Overview

Bluefin tunas (family Scombridae), such as Pacific bluefin tuna (PBT) (Thunnus orientalis), Atlantic bluefin tuna (Thunnus thynnus), and southern bluefin tuna (Thunnus maccoyii), are highly migratory, large-bodied and top pelagic predators species that represent one of the most important fishery resources that yield high market values across the world. We determined the genome sequence of the Pacific bluefin tuna, using next-generation sequencing technology. A total of 26,433 protein-coding genes were predicted from 16,802 assembled scaffolds (Nakamura et al., 2013). Based on the draft genome sequence, we developed the first 44K Pacific bluefin tuna oligonucleotide microarray (oligo-array). Our work has been published in the journal Gene (Special issue: Marine Genomics) on February 1, 2016.

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Predicted genes (Ver. 1) 　　　CDS: (11.7MB) 　　　Proteins: (7.4MB) Additional information (Ver. 1) 　　　Scaffold: (218MB) 　　　Augustus gene models: (6.5MB)

Published papers

Yoji Nakamura, Kazuki Mori, Kenji Saitoh, Kenshiro Oshima, Miyuki Mekuchi, Takuma Sugaya, Yuya Shigenobu, Nobuhiko Ojima, Shigeru Muta, Atushi Fujiwara, Motoshige Yasuike, Ichiro Oohara, Hideki Hirakawa, Vishwajit Sur Chowdhury, Takanori Kobayashi, Kazuhiro Nakajima, Motohiko Sano, Tokio Wada, Kosuke Tashiro, Kazuho Ikeo, Masahira Hattori, Satoru Kuhara, Takashi Gojobori, and Kiyoshi Inouye (2013) Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna. Proc. Natl. Acad. Sci. U. S. A., Volume 110, Pages 11061–11066
(doi: 10.1073/pnas.1302051110)

Motoshige Yasuike, Atushi Fujiwara, Yoji Nakamura, Yuki Iwasaki, Issei Nishiki, Takuma Sugaya, Akio Shimizu, Motohiko Sano, Takanori Kobayashi, Mitsuru Ototake (2016) A functional genomics tool for the Pacific bluefin tuna: Development of a 44K oligonucleotide microarray from whole-genome sequencing data for global transcriptome analysis. Gene. Volume 576,Issue 2, Part 1, Pages 603–609
(doi: 10.1016/j.gene.2015.10.023)

Abstract

Bluefin tunas are one of the most important fishery resources worldwide. Because of high market values, bluefin tuna farming has been rapidly growing during recent years. At present, the most common form of the tuna farming is based on the stocking of wild-caught fish. Therefore, concerns have been raised about the negative impact of the tuna farming on wild stocks. Recently, the Pacific bluefin tuna (PBT), Thunnus orientalis, has succeeded in completing the reproduction cycle under aquaculture conditions, but production bottlenecks remain to be solved because of very little biological information on bluefin tunas. Functional genomics approaches promise to rapidly increase our knowledge on biological processes in the bluefin tuna.

Here, we describe the development of the first 44K PBT oligonucleotide microarray (oligo-array), based on whole-genome shotgun (WGS) sequencing and large-scale expressed sequence tags (ESTs) data. In addition, we also introduce an initial 44K PBT oligo-array experiment using in vitro grown peripheral blood leukocytes (PBLs) stimulated with immunostimulants such as lipopolysaccharide (LPS: a cell wall component of Gram-negative bacteria) or polyinosinic:polycytidylic acid (poly I:C: a synthetic mimic of viral infection). This pilot 44K PBT oligo-array analysis successfully addressed distinct immune processes between LPS- and poly I:C- stimulated PBLs. Thus, we expect that this oligo-array will provide an excellent opportunity to analyze global gene expression profiles for a better understanding of diseases and stress, as well as for reproduction, development and influence of nutrition on tuna aquaculture production.

Contact Email

NRIFS - Tunas Genome Research Group
FRA-bioinfo@ml.affrc.go.jp