title: Deep sequencing, profiling and detailed annotation of microRNAs in Takifugu rubripes.
abstract: BACKGROUND
  microRNAs (miRNAs) in fish have not been as extensively studied as those in mammals. The fish species Takifugu rubripes is an intensively studied model organism whose genome has been sequenced. The T. rubripes genome is approximately eight times smaller than the human genome, but has a similar repertoire of protein-coding genes. Therefore, it is useful for identifying non-coding genes, including miRNA genes. To identify miRNA expression patterns in different organs of T. rubripes and give fundamental information to aid understanding of miRNA populations in this species, we extracted small RNAs from tissues and performed deep sequencing analysis to profile T. rubripes miRNAs. These data will be of assistance in functional studies of miRNAs in T. rubripes.
  
  
  RESULTS
  After analyzing a total of 139 million reads, we found miRNA species in nine tissues (fast and slow muscles, heart, eye, brain, intestine, liver, ovaries, and testes). We identified 1420 known miRNAs, many of which were strongly expressed in certain tissues with expression patterns similar to those described for other animals in previous reports. Most miRNAs were expressed in tissues other than the ovaries or testes. However, some miRNA families were highly abundant in the gonads, but expressed only at low levels in somatic tissue, suggesting specific function in germ cells. The most abundant isomiRs (miRNA variants) of many miRNAs had identical sequences in the 5' region. However, isomiRs of some miRNAs, including fru-miR-462-5p, varied in the 5' region in some tissues, suggesting that they may target different mRNA transcripts. Longer small RNAs (26-31 nt), which were abundant in the gonads, may be putative piRNAs because of their length and their origin from repetitive elements. Additionally, our data include possible novel classes of small RNAs.
  
  
  CONCLUSIONS
  We elucidated miRNA expression patterns in various organs of T. rubripes. Most miRNA sequences are conserved in vertebrates, indicating that the basic functions of vertebrate miRNAs share a common evolution. Some miRNA species exhibit different distributions of isomiRs between tissues, suggesting that they have a broad range of functions.
authors.affiliation: Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, 113-8657, Tokyo, Japan. tarnjew@gmail.com.
authors.forename: Chaninya
authors.initials: C
authors.lastname: Wongwarangkana
authors.affiliation: Bio-production Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, 305-8566, Japan. k-fujimori@aist.go.jp.
authors.forename: Kazuhiro E
authors.initials: KE
authors.lastname: Fujimori
authors.affiliation: Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, 113-8657, Tokyo, Japan. msk.scanner@gmail.com.
authors.forename: Masaki
authors.initials: M
authors.lastname: Akiba
authors.affiliation: Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, 113-8657, Tokyo, Japan. akino@mail.ecc.u-tokyo.ac.jp.
authors.forename: Shigeharu
authors.initials: S
authors.lastname: Kinoshita
authors.affiliation: Okinawa Cutting-edge Genome Project, Okinawa, Japan. trymrm@gmail.com.|Okinawa Industrial Technology Center, Okinawa, 904-2234, Japan. trymrm@gmail.com.
authors.forename: Morimi
authors.initials: M
authors.lastname: Teruya
authors.affiliation: Okinawa Cutting-edge Genome Project, Okinawa, Japan. nezuo@biojet.jp.|Biojet Co., Ltd, 315 Shioya, Uruma, 904-2231, Okinawa, Japan. nezuo@biojet.jp.
authors.forename: Maiko
authors.initials: M
authors.lastname: Nezuo
authors.affiliation: Okinawa Cutting-edge Genome Project, Okinawa, Japan. tsuka@biojet.jp.|Biojet Co., Ltd, 315 Shioya, Uruma, 904-2231, Okinawa, Japan. tsuka@biojet.jp.
authors.forename: Tsukahara
authors.initials: T
authors.lastname: Masatoshi
authors.affiliation: School of Marine Bioscience, Kitasato University, Minami, Sagamihara, 252-0373, Kanagawa, Japan. swatabe@kitasato-u.ac.jp.
authors.forename: Shugo
authors.initials: S
authors.lastname: Watabe
authors.affiliation: Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, 113-8657, Tokyo, Japan. asakawa@mail.ecc.u-tokyo.ac.jp.
authors.forename: Shuichi
authors.initials: S
authors.lastname: Asakawa
mesh_terms: D000818:Animals; D020869:Gene Expression Profiling / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D058977:Molecular Sequence Annotation / Q000379:methods; D034741:RNA, Small Interfering / Q000235:genetics; D023741:Takifugu / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D034741:RNA, Small Interfering