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

Oikopleura dioica is a globally prolific tunicate that harbors a small genome of <70MB.  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 ongoing 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 & RNA isolation/sequencing of field samples on NGS (Illumina & Nanopore) platforms. He has been successful in optimizing isolation conditions of typically low total-genomic DNA yields found in Oikopleura samples for high-quality long reads from a single individual.

Andrew Liu joined the unit in 2017, previously from Neurobiology Unit since starting at OIST in 2010 and RIKEN Center for Brain Science between 2005-2010. A crotchety old technician who remembers the days of laboring with Sanger sequencing using 32P end-labelled oligos and ridiculously large glass plates (and if the Gods were willing, achieving 600bp in a run). Provides culturing, fieldwork, molecular and cell biology support for the Oikopleura project. Also, involved with development of wet-lab automation in a Genomics setting.

Aleksandra Bliznina graduated from Moscow State University with her Masters degree in 2017 and began her PhD with the unit in 2018. She has been engaged and tasked with the analysis of Nanopore and Illumina sequencing data from a single Oikopleura dioica individual for assembly of the complete genome from telomere to telomere. Her work in this endeavor gave rise to a first authorship in BMC Genomics in 2021. She continues to work on complete annotation of the sequence assembly and synteny breakpoint analysis using sequencing data generated from previously published global and unit acquired local populations.

Dr Charles Plessy joined GRSU in late 2018 hailing from RIKEN Genomic Sciences Center in Yokohama. He brought with him nearly 20 years of genomic and transcript analysis proficiency along with a strong background in bioinformatics. While working with our unit, he established a streamlined pipeline using Nextflow for processing and compiling raw sequence data. As an enthusiastic group leader, he leads multiple projects within the unit, contributes his time to furthering the OIST's research community's scope, and promotes the Open Science Initiative.

Dr Michael Mansfield joined GRSU in 2020 after completion of his PhD in Biology at the University of Waterloo, Canada. His recent studies brought fresh bioinformatics knowledge to the unit that includes, genome assembly, structural annotation, phylogenetics, and the regulation of gene expression. During the past two years, he has provided significant contributions to the assembly and annotation pipeline while he continues to lead multiple collaborative inter-disciplinary projects. Additionally, he has given helpful guidance to students and interns. Currently, he is analyzing data collected from our population studies to determine evolutionary mechanisms of diversity and speciation.

Dr. Charlotte Capitanchik is a visiting researcher in GRSU, joining in 2022 after completing her PhD in Computational Biology at the Francis Crick Institute in London. She has a long-standing interest in the molecular mechanisms of RNA processing, with her previous studies focusing on mechanisms of pre-mRNA splicing, RNA modification and RNA-binding protein interactions with RNA. She brings experience of reproducible analysis and integration of a wide variety of functional genomics data, including RNA-Seq, QuantSeq, ribosome profiling, metabolic RNA profiling and CLIP methodologies. She is a contributing author to multiple bioinformatics tools that aim to simplify and speed up analyses for the wider research community. Her aim in the Luscombe unit is to produce and analyse long-read RNA sequencing data in Oikopleura Dioica to generate insights into the evolution of pre-mRNA processing mechanisms, such as splicing.  

Naohiro Yamauchi graduated from the University of Tokyo in 2022 and began his rotation in the unit in April. He is interested in how information processing occurs when microscopic molecules and cells in living organisms interact to form macroscopic phenotypes. In the unit, he is working on functional genomics of Oikopleura dioica, constructing Nextflow pipeline and analyzing transcriptome data.

J. Nicolaus Wibisana joined GRSU in 2022 as a rotation student working on regulatory element conservation in Oikopleura dioica. He previously worked on super-enhancer regulation mediated by the transcription factor NF-κB in B cell activation at Osaka University while working on his Masters before moving to OIST for PhD. He is both a wet and dry biologist who also has interest in 3D modeling and printing.