Dianchang Zhang

A preliminary study for identification of candidate AFLP markers under artificial selection for shell color in pearl oyster Pinctada fucata.

Pearl oyster Pinctada fucata is widely cultured to produce seawater pearl in South China, and the quality of pearl is significantly affected by its shell color. Thus the Pearl Oyster Selective Breeding Program (POSBP) was carried out for the shell color and growth traits. The black (B), gold (G), red (R) and white (W) shell strains with fast growth trait were achieved after five successive generation selection. In this study, AFLP technique was used to scan genome of four strains with different shell colors to identify the candidate markers under artificial selection. Eight AFLP primer combinations were screened and yielded 688 loci, 676 (98.26%) of which were polymorphic. In black, gold, red and white strains, the percentage of polymorphic loci was 90.41%, 87.79%, 93.60% and 93.31%, respectively, Neis gene diversity was 0.3225, 0.2829, 0.3221 and 0.3292, Shannons information index was 0.4801, 0.4271, 0.4825 and 0.4923, and the value of FST was 0.1805. These results suggested that the four different shell color strains had high genetic diversity and great genetic differentiation among strains, which had been subjected to the continuous selective pressures during the artificial selective breeding. Furthermore, six outlier loci were considered as the candidate markers under artificial selection for shell color. This study provides a molecular evidence for the inheritance of shell color of P. fucata.

Characterization of complete mitochondrial genome of fives tripe wrasse (Thalassoma quinquevittatum, Lay & Bennett, 1839) and phylogenetic analysis

To further supplement the genome-level features in related species, T. quinquevittatum complete mtDNA was firstly sequenced and de novo assembled by next-generation sequencing. The full-length mtDNA of T. quinquevittatum was a 16,896bp fragment, which was atypical of Labridae, with 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), 23 transfer RNA (tRNA) genes, and a major non-coding control region (D-loop region). Additionally, the mtDNA of T. quinquevittatum exhibited characteristics of A (27.1%), T (29.3%), G (17.8%), and C (25.8%) with a high A+T content (56.4%). Furthermore, the analysis of the average Ka/Ks in the 13 PCGs of three Labridae species indicated a strong purifying selection within this group. Additionally, the phylogenetic analysis based on 13 concatenated PCGs nucleotide and amino acid datasets, showed high value support for the following sister clade among the four genera (T. quinquevittatum, Halichoeres trimaculatus, Halichoeres melanurus, Parajulis poecilepterus). The complete mtDNA of the T. quinquevittatum provided important information for the study in population genetics and evolutionary theory.

The complete mitochondrial genome of banana shrimp Fenneropenaeus merguiensis with phylogenetic consideration

Abstract The complete mitochondrial genome sequence of Fenneropenaeus merguiensis was determined by shotgun assembly method. The complete mitochondrial DNA sequence is a circular molecule with 16,023 bp in length including 13 protein-coding genes, 22 transfer RNA genes, 2 rRNA genes and a control region. The gene arrangements are consistent with the pan crustacean ground pattern. The molecular analyses provided robust evidence for the monophyly of Fenneropenaeus, but Litopenaeus was not monophyletic. Phylogenetic analyses robustly supported the fact that genus Penaeus s.l. contains the two lineages: Marsupenaeus and Penaeus s.s+ Fenneropenaeus + Litopenaeus + Farfantepenaeus.

Shotgun assembly of the mitochondrial genome from Fenneropenaeus penicillatus with phylogenetic consideration.

The complete mitochondrial genome is of great importance for better understanding of the genome-level characteristics and phylogenetic relationships among related species. In this study, Fenneropenaeus penicillatus mitochondrial genome sequence was determined by next-generation sequencing. The complete genome DNA was 16,040 bp in length and consisted of a typical set of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a putative control region (CR). The gene arrangement is identical to the pancrustacean pattern. The overall base composition of its mitochondrial genome is estimated to be 34.1% for A, 34.1% for T, 12.5% for G and 19.3% for C with a high A+T content (68.2%). The analysis of the average Ka/Ks in the 13 mitochondrial protein-coding genes of penaeid shrimps indicated a strong purifying selection within this group. The phylogenetic analysis based on mitochondrial sequences and 13 concatenated protein-coding genes showed strong statistic support for the following relationship among the five genera ((Penaeus s.s+Fenneropenaeus)+(Litopenaeus+Farfantepenaeus))+Marsupenaeus. The sequence data of F. penicillatus can provide useful information for the studies on molecular systematics, population structure, stock evaluation and conservation genetics.

Isolation and characterization of 21 polymorphic microstatellites in golden pompano Trachinotus ovatus

The golden pompano Trachinotus ovatus is a most important marine fish in South China, and the wild population of T. Ovatus has been rapidly decreasing owing to overfishing recently, to understand the genetic status for the conservation, we isolated and characterized twenty-one polymorphic microsatellites from a (GT)13 enriched genomic library. The number of alleles ranged from 2 to 10. The observed and expected heterozygosities ranged from 0.083 to 0.792 and from 0.081 to 0.886, respectively. The PIC value ranged from 0.0767 to 0.8623. Six loci deviated from Hardy-Weinberg equilibrium. Finally, the 21 novel informative microsatellite markers could be used in future population genetic study of T. ovatus that might be useful in a context of marine biodiversity conservation.

Feed type regulates the fatty acid profiles of golden pompano Trachinotus ovatus (Linnaeus 1758)

ABSTRACT The aim of the present study was to evaluate the effect of different feed types on the fatty acid profiles of golden pompano (Trachinotus ovatus). Three feed types (pelleted feed, frozen squid and frozen fish) were assigned to triplicate groups of fish (146.22 ± 3.26 g) in a total of 9 floating cages (50 fish per cage). Analysis of the fatty acid profiles of the three feed types revealed that frozen squid had the highest levels of long-chain polyunsaturated fatty acids (LC-PUFA), while the pelleted feed and frozen fish had lower levels of LC-PUFA, in particular eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). After three months of being fed a specific feed type, the fatty acid profiles of golden pompano muscle tissues were analysed. The highest levels of LC-PUFA were detected in fish fed with frozen squid. Golden pompano fed with frozen fish had intermediate levels of LC-PUFA content. The results suggest that the fatty acid composition of prey items can significantly affect the muscle fatty acid composition of the consumer. Muscle fatty acid composition could also be used as an indicator of diet type for golden pompano in the aquaculture industry.

Functional characteristic and differential expression of myostatin in Chlamys nobilis

ABSTRACT Myostatin (MSTN) was a conserved negative regulatory protein of muscle growth and development in numerous species. In this study, the MSTN gene was cloned and characterized from a noble scallop, Chlamys nobilis, and it was named CN-MSTN. To investigate the molecular characterization of MSTN and its gene expression profile of spatio-temporal, we isolated the MSTN cDNA sequence in C. nobilis and analysed expression patterns using quantitative real-time PCR. CN-MSTN cDNA contained a 1,374 bp open reading frame that encoded a 458 amino acids. Furthermore, the result of 3D model indicated that CN-MSTN mature peptide was similar to that of Chlamys farreri. Additionally, based on both the nucleotide and amino acid datasets, phylogenetic trees indicated that C. nobilis has the highest similarity with homologues of C. farreri. The expression patterns of different stages showed that MSTN expression was markedly higher in the gastrulae period. Additionally, remarkable expression of MSTN was observed in adductor muscle than with other tissues. Our data would provide expression and phylogenetic information of this economical important sea food, noble scallop.

Shotgun assembly of the first mitochondrial genome of Metapenaeus (Metapenaeus ensis) with phylogenetic consideration

Abstract The first complete mitochondrial genome sequence of Metapenaeus was characterized from sand shrimp Metapenaeus ensis using shotgun assembly method. The complete mitochondrial DNA sequence is a 15 944 bp circular molecule, and contains 13 protein-coding genes, 22 transfer RNA genes, two rRNA genes, and a control region. The gene arrangements are consistent with the pancrustacean ground pattern. The phylogenetic trees were divided two clades besides outgroup, which belonged to Penaeus s.l. and Metapenaeus genus. The molecular analyses provided robust evidence for the monophyly of Fenneropenaeus, but Litopenaeus is not monophyletic.

The complete mitochondrial genome of mud carp Cirrhinus molitorella (Cypriniformes, Cyprinidae)

Abstract The complete mitochondrial genome of Cirrhinus molitorella was determined using the polymerase chain reaction. The complete mitochondrial DNA sequence is 16,602 bp in length. It consists of 13 protein-coding genes, 22 transfer RNA genes, 2 rRNA genes and 2 non-coding regions. Overall base composition of mitogenome is estimated to be 32.32% for A, 15.26% for G, 25.00% for T, 27.41% for C, respectively, with a high A + T content (57.32%). The control region contains a dinucleotide repeat motif, (TA)12, a termination-associated sequence and three conserved sequence blocks. The complete mitochondrial genome sequence of C. molitorella can provide a basic data for the studies on population structure, molecular systematic, stock evaluation and conservation genetics. It is also helpful to develop the rational management strategies for C. molitorella resource.

Genomic structure, expression pattern and polymorphisms of GILT in golden pompano Trachinotus ovatus (Linnaeus 1758)

The interferon-g-inducible lysosomal thiol reductase (GILT) plays a significant character in the processing and presentation of MHC class II restricted antigen (Ag) by catalyzing disulfide bond reduction in mammals. To explore the function of GILT in the immune system of fish, we cloned a GILT gene homologue from Trachinotus ovatus, the full-length cDNA of GILT, which consisted of 2, 747 bp with a 771 bp open reading frame, encoding a protein of 256 amino acids. Moreover, similar to other species GILT gene, 7 exons and 6 introns were identified in T. ovatus, the deduced protein also possessed a representative characteristic of known GILT proteins. The result of real-time quantitative PCR showed that GILT mRNA was dramatically expressed in immune-associated tissues, such as spleen (p < 0.01) and kidney (p < 0.05). Bacterial challenge revealed that GILT mRNA level remarkably up-regulation in liver, spleen, kidney and intestine after induction with Photobacterium damsela. Furthermore, based on cloned sequences and genome BLAST, only one SNP site (ToGILT-S1-g.148C>G) was identified, and the allele C was significantly associated with high-susceptibility (HS) group, nevertheless, the allele G was dramatically associated with high-resistance (HR) group, indicating potential application for disease resistant breeding selection in T. ovatus.