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Deep Dives into DNA of Marine Biology

Friday, July 27, 2018

What lies beneath? Photo by Ruben Gutierrez.

“Live every week like it’s Shark Week,” 30 Rock character Tracy Jordan once quipped to Kenneth the Page, referencing the week-long, dorsal-finned programming phenomenon that has become the Discovery Channel summer ratings mainstay.

If it involves diving deeply into the science of the maligned species, we’re all in favor. But why stop there?

On our companion long-form Medium blog, we hosted our own Marine Week to highlight recent scientific discoveries across the seas.

  • In “Healthy Marine Ecosystems Rely on Their Tiniest Inhabitants,” we explore how the health of ocean habitats relies on more than the activities of our finned friends. Just as human health is proving to be linked to the microbial communities in our guts, marine health is influenced by the bacteria in its ecosystems. A group of Thai scientists are studying the marine microbiology of coral reefs in the Gulf of Thailand and the Andaman Sea to glean the role bacteria might play in the health of the habitat and its responses to environmental stressors, such as elevated seawater temperature.
  • The orange clownfish, Amphiprion percula, may have been immortalized in the comedic film “Finding Nemo,” but its importance to the scientific community is no joke. In “Finding Nemo’s Genes: International Team Creates First Reference Genome of Orange Clownfish,” we visit an effort led by Tim Ravasi of King Abdullah University of Science and Technology in Saudi Arabia and Phil Munday of James Cook University in Australia, to create molecular resources for one of the most important species for studying the ecology and evolution of coral reef fishes, as well as a model species for social organization, sex change, mutualism, habitat selection, lifespan, and predator-prey interactions.
  • Aquaculture has become an increasingly important source of sustainable seafood. And similar to the city singles scene, its viability has a lot to do with sex. In “Deep in the Dating Pool,” we look at how studies into sex differentiation of two marine species — Nile tilapia (Oreochromis niloticus) and abalone (Haliotis discus hannai)– can help commercial and conservation breeding efforts. Long-read sequencing and the Iso-Seq method were key to the success of these efforts by two international research groups.
  • In “A Fish Tale: Tracing the Divergence of a Species,” we explore what it takes for one species to evolve into another, with medaka as the model. A popular pet since the 17th century because of its hardiness and pleasant coloration, scientists are more interested in the genetics of the medaka, but earlier attempts to sequence the fish’s 800 Mb genome were not the best quality, and had 97,933 gaps in their sequence. So researchers at the University of Tokyo started from scratch, using Single Molecule, Real-Time (SMRT) Sequencing. This advanced technology allowed them to study difficult-to-detect centromeres and changes in DNA structure that were missing in the previous genome assemblies.

Hungry for more? Head over to bioRxiv, where a team of Japanese and American researchers, led by Shawn Burgess at the NIH’s National Human Genome Research Institute, have reported on the assembly of the goldfish (Carassius auratus) genome and the evolution of its genes after whole genome duplication. As a very close relative of the common carp (Cyprinus carpio), goldfish share the recent genome duplication that occurred approximately 14-16 million years ago in their common ancestor, and the combination of centuries of breeding and a wide array of interesting body morphologies “is an exciting opportunity to link genotype to phenotype as well as understanding the dynamics of genome evolution and speciation,” the authors state.

Generating a high-quality draft sequence of a “Wakin” goldfish using 71-fold coverage PacBio long-reads, the team identified 70,324 coding genes and more than 11,000 non-coding transcripts and found that that two sub-genomes in goldfish retained extensive synteny and collinearity between goldfish and zebrafish. However, “ohnologous” genes were lost quickly after the carp whole-genome duplication, and the expression of 30% of the retained duplicated gene diverged significantly across seven tissues sampled.

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