Adaptive Evolution Patterns in the Pacific Oyster Crassostrea gigas

Contribution of HIF-1α to Heat Shock Response by Transcriptional Regulation of HSF1/HSP70 Signaling Pathway in Pacific Oyster, Crassostrea gigas

Ocean temperature rising drastically threatens the adaptation and survival of marine organisms, causing serious ecological impacts and economic losses. It is crucial to understand the adaptive mechanisms of marine organisms in response to high temperature. In this study, a novel regulatory mechanism that is mediated by hypoxia-inducible factor-1α (HIF-1α) was revealed in Pacific oyster (Crassostrea gigas) in response to heat stress. We identified a total of six HIF-1α genes in the C. gigas genome, of which HIF-1α and HIF-1α-like5 were highly induced under heat stress. We found that the HIF-1α and HIF-1α-like5 genes played critical roles in the heat shock response (HSR) through upregulating the expression of heat shock protein (HSP). Knocking down of HIF-1α via RNA interference (RNAi) inhibited the expression of heat shock factor 1 (HSF1) and HSP70 genes in C. gigas under heat stress. Both HIF-1α and HIF-1α-like5 promoted the transcriptional activity of HSF1 by binding to hypoxia response elements (HREs) within the promoter region. Furthermore, the survival of C. gigas under heat stress was significantly decreased after knocking down of HIF-1α. This work for the first time revealed the involvement of HIF-1α/HSF1/HSP70 pathway in response to heat stress in the oyster and provided an insight into adaptive mechanism of bivalves in the face of ocean warming.

Ecological significance of G protein-coupled receptors in the Pacific oyster (Crassostrea gigas): Pervasive gene duplication and distinct transcriptional response to marine environmental stresses

Marine ecosystems with ocean warming and industry pollution threaten the survival and adaptation of organisms. G protein-coupled receptors (GPCRs) play critical roles in various physiological and toxicological processes in vertebrates and invertebrates. The Pacific oyster (Crassostrea gigas) was widely used to study the adaptation of marine molluscs to coastal environments. In this work, we identified a total of 586 GPCRs in C. gigas genome. The C. gigas GPCRs were divided into five classes (including class A, B, C, E and F) with different degrees of expansion. Meta-analysis of multiple RNA-seq datasets revealed that transcriptional expression patterns of GPCRs in C. gigas were distinct in response to high temperature, salinity, air exposure, heavy metal, ostreid herpes virus 1 (OsHV-1) and Vibrio challenge. This work for the first time characterized the GPCR gene family and provided insights into the potential roles of GPCRs in adaptation of marine molluscs to stressful coastal environment.

Genome-Wide Identification of Long Non-coding RNAs in Crassostrea gigas and Their Association with Heat Stress

Oysters face a complex and changeable environment in the intertidal zone. Heat stress is the main cause of their mass summer deaths. Several important genes are identified to be associated with heat response for oysters. However, regulation of these heat response genes in oysters remains largely unknown. In this study, 27 RNA-seq datasets are used to give a relatively comprehensive of long noncoding RNA (lncRNA) sets for C. gigas. Then, the differential expressed genes and lncRNAs are identified under heat stress. Among all the heat shock proteins (HSPs) and inhibitor of apoptosis proteins (IAPs) in the C. gigas genome, 25 heat shock proteins and 14 IAPs are differential expressed. The Gene Ontology analysis reveals that differential expressed genes (DEGs) are enriched in 6, 7, and 7 GO terms in cellular components, molecular function, and biological process, respectively. Within these terms, cellular response to stimulus is the most abundant term. Furthermore, the potential cis target of the differential expressed lncRNAs (DELs) are predicted to investigate their functions. Of the 394 DELs, there are 80 DELs being found to be corresponded to 113 protein-coding genes. Of them, eight HSPs are found to be regulated by their lncRNA regulators under heat stress. This work provides valuable resource of lncRNA and their regulatory roles under heat stress in C. gigas and gives new insights into adaptive evolution in marine mollusks.

Genomic Landscape of Mutational Biases in the Pacific Oyster Crassostrea gigas

Mutation is a driving force of evolution that has been shaped by natural selection and is universally biased. Previous studies determined genome-wide mutational patterns for several species and investigated the heterogeneity of mutational patterns at fine-scale levels. However, little evidence of the heterogeneity of mutation rates over large genomic regions was shown. Hence, the mutational patterns of different large-scale genomic regions and their association with selective pressures still need to be explored. As the second most species-rich animal phylum, little is known about the mutational patterns in Mollusca, especially oysters. In this study, the mutational bias patterns are characterized by using whole-genome resequencing data in the Crassostrea gigas genome. I studied the genome-wide relative rates of the pair mutations and found that the predominant mutation is GC -> AT, irrespective of the genomic regions. This analysis reveals that mutational biases were associated with gene expression levels across the C. gigas genome. Genes with higher expression levels and breadth expression patterns, longer coding length, and more exon numbers had relatively higher GC -> AT rates. I also found that genes with larger dN/dS values had relatively higher GC -> AT rates. This work represents the first comprehensive research on the mutational biases in Mollusca species. Here, I comprehensively investigated the relationships between mutational biases with some intrinsic genetic factors and evolutionary indicators and proposed that selective pressures are important forces shaping the mutational biases across the C. gigas genome.

First de novo transcriptome assembly of Iwagaki oyster, Crassostrea nippona, and comparative evolutionary analysis of salinity-stress response genes in Crassostrea oysters

Crassostrea nippona is a commercially important oyster species in East Asia for it is edible during the summer when the other oyster species are unavailable. Salinity is one of the important limiting factors to the survival and distribution of this stenohaline species. In this study, 535 million reads (74G data) from C. nippona were produced and assembled into 66,742 transcripts. The number of 19,253 differentially expressed genes (DEGs) under salinity stress were identified as salinity stress-response genes. Through comparative evolutionary analysis in five Crassostrea species from East Asia, salinity stress-response genes were noticed to have higher adaptive evolution rates than other genes. This study presents the first de novo transcriptome of C. nippona. Furthermore, comparative evolutionary analysis implies that salinity plays an important role in speciation of Crassostrea species.

The evo-devo of molluscs: Insights from a genomic perspective

Molluscs represent one of ancient and evolutionarily most successful groups of marine invertebrates, with a tremendous diversity of morphology, behavior, and lifestyle. Molluscs are excellent subjects for evo-devo studies; however, understanding of the evo-devo of molluscs has been largely hampered by incomplete fossil records and limited molecular data. Recent advancement of genomics and other technologies has greatly fueled the molluscan "evo-devo" field, and decoding of several molluscan genomes provides unprecedented insights into molluscan biology and evolution. Here, we review the recent progress of molluscan genome sequencing as well as novel insights gained from their genomes, by emphasizing how molluscan genomics enhances our understanding of the evo-devo of molluscs.

Evaluation of Genomic Selection for Seven Economic Traits in Yellow Drum (Nibea albiflora)

Yellow drum (Nibea albiflora) is an important maricultural fish in China, and genetic improvement is necessary for this species. This research evaluated the application of genomic selection methods to predict the genetic values of seven economic traits for yellow drum. Using genome-wide single-nucleotide polymorphisms (SNPs), we estimated the genetic parameters for seven traits, including body length (BL), swimming bladder index (SBI), swimming bladder weight (SBW), body thickness (BT), body height (BH), body length/body height ratio (LHR), and gonad weight index (GWI). The heritability estimates ranged from 0.309 to 0.843. We evaluated the prediction performance of various statistical methods, and no one method provided the highest predictive ability for all traits. We then evaluated and compared the use of genome-wide association study (GWAS)-informative SNPs and random SNPs for prediction and found that GWAS-informative SNPs obviously increased. It only needed 5 and 100 informative SNPs for LHR and BT to achieve almost the same predictive abilities as using genome-wide SNPs, and for BL, SBI, SBW, BH, and GWI, about 1000 to 3000 informative SNPs were needed to achieve whole-genome level predictive abilities. It can be concluded from the test results that breeders can use fewer SNPs to save the breeding costs of genomic selection for some traits.