D-STEP & Symposium on Evolutionary Genetics and Omics

The SEGO will be held at National Institute of Genetics (NIG) in Japan on July 13 & 14, 2018. It covers a wide range of topics in evolutionary genetics and omics to discuss current research and to stimulate future international collaboration. All talks are invitation-based.

DDBJ also organizes a training session (DDBJ Supercomputer Training & Educational Program) jointly with this symposium. We accept max. 10 participants. Please apply from Application form.

Symposium on Evolutionary Genetics and Omics (SEGO)

  • Date : July 13, 14 2018 (Fri, Sat)
  • Venue : National Institute of Genetics, Mishima, Japan
  • Language : English (including the training course)

Program

July 13 (Friday)

11:00-12:00
Talks 1
Dynamics and Constraints of Protein Evolution
Nobuhiko Tokurik (The University of British Columbia, Canada)
12:00-13:15
Lunch and discussion
13:15-13:25
Introduction
Introduction
Tomoko Ohta (National Institute of Genetics(NIG), Japan)
13:25-13:55
Talks 2
Adaptation of A-to-I RNA editing and the impact on genome evolution
Jian Lu (Peking University, China)
13:55-14:25
Talks 3
Evolutionary patterns of polymorphic duplications in Drosophila melanogaster
JChau-Ti Ting (National Taiwan University, Taiwan)
14:25-14:45
Coffee and discussion
14:45-15:15
Talks 4
Evolution of three independent neo-sex chromosome systems in Drosophila
Masafumi Nozawa (Tokyo Metropolitan University, Japan)
15:15-15:45
Talks 5
The rises and falls of opsin genes in 59 ray-finned fish genomes and their implications for environmental adaptation
Jinn-Jy Lin (Academia Sinica, Taiwan)
15:45-16:05
Coffee and discussion
16:05-16:35
Talks 6
Ecological genomics of fungi and nematodes in Asia
Isheng Jason Tsai (Academia Sinica, Taiwan)
16:35-17:05
Talks 7
Searching for packaging signals in viruses with segmented genomes
Yoshiyuki Suzuki (Nagoya City University, Japan)
17:05-17:25
Coffee and discussion
17:25-17:55
Talks 8
Genomic and Molecular Insights into Evolutionary Innovation and Domestication of Birds
Chen Siang “Gene” Ng (National Tsing Hua University, Taiwan)

July 14 (Saturday)

9:15-9:45
Talks 9
A New Approach to Estimate Site Frequency Spectra to Infer Evolutionary Forces: applications to Drosophila genomes.
Tomotaka Matsumoto (National Institute of Genetics, Japan)
9:45-10:15
Talks 10
Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes.
Yuichiro Nakatani (The University of Dublin, Ireland)
10:15-10:30
Coffee and discussion
10:30-11:30
Talks 11
On the post-glacial spread and phenotypic changes of weedy Arabidopsis thaliana
Cheng-Ruei Lee (National Taiwan University, Taiwan)
10:30-11:30
Talks 12
Genetic adaptation and ancestry inference of the Taiwanese indigenous and Han peop
Yun-Hua Lo (National Yang-Ming University, Taiwan)
11:30-11:45
Coffee and discussion
11:45-12:15
Talks 13
Coalescent analysis of phylogenomic data resolves the species relationships in the Anopheles gambiae species complex
Ziheng Yang (University College London, England)
112:15-13:30
Lunch and discussion

2nd DDBJ Supercomputer Training & Educational Program training session

  • Date : July 14 (Saturday) 13:30 - 17:30
  • Venue : NIG Guest House 2F
  • Language : English
  • Capacity : 10
  • Apply : Application form

Program

July 14 (Saturday)

13:30-14:00
Talks 14
Introduction to NIG Supercomputer and DDBJ
Masanori Arita (National Institute of Genetics (NIG), Japan)
DDBJ is a part of International Nucleotide Sequence Database (INSD) in collaboration with NCBI and ENA/EBI since 1987. We provide not only traditional sequence information but also next-generation sequence data from Sequence Read Archive, research projects from BioProject, biological sources and materials from BioSample, and human genotype-phenotype information from JGA.
Our Supercomputer is open to Japanese researchers and foreign collaborators upon request, and over 500 registered users perform life science research. In this talk, I will introduce the overview of our services and explain how to use them.
14:00-14:30
Talks 15
Genome assembly and polymorphism analysis of plants
Hideki Hirakawa (Kazusa DNA Reserch Institute, japan)
Since Kazusa DNA Research Institute (KDRI) has been established in 1994, we have determined the genome sequences of several kinds of plants with low or high heterozygosity, such as model plants (Arabidopsis thaliana, Lotus japonicus etc.), cereal (buckwheat, quinoa etc.), vegetables (tomato, eggplant, daikon radish etc.), fruits (tomato, strawberry etc.), and flowers (carnation, wild rose etc.) by using Sanger or next-generation sequencers (NGSs). Recently, Sequel (Pacific Biosciences) known as a long-read sequencer has been installed in KDRI, and we have been trying to determine the genome sequences in pseudomolecule level by assembling the Sequel reads together with cross-linking DNA (Hi-C) and optical mapping (BioNano) technologies.
In addition, we are conducting de novo haplotype assemblies for a few plant species by using the 10x GemCode technology (10x Genomics). Currently, the quality of the genome sequences of diploid species has been increasing by using these technologies.
However, the genome assembly of polyploid species is still difficult due to the complexity of genome structure. After the genome assembly was finished, polymorphism analyses were conducted against several kinds of cultivars in genome sequencing projects. In this presentation, I will talk about the genome sequencing and polymorphism analysis of plants performed in KDRI.
14:30-15:00
Talks 16
Large-genome assembly using PacBio and Illumina reads
Yasukazu Nakamura (National Institute of Genetics (NIG), Japan)
Since 1987, the DNA Data Bank of Japan (DDBJ) at the National Institute of Genetics (NIG) has worked as a partner of the International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org). The INSDC, one of the longest-standing global alliances of biological databases, has been committed to collecting, preserving and providing access to comprehensive nucleotide sequence datasets. Current NGS platforms provide a way to access genomic information of many species at relatively low cost and ultra high speed. In the Sequence Read Archive (SRA) of the INSDC, NGS data has been accumulated exponentially. For analysis of large-scale sequence data, DDBJ Center operates the NIG supercomputer system. The NIG supercomputer offers computational infrastructure for the construction of DDBJ databases and analysis services, and provides researchers with a large-scale data analysis and supercomputing environment. In this talk, I will demonstrate how to construct a set of longer and accurate scaffolds using mixed data of a large amount of long and short reads on the NIG supercomputer system.
15:00-17:30
Demo
Tutorial for next-generation sequence analysis
Yasukazu Nakamura (National Institute of Genetics (NIG), Japan)
Using sample data, participants will trace the steps of NGS analysis. We also provide tips for computational analyses.

About the Symposium

Organizers

Sponsors and support