Dataset Information

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.

SUBMITTER: Nakamura Y

PROVIDER: S-EPMC3703999 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature

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Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna.

Nakamura Yoji Y Mori Kazuki K Saitoh Kenji K Oshima Kenshiro K Mekuchi Miyuki M Sugaya Takuma T Shigenobu Yuya Y Ojima Nobuhiko N Muta Shigeru S Fujiwara Atushi A Yasuike Motoshige M Oohara Ichiro I Hirakawa Hideki H Chowdhury Vishwajit Sur VS Kobayashi Takanori T Nakajima Kazuhiro K Sano Motohiko M Wada Tokio T Tashiro Kosuke K Ikeo Kazuho K Hattori Masahira M Kuhara Satoru S Gojobori Takashi T Inouye Kiyoshi K

Proceedings of the National Academy of Sciences of the United States of America 20130618 27

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 techno ...[more]

PMID: 23781100

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Project description:Accurate understanding of changing population dynamics associated with climate change is critical for managing highly migratory fish species. However, long-term data on population dynamics and the resulting recruitment variability is still lacking for many species, making it difficult to predict and integrate the effects of ocean warming into management schemes. In this study, high-resolution stable oxygen isotope (δ18O) analysis was performed on the otoliths of adult Pacific bluefin tuna Thunnus orientalis using secondary ion mass spectrometry (SIMS) to determine the natal origin of an individual fish. The core δ18Ootolith corresponding to the larval stage greatly varied among the individuals, indicating that the larvae experienced a wide range of thermal environments. The non-hierarchical cluster analysis performed on the core δ18Ootolith grouped fish into those with higher δ18Ootolith (lower temperature) and those with lower δ18Ootolith (higher temperature), most likely representing relative temperature difference experienced between fish born in the Sea of Japan and in the Nansei Islands area. The Nansei Islands area cluster showed more variability in the early otolith growth indicating a longer spawning season, which is consistent with the observed longer spawning duration in this area. The absolute temperature estimates based on the SIMS-measured core δ18Ootolith were significantly higher than those expected from sea surface temperature data, suggesting the effects of matrix-related bias on the temperature offsets. The relative temperature difference, however, matched well with the known spawning temperature range of the two spawning grounds. The recruitment contribution from each spawning ground (all year-classes pooled, n = 51) was 45% in the Sea of Japan and 55% in the Nansei Islands area. Overall, this study demonstrated the effectiveness of SIMS δ18Ootolith analysis for investigating the natal origin of fish and its potential application in fish population dynamics studies.

Project description:BackgroundThe Pacific bluefin tuna (Thunnus orientalis) is a regionally endothermic fish that maintains temperatures in their swimming musculature, eyes, brain and viscera above that of the ambient water. Within their skeletal muscle, a thermal gradient exists, with deep muscles, close to the backbone, operating at elevated temperatures compared to superficial muscles near the skin. Their heart, by contrast, operates at ambient temperature, which in bluefin tunas can range widely. Cardiac function in tunas reduces in cold waters, yet the heart must continue to supply blood for metabolically demanding endothermic tissues. Physiological studies indicate Pacific bluefin tuna have an elevated cardiac capacity and increased cold-tolerance compared to warm-water tuna species, primarily enabled by increased capacity for sarcoplasmic reticulum calcium cycling within the cardiac muscles.ResultsHere, we compare tissue-specific gene-expression profiles of different cardiac and skeletal muscle tissues in Pacific bluefin tuna. There was little difference in the overall expression of calcium-cycling and cardiac contraction pathways between atrium and ventricle. However, expression of a key sarcoplasmic reticulum calcium-cycling gene, SERCA2b, which plays a key role maintaining intracellular calcium stores, was higher in atrium than ventricle. Expression of genes involved in aerobic metabolism and cardiac contraction were higher in the ventricle than atrium. The two morphologically distinct tissues that derive the ventricle, spongy and compact myocardium, had near-identical levels of gene expression. More genes had higher expression in the cool, superficial muscle than in the warm, deep muscle in both the aerobic red muscle (slow-twitch) and anaerobic white muscle (fast-twitch), suggesting thermal compensation.ConclusionsWe find evidence of widespread transcriptomic differences between the Pacific tuna ventricle and atrium, with potentially higher rates of calcium cycling in the atrium associated with the higher expression of SERCA2b compared to the ventricle. We find no evidence that genes associated with thermogenesis are upregulated in the deep, warm muscle compared to superficial, cool muscle. Heat generation may be enabled by by the high aerobic capacity of bluefin tuna red muscle.

Dataset Information

Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna.

Publications

Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna.

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