A functional genomics tool for the Pacific bluefin tuna: Development of a 44K oligonucleotide microarray from whole-genome sequencing data for global transcriptome analysis

• Published in: Gene Vol. 576; no. 2; pp. 603 - 609
• Main Authors: Yasuike, Motoshige, Fujiwara, Atushi, Nakamura, Yoji, Iwasaki, Yuki, Nishiki, Issei, Sugaya, Takuma, Shimizu, Akio, Sano, Motohiko, Kobayashi, Takanori, Ototake, Mitsuru
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.02.2016
• Subjects: Animals; Aquaculture; Bluefin tuna; Gene prediction; Immune system; Marine; Oligonucleotide Array Sequence Analysis; Oligonucleotide microarray; Thunnus orientalis; Transcriptome; Tuna - genetics; I, Pacific; WGS; Transcriptome; UniProtKB; APPs; TNF; IRG1; CYP1A; ISGs; VNN; NCBI; HSD; KEGG; cDNA; BLAST; RPS-BLAST; PBT; IL; poly I:C; KAAS; G-CSF; PBLs; IRF; Aquaculture; RefSeq; UniProt; nr; nt; LPS; Bluefin tuna; IFN; Gene prediction; ABT; EC numbers; ANOVA; TLR; Cy3; Immune system; SBT; GDF15; GO; VLIG-1; SOCS-1; ESTs; RNA-Seq; Thunnus orientalis; RSIVD; PRIAM; PGRP-L1; Oligonucleotide microarray
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2015.10.023

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. •We developed the first 44K Pacific bluefin tuna (PBT) Thunnus orientalis oligonucleotide microarray (oligo-array).•The PBT oligo-array successfully revealed distinct immune processes between LPS - and poly I:C- stimulated PBLs.•We expect that this oligo-array is a valuable new tool for large-scale transcriptome studies in the PBT research community.