Projects

Comparative genetic analysis of Oikopleura dioca among local sub-populations.

Oikopleura dioica is a globally prolific tunicate that harbors a small genome of <80MB.  This surprisingly scant amount of DNA codes for a relatively complex organism (the body plan during its entire life cycle has features of a notochord and tail). Preliminary whole genome sequencing and analysis of the local populations that live in the seas surrounding Okinawa has shown some notable differences among them. Morphologically, they appear to be the same species but further investigation is on-going to determine the exact differences in the structure of their genomes and the evolutionary events that gave rise to the divergence. In time, the goal is to determine the mechanism that drives the local genetic diversity and potentially use this in a broader context for geographically-driven global speciation.

 

 

Aki Masunaga successfully established an impressive culturing facility for the long-term maintenance of Oikopleura dioica at GRSU since she began her career here in 2015. Currently, she is involved in whole genome DNA isolation/sequencing of field samples on NGS (Illumina & Nanopore) platforms and yet still manages to coordinate and conduct field-work required for the population study.
Dr Yongkai Tan has provided his expertise in NGS, gleaned while working for Beijing Genomic Institute in Kobe, to the GRSU group since starting in 2016. Currently, he is involved in whole genome DNA isolation/sequencing of field samples on NGS (Illumina & Nanopore) platforms and has successfully optimized the low total-genomic DNA samples yields found in Oikopleura samples for single individual reference sequencing and assemblies.
Dr Charles Plessy recently joined the GRSU late in 2018 from RIKEN Genomic Sciences Center in Yokohama and brings with him over 15 years of genomic and transcript analysis along with a strong background in bioinformatics.  He has established a streamlined pipeline for compiling and processing of raw sequence data and is the lead individual for the assembly and analysis of all transciptomes and genomes sequenced.