TY - JOUR
T1 - Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna
AU - Nakamura, Yoji
AU - Mori, Kazuki
AU - Saitoh, Kenji
AU - Oshima, Kenshiro
AU - Mekuchi, Miyuki
AU - Sugaya, Takuma
AU - Shigenobu, Yuya
AU - Ojima, Nobuhiko
AU - Muta, Shigeru
AU - Fujiwara, Atushi
AU - Yasuike, Motoshige
AU - Oohara, Ichiro
AU - Hirakawa, Hideki
AU - Chowdhury, Vishwajit Sur
AU - Kobayashi, Takanori
AU - Nakajima, Kazuhiro
AU - Sano, Motohiko
AU - Wada, Tokio
AU - Tashiro, Kosuke
AU - Ikeo, Kazuho
AU - Hattori, Masahira
AU - Kuhara, Satoru
AU - Gojobori, Takashi
AU - Inouye, Kiyoshi
PY - 2013/7/2
Y1 - 2013/7/2
N2 - 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.
AB - 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.
KW - Animal opsin
KW - Tuna genome
KW - Visual system
UR - http://www.scopus.com/inward/record.url?scp=84879723871&partnerID=8YFLogxK
U2 - 10.1073/pnas.1302051110
DO - 10.1073/pnas.1302051110
M3 - Article
C2 - 23781100
AN - SCOPUS:84879723871
SN - 0027-8424
VL - 110
SP - 11061
EP - 11066
JO - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
JF - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
IS - 27
ER -