Development of a DNA genotyping method using Next-Generation Sequencing and genome-wide DNA polymorphisms analysis

Representative Organization: Tohoku University

2014/06/01 - 2015/03/31

Sendai Bay, coast lines of Japan

Others

DNA markers using a huge amount of data produced by a Next Generation Sequencing platform IonTorrent PGM will be newly developped to evaluate genetic diversity of aquatic organisms inhabiting Tohoku area. Based on the spatial and temporal sampling collection, the genetic diversity and its dynamics before and after the impact will be investigated. The species of interest are Pseudopleuronectes yokohamae, Onchoryncus keta, seaweed, and invertebrate animals.

Genetic differentiation was observed along the Pacific Ocean coasts, especially between the east and west sides of Boso peninsula, among which the populations were further diverged at each side of the peninsula (pairwise FST = 0.02305 - 0.19784). At the east side, significant divergences were found between Mutsu Bay and others (FST = 0.03829), but not over the area from Onagawa Bay to Choshi, suggesting the broad gene flow. The genetic diversity of the Sendai Bay populations (HE = 0.5061 - 0.5463) was not drastically changed over time (April 2012 - February 2014) and relatively higher than those of the populations collected from the western localities of Boso peninsula (HE = 0.3817 - 0.4557). These results present that the effects of the massive tsunami on the genetic diversity of the marbled flounder populations in Sendai Bay were likely minimal.

FY2014 Development of a DNA genotyping method using Next-Generation Sequencing and genome-wide DNA polymorphisms analysis

Pseudopleuronectes yokohamae (Pleuronectiformes; Pleuronectidae) draft genome sequence data and RAD-tag reads data