FY2014 Annual Report

DNA Sequencing Section

Abstract

The mission of the DNA Sequencing Section (hereinafter referred to as SQC) is to promote advances in biological science by providing researchers with state-of-the-art genomic technologies. SQC offers OIST researchers genome analysis services in a wide range of the applications including de novo genome sequencing, re-sequencing, RNA sequencing, ChIP sequencing and bisulfite sequencing. We help researchers with their planning, library preparation, library quantification and subsequent sequencing. In addition, SQC provides access to genome analysis instruments such as Illumina MiSeq.

The major achievements/updates in the fiscal year 2014 are as following:

a) Members and NGS platform

  • 2 technical and 1 administrative staffs joined.
  • 1 instrument of Illumina HiSeq2500 was installed in August.
  • 1 instrument of BioNano Genomics Irys System was installed in December.
  • 1 instrument of Pacific Biosciences RSII was installed in February.

b) Activities

  • Bisulfate library preparation and sequencing service had started (December, 2014).
  • SQC had provided our services to 12 research units in OIST for this fiscal year.

c) Publications

  • 1 contribute article to the journal
  • 4 papers, SQC members listed in author
  • 3 paper, SQC appeared in acknowledgement
  • 9 oral presentations including 3 invited talks
  • 3 poster presentations

d) Meetings and Events

  • 5 training session was organized by SQC (OIST internal).

1. Members and NGS / NGM platforms

 

1.1 Members

Section Leader :
Hiroki Goto

Technical Expert :
Manabu Fujie

Staff :
Shinichi Yamasaki
Nana Arakaki
Ryo Koyanagi
Hiroko Yuki
Wakana Oshiro (from May, 2014)
Mayumi Kawamitsu (from December, 2014)
Miyuki Kanda (from January, 2015)

​1.2 NGS platform

As of March 2015, SQC has been equipped with eight next-generation sequencing instruments shown in the table below. An Ilumina Hiseq2500 was additionally installed in August, and a Pacific Biosciences RSII was newly installed in March. Two of three Roche Genome Sequencer FLX+ and one Illumina Genome Analyzer IIx were terminated because of no demand due to the high sequencing cost and almost no advantage of their specifications.

                           Model Name                                   Manufacturer              Qty.
Genome Sequencer FLX+ Roche 1
HiSeq 2500 Illumina 2
MiSeq Illumina 2
Ion Proton Life Technologies 1
PacBio RSII Pacific Biosciences 1
Irys System BioNano 1

2. Activities

2.1 Sequencing services

SQC offered the following sequencing and library preparation services:

  • DNA Shotgun Sequencing (PCR)
  • DNA Shotgun Sequencing (PCR-Free)
  • RNA Sequencing (Strand-Specific)
  • Small RNA Sequencing
  • ChIP Sequencing
  • Amplicon Sequencing
  • Metagenomic Sequencing
  • Bisulfate sequencing (PBAT)
  • DNA Mate pair Sequencing
  • Restriction-site Associated DNA Sequencing (RAD-Seq)

SQC provided our services to the following units:

  • Goryanin Unit
  • Jenke-Kodama Unit
  • Luscombe Unit
  • Maruyama Unit
  • Mikheyev Unit
  • Mitarai Unit
  • Rokhsar Unit
  • Samatey Unit
  • Satoh Unit
  • Saze Unit
  • VanVactor Unit
  • Yamamoto Unit

The summary statistics for SQC services are shown below:

2.2 Other activities

Nothing to report

3. Publications

3.1 Journal

* The articles were published by OIST researchers used our sequencing services (SQC members were underlined).

3.1.1 Publications by SQC

Arakaki, N.
Introduction of DNA Sequencing Section in OIST
Journal of the Society of Tropical Resources and Technologists, Vol.29 No.1, P13-15, 2014.

3.1.2 SQC members in Authors

Shinzato, C., Yasuoka, Y., Mungpakdee, S., Arakaki, N., Fujie, M., Nakajima, Y., and Satoh, N.
Development of novel, cross-species microsatellite markers for Acropora corals using next-generation sequencing technology
Frontiers in Marine Science, 2014 May 23. DOI: org/10.3389/fmars.2014.00011

Mungpakdee, S., Shinzato, C., Takeuchi, T., Kawashima, T., Koyanagi, R., Hisata, K., Tanaka, M., Goto, H., Fujie, M., Lin, S., Satoh, N., and Shoguchi, E.
Massive gene transfer and extensive RNA editing of a symbiotic dinoflagellate plastid genome
Genome Biology and Evolution, 2014 May 31;6(6):1408-22. DOI:10.1093/gbe/evu109.

Gusev, O., Suetsugu, Y., Cornette, R., Kawashima, T., Logacheva, MD., Kondrashov, AS., Penin, AA., Hatanaka, R., Kikuta, S., Shimura, S., Kanamori, H., Katayose, Y., Matsumoto, T., Shagimardanova, E., Alexeev, D., Govorun, V., Wisecaver, J., Mikheyev, A., Koyanagi, R., Fujie, M., Nishiyama, T., Shigenobu, S., Shibata, T., Golygina, V., Hasebe, M., Okuda, T., Satoh, N., and Kikawada. T.
Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge
Nature Communications, 2014 Sep 12;5:4784. DOI: 10.1038/ncomms5784.

Satou, Y., Hirayama, K., Mita, K., Fujie, M.,  Chiba, S., Yoshida, R., Endo, T., Sasakura, Y., Inaba, K., Satoh, N.
Sustained Heterozygosity Across a Self-Incompatibility Locus in an Inbred Ascidian
Molecular Biology and Evolution, 2015 Jan;32(1):81-90. DOI: 10.1093/molbev/msu268.

3.1.3 SQC in Acknowledgement

Baughman, KW., McDougall, C., Cummins, SF., Hall, M., Degnan, BM., Satoh, N., and Shoguchi, E.
Genomic organization of Hox and ParaHox clusters in the echinoderm, Acanthaster planci
Genesis, 2014 Dec;52(12):952-8. DOI: 10.1002/dvg.22840

Tin, MM., Economo, EP., and Mikheyev, AS.
Sequencing degraded DNA from non-destructively sampled museum specimens for RAD-tagging and low-coverage shotgun phylogenetics
PLoS One, 2014 May 14:9(5):e96793. DOI:10.1371/journal.pone.0096793.

Barker, CS., Meshcheryakova, IV., Sasaki, T., Roy MC., Sinha, PK., Yagi, T., and Samatey, FA.
Randomly selected suppressor mutations in genes for NADH:quinone oxidoreductase-1, which rescue motility of a Salmonella ubiquinone-biosynthesis mutant strain
Microbiology, 2014 Jun;160(Pt 6):1075-86. DOI:10.1099/mic.0.075945-0.

3.2 Book and other on-time publication

3.2.1 Book

Fujie, M., and Yamasaki, S.
Experimental Medicine, Special Topic Book, Standard protocols on Next Generation Sequencing-WET&DRY-
Chapter V. Protocols -Environment・Evolution・Natural Resources-4.
P277-289 Published on September 10, 2014

3.3 Oral and Poster Presentations

* Speaker was put a circle on the name.

[Invited] Fujie, M.
Changes in the de novo sequencing strategy promoted by innovation​
NGS Session in “For the Better Forum 2014 ～Customer Insight～”
The event of Perkin Elmer Japan, Toranomon hills forum, Tokyo, Japan, November 11, 2014.

[Invited] Fujie, M.​
NGS library quantification using digital PCR
The 1st BioRad Digital PCR User Forum,Tennouzu Central Tower Hall 27, Tokyo, July 17, 2014.

[Invited] Koyanagi, R.
Exploring Metazoan Evolution with Genome Maps
International Plant & Animal Genome XXIII, Town and Country Hotel, San Diego, CA, USA, January 12, 2015

Yasuoka, Y., Koyanagi, R., Yasuoka, Y., Shinzato, C., and Satoh, N.
Functional analysis of the T-box transcription factor Brachyury in coral gastrula embryos
The 47th annual meeting of the Japanese Society of Developmental Biologists
WINC Aichi, Nagoya, Japan, May 27-30, 2014.

Shinzato, C., Yasuoka, Y., Mungpakdee, S., Zayasu, Y., Arakaki, N., Fujie, M., Nakajima, Y., and Satoh N.
Development of novel, cross species microsatellite markers for Acropora corals using next generation sequencing technology
The 85th Annual Meeting of the Zoological Society of Japan, Tohoku University, Sendai, Japan, Sep 11-13, 2014.

Satou, Y., Hirayama, K., Mita, K., Fujie, M., Chiba, S., Yoshida, R., Endo, T., Sasakura, Y., Inaba, K., and Satoh, N.
Sustained heterozygosity across a self-incompatibility locus in an inbred ascidian
The 85th Annual Meeting of the Zoological Society of Japan, Tohoku University, Sendai, Japan, Sep 11-13, 2014.

Luo, Y., Takeuchi, T., Koyanagi, R., Tanaka, M., Khalturina, M., Fujie, M., Yamasaki, S., Yamada, L., Sawada, H., Endo, K., and Satoh, N.
The Lingula genome and the evolution of lophotrochozoans and biomineralization
The 85th Annual Meeting of the Zoological Society of Japan, Tohoku University, Sendai, Japan, Sep 11-13, 2014.

Kanda, M., Koyanagi, R.，Fujie, M., Sakamoto, T., Sakamoto, H., Satoh, N.
Genome decoding of a phoronida Phoronis australis and a nemertea Lineus geniculatus​
Microbiology, 2014 Jun;160(Pt 6):1075-86. DOI:10.1099/mic.0.075945-0.

Koyanagi, R., Kanda, M., Fujie, M., Suzuki, T., Satoh, Nori.
Genome decoding of a gastroricha, Ichthydium podura
The 85th Annual Meeting of the Zoological Society of Japan, Tohoku University, Sendai, Japan, Sep 11-13, 2014.

3.3.2 Poster presentations

Ueki, R., Fujie, M., and Satoh, N.
Metagenome analysis of gut bacteria flora in Ascidia kreagra 
The 16th Annual Meeting of the Japanese Society for Marine Biotechnology
Faculty of Bioresources, Mie University, Mie Prefecture, Japan, May 31-June 1, 2014.

Shinzato, C., Yasuoka, Y., Mungpakdee, S., Zayasu, Y., Arakaki, N., Fujie, M., Nakajima, Y., and Satoh, N.
Development of novel, cross-species microsatellite markers for Acropora corals using next-generation sequencing technology​
The 17th Japanese coral reef society meeting, Kochijyo hall, Kochi, Japan, From Sept. 27 to Dec. 1, 2014.

Koyanagi, R.
“Multicellular eukaryotic genome assembly supported by optical mapping”
The 37th annual meeting of Molecular Biology Society Japan, Pacifico Yokohama, Yokohama, Japan, Nov, 2014.

3.4 Statistics

3.3.2 Cumulative number of scientific publications

 

3.3.2 Cumulative number of scientific presentations

4. Meetings and Events

 

  • Brief training session for Life Technologies StepOne plus, in Japanese (OIST internal, organized by SQC), May 18, 2014
  • Brief training session for Life Technologies StepOne plus, in English (OIST internal, organized by SQC), July 3, 2014
  • Technical Seminar for Recent developments of PacBio RSII by Dr. Steve Turmer (Pacific Biosciences founder and CTO) (OIST internal, organized by SQC), September 3, 2014
  • Brief training session for an automated DNA fractionation instrument (OIST internal, organized by SQC), December 15, 2014
  • One-on-one training session for MiSeq (OIST internal, organized by SQC), January 22, 2015
  • One-on-one training session for MiSeq (OIST internal, organized by SQC), February 6, 2015