Effect of the Liquid Density Difference on Interface Shape of Double-Liquid Lens

Meimei Kong,Lingfeng Zhu,Dan Chen,Zhongcheng Liang,Rui Zhao,Enming Xu 한국광학회 2016 Current Optics and Photonics Vol.20 No.3

The effect of the liquid density difference on interface shape of a double-liquid lens is analyzed indetail. The expressions of interface shape of two liquids with liquid density difference are analyzed andfitted with “even asphere”. The imaging analysis of the aspheric interface shape of a double-liquid lensis presented. The results show that the density difference of two liquids can cause the interface to bean aspheric surface, which can improve the image quality of a double-liquid lens. The result providesa new selection for the related further research and a wider application field for liquid lenses.

Mitogenome evidence for the existence of cryptic species in Coelomactra antiquata

Yang Yuan,Lingfeng Kong,Qi Li 한국유전학회 2013 Genes & Genomics Vol.35 No.6

Cryptic species which improve our understanding of species diversity and evolutionary histories within marine animals have been increasingly revealed in the marine realm. Coelomactra antiquate is an important commercial bivalve species, but has been suffering from severe population decline due to over-exploitation and deterioration of environmental conditions. To test the hypothesis that cryptic species might exist in C. antiquate presented in previous study, four complete mitogenomes of C. antiquate from northern and southern China were determined here. Comprehensive comparative analysis of the mitochondrial genomes of C. antiquate between northern and southern population reveals significant differences in genome composition,protein coding genes, tRNA genes, non-coding regions, genetic divergence and phylogenetic analysis. The results provide strong mitogenome evidence for the existence of cryptic species in C. antiquate. Besides, our results also support that comprehensive comparative analysis of mtDNA represents an accessible and powerful tool to identify cryptic species.

DNA methylation changes detected by methylation-sensitive amplified polymorphism in the Pacific oyster (Crassostrea gigas) in response to salinity stress

Xin Zhang,Lingfeng Kong,Hong Yu,Qi Li 한국유전학회 2017 Genes & Genomics Vol.39 No.11

Salinity is a considerable factor to the survival and distribution for a majority of marine organisms, the drawbacks of which are becoming a serious issue of aquaculture. DNA methylation, an extensively studied epigenetic modification in eukaryotes, plays a significant role in the regulation of gene expression in responding to environmental changes and triggering evolutionary consequences. The Pacific oyster Crassostrea gigas, as a eurythermal and euryhaline species, is considered to be tolerant to salinity fluctuation. In this study, fluorescent-labeled methylation-sensitive amplified polymorphism (F-MSAP) analysis was used to investigate the frequency and variation of DNA methylation in C. gigas under different salinity and time. The results showed that total methylation level was generally on a downward trend. At lower salinity, the total methylation level decreased at the earlier process and then increased during experiment process, but continued to shrink at the rest salinity. Fully methylation tended to better reflect the dynamics of total methylation. Recovery treatment showed that the extent and pattern of DNA methylation were difficult to return to the normal level in this research. The sequencing and BLAST analysis indicated that in salt stress most of the selected bands were closely related to the metabolism of nucleic acids and proteins, tropomyosin, and cellular transport, effecting on different biological processes of C. gigas. This work provides useful data to further elucidate the molecular mechanisms of salt stress response and tolerance in invertebrates.

Isolation and characterization of polymorphic microsatellite loci in the grand jackknife clam Solen grandis (Bivalvia: Veneroida)

Yang Yuan,Lingfeng Kong,Xiaodong Zheng,Qi Li 한국유전학회 2010 Genes & Genomics Vol.32 No.3

The grand jackknife clam Solen grandis (Dunker, 1861) is an overexploited bivalve species. In order to promote a conservation program for this species, it is necessary to evaluate its genetic diversity and population genetics. For this purpose,we isolated the first set of 18 polymorphic microsatellite markers and examined their allelic variation using a total of 30wild individuals collected from one locality. The number of alleles per locus ranged from 5 to 24, and the observed and expected heterozygosity varied from 0.300 to 0.967 and from 0.721 to 0.952, respectively. The high variabilities at these loci indicated that they would be use

Genetic and epigenetic variation in mass selection populations of Pacific oyster Crassostrea gigas

Qun Jiang,Qi Li,Hong Yu,Lingfeng Kong 한국유전학회 2013 Genes & Genomics Vol.35 No.5

Selective breeding often produces an improvementin phenotype. Much of the phenotypic change withina species is a consequence of genetic variation. However,there is growing evidence for phenotypic change even inthe absence of DNA sequence polymorphisms, termedepigenetic variation. This study’s goal was to investigatethe genetic and epigenetic variation in the mass selectionpopulations of the Pacific oyster (Crassostrea gigas),determine if any correlation exists between the genetic andepigenetic variations. This can serve as a first step ininvestigating the potential role epigenetic variations havein selective breeding. Amplified fragment length polymorphismanalysis and methylation-sensitive amplifiedpolymorphism methodology were used to monitor geneticand epigenetic variation in two populations (the base stockand the third selected generation) from a mass selectionline in the Pacific oyster. The correlation between geneticand epigenetic variation was evaluated by Co-InertiaAnalysis. The genetic difference was mainly found in thegene frequency shift revealed by the FST value (0.0151,P\0.01) and no significant reduction in genetic diversitywas detected. The percentage of methylation in C. gigaswas 26.4 %. No significant difference was observed on theaverage state of methylation, but a few bands showed differentfrequencies between the two populations. Co-InertiaAnalysis revealed a significant association between thegenetic and epigenetic profiles (P\0.01). Selective breeding often produces an improvement in phenotype. Much of the phenotypic change within a species is a consequence of genetic variation. However, there is growing evidence for phenotypic change even in the absence of DNA sequence polymorphisms, termed epigenetic variation. This study’s goal was to investigate the genetic and epigenetic variation in the mass selection populations of the Pacific oyster (Crassostrea gigas), determine if any correlation exists between the genetic and epigenetic variations. This can serve as a first step in investigating the potential role epigenetic variations have in selective breeding. Amplified fragment length polymorphism analysis and methylation-sensitive amplified polymorphism methodology were used to monitor genetic and epigenetic variation in two populations (the base stock and the third selected generation) from a mass selection line in the Pacific oyster. The correlation between genetic and epigenetic variation was evaluated by Co-Inertia Analysis. The genetic difference was mainly found in the gene frequency shift revealed by the FST value (0.0151, P\0.01) and no significant reduction in genetic diversity was detected. The percentage of methylation in C. gigas was 26.4 %. No significant difference was observed on the average state of methylation, but a few bands showed different frequencies between the two populations. Co-Inertia Analysis revealed a significant association between the genetic and epigenetic profiles (P\0.01).

Expression and DNA methylation pattern of reproduction-related genes in partially fertile triploid Pacific oysters Crassostrea gigas

Qun Jiang,Qi Li,Hong Yu,Lingfeng Kong 한국유전학회 2017 Genes & Genomics Vol.39 No.9

Partial or complete sterility is an obvious feature in triploid Pacific oyster (Crassostrea gigas) which contributes to improving rearing performances. Despite the significance of sterility, the molecular mechanism behind it remains elusive and related research was limited. This study focused on six reproduction-related genes and compared their different behavior in gene expression and DNA methylation pattern between triploid and diploid oysters in order to provide more molecular information. The gonadal development of triploid oyster was examined by histology before molecular analysis. Gametogenesis disturbance was observed in triploid oysters at different development stages (stage II and III) with more serious impairment in females. QPCR showed significant gene expression difference between diploid and triploid in two genes: putative Vg and cgER. Gene expression of putative Vg was delayed in triploids while for cgER triploid oyster showed higher expression and the difference was significant at stage III. DNA methylation pattern of these two genes were further investigated by bisulfite sequencing. Between diploid and triploid oysters, no difference was observed in total methylation level but some individual loci showed different patterns: significantly high methylation rate of loci 2284 in cgER was observed in triploid oyster which has a higher expression of this gene. This study indicated that putative Vg and cgER might play a role in partial sterile in triploid C. gigas. Gene expression could be regulated by the methylation pattern at specific individual locus, which deserves equivalent attention as well as total DNA methylation level.

Development, inheritance and evaluation of 55 novel single nucleotide polymorphism markers for parentage assignment in the Pacific oyster (Crassostrea gigas)

Yu-Lin Jin,Qi Li,Lingfeng Kong,Hong Yu 한국유전학회 2014 Genes & Genomics Vol.36 No.2

Expressed sequence tags (ESTs) are essential toascertain gene function, but also to identify polymorphicgene-associated single nucleotide polymorphisms (SNPs)(type I markers) suitable for map construction and populationanalysis in the Pacific oyster (Crassostrea gigas). Inthis study, a total of 48,769 putative SNPs were detectedfrom 46,171 ESTs of the Pacific oyster. Fifty-five genederivedSNPs were isolated and characterized by means ofhigh resolution melting analysis. The observed andexpected heterozygosities ranged from 0.063–0.563 and0.091–0.448, with an average of 0.284 and 0.279, respectively. The SNPs were tested on 6 families of C. gigas forexamination of inheritance mode of SNPs. One hundredand thirty-two tests of segregation ratios at 48 loci revealed30 (22 %) significant departures from expected Mendelianratios, but no null allele was detected. The power of theseSNPs in parentage assignment was evaluated, and the realdata demonstrated that 17 % of all real offspring wereunambiguously assigned parents with 30 SNPs, and 100 %of the offspring were correctly allocated to their parentswhen 40 or more SNPs were used. The results obtained inthis study suggest that gene-derived SNPs will complementthe currently available microsatellite markers and may beuseful for comparative mapping, marker-assisted selectionand evolutionary studies.

Complete mitochondrial genome sequence of Cucullaea labiata (Arcoida: Cucullaeidae) and phylogenetic implications

Yanwei Feng,Qi Li,Hong Yu,Lingfeng Kong 한국유전학회 2017 Genes & Genomics Vol.39 No.8

The complete mitochondrial genome of Cucullaea labiata (Arcoida: Cucullaeidae) was firstly determined in this study in order to better understand the phylogenetic relationship between Cucullaeidae and Arcidae. The C. labiata mitochondrial genome was 25,845 bp in size and contained 12 protein-coding genes, 2 rRNA and 22 tRNA genes. The number and the location of the tRNA genes were different from three Arcidae species (Scapharca broughtonii, Scapharca kagoshimensis and Tegillarca granosa). Gene arrangement also differed dramatically. The length of the non-coding regions was 10,559 bp, in which the largest one (6057 bp) included eight point nine copies of a 659 bp repeat motif. The number of repeated sequences was different in different individuals, similar to the findings from the mitochondrial genome of S. broughtonii and Placopecten magellanicus. One intron was found in cox1 gene both in CL_98 and in CL_99 individuals of C. labiata. The reason why mitochondrial introns are retained so scarcely in bivalve taxa needs further research. Phylogenetic analyses based on 12 concatenated amino acid sequences of protein-coding genes supported Cucullaeidae was the sister group of Arcidae.