Caiyan Zhu

Characterization and expression analysis of a chitinase gene (PmChi-4) from black tiger shrimp (Penaeus monodon) under pathogen infection and ambient ammonia nitrogen stress.

ABSTRACT Chitinase is a multi‐gene family, which play important physiological roles in crustaceans, involved in several biological processes, including digestion, molting and defense against viruses. In the present study, a chitinase‐4 gene (PmChi‐4) was cloned from Penaeus monodon by rapid amplification of cDNA ends (RACE). The full length of PmChi‐4 cDNA was 2178 bp, including an 1815 bp open reading frame (ORF) which encoded 604 amino acid residues. The predicted PmChi‐4 protein was 67.7 kDa and shared 61%–88% identity with the type of Chi‐4s from other crustaceans. Quantitative real‐time (qRT‐PCR) analysis indicated that PmChi‐4 was expressed ubiquitously with the high expression level in hepatopancreas. PmChi‐4 was expressed throughout the whole larvae stages, and the highest level of PmChi‐4 transcripts was detected at Mysis3 stage, which indicated that PmChi‐4 may be involved in larval metamorphosis. In order to know whether PmChi‐4 was related to the immune response of shrimp, Streptococcus agalactiae and Vibrio harveyi were chosen to challenge the shrimp, PmChi‐4 transcripts were significantly increased and reached to the maximum at 6 h in hepatopancreas and at 12 h in gill, respectively. The results suggested that PmChi‐4 participated in the immune defenses to pathogen infection. Besides, the ammonia nitrogen stress treatment was also carried out, PmChi‐4 transcripts were significantly decreased in hepatopancreas and gill and the result showed that PmChi‐4 may be involved in ammonia nitrogen stress in P. monodon. Overall, our present study lay a foundation for further research into the biological function and regulation of chitinase in P. monodon. HighlightsA chitinase‐4 gene was cloned from P. monodon by RACE method.The full length of PmChi‐4 cDNA was 2178 bp, including an 1815 bp ORF.qRT‐PCR was performed to study the PmChi‐4 expression pattern in different tissues and larvae stages.PmChi‐4 expression level increased after S. agalactiae and V. harveyi infection.PmChi‐4 expression level declined after ammonia nitrogen stress treatment.

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.

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.

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.

Complete mitochondrial genome sequence of golden pompano Trachinotus ovatus

Abstract The complete mitochondrial genome of Trachinotus ovatus was determined by the polymerase chain reaction (PCR). The mitogenome is 16,564 bp long and has the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one control region. The overall base composition of mitogenome is estimated to be 29.0% for A, 28.9% for C, 26.2% for T, 15.9% for G, respectively, with a high A + T content (55.2%). With the exception of ND6 and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. The control region contains a dinucleotide repeat motif, (AT)5. This mitogenome sequence would play an important role in population genetics and the molecular taxonomy of T. ovatus.