title: Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna.
abstract: Tunas are migratory fishes in offshore habitats and top predators with unique features. Despite their ecological importance and high market values, the open-ocean lifestyle of tuna, in which effective sensing systems such as color vision are required for capture of prey, has been poorly understood. To elucidate the genetic and evolutionary basis of optic adaptation of tuna, we determined the genome sequence of the Pacific bluefin tuna (Thunnus orientalis), using next-generation sequencing technology. A total of 26,433 protein-coding genes were predicted from 16,802 assembled scaffolds. From these, we identified five common fish visual pigment genes: red-sensitive (middle/long-wavelength sensitive; M/LWS), UV-sensitive (short-wavelength sensitive 1; SWS1), blue-sensitive (SWS2), rhodopsin (RH1), and green-sensitive (RH2) opsin genes. Sequence comparison revealed that tuna's RH1 gene has an amino acid substitution that causes a short-wave shift in the absorption spectrum (i.e., blue shift). Pacific bluefin tuna has at least five RH2 paralogs, the most among studied fishes; four of the proteins encoded may be tuned to blue light at the amino acid level. Moreover, phylogenetic analysis suggested that gene conversions have occurred in each of the SWS2 and RH2 loci in a short period. Thus, Pacific bluefin tuna has undergone evolutionary changes in three genes (RH1, RH2, and SWS2), which may have contributed to detecting blue-green contrast and measuring the distance to prey in the blue-pelagic ocean. These findings provide basic information on behavioral traits of predatory fish and, thereby, could help to improve the technology to culture such fish in captivity for resource management.
authors.affiliation: Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, Kanazawa, Yokohama 236-8648, Japan. yojnakam@affrc.go.jp
authors.forename: Yoji
authors.initials: Y
authors.lastname: Nakamura
authors.forename: Kazuki
authors.initials: K
authors.lastname: Mori
authors.forename: Kenji
authors.initials: K
authors.lastname: Saitoh
authors.forename: Kenshiro
authors.initials: K
authors.lastname: Oshima
authors.forename: Miyuki
authors.initials: M
authors.lastname: Mekuchi
authors.forename: Takuma
authors.initials: T
authors.lastname: Sugaya
authors.forename: Yuya
authors.initials: Y
authors.lastname: Shigenobu
authors.forename: Nobuhiko
authors.initials: N
authors.lastname: Ojima
authors.forename: Shigeru
authors.initials: S
authors.lastname: Muta
authors.forename: Atushi
authors.initials: A
authors.lastname: Fujiwara
authors.forename: Motoshige
authors.initials: M
authors.lastname: Yasuike
authors.forename: Ichiro
authors.initials: I
authors.lastname: Oohara
authors.forename: Hideki
authors.initials: H
authors.lastname: Hirakawa
authors.forename: Vishwajit Sur
authors.initials: VS
authors.lastname: Chowdhury
authors.forename: Takanori
authors.initials: T
authors.lastname: Kobayashi
authors.forename: Kazuhiro
authors.initials: K
authors.lastname: Nakajima
authors.forename: Motohiko
authors.initials: M
authors.lastname: Sano
authors.forename: Tokio
authors.initials: T
authors.lastname: Wada
authors.forename: Kosuke
authors.initials: K
authors.lastname: Tashiro
authors.forename: Kazuho
authors.initials: K
authors.lastname: Ikeo
authors.forename: Masahira
authors.initials: M
authors.lastname: Hattori
authors.forename: Satoru
authors.initials: S
authors.lastname: Kuhara
authors.forename: Takashi
authors.initials: T
authors.lastname: Gojobori
authors.forename: Kiyoshi
authors.initials: K
authors.lastname: Inouye
mesh_terms: D000818:Animals; D001483:Base Sequence; D055253:Color Vision / Q000235:genetics / Q000502:physiology; D019143:Evolution, Molecular; D029941:Fish Proteins / Q000235:genetics*; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D008297:Male; D008969:Molecular Sequence Data; D055355:Opsins / Q000235:genetics; D010802:Phylogeny; D011235:Predatory Behavior / Q000502:physiology; D012168:Retinal Pigments / Q000235:genetics*; D014413:Tuna / Q000235:genetics* / Q000502:physiology
chemical_list: D029941:Fish Proteins; D055355:Opsins; D012168:Retinal Pigments
keywords: animal opsin; tuna genome; visual system