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Relaxation of Selective Constraint on the Ultra-Large Mitochondrial Genomes of Arcidae (Mollusca: Bivalvia)

Journal of Ocean University of China 2021年第5期20卷 1157-1166页

作者： SUN Shao’e LI Qi kong lingfeng Key Laboratory of Mariculture Ministry of EducationOcean University of ChinaQingdao 266003China Laboratory for Marine Fisheries Science and Food Production Processes Pilot National Laboratory for Marine Science and Technology(Qingdao)Qingdao 266237China

The mitochondrial genomes(mitogenomes)are purportedly under selection for smaller size to improve their replica-tion and translation ***,the mitogenomes of Arcidae species are larger than those of other bivalves,and are among the largest metazoan mitogenomes reported to *** order to explore the differences of base composition and selective constraints between the large and small mitogenomes,we compared the mitogenomes of 9 large arcid mitogenomes and 77 small bivalves *** composition analyses indicated that Arcidae mitogenomes have significantly greater GC skews in both their whole genomes and coding *** result suggests that the replication of the large mitogenomes in Arcidae may be slower than those in other bivalves,exposing the parental strand to deamination for a longer *** pressure analyses showed that the mitochondrial protein-coding genes of Arcidae species have significantly higher Ka/Ks ratios than other bivalves,suggesting that they have accumulated more nonsynonymous nucleotide *** protein-coding genes(atp6,cox1-3,nad1,nad4 and nad5)show significant difference for Ka/Ks ratios between the Arcidae and non-Arcidae ***,these divergences are not observed in the nuclear gene within histone *** these observations,we concluded that the large mitoge-nomes of Arcidae species experienced more relaxed selective *** some Arcidae species are more tolerant to hypoxia that can lead to low metabolic rate,the relaxed selective constraints of mitogenomes may be *** study provides new insights into the evolution of Arcidae mitogenomes.

关键词： Arcidae mitochondrial genome genome size relaxed selective constraint

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Reproductive Cycle and Seasonal Variations in Lipid Content and Fatty Acid Composition in Gonad of the Cockle Fulvia mutica in Relation to Temperature and Food

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Journal of Ocean University of China 2013年第3期12卷 427-433页

作者： LIU Wenguang LI Qi kong lingfeng Key Laboratory of Marine Bio-resources Sustainable Utilization South China Sea Institute of OceanologyChinese Academy of Sciences Key Laboratory of Mariculture Ministry of EducationOcean University of China

From March 2004 to February 2005,seasonal variations in lipid content and fatty acid composition of gonad of the cockle Fulvia mutica(Reeve) were studied on the eastern coast of China in relation to the reproductive cycle and environment conditions(e.g.,temperature and food availability).Histological analysis as well as lipid and fatty acid analyses were performed on neutral and polar lipids of the *** showed that gametogenesis occurred in winter and spring at the expense of lipids previously accumulated in summer and autumn,whereas spawning occurred in summer(20.4-24.6℃).The seasonal variation in lipid content was similar to that of the mean oocyte *** both neutral and polar lipids,the 20:5n-3 and 22:6n-3 levels were relatively higher than saturated fatty acids,and polyunsaturated fatty acids were abundant,with series n-3 as the predominant *** variations in the 20:5n-3 and 22:6n-3 levels and the principal n-3 fatty acids were clearly related to the reproductive *** ∑(n-3) and ∑(n-6) values were relatively high during January-May,and the associated unsaturation index was significantly higher than that in other *** results suggest that fatty acids play an important role in the gametogenesis of ***.

关键词： Fulvia mutica lipids fatty acids reproductive cycle food temperature

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Molecular Identification of Dried Shellfish Products Sold on the Market Using DNA Barcoding

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Journal of Ocean University of China 2021年第4期20卷 931-938页

作者： SUN Shao’e ZHANG Xiaojie kong lingfeng LI Qi Key Laboratory of Mariculture Ministry of EducationOcean University of ChinaQingdao 266003China Laboratory for Marine Fisheries Science and Food Production Processes Pilot National Laboratory for Marine Science and Technology(Qingdao)Qingdao 266237China

The dried shellfish products with rich nutrients and low-calorie content are favorite food in China,especially in coastal ***,the species of dried shellfish products in the market are usually unknown,as the taxonomic features were removed during the production *** study described the application of DNA barcoding technique to the identification of 100 dried shellfish(scallop,squid,octopus and cuttlefish)products in *** were authenticated by comparing mitochondrial cytochrome oxidase subunit I(COI)gene and 16S ribosomal RNA(16S rRNA)gene sequences with public reference taxonomic *** results showed that all the 100 products can be identified at species *** four scallop adductor products were processed using the bay scallop,Argopecten irradians,and one was from Portuguese oyster,Crassostrea *** the 27 squid,2 cuttlefish and 6 octopus products were produced by the Jumbo flying squid,Dosidicus *** neighbour-joining tree is in agreement with the results of DNA barcoding *** 64 scallop samples formed one *** cluster,leaving Sca65 clustered with the reference oyster sequence ***(MH997922).All the 35 cephalopod(squid,octopus and cuttlefish)samples formed a *** *** investigation revealed a low variety of dried shellfish products sold on the market,and highlighted the high rate of mislabeling and species *** present work provides a practical method for tracing and authenticating shellfish products.

关键词： dried shellfish product DNA barcoding species identification mislabeling species substitution

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Biochemical Composition and Nutritional Value of Different Shell Color Strains of Pacific Oyster Crassostrea gigas

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Journal of Ocean University of China 2018年第4期17卷 897-904页

作者： ZHU Yijing LI Qi YU Hong kong lingfeng Key Laboratory of Mariculture of Ministry of Education Ocean University of China

The shell color of Pacific oyster(Crassostrea gigas) is a desirable trait; but the nutritional studies on C. gigas with different shell colors have not been conducted. Through successive selective breeding, five shell color strains of black(B), purple(P), orange(O), golden(G) and white(W) C. gigas have been developed. The aim of this study was to evaluate the chemical composition and nutritional value of five shell color strains and one commercial population with a common color. The biochemical composition including moisture, total protein, glycogen, ash, total fat, fatty acids(FA), amino acids and minerals was detected. The results indicated that the protein(50.76%–56.57%) was the major component. The content of glycogen showed a significant difference between orange shell and golden shell strains, as well as between commercial population and golden shell strain. In addition, all shell color strains contained a large amount of essential amino acids(12.20–14.15 g(100 g)^(-1)), of them leucine(2.81–3.29 g(100 g)^(-1)) and lysine(2.79–3.28 g(100 g)^(-1)) were predominant. The oysters were rich in polyunsaturated fatty acids(42.26%–45.24% of total fatty acid) with high levels of DHA(18.53%–21.16% of total fatty acid) and EPA(17.23%–18.68% of total fatty acid). Significant differences of mineral contents(Mg, Zn, Fe and Cu) were identified among the six populations. These results indicated that C. gigas with different shell colors presented rich nutritional value with high protein, glycogen, essential amino acids and polyunsaturated fatty acids. The biochemical composition obtained in this study is useful for selective breeding of C. gigas with different shell colors.

关键词： Crassostrea gigas biochemical composition nutrition value shell color selective breeding

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The Clam Cyclina sinensis (Gmelin) Phylogeography Study with 28S rRNA Gene and Potential of Nuclear rRNA Genes in Genetic Assessments of Molluscs

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Journal of Ocean University of China 2022年第2期21卷 395-399页

作者： NI Gang LI Qi kong lingfeng YU Hong The Key Laboratory of Mariculture Ministry of EducationOcean University of ChinaQingdao 266003China Laboratory for Marine Fisheries Science and Food Production Processes Qingdao National Laboratory for Marine Science and TechnologyQingdao 266003China Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering Sanya Oceanographic InstitutionOcean University of ChinaSanya 572000China

Intraspecific diversity of molluscan species is usually studied based on maternally inherited mitochondrial DNA,from which only part of the evolutionary history can be *** nuclear ribosomal RNA genes such as 28S rRNA represent poten-tial candidates that can be easily applied in phylogeography because of lacking intraindividual ***,considering their low polymorphism,genetic appraisals on whether and how they can be used in population studies are ***,we applied a short 28S rRNA to assess genetic patterns of the clam Cyclina sinensis along the coast of China and compared the results with a for-mer study based on COI and ITS-1 *** results revealed the 28S rRNA data set was characterized by an extremely low level of variation,with only seven haplotypes defined for 93 *** and nucleotide diversity for each population was al-most the lowest when compared with the other two ***,the distribution of two dominant haplotypes showed clear geo-graphic patterns,and significant population differentiation was revealed between the East China Sea and the South China *** patterns were highly concordant with findings of the former study that populations of *** were historically separated by land bridges among sea *** study suggested that although the nuclear rRNAs have shortcomings such as low variation,they have advantages including lack of intraindividual variation and high amplification *** rRNA genes can enrich the toolbox of nuclear markers in molluscan phylogeographic studies.

关键词： marine phylogeography molluscs nuclear gene genetic break

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Relationship Between Single Nucleotide Polymorphism of Glycogen Synthase Gene of Pacific Oyster Crassostrea gigas and Its Glycogen Content

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Journal of Ocean University of China 2017年第1期16卷 168-174页

作者： LIU Siwei LI Qi YU Hong kong lingfeng Key Laboratory of Mariculture of Ministry of Education Ocean University of ChinaQingdao 266003P.R.China

Glycogen is important not only for the energy supplementary of oysters, but also for human consumption. High glycogen content can improve the stress survival of oyster. A key enzyme in glycogenesis is glycogen synthase that is encoded by glycogen synthase gene GYS. In this study, the relationship between single nucleotide polymorphisms(SNPs) in coding regions of Crassostrea gigas GYS(Cg-GYS) and individual glycogen content was investigated with 321 individuals from five full-sib families. Single-strand conformation polymorphism(SSCP) procedure was combined with sequencing to confirm individual SNP genotypes of Cg-GYS. Least-square analysis of variance was performed to assess the relationship of variation in glycogen content of C. gigas with single SNP genotype and SNP haplotype. As a consequence, six SNPs were found in coding regions to be significantly associated with glycogen content(P < 0.01), from which we constructed four main haplotypes due to linkage disequilibrium. Furthermore, the most effective haplotype H2(GAGGAT) had extremely significant relationship with high glycogen content(P < 0.0001). These findings revealed the potential influence of Cg-GYS polymorphism on the glycogen content and provided molecular biological information for the selective breeding of good quality traits of C. gigas.

关键词： Crassostrea gigas glycogen content glycogen synthase gene SNP

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Development of Three Multiplex PCR Primer Sets for Ark Shell(Scapharca broughtonii)and Their Validation in Parentage Assignment

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Journal of Ocean University of China 2016年第2期15卷 311-317页

作者： LINing LI Qi kong lingfeng YU Hong Key Laboratory of Mariculture of Ministry of Education Ocean University of ChinaQingdao 266003P.R.China

Scapharca broughtonii is a commercially important and over-exploited *** order to investigate its genetic diversity and population structure,43 novel polymorphic microsatellites were isolated and *** number of alleles per locus ranged from 3 to 22 with an average of 6.93,and the observed and expected heterozygosities varied between 0.233 and 1.000,and 0.250 and 0.953,with an average of 0.614 and 0.707,*** highly informative multiplex PCRs were developed from nine of those microsatellites for *** evaluated and validated these multiplex PCRs in 8 full-sib *** average polymorphism information content(PIC) was *** frequency of null alleles was estimated as 3.13% of all the alleles segregation based on a within-family analysis of Mendelian segregation *** analysis of real offspring demonstrated that 100% of all offspring were unambiguously allocated to a pair of parents based on 3 multiplex *** 43 microsatellite loci with high variability will be helpful for the analysis of population genetics and conservation of wild stock of *** 3 sets of multiplex PCRs could be an important tool of pedigree reconstruction,population genetic analysis and brood stock management.

关键词： Seapharca broughtonii microsatellites multiplex PCR parentage assignment

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Dietary Supplementation of β-Carotene Reveals miRNAs Involved in the Regulation of Carotenoid Metabolism in Crassostrea gigas

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Journal of Ocean University of China 2024年第4期23卷 1045-1053页

作者： SUN Dongfang WAN Sai YU Hong kong lingfeng LI Qi Key Laboratory of Mariculture Ministry of EducationOcean University of ChinaQingdao 266003China Laboratory for Marine Fisheries Science and Food Production Processes Laoshan LaboratoryQingdao 266237China

Carotenoids play crucial physiological roles in animals.A comprehensive investigation into the mechanism of carotenoid metabolism in oysters will establish a theoretical foundation for further development of its carotenoid-rich ***,the information on the function of miRNA in β-carotene metabolism in oysters is *** elucidate the mechanisms underlying miRNA regulation of carotenoid metabolism in oysters,we compared the expressions of miRNA in digestive gland tissues of Pacific oyster(Crassostrea gigas)fed with aβ-carotene supplemented diet and a normal diet,respectively.A total of 690 candidate miRNAs in the Pacific oyster digestive gland tissues were identified,including 590 known miRNAs and 111 unknown *** differentially expressed miRNAs were obtained in the carotenoid-fed and normal groups,associated to 137 differentially expressed target ***,the GO enrichment analysis revealed that the differentially expressed target genes were mainly involved in transmembrane transport *** enrichment showed that the differentially expressed target genes were involved in ABC *** of the mRNA-miRNA network revealed that novel0025 played a central role in carotenoid metabolism,and it was negatively correlated with the expression of 46 *** addition,down-regulated expression of novel0025 upregulated the expression of the lipoprotein gene LOC105342186,suggesting a potential regulatory role in carotenoid *** results provide useful information for elucidating the miRNA regulation mechanism during carotenoids metabolism in the Pacific oyster.

关键词： Crassostrea gigas β-carotene microRNA carotenoid metabolism

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Genetic Variation Assessed with Microsatellites in Mass Selection Lines of the Pacific Oyster (Crassostrea gigas) in China

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Journal of Ocean University of China 2016年第6期15卷 1039-1045页

作者： WANG Xubo LI Qi YU Hong kong lingfeng Key Laboratory of Mariculture Ministry of Education Ocean University of China Qingdao 266003 P. R. China

Abstract Four successive mass selection lines of the Pacific oyster, Crassostrea gigas, selected for faster growth in breeding pro- grams in China were examined at ten polymorphic microsatellite loci to assess the level of allelic diversity and estimate the effective population size. These data were compared with those of their base population. The results showed that the genetic variation of the four generations were maintained at high levels with an average allelic richness of 18.8-20.6, and a mean expected heterozygosity of 0.902-0.921. They were not reduced compared with those of their base population. Estimated effective population sizes based on temporal variances in microsatellite frequencies were smaller to that of sex ratio-corrected broodstock count estimates. Using a rela- tively large number ofbroodstock and keeping an equal sex ratio in the broodstock each generation may have contributed to retaining the original genetic diversity and maintaining relatively large effective population size. The results obtained in this study showed that the genetic variation was not affected greatly by mass selection progress and high genetic variation still existed in the mass selection lines, suggesting that there is still potential for increasing the gains in future generations of C. gigas. The present study provided im- portant information for future genetic improvement by selective breeding, and for the design of suitable management guidelines for genetic breeding of C. gigas.

关键词： Pacific oyster genetic variation microsatellite mass selection line effective population size

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Response to Selection for Fast Growth in the Second Generation of Pacific Oyster (Crassostrea gigas)

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Journal of Ocean University of China 2012年第3期11卷 413-418页

作者： WANG Qingzhi LI Qi kong lingfeng YU Ruihai Liaoning Ocean and Fishery Science Research Institute Dalian 116023P.R.China Key Laboratory of Mariculture Ministry of EducationOcean University of ChinaQingdao 266003P.R.China

Mass selection for fast growth was conducted in three Pacific oyster (Crassostrea gigas) stocks from China, Japan and Korea using previously established lines (CS1, JS1, and KS1). To determine whether continuous progress can be achieved by selection for growth, the progeny of three second-generation Pacific oyster lines was selected for shell height and evaluated via a 400-day farming experiment. When harvested at the end of the experiment, the selected crosses of CS2, JS2, and KS2 lines grew by 9.2%, 10.2% and 9.6% larger than the control crosses, respectively. During grow-out stage, the genetic gain of three selected lines was (10.2 ± 1.4)%, (10.4 ± 0.3)%, and (8.4 ± 1.6)%, respectively; and the corresponding realized heritability was 0.457 ± 0.143, 0.312 ± 0.071 and 0.332 ± 0.009, respectively. These results indicated that the selection for fast growth achieved steady progress in the second generation of oyster. Our work provides supportive evidence for the continuity of the Pacific oyster selective breeding program.

关键词： Pacific oyster Crassostrea gigas mass selection second generation genetic gain realized heritability

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