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Ocean Sunfish Genome Offers Clues to Large Bony Fish Features
Friday, September 9, 2016
NEW YORK (GenomeWeb) – An international team led by investigators at BGI-Shenzhen and A*STAR in Singapore has sequenced the genome of the ocean sunfish, Mola mola, the largest known living bony fish species.
The ocean sunfish is known for its unusual appearance, rapid growth, and large size, often reaching more than two tons. When they compared the genome with sequences from other ray-finned fish — including the fugu or pufferfish, a fish with far different physical features that was sequenced in 2002 — the researchers uncovered sunfish-specific adaptations involving growth-related hormone signaling pathways and cartilage formation rather than alterations to HOX genes. The results appeared in the journal GigaScience last night.
"[W]e were keen to sequence the ocean sunfish genome and compare it with the pufferfish genome, to identify genetic changes that have occurred in the ocean sunfish lineage and that might give clues to the highly derived phenotype of the ocean sunfish," co-senior author Byrappa Venkatesh, a comparative genomics researcher at A*STAR's Institute of Molecular and Cell Biology, said in a statement.
Venkatesh and colleagues used the Illumina HiSeq 2000 to do paired-end sequencing on eight ocean sunfish DNA libraries. They put the resulting reads together into a 642 million base assembly. The full sunfish genome has been estimated at 730 million bases.
The team's analysis uncovered 19,605 predicted protein-coding genes, though roughly 11 percent of the genome appeared to be comprised of repetitive sequences such as transposable elements.
Conducting a comparative analysis of the sunfish and seven other ray-finned fish, which focused on nearly 1,700 ray-finned fish gene orthologues, the researchers considered relationships and divergence times for the fish. For example, they estimated that the ocean sunfish lineage split from the pufferfish lineage roughly 68 million years ago.
Meanwhile, their search for genes under positive selection and/or particularly speedy evolution in the sunfish led to growth hormone, insulin growth factor, extracellular matrix, and collagen/cartilage formation-related genes.
On the other hand, the team did not detect a decrease in Hox genes or Hox gene clusters in the sunfish genome, suggesting that the loss of such segmental identity-defining genes is not behind the sunfish's unusual shape.
"We still have a lot to learn from the ocean sunfish genome assembly," Venkatesh noted. "One way to pinpoint more genetic changes specific to ocean sunfish would be to sequence more closely related species such as porcupine fish, box fish, triggerfish, and triplespines."
Dozens of fish genomes have now been sequenced as part of the Genome 10K (G10K) project. Members of the G10K Consortium sequenced 100 vertebrate genomes for the first stage of the project. Last fall, G10K and BGI announced plans to sequence 10,000 vertebrates by 2020.
Originally posted on genomeweb
Photo: Oliver Dodd