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Japanese Flounder Genome, Comparative Analysis Reveal Genetic Underpinnings of Body Asymmetry

NEW YORK (GenomeWeb) – Clues to the genetics behind the unusual asymmetry found in flatfish are coming out of a new genome assembly and comparative genomic analysis of the Japanese flounder, Paralichthys olivaceus.

As reported today in Nature Genetics, an international team led by investigators in China, Germany, the US, and Portugal put together a genome assembly for the Japanese flounder that housed almost 22,000 predicted protein-coding genes.

When they analyzed the flounder genome and transcriptome alongside sequences from another flatfish, the investigators identified pathways that appear to contribute to developmental events that lead to the migration of one eye to the opposite side of the body and to the fish's pancake-like body shape.

"[T]he establishment of a high-quality genome of the Japanese flounder and its comparison to the genome of another flatfish, the Chinese tongue sole, led to the identification of genes and developmental pathways that regulate metamorphosis and establish body asymmetry," the authors wrote.

Using the Illumina HiSeq 2000 instrument, the researchers sequenced the genome of a female Japanese flounder, generating a high-quality assembly that spanned some 546 million bases. They also sequenced RNA from pigmented and unpigmented tissue from the Japanese flounder and from the Chinese tongue sole (Cynoglossus semilaevis), a distantly related flatfish and the first to have its genome sequenced, in 2014.

With help from the RNA sequences, the team annotated 21,787 protein-coding Japanese flounder genes, including genes from families shared with the Chinese tongue sole or families that were expanded in both flatfish. Although the two fish lineages split some 70 million years ago, the genomes still appeared to contain nearly 400 million bases of syntenic sequence.

By comparing sequences in the Japanese flounder, Chinese tongue sole, and other teleost fish, the researchers narrowed in on more than 100 genes that appeared to be under positive selection in the flatfish lineage — a set that contained genes related to skeletal and muscular patterns, body symmetry, and hormone signaling.

The team's analysis of genomic and transcriptomic patterns in the flatfish, combined with follow-up immunohistochemistry, immunofluorescence, microinjection, and other experiments, offered a look at the molecular underpinnings for some characteristic flatfish features. For example, the results suggested that retinoic acid gradients and uneven coloring in flatfish skin are helped along by the expression of light-sensing opsin, while interplay between retinoic acid and thyroid hormone signaling pathways seemed to contribute to the movement of one eye to the opposite side of the body during flatfish development.

"We demonstrate that retinoic acid is critical in establishing asymmetric pigmentation and, via cross-talk with thyroid hormones, in modulating eye migration," the authors wrote. "The unexpected expression of the visual opsins from the phototransduction pathway in the skin translates illumination differences and generates retinoic acid gradients that underlie the generation of asymmetry."