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Wednesday, June 27, 2018

Plant and Animal SMRT Grant Will Enable Insight Into Sightless Fish

When German diver Joachim Kreiselmaier reached the deepest parts of the Danube-Aach cave system, he couldn’t believe his eyes: a “strange fish,” with a pale body coloration and smaller eyes and larger nares and barbels than the loaches typically spotted nearby. He had discovered the first cavefish in Europe, and the northernmost in the world. “This is spectacular, as it was believed that the Pleistocene glaciations prevented fish from colonizing subterranean habitats north of 41° latitude,” said ecologist Jasminca Behrmann-Godel of the Limnological Institute of the University of Konstanz, who examined the fish Kreiselmaier brought back to the surface. “Initial…

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Monday, May 14, 2018

Codfish Study Employs Target Capture and SMRT Sequencing to Explore Evolution

Many investigators rely on targeted sequencing approaches for deep dives into genomic regions of interest. By designing specific probes -- often using short-read sequences directed towards the exome and supported by existing reference genomes or transcriptome assemblies -- scientists can home in on exactly the area they want to explore. But what about sequences in intergenic regions not covered by short reads, which could contain crucial regulatory elements varying between populations that might be of functional and evolutionary importance? Or, what about species lacking high-quality reference genomes to guide probe design? A team of Norwegian researchers are tackling these challenges…

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Thursday, December 14, 2017

A Fish Tale: Centromeres Prove Central to the Divergence of a Species

The ability to study the speciation of an animal in real-time is a dream come true for evolutionary and developmental biologists. A group of Japanese researchers has gotten that opportunity, thanks in part to SMRT Sequencing. Scientists at the University of Tokyo were the first to create a reference genome for an inbred strain of the medaka fish (Oryzias latipes), genome size ~800 Mb, in 2007. The genome assembly was created using Sanger sequencing, but contained low-quality regions and 97,933 sequence gaps. So, the team started from scratch with long-read sequencing to generate genome assemblies with far less missing sequence.…

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