The Experts below are selected from a list of 2823 Experts worldwide ranked by ideXlab platform
Guofan Zhang - One of the best experts on this subject based on the ideXlab platform.
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de novo transcriptome sequencing reveals candidate genes involved in orange shell coloration of bay scallop Argopecten irradians
Journal of Oceanology and Limnology, 2018Co-Authors: Wen Teng, Rihao Cong, Huayong Que, Guofan ZhangAbstract:Molluscan shell color has received persistent attention for its distinctive diversity and complexity. In the present study, six transcriptome libraries obtained from two developmental stages, pre-pigmentation and post-pigmentation, were used for paired-end sequencing in the bay scallop Argopecten irradians. In total, 289 839 646 paired-end reads were assembled into 70 929 transcripts. Using BLASTX and BLASTN, 30 896 unigenes were successfully annotated against the SWISS-PROT, NR, and KOG database. Gene ontology annotation and Kyoto Encyclopedia of Genes and Genomes classification identified numbers of unigenes involved in biomineralization and pigmentation. Digital gene expression analysis revealed that melanin, trace metal elements and porphyrins are potentially involved in shell coloration of A. irradians.
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snp identification by transcriptome sequencing and candidate gene based association analysis for heat tolerance in the bay scallop Argopecten irradians
PLOS ONE, 2014Co-Authors: Shoudu Zhang, Fei Meng, Guofan ZhangAbstract:The northern bay scallop Argopecten irradians irradians (Lamarck) and the southern bay scallop Argopecten irradians concentricus (Say) were introduced into China in the 1980s and 1990s, and are now major aquaculture molluscs in China. Here, we report the transcriptome sequencing of the two subspecies and the subsequent association analysis on candidate gene on the trait of heat tolerance. In total, RNA from six tissues of 67 and 42 individuals of northern and southern bay scallops, respectively, were used and 55.5 and 34.9 million raw reads were generated, respectively. There were 82,267 unigenes produced in total, of which 32,595 were annotated. Altogether, 32,206 and 23,312 high-quality SNPs were identified for northern and southern bay scallops, respectively. For case-control analysis, two intercrossed populations were heat stress treated, and both heat-susceptible and heat-resistant individuals were collected. According to annotation and SNP allele frequency analysis, 476 unigenes were selected, and 399 pairs of primers were designed. Genotyping was conducted using the high-resolution melting method, and Fisher’s exact test was performed for allele frequency comparison between the heat-susceptible and heat-resistant groups. SNP all-53308-760 T/C showed a significant difference in allele frequency between the heat-susceptible and heat-resistant groups. Notably, considerable difference in allele frequency at this locus was also observed between the sequenced natural populations. These results suggest that SNP all-53308-760 T/C may be related to the heat tolerance of the bay scallop. Moreover, quantitative expression analysis revealed that the expression level of all-53308 was negatively correlated with heat tolerance of the bay scallop.
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BROADENING OF THE GENETIC BASIS OF THE ATLANTIC BAY SCALLOP Argopecten IRRADIANS AFTER INTERSPECIFIC HYBRIDIZATION AND BACKCROSSING
Journal of Shellfish Research, 2014Co-Authors: Shoudu Zhang, Guofan ZhangAbstract:The growth characteristics and morphological features of the Atlantic bay scallop (Argopecten irradians irradians Lamarck), Chilean scallop (Argopecten purpuratus Lamarck), F1 hybrids of these species, and the offspring produced via 2 cycles of backcrossing between hybrid populations and the Atlantic bay scallop were examined to determine the feasibility of broadening the genetic basis of the bay scallop. Bidirectional fertilization and successful hatching were observed in F1 hybrids. Notable heterosis (i.e., >1% of the midparent values) was detected in growth and survival throughout the whole life span of the scallops. The F1 hybrids showed universal feminization, but with low fertilization and hatching rates observed in backcrosses with bay scallops (partial sterility). Hematoxylin-eosin staining of paraffin sections of the feminine gonads of the hybrids was performed in this study. The male gonad was found to be vestigial, without any active sperm, whereas the female gonad was well developed and presented abundant eggs with a normal appearance. Increasing fertilization and hatching rates were observed in the second generation of backcrosses between hybrid populations and bay scallops compared with the first backcrosses. At the same time, a growth advantage and low temperature resistance were regained in the offspring produced from backcrossed breeding. This study describes a promising way to broaden the genetic basis of bay scallops with the aim of improving the growth characteristics of cultured scallop stocks.
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A set of polymorphic microsatellite loci for the bay scallop, Argopecten irradians
Molecular Ecology Notes, 2006Co-Authors: Xiao Liu, Zhenmin Bao, Guofan ZhangAbstract:The method of creating enriched microsatellite libraries can supply an abundant source of microsatellite sequences at a considerably reduced cost. Here we report the development of 15 polymorphic microsatellite loci from the bay scallop, Argopecten irradians, using enrichment protocol. Polymorphism was assessed in a sample of hatchery population (n = 38) revealing three to seven alleles per locus. The expected and observed heterozygosities ranged from 0.198 to 0.813 and from 0.083 to 0.833, respectively. These markers will be useful for genetic variation monitoring and parentage analysis.
Chunde Wang - One of the best experts on this subject based on the ideXlab platform.
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transcriptomic and proteomic analyses of genetic factors influencing adductor muscle coloration in qn orange scallops
BMC Genomics, 2019Co-Authors: Junlin Song, Chunde WangAbstract:Background Color polymorphism, a high-valued trait, is frequently observed in molluscan shellfish. The QN Orange scallop, a new scallop strain successively selected from the interspecific hybrids of the bay scallop (Argopecten irradians irradians) and the Peruvian scallop (Argopecten purpuratus), is distinguished from other scallops by its orange adductor muscles. In this study, to reveal the mechanisms of the formation of adductor muscle coloration in the QN Orange scallops, we compared the proteome and transcriptome of orange adductor muscles of the QN Orange and those of white adductor muscles of the Bohai Red scallop, another strain selected from the interspecific hybrids of the bay scallop and the Peruvian scallop.
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Genome annotation for Argopecten irradians irradians and Argopecten irradians concentricus
2019Co-Authors: Chunde Wang, Xiao Liu, Min Chen, Bo Liu, Guilong Liu, Zhaoshan Zhong, Qiong ShiAbstract:Genome annotation for Argopecten irradians irradians and Argopecten irradians concentricu
Thomas R Famula - One of the best experts on this subject based on the ideXlab platform.
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characterization of 35 microsatellite loci in the pacific lion paw scallop nodipecten subnodosus and their cross species amplification in four other scallops of the pectinidae family
Molecular Ecology Notes, 2006Co-Authors: Ana Maria Ibarra, Jessica L Petersen, Thomas R FamulaAbstract:Four microsatellite-enriched DNA libraries yielded 35 microsatellite loci from 100 primer pairs designed for Pacific lion-paw scallop, Nodipecten subnodosus . The number of alleles ranged from four to 28. Three of the 35 loci were not in Hardy–Weinberg equilibrium and linkage disequilibrium was found for one pair of loci. These microsatellites will be used to analyse the population structure of the species in Mexico’s Baja Peninsula to propose management strategies for scallop aquaculture development. Twenty-six primer pairs cross-amplified in Nodipecten nodosus , whereas none ( Argopecten ventricosus ) or few crossamplified in the Argopecten species.
Zhenmin Bao - One of the best experts on this subject based on the ideXlab platform.
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RESEARCH ARTICLE
2016Co-Authors: Xiaoting Huang, Lingling Zhang, Shi Wang, Zhenmin BaoAbstract:Genomic in situ hybridization identifies parental chromosomes in hybrid scallop... 189 Genomic in situ hybridization identifies parental chromosomes in hybrid scallop (Bivalvia, Pectinoida, Pectinidae) between female Chlamys farreri and male Argopecten irradians irradian
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genomic in situ hybridization identifies parental chromosomes in hybrid scallop bivalvia pectinoida pectinidae between female chlamys farreri and male Argopecten irradians irradians
Comparative Cytogenetics, 2015Co-Authors: Xiaoting Huang, Lingling Zhang, Shi Wang, Zhenmin BaoAbstract:Interspecific crossing was artificially carried out between Chlamys farreri (Jones & Preston, 1904) ♀ and Argopecten irradians irradians (Lamarck, 1819) ♂, two of the dominant cultivated scallop species in China. Genomic in situ hybridization (GISH) was used to examine the chromosome constitution and variation in hybrids at early embryonic stage. The number of chromosomes in 66.38% of the metaphases was 2n = 35 and the karyotype was 2n = 3 m + 5 sm + 16 st + 11 t. After GISH, two parental genomes were clearly distinguished in hybrids, most of which comprised 19 chromosomes derived from their female parent (Chlamys farreri) and 16 chromosomes from their male parent (Argopecten irradians irradians). Some chromosome elimination and fragmentation was also observed in the hybrids.
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Molecular genetic analysis of heterosis in interspecific hybrids of Argopecten purpuratus x A. irradians irradians.
Genetics and Molecular Research, 2015Co-Authors: Xiaoting Huang, Wang Chunde, Yan Sun, Junxia Mao, Shenhai Wang, Zhenmin BaoAbstract:Argopecten purpuratus and Argopecten irradians irradians hybridization was successfully performed and the hybrid offspring displayed apparent heterosis in growth traits. To better understand the genetic basis of heterosis, the genomic composition and genetic variation of the hybrids were analyzed with amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers. Seven of eight universal SSR primers displayed polymorphism in the hybrids and their parental groups, and hybrids inherited both parental geno-types at each locus. Using five primer combinations in AFLP analysis, 433 loci were amplified in the hybrids and their parental groups. The frequency of polymorphisms was 88.22%. F1 hybrids inherited 88.11 and 92.88% of AFLP bands from their parents. Some loci did not follow Mendelian Law, including 48 loci in parents that were lost, and 11 new loci that were amplified in the hybrids. The parameters of Nei's gene diversity, Shannon's Information index, genetic distance, and molecular variance between groups were calculated. The genetic differentiation between two hybrid groups (0.253) was smaller than that between hybrids and their parents (0.554 to 0.645), and was especially smaller than that between two parental groups (0.769). The high genetic similarity (0.9347) and low genetic differentiation (0.2531) between two hybrid groups suggests that these hybrid groups were genetically very close. Heterozygosities of hybrid groups were higher than those of parental groups, indicating that the hybrids had increased genetic diversity.
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Genomic in situ hybridization identifies parental chromosomes in hybrid scallop (Bivalvia, Pectinoida, Pectinidae) between female Chlamys farreri and male Argopecten irradians irradians
Pensoft Publishers, 2015Co-Authors: Xiaoting Huang, Lingling Zhang, Shi Wang, Zhenmin BaoAbstract:Interspecific crossing was artificially carried out between Chlamys farreri (Jones & Preston, 1904) ♀ and Argopecten irradians irradians (Lamarck, 1819) ♂, two of the dominant cultivated scallop species in China. Genomic in situ hybridization (GISH) was used to examine the chromosome constitution and variation in hybrids at early embryonic stage. The number of chromosomes in 66.38% of the metaphases was 2n = 35 and the karyotype was 2n = 3 m + 5 sm + 16 st + 11 t. After GISH, two parental genomes were clearly distinguished in hybrids, most of which comprised 19 chromosomes derived from their female parent (C. farreri) and 16 chromosomes from their male parent (A. i. irradians). Some chromosome elimination and fragmentation was also observed in the hybrids
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A set of polymorphic microsatellite loci for the bay scallop, Argopecten irradians
Molecular Ecology Notes, 2006Co-Authors: Xiao Liu, Zhenmin Bao, Guofan ZhangAbstract:The method of creating enriched microsatellite libraries can supply an abundant source of microsatellite sequences at a considerably reduced cost. Here we report the development of 15 polymorphic microsatellite loci from the bay scallop, Argopecten irradians, using enrichment protocol. Polymorphism was assessed in a sample of hatchery population (n = 38) revealing three to seven alleles per locus. The expected and observed heterozygosities ranged from 0.198 to 0.813 and from 0.083 to 0.833, respectively. These markers will be useful for genetic variation monitoring and parentage analysis.
Ana Maria Ibarra - One of the best experts on this subject based on the ideXlab platform.
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Thirty-seven additional microsatellite loci in the Pacific lion-paw scallop (Nodipecten subnodosus) and cross-amplification in other pectinids
Conservation Genetics Resources, 2009Co-Authors: Jessica L Petersen, Ana Maria IbarraAbstract:We characterized 37 new microsatellite markers in the Pacific lion-paw scallop ( Nodipecten subnodosus ) and tested for cross-amplification in four other species. Genetic diversity was estimated using 24 individuals from the Lagoon Ojo de Liebre, B.C.S., Mexico. Allelic richness varied from 5 to 27 alleles per locus and the average expected heterozygosity was 0.76. Ten loci exhibited significant departure from Hardy–Weinberg equilibrium likely due to the presence of null alleles. Sixteen of these markers cross-amplified in closely related N. nodosus , while little or no amplification was observed in three Argopecten species.
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characterization of 35 microsatellite loci in the pacific lion paw scallop nodipecten subnodosus and their cross species amplification in four other scallops of the pectinidae family
Molecular Ecology Notes, 2006Co-Authors: Ana Maria Ibarra, Jessica L Petersen, Thomas R FamulaAbstract:Four microsatellite-enriched DNA libraries yielded 35 microsatellite loci from 100 primer pairs designed for Pacific lion-paw scallop, Nodipecten subnodosus . The number of alleles ranged from four to 28. Three of the 35 loci were not in Hardy–Weinberg equilibrium and linkage disequilibrium was found for one pair of loci. These microsatellites will be used to analyse the population structure of the species in Mexico’s Baja Peninsula to propose management strategies for scallop aquaculture development. Twenty-six primer pairs cross-amplified in Nodipecten nodosus , whereas none ( Argopecten ventricosus ) or few crossamplified in the Argopecten species.