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Fishes
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Mollusk Genetic Diversity and Breeding Technology
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Mollusk Genetic Diversity and Breeding Technology

A special issue of Fishes (ISSN 2410-3888). This special issue belongs to the section "Genetics and Biotechnology".

Deadline for manuscript submissions: closed (15 November 2023) | Viewed by 11946

Special Issue Editors

Dr. Chunsheng Liu

E-Mail Website
Guest Editor
College of Marine Science, Hainan University, Haikou 570228, China
Interests: aquaculture technology and environmental adaptation of tropical mollusks
Dr. Yi Yang

E-Mail Website
Guest Editor
College of Marine Science, Hainan University, Haikou 570228, China
Interests: Taxonomy, phylogeny and phylogeography of marine mollusks; Shellfish genetics and breed
Dr. Biao Wu

E-Mail Website
Guest Editor
Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
Interests: genetic breeding of marine mollusks

Special Issue Information

Dear Colleagues,

Mollusks are the second most diverse group in the animal kingdom and include many economically important aquatic species. To better develop and utilize such consumed mollusks, it is important to focus on their germ plasm resources, which involves the exploration of genetic diversity. The conservation of genetic diversity is an essential prerequisite for developing new breeds with desirable traits. Meanwhile, mollusks have a high yield in the aquatic industry, providing low-fat and protein-rich seafood for humans. The culture of economic mollusks, including bivalves, gastropods and cephalopods, is a globally important industry. In general, mollusk farming techniques include elevated culture on racks, trestles and other structures.

I am pleased to invite you to contribute to the Special Issue “Mollusk Genetic Diversity and Breeding Technology”, which will be published in the journal Fishes. We welcome the submission of original research articles, reviews, mini-reviews, and perspective articles on topics including (but not limited to) the following:

  • Population genetics analysis of mollusks derived from mitochondrial DNA and nuclear markers;
  • Evaluation of the genetic resources of mollusks;
  • Farming techniques and farming patterns of mollusks;
  • Physiological and biochemical responses of mollusks to environmental stress.

Dr. Chunsheng Liu
Dr. Yi Yang
Dr. Biao Wu
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Fishes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • genetic diversity
  • phylogeny
  • breeding technology
  • environmental adaptation

Published Papers (7 papers)

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Research

13 pages, 3000 KiB  
Article
Aminotransferase Class I and II Gene Family in the Jinjiang Oyster (Crassostrea ariakensis): Genomewide Identification, Phylogenetic Analysis and Expression Profiles after Salinity Stress
by Guangyu Ge, Zhihong Liu, Tao Yu, Liqing Zhou, Xiujun Sun, Zhuanzhuan Li and Yanxin Zheng
Fishes 2023, 8(9), 459; https://0-doi-org.brum.beds.ac.uk/10.3390/fishes8090459 - 14 Sep 2023
Cited by 1 | Viewed by 1088
Abstract
Aminotransferases are enzymes found in living organisms that catalyze transfer reactions between amino acids and keto acids, crucial for amino acid metabolism and synthesis. Aminotransferase classes I and II play a vital role in regulating osmolarity, protecting cells, and improving metabolic homeostasis and [...] Read more.
Aminotransferases are enzymes found in living organisms that catalyze transfer reactions between amino acids and keto acids, crucial for amino acid metabolism and synthesis. Aminotransferase classes I and II play a vital role in regulating osmolarity, protecting cells, and improving metabolic homeostasis and cellular fitness. To investigate the characteristics of the aminotransferase class I and II gene family and their roles in osmotic pressure regulation in the Jinjiang oyster (Crassostrea ariakensis), the gene structure, chromosomal localization, and phylogeny were characterized and the genes’ expression in the gill under high-salt stress was analyzed. In this study, eighteen Aminotransferase class I and II genes, including SPTLCa and SPTLCb, SPTa and SPTb, ALAT2a and ALAT2b, KAT3a and KAT3b, and ASTa, ASTb and ASTc, were identified. The physicochemical properties of 11 family members were stable, with their instability factors less than 40. Subcellular localization prediction showed that aminotransferase classes I and II were localized in the cytoplasm or mitochondria. Chromosomal localization results showed that the 18 aminotransferase class I and II genes were located on eight chromosomes. All members of this gene family had the Aminotran_1_2 structural domain which is associated with osmotic pressure regulation by adjusting the conversion reaction between amino acids and keto acids. Most gene expressions showed an initial increase followed by a decrease from 0 h to 12 h when the oysters were challenged by acute stress using artificial seawater with a salinity of 40. However, the expression of CarAGT2 and CarKAT3b genes showed an increased trend with increasing stress time. This study systematically investigated the bioinformatics characteristics of the aminotransferase class I and II gene family in C. ariakensis and their role in osmotic pressure regulation, which provides scientific data for understanding the potential functions of these genes in physiological adaptation, thereby expanding the research on osmoregulation in bivalves. Full article
(This article belongs to the Special Issue Mollusk Genetic Diversity and Breeding Technology)
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16 pages, 2839 KiB  
Article
Hypoxia Activates HIF-1α and Affects Gene Expression and Transcriptional Regulation of PHD in Tegillarca granosa
by Zhilan Peng, Xiaomin Liu, Ming Jin, Yu Zhan, Xiaolin Zhang, Yongbo Bao and Minhai Liu
Fishes 2023, 8(7), 359; https://0-doi-org.brum.beds.ac.uk/10.3390/fishes8070359 - 11 Jul 2023
Viewed by 1282
Abstract
Hypoxia is a common challenge faced by mollusks, and the role of hypoxia-inducible factor-1α (HIF-1α) in regulating related target genes under hypoxia in Tegillarca granosa (Tg) remains unclear. In this study, we identified gene HIF-1α and further explored its function. qRT-PCR [...] Read more.
Hypoxia is a common challenge faced by mollusks, and the role of hypoxia-inducible factor-1α (HIF-1α) in regulating related target genes under hypoxia in Tegillarca granosa (Tg) remains unclear. In this study, we identified gene HIF-1α and further explored its function. qRT-PCR was performed to determine the mRNA expression of HIF-1α, prolyl 4-hydroxylases (PHD), hemoglobin (Hb), and myoglobin (Mb) in response to hypoxia. Dual-luciferase reporter analysis was used to assess the transcriptional activity of HIF-1α on the PHD and Hb genes during hypoxia. Results showed that the expression levels of HIF-1α and PHD mRNAs were highest in the gill and lowest in the adductor muscle. Under hypoxic conditions, HIF-1α and PHD mRNAs were both induced, and their expression levels increased significantly, peaking at 8 h and gradually decreasing thereafter. The transcription of Tg-PHD was induced by hypoxia and was Tg-HIF-1α dependent. Notably, the expression of Hb decreased in hemocytes (p < 0.01) after 8 h at 0.5 mg/L, while the expression of MbI and MbII increased (p < 0.01) in the hepatopancreas after 24 h and 120 h, respectively. Moreover, Tg-HIF-1α could transactivate the PHD promoter but not that of Hb. These findings provide valuable insights into the regulatory role of Tg-HIF-1α on Tg-PHD, safeguarding it from degradation by PHD and offering significant contributions to the understanding of HIF-1α’s function. Nonetheless, the expression of Tg-HIF-1α protein was not detected under hypoxic conditions, and additional investigations are required to quantify Tg-HIF-1α protein dynamics and establish the correlation between mRNA expression and protein levels. Full article
(This article belongs to the Special Issue Mollusk Genetic Diversity and Breeding Technology)
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15 pages, 4234 KiB  
Article
Identification and Characterization of GYS and GSK3β Provides Insights into the Regulation of Glycogen Synthesis in Jinjiang Oyster Crassostrea ariakensis
by Yan Wang, Zhihong Liu, Xi Chen, Liqing Zhou, Xiujun Sun, Tao Yu, Xiaomei Wang, Yanxin Zheng and Biao Wu
Fishes 2023, 8(2), 65; https://0-doi-org.brum.beds.ac.uk/10.3390/fishes8020065 - 21 Jan 2023
Cited by 3 | Viewed by 1538
Abstract
Glycogen, a stored form of glucose, is an important form of energy for aquatic shellfish, contributing to the flavor and quality of the oyster. The glycogen synthase (GYS) and glycogen synthase kinase 3β (GSK3β) are two major enzymes in the glycogenesis. However, the [...] Read more.
Glycogen, a stored form of glucose, is an important form of energy for aquatic shellfish, contributing to the flavor and quality of the oyster. The glycogen synthase (GYS) and glycogen synthase kinase 3β (GSK3β) are two major enzymes in the glycogenesis. However, the information of the two genes in the Jinjiang oyster Crassostrea ariakensis remains limited. In this study, we identified the genes of GYS and GSK3β and further explored their function in the glycogen synthesis of C. ariakensis. The GYS and GSK3β were distributed in all tested tissues, and high expression of GYS and glycogen content were detected in the gonad, labial palp, hepatopancreas, and mantle, while the high expression of GSK3β was observed in the gill and adductor muscle. The expression of GYS was positively correlated with the glycogen content, while GSK3β was negatively correlated. Additionally, knockdown of GSK3β using RNAi decreased the GYS expression, revealing the negative regulatory effect of GSK3β on GYS. These findings enrich the research data of GSK3β and GYS involved in glycogen synthesis, providing valuable information for further research on the function of GSK3β and GYS in the glycogen synthesis process of oyster. Full article
(This article belongs to the Special Issue Mollusk Genetic Diversity and Breeding Technology)
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10 pages, 1146 KiB  
Article
Evaluating the Utility of Five Gene Fragments for Genetic Diversity Analyses of Mytella strigata Populations
by Chenxia Zuo, Tingting Zhang, Chenchen Zhang, Daotan Zhao, Yi Zhu, Xiaojie Ma, Haiyan Wang, Peizhen Ma and Zhen Zhang
Fishes 2023, 8(1), 34; https://0-doi-org.brum.beds.ac.uk/10.3390/fishes8010034 - 3 Jan 2023
Cited by 3 | Viewed by 1754
Abstract
Mytella strigata (Hanley, 1843) is an invasive mussel species that has rapidly spread in China in recent years. Here, we tested the utility of three mitochondrial gene fragments, COI, 12S, and 16S, and two nuclear gene fragments, D1 28S and [...] Read more.
Mytella strigata (Hanley, 1843) is an invasive mussel species that has rapidly spread in China in recent years. Here, we tested the utility of three mitochondrial gene fragments, COI, 12S, and 16S, and two nuclear gene fragments, D1 28S and 18S-ITS1, for characterizing the levels of genetic diversity among and within populations using 191 M. strigata specimens collected in China to aid ongoing efforts to identify the origin of the invasion as well as molecular genetic studies. M. strigata exhibited two sex-associated haplogroups according to the COI and 12S sequences. The ratio of female-lineage to male-lineage COI and 12S sequences was 149:22 and 72:7, and the genetic distances between haplogroups were 6.56 and 9.17, respectively. Only one haplotype was detected among the 18S-ITS1 sequences (413 bp), and three haplotypes were detected among the D1 28S sequences (296 bp). The haplotype diversity of both the female-lineage COI and 12S sequences was greater than 0.5, and the nucleotide diversity of the 12S, 16S, D1 28S, and 18S-ITS1 sequences was less than 0.005 in all six populations in China. Our findings indicated that COI is the most useful gene fragment for genetic diversity studies of M. strigata populations; D1 28S and 18S-ITS1 sequences would be useful for species identification because of their low intraspecific diversity. Our genetic analysis of the COI sequences revealed Colombia as the most likely origin of M. strigata in China and showed that the invasive populations in China have recently experienced or are currently experiencing a population bottleneck. Full article
(This article belongs to the Special Issue Mollusk Genetic Diversity and Breeding Technology)
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15 pages, 3942 KiB  
Article
First Report on Genome Analysis and Pathogenicity of Vibrio tubiashii FP17 from Farmed Ivory Shell (Babylonia areolata)
by Chen Dai, Xiaoxin Li, Dapeng Luo, Qingming Liu, Yun Sun, Zhigang Tu and Minghui Shen
Fishes 2022, 7(6), 396; https://0-doi-org.brum.beds.ac.uk/10.3390/fishes7060396 - 17 Dec 2022
Cited by 3 | Viewed by 1938
Abstract
Ivory shell (Babylonia areolata) is a commercially important aquaculture species mainly found on the southeast coast of China. However, it has been greatly affected by vibriosis in recent years. In this study, FP17 (a potential pathogen) was isolated from a dying [...] Read more.
Ivory shell (Babylonia areolata) is a commercially important aquaculture species mainly found on the southeast coast of China. However, it has been greatly affected by vibriosis in recent years. In this study, FP17 (a potential pathogen) was isolated from a dying ivory shell with “acute death syndrome” and confirmed as a pathogen via infectious experiment. Furthermore, phylogenetic analysis based on the average nucleotide identity (ANI) sequencing of the 16S rRNA gene and housekeeping genes (ftsz, gapA, gyrB, mreB, pyrH, rpoA, and topA) indicated that FP17 was identical to Vibrio tubiashii. Transmission electron microscopy showed that FP17 is curved and has a short rod shape, with a single flagellum. Besides, the calculated LD50 after the intramuscular injection of FP17 was 2.11 × 106 CFU/g at 14 d. The genome of the FP17 strain consists of two chromosomes and one plasmid with 5,261,336 bp and 45.08% GC content, including 4824 open reading frames (ORFs) and 150 non-coding RNAs (ncRNA). Genome mining revealed that 120 candidate gene clusters, including vibrioferrin and flagellum-related proteins, are responsible for virulence. Comparative genomic analysis showed that vibrioferrin genes, such as pvs and type Ⅵ secretion system protein genes (vas), are specific in V. tubiashii FP17 but not in the ATCC19109 strain. Furthermore, 92 antimicrobial resistance (AMR) genes, such as tufA, tet(35), crp, etc., were mapped within the genome as the potential candidate for virulence, consistent with antibiotic susceptibility assay. This is the first study to describe the complete genome sequence of V. tubiashii infecting ivory shell. The genetic characteristics, virulence factors, and antimicrobial resistance of the V. tubiashii strain FP17 were also explored. Full article
(This article belongs to the Special Issue Mollusk Genetic Diversity and Breeding Technology)
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9 pages, 612 KiB  
Article
Host Fish Suitability for Freshwater Bivalve Anodonta woodiana Breeding Programs
by Xiubao Chen, Guochao Duan, Mingjun Yan, Hongbo Liu, Tao Jiang and Jian Yang
Fishes 2022, 7(6), 329; https://0-doi-org.brum.beds.ac.uk/10.3390/fishes7060329 - 10 Nov 2022
Cited by 2 | Viewed by 1305
Abstract
The freshwater bivalve Anodonta woodiana is native to China and widely distributed in Asia, Europe, and North America. However, natural populations of A. woodiana in China have dramatically declined recently. Several fish species have been used as potential hosts in breeding programs; nonetheless, [...] Read more.
The freshwater bivalve Anodonta woodiana is native to China and widely distributed in Asia, Europe, and North America. However, natural populations of A. woodiana in China have dramatically declined recently. Several fish species have been used as potential hosts in breeding programs; nonetheless, the optimal host species is yet to be identified. In this study, we examined the suitability of five potential host fish species (bighead carp, common carp, crucian carp, yellow catfish, and tilapia) for A. woodiana under laboratory conditions. No significant difference was found in the number of glochidia attached to the five fish species; however, tilapia hosted more transformed juveniles than bighead carp, common carp, or yellow catfish (p < 0.05), with bighead carp hosting the least (p < 0.05). Yellow catfish had the highest host capacity index (the number of successfully transformed juveniles/the weight of the host fish × the survival rate of the host fish), 133 times higher than bighead carp and 1.3–2.9 times higher than the other species. The shell length and height of freshly transformed juveniles from yellow catfish were significantly larger than those of other host fish (p < 0.05). The juvenile index (shell length × shell height) of yellow catfish was significantly higher than that of other fish species (p < 0.05). In conclusion, yellow catfish appears to be the most suitable host fish out of the five species tested here. Full article
(This article belongs to the Special Issue Mollusk Genetic Diversity and Breeding Technology)
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28 pages, 7804 KiB  
Article
Combined Effects of Temperature and Salinity on Antioxidants in the Immune System of the Pearl Oyster Pinctada fucata
by Jingru Yang, Zhengyi Fu, Gang Yu, Zhenhua Ma and Xiaomei Wang
Fishes 2022, 7(5), 260; https://0-doi-org.brum.beds.ac.uk/10.3390/fishes7050260 - 27 Sep 2022
Cited by 2 | Viewed by 1763
Abstract
A water environment can impact many physiological processes of aquatic animals. The antioxidant response of immune system of the pearl oyster to temperature and salinity is of great significance to health. This study analyzed the physiological changes and immune responses under different temperature [...] Read more.
A water environment can impact many physiological processes of aquatic animals. The antioxidant response of immune system of the pearl oyster to temperature and salinity is of great significance to health. This study analyzed the physiological changes and immune responses under different temperature and salinity levels (temperature: 20, 25, and 30 °C; salinity: 23, 28, and 33‰) in the short term (7 d) in the hepatopancreas and other tissues of 405 pearl oysters. The combined effects of temperature and salinity on antioxidants in the immune system of the pearl oyster were evaluated via response surface methodology and Box–Benhnken design (BBD) under laboratory conditions. The secondary effects of salinity on the activities of glutathione peroxidase (GSH-PX), catalase (CAT), and superoxide dismutase (SOD) were significant, and CAT and SOD showed an inverted U-shaped trend with the increase in salinity. Temperature significantly impacted GSH-PX, CAT, glutathione (GSH), and SOD in primary and secondary effects, and the maximum values of CAT, GSH, and SOD were observed. The phenoloxidase (POX) and alkaline phosphatase (AKP) activities increased with the increasing temperatures. The interaction of temperature and salinity was significant on CAT and SOD, but was not significant on GSH-PX. The interaction between salinity and temperature on AKP was significant, which was contrary to the results of AKP in the hemolymph. The expression levels of antioxidant genes varied between tissues, and the expression levels of different genes in the same tissue were different. Appropriate immunity and antioxidant index models were established under the combined temperature and salinity conditions. The optimal combination of temperature and salinity was 24.95 °C and 28.11‰, respectively, and the desirability was 0.803. This study provides theoretical reference points for the pearl oyster to respond to temperature and salinity changes and can be used to establish an index model for shellfish aquaculture. Full article
(This article belongs to the Special Issue Mollusk Genetic Diversity and Breeding Technology)
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