understanding of the molecular basis of muscle contraction and its regulation in non-model invertebrates.
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Affiliation(s)
- Xiujun Sun
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, People's Republic of China
| | - Zhihong Liu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, People's Republic of China
| | - Biao Wu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, People's Republic of China
| | - Liqing Zhou
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, People's Republic of China
| | - Qi Wang
- College of Fisheries, Ocean University of China, Qingdao, 266003, China
| | - Wei Wu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, People's Republic of China
| | - Aiguo Yang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China. .,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, People's Republic of China.
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13
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Feng D, Li Q, Yu H, Kong L, Du S. Transcriptional profiling of long non-coding RNAs in mantle of Crassostrea gigas and their association with shell pigmentation. Sci Rep 2018; 8:1436. [PMID: 29362405 PMCID: PMC5780484 DOI: 10.1038/s41598-018-19950-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 01/10/2018] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) play crucial roles in diverse biological processes and have drawn extensive attention in the past few years. However, lncRNAs remain poorly understood about expression and roles in Crassostrea gigas, a potential model organism for marine molluscan studies. Here, we systematically identified lncRNAs in the mantles of C. gigas from four full-sib families characterized by white, black, golden, and partially pigmented shell. Using poly(A)-independent and strand-specific RNA-seq, a total of 441,205,852 clean reads and 12,243 lncRNA transcripts were obtained. LncRNA transcripts were relatively short with few exons and low levels of expression in comparison to protein coding mRNA transcripts. A total of 427 lncRNAs and 349 mRNAs were identified to differentially express among six pairwise groups, mainly involving in biomineralization and pigmentation through functional enrichment. Furthermore, a total of 6 mRNAs and their cis-acting lncRNAs were predicted to involve in synthesis of melanin, carotenoid, tetrapyrrole, or ommochrome. Of them, chorion peroxidase and its cis-acting lincRNA TCONS_00951105 are implicated in playing an essential role in the melanin synthetic pathway. Our studies provided the first systematic characterization of lncRNAs catalog expressed in oyster mantle, which may facilitate understanding the molecular regulation of shell colour diversity and provide new insights into future selective breeding of C. gigas for aquaculture.
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Affiliation(s)
- Dandan Feng
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Shaojun Du
- Institute of Marine and Environmental Technology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, United States
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14
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Zhao L, Li Y, Li Y, Yu J, Liao H, Wang S, Lv J, Liang J, Huang X, Bao Z. A Genome-Wide Association Study Identifies the Genomic Region Associated with Shell Color in Yesso Scallop, Patinopecten yessoensis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:301-309. [PMID: 28527015 DOI: 10.1007/s10126-017-9751-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/19/2017] [Indexed: 06/07/2023]
Abstract
The shell color polymorphism widely exists in economic shellfish, which not only results in a better visual perception but also shows great value as an economic trait for breeding. Small numbers of reddish-orange shell Yesso scallops, Patinopecten yessoensis, were found in cultured populations compared to the brown majority. In this study, a genome-wide association study was conducted to understand the genetic basis of shell color. Sixty-six 2b-RAD libraries with equal numbers of reddish-orange and brown shell individuals were constructed and sequenced using the Illumina HiSeq 2000 platform. A total of 322,332,684 high-quality reads were obtained, and the average sequencing depth was 18.4×. One genomic region on chromosome 11 that included 239 single-nucleotide polymorphisms (SNPs) was identified as significantly associated with shell color. After verification by high-resolution melting in another population, two SNPs were selected as specific loci for reddish-orange shell color. These two SNPs could be used to improve the selective breeding progress of true-breeding strains with complete reddish-orange scallops. In addition, within the significantly associated genomic region, candidate genes were identified using marker sequences to search the draft genome of Yesso scallop. Three genes (LDLR, FRIS, and FRIY) with known functions in carotenoid metabolism were identified. Further study using high-performance liquid chromatography proved that the relative level of carotenoids in the reddish-orange shells was 40 times higher than that in the brown shells. These results suggested that the accumulation of carotenoids contributes to the formation of reddish-orange shells.
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Affiliation(s)
- Liang Zhao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yangping Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yajuan Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jiachen Yu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Huan Liao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Shuyue Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jia Lv
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jun Liang
- Dalian Zhangzidao Fishery Group Co., Ltd., Dalian, China
| | - Xiaoting Huang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
| | - Zhenmin Bao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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