FY2013 Annual Report

Abstract

 

The mission of the DNA Sequencing Section (hereinafter referred to as SQC) is to promote advances in biological science by providing researchers in genomic analyses with the latest and most advanced technologies. SQC offers OIST researchers next-generation sequencing (hereinafter abbreviated as NGS) services in a wide range of NGS 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. The major achievements/updates in the fiscal year 2013 are as following:

 

a) Members and NGS platform

- 1 technical  staff joined in May.

- 3 instruments of Roche 454 GS FLX titanium were upgraded to FLX+, which enabled us to perform

longer-read sequencing.

- 1 instrument of Illumina HiSeq 2000 was upgraded to HiSeq2500 in July, which enabled us to

perform Rapid Run mode sequencing.

- 1 instrument of Illumina MiSeq was installed in October.

 

b) Activities

- Bisulfate library preparation and sequencing service had started.

- SQC had provided our services to 11 units including 1 new unit.

 

c) Publications

- 8 papers, SQC members listed in author

- 1 paper, SQC appeared in acknowledgement

- 4 application notes described by SQC

- 10 oral presentations including 3 invited talks

- 4 poster presentations

 

d) Meetings and Events

- 2 meeting of Okinawa NGS technical exchange were held.

- 1 training session was organized by SQC (OIST internal).

 

1. Members and NGS platforms

 

1.1 Members

Section Leader :

Takanari Ichikawa

 

Acting Section Leader :

Hiroki Goto (from November 1st, 2013)

 

Technical Expert :  

Manabu Fujie

 

Staff :    

Shinichi Yamasaki

Nana Arakaki

Ryo Koyanagi

Hiroko Yuki (from May 1st, 2014)

 

1.2 NGS platform

 

As of March 2014, SQC has been equipped with eight next-generation sequencing instruments shown in the table below. For this fiscal year, Roche 454 GS FLX titanium and Illumina HiSeq 2000 were upgraded to FLX+ and HiSeq 2500, respectively. An Illumina MiSeq instrument was newly installed in October.

 

 Model Name  Manufacturer        Qty.
Genome Sequencer FLX+ Roche      3
Genome Analyzer IIx  Illumina       1
HiSeq2500 Illumina       1
MiSeq Illumina       2
Ion Proton   Life Technologies      1

2. Activities

 

2.1 Sequencing services

SQC offered the following sequencing and library preparation services.

● De novo sequencing

● Re-sequencing

● Transcriptome

● ChIP-seq

● miRNA-seq

● Bisulfite sequencing

● Library preparations (shotgun, mate-pair/paired-end, mRNA, small RNA with/without multiplexing, and bisulfite)

 

For this fiscal year, SQC provided our services to the following units:

  • Brenner Unit

  • Goryanin Unit

  • Luscombe Unit

  • Mikheyev Unit

  • Satoh Unit

  • Saze Unit

  • Sinclair Unit

  • VanVactor Unit

  • Yanagida Unit

  • Yamamoto Unit

  • Jenke-kodama Unit (new)

 

Here’s the summary statistics for FY2013 SQC services.

  • Library construction: 184

  • Total data amount: 44,164 Gb

 

2.2 Other activities

 

2.2.1 Application Note

SQC provided manufacturers with the results of analysis for quality improvement of library preparation or sequencing using their newly-marketed instruments. The methods and the results were introduced at application note issued by each manufacturer. (See. 4.2 Books and other on-time publications)

 

2.2.2 Technical Exchange Meeting of Okinawa NGS

Continuing from 2012, we had the periodic meeting of NGS-technical exchange among the following four institutes/universities in Okinawa: Okinawa Industrial Technology Center, Okinawa Prefectural Agricultural Research Center, the University of the Ryukyus (Tropical Biosphere Research Center and Faculty of Medicine), and us (OIST SQC). The meeting was held twice in FY2013 (See 6. Meetings and Events).

 

2.2.3 Genome Resources Committee

In December 2013, Genome Resources Committee has been launched for deliberating and making recommendations on the policies of utilization and scheduling, and future plans of equipment and infrastructure for all genome sequencing and analysis resources funded by OIST. SQC is ensured by the committee to deliver the best possible service and support to meet genomic analysis requirements at OIST.

 

3. Publications

3.1 Journal

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


 

3.1.1 SQC members in Authors

 

Matsumae, H., Hamada, M., Fujie, M., Niimura, Y., and Kawashima, T.

A methodical microarray design enables surveying of expression of a broader range of genes in Ciona intestinalis.

Gene, Volume 519, Issue 1 : 82-90, April 25, 2013.

 

Husnik, F., Nikoh, N., Koga, R., Ross, L., Duncan, R. P., Fujie, M., Tanaka, M., Satoh, N., Bachtrog, D., Wilson, A. C., Dohlen, C. D., Fukatsu, T., and McCutcheon, J. P.

Horizontal gene transfer from diverse bacteria to an insect genome enables a tripartite nested mealybug symbiosis.

Cell, Volume 153, Issue 7 : 1567-1578, June 20, 2013.

 

Shoguchi, E., Shinzato, C., Kawashima, T., Gyoja, F., Mungpakdee, S., Koyanagi, R., Takeuchi, T., Hisata, K., Tanaka, M., Fujiwara, M., Hamada, M., Azadeh, S., Fujie, M., Usami, T., Goto, H., Yamasaki, S., Arakaki, N., Suzuki, Y., Sugano, S., Toyoda, A., Kuroki, Y., Fujiyama, A., Medina, M., Coffroth, M. A., Bhattacharya, D., and Satoh, N.

Draft assembly of the Symbiodinium minutum nuclear genome reveals dinoflagellate gene structure.

Current Biology, Volume 23, Issue 15 : 1399-1408, August 5, 2013.

 

Mehta, T. K., Ravi, V., Yamasaki, Y., Lee, A. P., Lian, M. M., Tay, B. H., Tohari, S., Yanai, S., Tay, S., Brenner, S., and Venkatesh, B.

Evidence for at least six Hox clusters in the Japanese lamprey (Lethenteron japonicum).

Proceedings of the National Academy of Sciences, Volume 110, Issue 40 : 16044-16049, October 1, 2013.

 

Kawashima, T., Takeuchi, T., Koyanagi, R., Kinoshita, S., Endo, H., and Endo, K.

Initiating the mollusk genomics annotation community: toward creating the complete curated gene-set of the Japanese Pearl Oyster, Pinctada fucata.

Zoological Science, Volume 30, Issue 10, 794-796, October 2013.

 

Koyanagi, R., Takeuchi, T., Hisata, K., Gyoja, F., Shoguchi, E., and Kawashima, T.

MarinegenomicsDB: an integrated genome viewer for community-based annotation of genomes.

Zoological Science, Volume 30, Issue 10 : 797-800, October 2013.

 

Nishi, S., Tsubouchi, T., Takaki, Y., Koyanagi, R., Satoh, N., Maruyama, T., and Hatada, Y.

Draft genome sequence of Loktanella cinnabarina LL-001T, isolated from deep-sea floor sediment

Genome Announcements, Volume 1, Issue 6 : November 14, 2013


 

3.1.2 SQC in Acknowledgement

 

Aird, S. D., Watanabe, Y., Villar-Briones, A., Roy, M. C., Terada, K., and Mikheyev, A. S.

Quantitative high-throughput profiling of snake venom gland transcriptomes and proteomes (Ovophis okinavensis and Protobothrops flavoviridis)

BMC Genomics, Volume 14, Issue 790 : November 14, 2013

 

3.2 Book and other on-time publication

None


 

3.2.1 Application note

 

Koyanagi, R.

Benefit of precise size selection on Ion Torrent PGM sequencing library using Pippin Prep

Labcab, Vol.5, December 2013.

 

Yuki, H.

DNA extraction with Maxwell 16 - Practical example on yeast

Labcab, Vol.5, December 2013.

 

Koyanagi, R.

Benefit of precise size selection on Ion Torrent PGM sequencing library using Pippin Prep

Application Note 2013 <05>, Nippon Genetics Co., Ltd., July 2013.

 

Fujie, M.

Application of Digital PCR : Library Quantification for next generation sequencers

BioRad News, Vol.3, May 2013.

 

3.3 Oral and Poster Presentations

* Speaker was put a circle on the name.

 

3.3.1 Oral Presentations

 

[Invited] ○Yamasaki, S., Koyanagi, R., Fujie, M., Shinzato, C. Takeuchi, T.

Master of De novo

Academic session in the 3rd meeting of NGS field, Kobe International Conference Center, Hyogo, Japan. September 4-5, 2013.

 

[Invited] ○Yamasaki, S.

“Is your rival "Human" ? or … ?”

Keynote lecture in Kosen conference in Okinawa, Ounoyama-koen Budokan, Okinawa, Japan. June 29, 2013.

 

Goto, H., Yamasaki, S., Arakaki, N., Koyanagi, R., ○Fujie, M., Yuki, H.

Technological advances in de novo sequencing

Symposium 1 : Marinegenomics, it’s new dynamism in the 13th Japanese Society of Marine Biotechnology meeting, Jichikaikan, Okinawa, Japan. June 1, 2013.


 

○Iwasaka, H., Koyanagi, R., Aki, T.

Genome decoding of valuable microalgae and its application

Symposium 1 : Marinegenomics, it’s new dynamism in the 13th Japanese Society of Marine Biotechnology meeting, Jichikaikan, Okinawa, Japan. June 1, 2013

 

[Invited] ○Koyanagi, R., ○Fujie, M.

De novo sequencing on the MiSeq system

De novo series (Invited by Illumina K.K.) in Illumina webinar (http://www.illuminakk.co.jp/events/webinar_japan.ilmn?ws=ws), April 12, 2013.

 

○Goto, H., Arakaki, N., Koyanagi, R., Fujie, M., Yamasaki, S., Yuki, H.

Genome analysis on natural resource use

2013 annual meeting of the Society of Tropical Resources Technologists, Okinawa Industrial Technology Center, Okinawa, Japan. November 29, 2013.


 

○Satoh, N., Sakamoto, T., Sakamoto, H., Endo, K., Goto, T.,Suzuki, T., Furuya, H., Sasakura, Y., Katayama, T., Kawashima, T., Fujie, M., and Koyanagi, R.

Towards genome decoding of all the animal phyla: (1) Overview

The 84th annual meeting of the zoological society of Japan, Okayama University, Okayama, Japan. September 26-28, 2013.

 

○Luo, Y. J., Endo, K., Tanaka, M., Fujie, M., Koyanagi, R., and Satoh, N.

Towards genome decoding of all the animal phyla: (2) A brachiopod, Lingula anatina

The 84th annual meeting of the zoological society of Japan, Okayama University, Okayama, Japan. September 26-28, 2013.


 

○Koyanagi, R., Sakamoto, T., Sakamoto, H., Satoh, N.              

Towards genome decoding of all the animal phyla: (3) A phoronid, Phoronius australis

The 84th annual meeting of the zoological society of Japan, Okayama University, Okayama, Japan. September 26-28, 2013.


 

○Kanda, M., Katayama, M., Hikosaka, A., Tagawa, K., Ueki, T., Yoshida, M., Nakano, H.,

Koyanagi, R., Fujie, M., amd Satoh, N.

Towards genome decoding of all the animal phyla: (4) Acoelomorphs, Waminoa and Praesagittifera

The 84th annual meeting of the zoological society of Japan, Okayama University, Okayama, Japan. September 26-28, 2013.


 

3.3.2 Poster presentations

 

○Koyanagi, R., Seidi, A., Fujie, M., and Satoh, N.

Genome Sequencing of Botryococcus and Aurantiochytrium

R&D cluster meeting, Okinawa, Japan. December 19, 2013.

 

○Kanda, M., Koyanagi, R., Fujie, M., Satoh, N.

Problems caused to the library preparation of marine invertebrate genome

The 3rd meeting of NGS Field, Kobe International Conference Center, Hyogo, Japan. September 4-5, 2013.


 

○Yuki, H., Goto, H., Fujie, M., Yamasaki, S., Koyanagi, R., Arakaki, N., Yokoi, T. and Sajiki, K.

A high throughput DNA extraction method for NGS from fission yeast

The 3rd meeting of NGS Field, Kobe International Conference Center, Hyogo, Japan. September 4-5, 2013.

 

○Arakaki, N., Goto, H., Fujie, M., Yamasaki, S., Koyanagi, R., Yuki, H., Motegi, T., and

Kobayashi, M.

Cooperation with machines　~Automated massive library prep~

The 3rd meeting of NGS Field, Kobe International Conference Center, Hyogo, Japan. September 4-5, 2013.

 

4. Meetings and Events

 

8th NGS Technical Exchange Meeting of Okinawa

Attendees: Yuki, H., Arakaki, N.

Okinawa Life Science Center, Okinawa, Japan. August 8, 2013.

 

9th NGS Technical Exchange Meeting of Okinawa

Attendees: Fujie, M., Yuki, H.

Okinawa Industrial Technology Center, Okinawa, Japan, March 19, 2014.


Brief training session for a new DNA shearing instrument (OIST internal, organized by SQC), March 10, 2014