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Guofan Zhang – One of the best experts on this subject based on the ideXlab platform.
de novo transcriptome sequencing reveals candidate genes involved in orange shell coloration of bay scallop Argopecten irradiansJournal 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.
snp identification by transcriptome sequencing and candidate gene based association analysis for heat tolerance in the bay scallop Argopecten irradiansPLOS 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.
BROADENING OF THE GENETIC BASIS OF THE ATLANTIC BAY SCALLOP Argopecten IRRADIANS AFTER INTERSPECIFIC HYBRIDIZATION AND BACKCROSSINGJournal 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.
Chunde Wang – One of the best experts on this subject based on the ideXlab platform.
transcriptomic and proteomic analyses of genetic factors influencing adductor muscle coloration in qn orange scallopsBMC Genomics, 2019Co-Authors: Junlin Song, Chunde WangAbstract:
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.
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.
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 familyMolecular 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.