NEW YORK (GenomeWeb) – In PLOS Genetics, researchers from BGI-Shenzhen and other centers in China reported on efforts to sequence and analyze the genome of a bony fish called the large yellow croaker, Larimichthys crocea.
The team put together a genome assembly for the environmentally sensitive, but economically valuable fish, using sequences generated from wild L. crocea caught off China's coast. Together with transcriptome sequence data and proteomic profiling on mucus samples from air-exposed large yellow croakers, the genome provided a peek at the basis for characteristic L. crocea features — from its acute eyesight to its physiological responses in low oxygen conditions.
"Our results reveal the molecular and genetic basis of fish adaptation and response to hypoxia and air exposure," co-senior authors Jun Wang, Jian-Zhong Shao, and Xinhua Chen, and their colleagues wrote. "The data generated by this study will provide valuable resources for the genetic improvement of stress resistance and yield potential in L. crocea."
The large yellow croaker's natural distribution spans the northern region of the South China Sea, the southern Yellow Sea, and the East China Sea. It is also grown extensively in aquaculture operations in China and other parts of East Asian, where large yellow croaker meat is sought after for its selenium content and other nutritional properties.
The species is adapted to temperate waters, the researchers explained, but displays sensitivity to air and low oxygen conditions. It is also averse to sound, despite its own ability to produce the relatively loud "croaks" that give it its name.
In an effort to gain insight into the large yellow croaker's responses to environmental stress, along with features that might render it more resistant to disease in an aquaculture setting, the team used a combination of bacterial artificial chromosome sequencing and whole-genome shotgun sequencing with the Illumina HiSeq 2000 to tackle DNA from wild L. crocea representatives caught near Ningde, China.
The researchers also did transcriptome sequencing on 11different tissue types taken from male and female fish, as well as transcriptome sequencing and real-time PCR-based expression analyses on brain samples from fish exposed to low oxygen conditions over different stretches of time.
The resulting genome assembly spanned some 679 million bases of L. crocea's estimated 691 million base pair genome at 563-fold coverage, on average.
The team's analysis uncovered nearly 1.5 million repeat sequences and 25,401 predicted protein-coding genes, including representatives from almost 15,000 orthologous gene families found in seven teleost fish species sequenced previously.
Through sequence comparisons, the researchers not only delineated L. crocea's position in the teleost fish phylogeny, but also detected gene family expansions in the large yellow croaker genome that appear to account for the fish's keen vision, sensitive hearing, and knack for olfaction.
From their hypoxia experiments, meanwhile, the investigators got a glimpse at some of the immune, hormone, and metabolic pathways involved in maintaining oxygen to the brain as the animal's blood pressure and inflammatory responses ramp up in low oxygen conditions.
Finally, liquid chromatography and tandem mass spectrometry analysis indicated that the mucus produced by the large yellow croaker following exposure to air is comprised of a combination of more than 3,200 proteins — a set that includes immune players, oxidoreductase enzymes, and proteins suspected of binding oxygen and/or ions.
"The increase in secretion of the skin mucus of L. crocea under air exposure may reflect a physiological adjustment of the fish to cope with environmental changes," the study's authors speculated, "and the complex components suggest that the skin mucus exerts multiple protective mechanisms, which are involved in antioxidant functions, oxygen transport, immune defense, and osmotic and ionic regulation."