NEW YORK (GenomeWeb News) – In a study appearing online today in Nature, an international team led by investigators in China, Denmark, the US, and Hong Kong described findings from its genomic, transcriptomic, and proteomic study of the Pacific oyster, Crassostrea gigas.
The team's sequencing and assessment of the draft oyster genome revealed a sequence rife with polymorphisms and repetitive sequences. In addition to using the genome to define oyster genes — and exploring their expression in different tissues, circumstances, and stages of development — the group did proteomic profiling on oyster shell samples to learn more about the development of this complex structure.
Those involved in the study say the availability of an oyster genome sequence should serve to spur additional genomics research on other animals in the Mollusca phylum as well as the broader Lophotrochozoa super-phylum to which they belong.
"The oyster genome sequence and comprehensive transcriptome data provide valuable resources for studying molluscan biology and lophotrochozoan evolution," senior author Jun Wang and his colleagues wrote, "and for genetic improvement of oysters and other important aquaculture species."
Wang is currently BGI's executive director. He is also affiliated with the University of Copenhagen.
In addition to the value placed on oysters and other molluscs as a food source, animals in this species-rich phylum are used to produce a range of products — from dyes to decorative items such as pearls and showy shells, Wang and his co-authors explained. They are also important from a research perspective, informing ecological studies as well as investigations aimed at understanding specific physiological processes.
"Many molluscs are important fishery and aquaculture species, as well as models for studying neurobiology, ocean acidification, and adaptation to coastal environments under climate change," the researchers noted.
Given these and other motivations for understanding the mollusc genetics, the team decided to sequence the Pacific oyster, C. gigas, starting with genomic DNA from an inbred female individual.
In their first crack at this, the investigators used whole-genome shotgun sequencing to drum up enough Illumina short-reads to cover the oyster genome to a depth of around 155-fold.
Because of the profusion of polymorphisms and repeat sequences in the genome, assembling the sequence took some special tricks: to accomplish that, the researchers turned to a method that involved independent sequencing and assembly of fosmid pools. Those contigs could then be combined with shotgun sequence reads to develop consensus sequences and cobble together increasingly longer pieces of the genome.
"Fosmid pooling has been used for re-sequencing," the team noted, "and our results show that the combination of fosmid pooling, [next-generation sequencing], and hierarchical assembly provides a new, cost-effective alternative for de novo sequencing and assembly of complex genomes."
After putting together a 559 million base draft assembly for the inbred oyster, the group went on to re-sequence the genome of a wild oyster.
To complement their genome sequence data, researchers generated transcriptome sequence data for seven adult oyster organs, along with tissues from dozens of developmental stages and samples from adult oysters facing various environmental stressors. They also produced proteomic profiles of oyster shell samples by mass spectrometry.
Analyses of the inbred oyster's genome uncovered 3.1 million SNPs and nearly 260,000 small insertions and deletions, they reported, while the wild oyster sequence contained 3.8 million SNPs as well as almost 240,000 indels.
The team also saw a slew of transposable elements in the oyster genome, including some seemingly active elements suspected of influencing the introduction of new variants in the animal's genetic sequences.
In its analyses of coding sequences, the group identified more than 28,000 genes coding for polypeptides that are at least 50 amino acids long. Among them: 8,654 genes that seem to be oyster-specific based on comparisons with genome sequences from several other sequenced animals.
The oyster genome houses a larger-than-usual repertoire of heat shock proteins and proteins that impede apoptosis, the team noted. Other peculiarities in the genome included fragmentation of Hox developmental genes — which are found in a lone cluster in most animals — into four distinct stretches of sequence surrounded by other kinds of genes.
Meanwhile, folding in transcriptome information offered researchers the chance to begin asking more in-depth questions about oyster biology. For instance, they defined shifts in gene expression related to environmental stresses such as temperature, heavy metal exposure, and salinity, providing transcriptional clues to the adaptations oyster use to survive some of the sites it inhabits.
And by tapping into oyster shell proteomic data, the study's authors learned more about the particulars of oyster shell formation during development — a biomineralization process of interest to those trying to gauge the possible consequences of ocean acidification on molluscs.
Results from that analysis "indicate that oyster shell matrix is not formed simply by self-assembling silk-like proteins," the team reported. Instead, shell formation appears to be far more complicated, bringing together assembly and modification steps achieved by specific cell types in collaboration with vesicles known as exosomes.