Shoudu Zhang

The oyster genome reveals stress adaptation and complexity of shell formation

The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster’s adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa.

Laboratory Hybridization between Crassostrea ariakensis and C. Sikamea

ABSTRACT To understand possible reproductive interaction between Crassostrea ariakensis (Fujita, 1913) and C. sikamea (Amemiya, 1928), which coexist in estuaries of China and Japan, we conducted 2 × 2 factorial crosses between the two species. Asymmetry in fertilization success was observed, where C. sikamea eggs can be fertilized by C. ariakensis sperm, and the reciprocal cross resulted in no fertilization. Fertilization success in C. sikamea female × C. ariakensis male (SA) crosses was lower than that in the two intraspecific crosses and produced larvae that had similar growth rate as their maternal species during the first nine days because of maternal effects. After that, genome incompatibility casted negative effects on the growth and survival of the hybrid larvae. Most hybrid larvae died during metamorphosis, but a small number of spat survived. Genetic analysis revealed that the survived SA spat contained DNA from both species and were true hybrids. This study demonstrates that hybridization between C. ariakensis and C. sikamea is possible in one direction.

SNP identification by transcriptome sequencing and candidate gene-based association analysis for heat tolerance in the bay scallop Argopecten irradians.

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.

Yield trait improvement of bay scallops following complete diallel crosses between different scallop stocks

This study describes the complete diallel hybridization between newly introduced bay scallop stock (W) from Canada and local commercial stock (D) grown under laboratory conditions, in China. Larval survival and growth during all life stages (larvae, spat, and adult) were compared among hybrid (DW, WD) and purebred (DD, WW) populations. Significant heterosis was detected for survival during the larval stage (>1% of the mid-parent values). The mean heterosis (Hm) varied in growth throughout the life span. More than 50% of the Hm values were positive and negative in the DW and WD groups, respectively. The influence of maternal effects and mating types (intrapopulation vs. interpopulation crosses) on growth for all life stages was not consistent. Larval survival did not differ significantly (P>0.05) with maternal effect or mating type. In the harvest stage, shell length (SL), shell height (SH), shell width (SW), and total weight (TW) were larger in the hybrid compared with the inbred groups. Positive Hm values were observed in SL (1.5%), SW (5.8%), and TW (12.3%), and were more significant in the DW groups (6.1%, 4.5%, 6.8%, and 27.2%). These results suggest that hybridization between two geographic populations is a good tool for improving bay scallop growth. However, unstable heterosis between the two populations requires further study.

Broadening the Genetic Basis of the Atlantic Bay Scallop Argopecten Irradians after Interspecific Hybridization and Backcrossing

The above noted paper is being officially retracted as a publication in the Journal of Shellfish Research. The paper was originally published in Marine Sciences, Volume 36 (8) in 2012 in Chinese with an English Abstract. This constitutes duplicate publication. The authors have agreed to this retraction. The paper is no longer citeable.

Divergence and plasticity shape adaptive potential of the Pacific oyster

The interplay between divergence and phenotypic plasticity is critical to our understanding of a species’ adaptive potential under rapid climate changes. We investigated divergence and plasticity in natural populations of the Pacific oyster Crassostrea gigas with a congeneric oyster Crassostrea angulata from southern China used as an outgroup. Genome re-sequencing of 371 oysters revealed unexpected genetic divergence in a small area that coincided with phenotypic divergence in growth, physiology, heat tolerance and gene expression across environmental gradients. These findings suggest that selection and local adaptation are pervasive and, together with limited gene flow, influence population structure. Genes showing sequence differentiation between populations also diverged in transcriptional response to heat stress. Plasticity in gene expression is positively correlated with evolved divergence, indicating that plasticity is adaptive and favoured by organisms under dynamic environments. Divergence in heat tolerance—partly through acetylation-mediated energy depression—implies differentiation in adaptive potential. Trade-offs between growth and survival may play an important role in local adaptation of oysters and other marine invertebrates.Adaptive differentiation is poorly understood in marine systems. Here, the authors combine genome sequencing with gene expression and physiology to show that genetic divergence and plasticity contribute to local adaptation of Pacific oyster populations.