1
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Chau KD, Hauser FE, Van Nynatten A, Daane JM, Harris MP, Chang BSW, Lovejoy NR. Multiple Ecological Axes Drive Molecular Evolution of Cone Opsins in Beloniform Fishes. J Mol Evol 2024; 92:93-103. [PMID: 38416218 DOI: 10.1007/s00239-024-10156-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 01/12/2024] [Indexed: 02/29/2024]
Abstract
Ecological and evolutionary transitions offer an excellent opportunity to examine the molecular basis of adaptation. Fishes of the order Beloniformes include needlefishes, flyingfishes, halfbeaks, and allies, and comprise over 200 species occupying a wide array of habitats-from the marine epipelagic zone to tropical rainforest rivers. These fishes also exhibit a diversity of diets, including piscivory, herbivory, and zooplanktivory. We investigated how diet and habitat affected the molecular evolution of cone opsins, which play a key role in bright light and colour vision and are tightly linked to ecology and life history. We analyzed a targeted-capture dataset to reconstruct the evolutionary history of beloniforms and assemble cone opsin sequences. We implemented codon-based clade models of evolution to examine how molecular evolution was affected by habitat and diet. We found high levels of positive selection in medium- and long-wavelength beloniform opsins, with piscivores showing increased positive selection in medium-wavelength opsins and zooplanktivores showing increased positive selection in long-wavelength opsins. In contrast, short-wavelength opsins showed purifying selection. While marine/freshwater habitat transitions have an effect on opsin molecular evolution, we found that diet plays a more important role. Our study suggests that evolutionary transitions along ecological axes produce complex adaptive interactions that affect patterns of selection on genes that underlie vision.
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Affiliation(s)
- Katherine D Chau
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, Toronto, ON, Canada
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada
- Department of Biology, York University, Toronto, ON, Canada
| | - Frances E Hauser
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada
| | - Alexander Van Nynatten
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada
- Department of Biology, University of Victoria, Victoria, Canada
| | - Jacob M Daane
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | | | - Belinda S W Chang
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Nathan R Lovejoy
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, Toronto, ON, Canada.
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada.
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.
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2
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Wu B, Gao X, Hu M, Hu J, Lan T, Xue T, Xu W, Zhu C, Yuan Y, Zheng J, Qin T, Xin P, Li Y, Gong L, Feng C, He S, Liu H, Li H, Wang Q, Ma Z, Qiu Q, Wang K. Distinct and shared endothermic strategies in the heat producing tissues of tuna and other teleosts. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2629-2645. [PMID: 37273070 DOI: 10.1007/s11427-022-2312-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/28/2023] [Indexed: 06/06/2023]
Abstract
Although most fishes are ectothermic, some, including tuna and billfish, achieve endothermy through specialized heat producing tissues that are modified muscles. How these heat producing tissues evolved, and whether they share convergent molecular mechanisms, remain unresolved. Here, we generated a high-quality genome from the mackerel tuna (Euthynnus affinis) and investigated the heat producing tissues of this fish by single-nucleus and bulk RNA sequencing. Compared with other teleosts, tuna-specific genetic variation is strongly associated with muscle differentiation. Single-nucleus RNA-seq revealed a high proportion of specific slow skeletal muscle cell subtypes in the heat producing tissues of tuna. Marker genes of this cell subtype are associated with the relative sliding of actin and myosin, suggesting that tuna endothermy is mainly based on shivering thermogenesis. In contrast, cross-species transcriptome analysis indicated that endothermy in billfish relies mainly on non-shivering thermogenesis. Nevertheless, the heat producing tissues of the different species do share some tissue-specific genes, including vascular-related and mitochondrial genes. Overall, although tunas and billfishes differ in their thermogenic strategies, they share similar expression patterns in some respects, highlighting the complexity of convergent evolution.
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Affiliation(s)
- Baosheng Wu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Xueli Gao
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Mingling Hu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Jing Hu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Tianming Lan
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150006, China
| | - Tingfeng Xue
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Wenjie Xu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Chenglong Zhu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Yuan Yuan
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Jiangmin Zheng
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Tao Qin
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Peidong Xin
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Ye Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Chenguang Feng
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Shunping He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150006, China
| | - Haimeng Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhenhua Ma
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China.
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China.
| | - Kun Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China.
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3
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Hayashida T, Soma S, Nakamura Y, Higuchi K, Kazeto Y, Gen K. Transcriptome characterization of gonadal sex differentiation in Pacific bluefin tuna, Thunnus orientalis (Temminck et Schlegel). Sci Rep 2023; 13:13867. [PMID: 37620512 PMCID: PMC10449831 DOI: 10.1038/s41598-023-40914-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/18/2023] [Indexed: 08/26/2023] Open
Abstract
Tunas (genus Thunnus) are one of the most ecologically and commercially important fish worldwide. To establish a biological basis for reproduction in this globally essential species, we have recently studied crucial reproductive aspects of the Pacific bluefin tuna (T. orientalis; PBT), as a model of tuna species, based on our closed-cycle aquaculture technology. In this study, we clarified the global expression profile of the genes regulating gonadal sex differentiation in PBT, as this developmental process is vital to sexual reproduction. Based on the results of our comparative (RNA-sequencing) and temporal (qRT-PCR) transcriptome analyses using the updated genome dataset, we propose the molecular mechanisms of gonadal sex differentiation in PBT. In female gonads, foxl2 and cyp19a1a (coding aromatase) are expressed at the onset of sex differentiation. Active aromatase-mediated estrogen biosynthesis, which includes positive regulation of cyp19a1a expression by Foxl2, induces ovarian differentiation. By contrast, dmrt1 and gsdf are upregulated in differentiating male gonads lacking active estrogen synthesis. Dmrt1 and Gsdf would mainly promote testicular differentiation. Furthermore, androgen biosynthesis is upregulated in differentiating male gonad. Endogenous androgens may also be vital to testicular differentiation. This study provides the first comprehensive data clarifying the molecular basis for gonadal sex differentiation in tunas.
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Affiliation(s)
- Takao Hayashida
- Nagasaki Field Station, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 1551-8 Taira-machi, Nagasaki, Nagasaki, 851-2213, Japan.
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan.
| | - Satoshi Soma
- Yokohama Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fuku-ura, Yokohama, Kanagawa, 236-8648, Japan
| | - Yoji Nakamura
- Yokohama Field Station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fuku-ura, Yokohama, Kanagawa, 236-8648, Japan
| | - Kentaro Higuchi
- Nagasaki Field Station, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 1551-8 Taira-machi, Nagasaki, Nagasaki, 851-2213, Japan
- Minamiizu Field Station, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 183-2 Minamiizu, Kamo, Shizuoka, 415-0156, Japan
| | - Yukinori Kazeto
- Minamiizu Field Station, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 183-2 Minamiizu, Kamo, Shizuoka, 415-0156, Japan
| | - Koichiro Gen
- Nagasaki Field Station, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 1551-8 Taira-machi, Nagasaki, Nagasaki, 851-2213, Japan
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4
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Kon T, Fukuta K, Chen Z, Kon-Nanjo K, Suzuki K, Ishikawa M, Tanaka H, Burgess SM, Noguchi H, Toyoda A, Omori Y. Single-cell transcriptomics of the goldfish retina reveals genetic divergence in the asymmetrically evolved subgenomes after allotetraploidization. Commun Biol 2022; 5:1404. [PMID: 36572749 PMCID: PMC9792465 DOI: 10.1038/s42003-022-04351-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 12/08/2022] [Indexed: 12/28/2022] Open
Abstract
The recent whole-genome duplication (WGD) in goldfish (Carassius auratus) approximately 14 million years ago makes it a valuable model for studying gene evolution during the early stages after WGD. We analyzed the transcriptome of the goldfish retina at the level of single-cell (scRNA-seq) and open chromatin regions (scATAC-seq). We identified a group of genes that have undergone dosage selection, accounting for 5% of the total 11,444 ohnolog pairs. We also identified 306 putative sub/neo-functionalized ohnolog pairs that are likely to be under cell-type-specific genetic variation at single-cell resolution. Diversification in the expression patterns of several ohnolog pairs was observed in the retinal cell subpopulations. The single-cell level transcriptome analysis in this study uncovered the early stages of evolution in retinal cell of goldfish after WGD. Our results provide clues for understanding the relationship between the early stages of gene evolution after WGD and the evolution of diverse vertebrate retinal functions.
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Affiliation(s)
- Tetsuo Kon
- grid.419056.f0000 0004 1793 2541Laboratory of Functional Genomics, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Japan ,grid.10420.370000 0001 2286 1424Present Address: Department of Neurosciences and Developmental Biology, University of Vienna, Vienna, Austria
| | - Kentaro Fukuta
- grid.418987.b0000 0004 1764 2181Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Japan
| | - Zelin Chen
- grid.280128.10000 0001 2233 9230Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD USA ,grid.9227.e0000000119573309Present Address: CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Koto Kon-Nanjo
- grid.10420.370000 0001 2286 1424Department of Neurosciences and Developmental Biology, University of Vienna, Vienna, Austria
| | - Kota Suzuki
- Yatomi Station, Aichi Fisheries Research Institute, Yatomi, Japan
| | | | | | - Shawn M. Burgess
- grid.280128.10000 0001 2233 9230Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD USA
| | - Hideki Noguchi
- grid.418987.b0000 0004 1764 2181Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Japan ,grid.288127.60000 0004 0466 9350Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
| | - Atsushi Toyoda
- grid.288127.60000 0004 0466 9350Advanced Genomics Center, National Institute of Genetics, Mishima, Japan ,grid.288127.60000 0004 0466 9350Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Yoshihiro Omori
- grid.419056.f0000 0004 1793 2541Laboratory of Functional Genomics, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Japan
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5
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Zhao X, Huang Y, Bian C, You X, Zhang X, Chen J, Wang M, Hu C, Xu Y, Xu J, Shi Q. Whole genome sequencing of the fast-swimming Southern bluefin tuna (Thunnus maccoyii). Front Genet 2022; 13:1020017. [DOI: 10.3389/fgene.2022.1020017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
The economically important Southern bluefin tuna (Thunnus maccoyii) is a world-famous fast-swimming fish, but its genomic information is limited. Here, we performed whole genome sequencing and assembled a draft genome for Southern bluefin tuna, aiming to generate useful genetic data for comparative functional prediction. The final genome assembly is 806.54 Mb, with scaffold and contig N50 values of 3.31 Mb and 67.38 kb, respectively. Genome completeness was evaluated to be 95.8%. The assembled genome contained 23,403 protein-coding genes and 236.1 Mb of repeat sequences (accounting for 29.27% of the entire assembly). Comparative genomics analyses of this fast-swimming tuna revealed that it had more than twice as many hemoglobin genes (18) as other relatively slow-moving fishes (such as seahorse, sunfish, and tongue sole). These hemoglobin genes are mainly localized in two big clusters (termed as “MNˮ and “LAˮ respectively), which is consistent with other reported fishes. However, Thr39 of beta-hemoglobin in the MN cluster, conserved in other fishes, was mutated as cysteine in tunas including the Southern bluefin tuna. Since hemoglobins are reported to transport oxygen efficiently for aerobic respiration, our genomic data suggest that both high copy numbers of hemoglobin genes and an adjusted function of the beta-hemoglobin may support the fast-swimming activity of tunas. In summary, we produced a primary genome assembly and predicted hemoglobin-related roles for the fast-swimming Southern bluefin tuna.
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6
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Photoreceptor distributions, visual pigments and the opsin repertoire of Atlantic halibut (Hippoglossus hippoglossus). Sci Rep 2022; 12:8062. [PMID: 35577858 PMCID: PMC9110347 DOI: 10.1038/s41598-022-11998-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 05/03/2022] [Indexed: 11/15/2022] Open
Abstract
Fishes often have cone photoreceptors organized in lattice-like mosaic formations. In flatfishes, these lattices undergo dramatic changes during metamorphosis whereby a honeycomb mosaic of single cones in the larva is replaced by a square mosaic of single and double cones in the adult. The spatio-temporal dynamics of this transition are not well understood. Here, we describe the photoreceptors and mosaic formations that occur during the larva to juvenile transition of Atlantic halibut from the beginning of eye migration to its completion. To gauge the possibility of colour vision, visual pigments in juveniles were measured by microspectrophotometry and the opsin repertoire explored using bioinformatics. At the start of eye migration, the larva had a heterogeneous retina with honeycomb mosaic in the dorsonasal and ventrotemporal quadrants and a square mosaic in the ventronasal and dorsotemporal quadrants. By the end of metamorphosis, the square mosaic was present throughout the retina except in a centrodorsotemporal area where single, double and triple cones occurred randomly. Six cone visual pigments were found with maximum absorbance (λmax, in nm) in the short [S(431) and S(457)], middle [M(500), M(514) and M(527)], and long [L(550)] wavelengths, and a rod visual pigment with λmax at 491 nm. These pigments only partially matched the opsin repertoire detected by query of the Atlantic halibut genome. We conclude that the Atlantic halibut undergoes a complex re-organization of photoreceptors at metamorphosis resulting in a multi-mosaic retina adapted for a demersal life style.
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7
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Liang Q, Afriyie G, Chen Z, Xu Z, Dong Z, Guo Y, Wang Z. Analysis of opsin gene family of Crimson snapper (Lutjanus erythropterus). Gene 2022; 807:145960. [PMID: 34509581 DOI: 10.1016/j.gene.2021.145960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 08/27/2021] [Accepted: 09/07/2021] [Indexed: 11/30/2022]
Abstract
Opsin is a fellow of the G protein-coupled receptors (GPCRs) superfamily. It can be divided into visual and non-visual opsin according to whether it is directly involved in visual imaging. Opsin plays an important role in visual image formation and the regulation of non-image forming functions such as circadian entrainment in the growth, development and evolution of fish. Crimson snapper belongs to Perciforme mainly found in the Indo-West Pacific and the South China Sea. It is one of the most influential economic fishes in the South China Sea. In order to study the existence and expression of opsin gene in Crimson snapper, we sequenced the genome and tissue sample transcriptome of Crimson snapper. In this study, 32 opsin genes were identified from the genome of Crimson snapper. The length of these genes ranged from 1061 bp to 86203 bp and were distributed on 15 different chromosomes. The analysis of opsin gene family of Crimson snapper showed that the sws2 had two extra copies as compared with that of Zebrafish. Domain and motif analysis revealed that all the 32 opsin genes have seven-(pass)-transmembrane domain receptors (7TM receptors) each, and the opsin family contained 10 common motifs. The expression level of opsin gene, confirmed by RT-qPCR, was analyzed by using nine tissues transcriptome databases of Crimson snapper. The results showed that almost all opsin genes were highly expressed in the retina and brain, except opn7a and opn7b which were expressed in intestine and red skin, and almost no expression in other tissues. Our results provide a comprehensive basic knowledge for the opsin gene family of Crimson snapper, which has significance for the study of the function of opsin in Lutjanidaes.
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Affiliation(s)
- Qiulu Liang
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
| | - Gyamfua Afriyie
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
| | - Zizhao Chen
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
| | - Zhenmin Xu
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
| | - Zhongdian Dong
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China
| | - Yusong Guo
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China.
| | - Zhongduo Wang
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China.
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8
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Nakamura Y, Higuchi K, Kumon K, Yasuike M, Takashi T, Gen K, Fujiwara A. Prediction of the Sex-Associated Genomic Region in Tunas ( Thunnus Fishes). Int J Genomics 2021; 2021:7226353. [PMID: 34957293 PMCID: PMC8693018 DOI: 10.1155/2021/7226353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/28/2021] [Accepted: 11/13/2021] [Indexed: 11/17/2022] Open
Abstract
Fish species have a variety of sex determination systems. Tunas (genus Thunnus) have an XY genetic sex determination system. However, the Y chromosome or responsible locus has not yet been identified in males. In a previous study, a female genome of Pacific bluefin tuna (T. orientalis) was sequenced, and candidates for sex-associated DNA polymorphisms were identified by a genome-wide association study using resequencing data. In the present study, we sequenced a male genome of Pacific bluefin tuna by long-read and linked-read sequencing technologies and explored male-specific loci through a comparison with the female genome. As a result, we found a unique region carrying the male-specific haplotype, where a homolog of estrogen sulfotransferase gene was predicted to be encoded. The genome-wide mapping of previously resequenced data indicated that, among the functionally annotated genes, only this gene, named sult1st6y, was paternally inherited in the males of Pacific bluefin tuna. We reviewed the RNA-seq data of southern bluefin tuna (T. maccoyii) in the public database and found that sult1st6y of southern bluefin tuna was expressed in all male testes, but absent or suppressed in the female ovary. Since estrogen sulfotransferase is responsible for the inactivation of estrogens, it is reasonable to assume that the expression of sult1st6y in gonad cells may inhibit female development, thereby inducing the individuals to become males. Thus, our results raise a promising hypothesis that sult1st6y is the sex determination gene in Thunnus fishes or at least functions at a crucial point in the sex-differentiation cascade.
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Affiliation(s)
- Yoji Nakamura
- Bioinformatics and Biosciences Division, Fisheries Stock Assessment Center, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fuku-ura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan
| | - Kentaro Higuchi
- Tuna Aquaculture Division, Aquaculture Research Department, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 1551-8 Taira-machi, Nagasaki 851-2213, Japan
| | - Kazunori Kumon
- Amami Field Station, Tuna Aquaculture Division, Aquaculture Research Department, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 955-5 Hyousakiyamahara, Setouchi, Kagoshima 894-2414, Japan
| | - Motoshige Yasuike
- Bioinformatics and Biosciences Division, Fisheries Stock Assessment Center, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fuku-ura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan
| | - Toshinori Takashi
- Tuna Aquaculture Division, Aquaculture Research Department, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 1551-8 Taira-machi, Nagasaki 851-2213, Japan
| | - Koichiro Gen
- Tuna Aquaculture Division, Aquaculture Research Department, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 1551-8 Taira-machi, Nagasaki 851-2213, Japan
| | - Atushi Fujiwara
- Aquatic Breeding Division, Aquaculture Research Department, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 422-1 Nakatsuhamaura, Minami-ise, Mie 516-0193, Japan
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9
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Wu B, Feng C, Zhu C, Xu W, Yuan Y, Hu M, Yuan K, Li Y, Ren Y, Zhou Y, Jiang H, Qiu Q, Wang W, He S, Wang K. The Genomes of Two Billfishes Provide Insights into the Evolution of Endothermy in Teleosts. Mol Biol Evol 2021; 38:2413-2427. [PMID: 33533895 PMCID: PMC8136490 DOI: 10.1093/molbev/msab035] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Endothermy is a typical convergent phenomenon which has evolved independently at least eight times in vertebrates, and is of significant advantage to organisms in extending their niches. However, how vertebrates other than mammals or birds, especially teleosts, achieve endothermy has not previously been fully understood. In this study, we sequenced the genomes of two billfishes (swordfish and sailfish), members of a representative lineage of endothermic teleosts. Convergent amino acid replacements were observed in proteins related to heat production and the visual system in two endothermic teleost lineages, billfishes and tunas. The billfish-specific genetic innovations were found to be associated with heat exchange, thermoregulation, and the specialized morphology, including elongated bill, enlarged dorsal fin in sailfish and loss of the pelvic fin in swordfish.
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Affiliation(s)
- Baosheng Wu
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chenguang Feng
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China.,The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chenglong Zhu
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Wenjie Xu
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Yuan Yuan
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Mingliang Hu
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Ke Yuan
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Yongxin Li
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Yandong Ren
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Yang Zhou
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Haifeng Jiang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qiang Qiu
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Wen Wang
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Shunping He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Kun Wang
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
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10
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Mitchell LJ, Cheney KL, Luehrmann M, Marshall NJ, Michie K, Cortesi F. Molecular evolution of ultraviolet visual opsins and spectral tuning of photoreceptors in anemonefishes (Amphiprioninae). Genome Biol Evol 2021; 13:6347585. [PMID: 34375382 PMCID: PMC8511661 DOI: 10.1093/gbe/evab184] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2021] [Indexed: 11/29/2022] Open
Abstract
Many animals including birds, reptiles, insects, and teleost fishes can see ultraviolet (UV) light (shorter than 400 nm), which has functional importance for foraging and communication. For coral reef fishes, shallow reef environments transmit a broad spectrum of light, rich in UV, driving the evolution of diverse spectral sensitivities. However, the identities and sites of the specific visual genes that underly vision in reef fishes remain elusive and are useful in determining how evolution has tuned vision to suit life on the reef. We investigated the visual systems of 11 anemonefish (Amphiprioninae) species, specifically probing for the molecular pathways that facilitate UV-sensitivity. Searching the genomes of anemonefishes, we identified a total of eight functional opsin genes from all five vertebrate visual opsin subfamilies. We found rare instances of teleost UV-sensitive SWS1 opsin gene duplications that produced two functionally coding paralogs (SWS1α and SWS1β) and a pseudogene. We also found separate green sensitive RH2A opsin gene duplicates not yet reported in the family Pomacentridae. Transcriptome analysis revealed false clown anemonefish (Amphiprion ocellaris) expressed one rod opsin (RH1) and six cone opsins (SWS1β, SWS2B, RH2B, RH2A-1, RH2A-2, LWS) in the retina. Fluorescent in situ hybridization highlighted the (co-)expression of SWS1β with SWS2B in single cones, and either RH2B, RH2A, or RH2A together with LWS in different members of double cone photoreceptors (two single cones fused together). Our study provides the first in-depth characterization of visual opsin genes found in anemonefishes and provides a useful basis for the further study of UV-vision in reef fishes.
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Affiliation(s)
- Laurie J Mitchell
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Karen L Cheney
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Martin Luehrmann
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - N Justin Marshall
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kyle Michie
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia.,King's College, Cambridge, CB2 1ST, UK
| | - Fabio Cortesi
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
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11
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Qu M, Liu Y, Zhang Y, Wan S, Ravi V, Qin G, Jiang H, Wang X, Zhang H, Zhang B, Gao Z, Huysseune A, Zhang Z, Zhang H, Chen Z, Yu H, Wu Y, Tang L, Li C, Zhong J, Ma L, Wang F, Zheng H, Yin J, Witten PE, Meyer A, Venkatesh B, Lin Q. Seadragon genome analysis provides insights into its phenotype and sex determination locus. SCIENCE ADVANCES 2021; 7:eabg5196. [PMID: 34407945 PMCID: PMC8373133 DOI: 10.1126/sciadv.abg5196] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 07/01/2021] [Indexed: 05/29/2023]
Abstract
The iconic phenotype of seadragons includes leaf-like appendages, a toothless tubular mouth, and male pregnancy involving incubation of fertilized eggs on an open "brood patch." We de novo-sequenced male and female genomes of the common seadragon (Phyllopteryx taeniolatus) and its closely related species, the alligator pipefish (Syngnathoides biaculeatus). Transcription profiles from an evolutionary novelty, the leaf-like appendages, show that a set of genes typically involved in fin development have been co-opted as well as an enrichment of transcripts for potential tissue repair and immune defense genes. The zebrafish mutants for scpp5, which is lost in all syngnathids, were found to lack or have deformed pharyngeal teeth, supporting the hypothesis that the loss of scpp5 has contributed to the loss of teeth in syngnathids. A putative sex-determining locus encoding a male-specific amhr2y gene shared by common seadragon and alligator pipefish was identified.
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Affiliation(s)
- Meng Qu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458 Guangzhou, China
| | - Yali Liu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458 Guangzhou, China
| | - Yanhong Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458 Guangzhou, China
| | - Shiming Wan
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458 Guangzhou, China
| | - Vydianathan Ravi
- Institute of Molecular and Cell Biology, A*STAR, 138673 Biopolis, Singapore
| | - Geng Qin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458 Guangzhou, China
| | - Han Jiang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- University of Chinese Academy of Sciences, 100101 Beijing, China
| | - Xin Wang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458 Guangzhou, China
| | - Huixian Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458 Guangzhou, China
| | - Bo Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458 Guangzhou, China
| | - Zexia Gao
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, 430070 Wuhan, China
| | - Ann Huysseune
- Department of Biology, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Zhixin Zhang
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Minato, Tokyo, Japan
| | - Hao Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458 Guangzhou, China
| | - Zelin Chen
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458 Guangzhou, China
| | - Haiyan Yu
- Biomarker Technologies Corporation, 101300 Beijing, China
| | - Yongli Wu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- University of Chinese Academy of Sciences, 100101 Beijing, China
| | - Lu Tang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- University of Chinese Academy of Sciences, 100101 Beijing, China
| | - Chunyan Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458 Guangzhou, China
| | - Jia Zhong
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458 Guangzhou, China
| | - Liming Ma
- Biomarker Technologies Corporation, 101300 Beijing, China
| | - Fengling Wang
- Biomarker Technologies Corporation, 101300 Beijing, China
| | - Hongkun Zheng
- Biomarker Technologies Corporation, 101300 Beijing, China
| | - Jianping Yin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
| | - Paul Eckhard Witten
- Department of Biology, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Axel Meyer
- Department of Biology, University of Konstanz, 78464 Konstanz, Germany.
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, A*STAR, 138673 Biopolis, Singapore.
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458 Guangzhou, China
- University of Chinese Academy of Sciences, 100101 Beijing, China
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12
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Matsumoto Y, Oda S, Mitani H, Kawamura S. Orthologous Divergence and Paralogous Anticonvergence in Molecular Evolution of Triplicated Green Opsin Genes in Medaka Fish, Genus Oryzias. Genome Biol Evol 2021; 12:911-923. [PMID: 32467976 PMCID: PMC7337190 DOI: 10.1093/gbe/evaa111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2020] [Indexed: 11/30/2022] Open
Abstract
Gene duplication of green (RH2) opsin genes and their spectral differentiation are well documented in many teleost fish. However, their evolutionary divergence or conservation patterns among phylogenetically close but ecologically diverse species is not well explored. Medaka fish (genus Oryzias) are broadly distributed in fresh and brackish waters of Asia, with many species being laboratory-housed and feasible for genetic studies. We previously showed that a Japan strain (HNI) of medaka (Oryzias latipes) possessed three RH2 opsin genes (RH2-A, RH2-B, and RH2-C) encoding spectrally divergent photopigments. Here, we examined the three RH2 opsin genes from six Oryzias species representing three species groups: the latipes, the celebensis, and the javanicus. Photopigment reconstitution revealed that the peak absorption spectra (λmax) of RH2-A were divergent among the species (447–469 nm), whereas those of RH2-B and RH2-C were conservative (516–519 and 486–493 nm, respectively). For the RH2-A opsins, the largest spectral shift was detected in the phylogenetic branch leading to the latipes group. A single amino acid replacement T94C explained most of the spectral shift. For RH2-B and -C opsins, we detected tracts of gene conversion between the two genes homogenizing them. Nevertheless, several amino acid differences were maintained. We showed that the spectral difference between the two opsins was attributed to largely the E/Q amino acid difference at the site 122 and to several sites with individually small spectral effects. These results depict dynamism of spectral divergence of orthologous and paralogous green opsin genes in phylogenetically close but ecologically diverse species exemplified by medaka.
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Affiliation(s)
- Yoshifumi Matsumoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.,Live Imaging Center, Central Institute for Experimental Animals (CIEA), Kawasaki, Kanagawa, Japan
| | - Shoji Oda
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Hiroshi Mitani
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Shoji Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
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13
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Wang Y, Zhou L, Wu L, Song C, Ma X, Xu S, Du T, Li X, Li J. Evolutionary ecology of the visual opsin gene sequence and its expression in turbot (Scophthalmus maximus). BMC Ecol Evol 2021; 21:114. [PMID: 34098879 PMCID: PMC8186084 DOI: 10.1186/s12862-021-01837-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/24/2021] [Indexed: 11/27/2022] Open
Abstract
Background As flatfish, turbot undergo metamorphosis as part of their life cycle. In the larval stage, turbot live at the ocean surface, but after metamorphosis they move to deeper water and turn to benthic life. Thus, the light environment differs greatly between life stages. The visual system plays a great role in organic evolution, but reports of the relationship between the visual system and benthic life are rare. In this study, we reported the molecular and evolutionary analysis of opsin genes in turbot, and the heterochronic shifts in opsin expression during development. Results Our gene synteny analysis showed that subtype RH2C was not on the same gene cluster as the other four green-sensitive opsin genes (RH2) in turbot. It was translocated to chromosome 8 from chromosome 6. Based on branch-site test and spectral tuning sites analyses, E122Q and M207L substitutions in RH2C, which were found to be under positive selection, are closely related to the blue shift of optimum light sensitivities. And real-time PCR results indicated the dominant opsin gene shifted from red-sensitive (LWS) to RH2B1 during turbot development, which may lead to spectral sensitivity shifts to shorter wavelengths. Conclusions This is the first report that RH2C may be an important subtype of green opsin gene that was retained by turbot and possibly other flatfish species during evolution. Moreover, E122Q and M207L substitutions in RH2C may contribute to the survival of turbot in the bluish colored ocean. And heterochronic shifts in opsin expression may be an important strategy for turbot to adapt to benthic life. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01837-2.
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Affiliation(s)
- Yunong Wang
- College of Fisheries, Ocean University of China, Qingdao, 266003, People's Republic of China.,CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, PR China
| | - Li Zhou
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, PR China
| | - Lele Wu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, PR China
| | - Changbin Song
- Institute of Semiconductors, Chinese Academy of Science, Beijing, 100083, People's Republic of China
| | - Xiaona Ma
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China
| | - Shihong Xu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China
| | - Tengfei Du
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, PR China
| | - Xian Li
- College of Fisheries, Ocean University of China, Qingdao, 266003, People's Republic of China. .,CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China.
| | - Jun Li
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, People's Republic of China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, PR China
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14
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Zheng S, Shao F, Tao W, Liu Z, Long J, Wang X, Zhang S, Zhao Q, Carleton KL, Kocher TD, Jin L, Wang Z, Peng Z, Wang D, Zhang Y. Chromosome-level assembly of southern catfish (silurus meridionalis) provides insights into visual adaptation to nocturnal and benthic lifestyles. Mol Ecol Resour 2021; 21:1575-1592. [PMID: 33503304 DOI: 10.1111/1755-0998.13338] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 01/13/2021] [Accepted: 01/22/2021] [Indexed: 01/07/2023]
Abstract
The Southern catfish (Silurus meridionalis) is a nocturnal and benthic freshwater fish endemic to the Yangtze River and its tributaries. In this study, we constructed a chromosome-level draft genome of S. meridionalis using 69.7-Gb Nanopore long reads and 49.5-Gb Illumina short reads. The genome assembly was 741.2 Mb in size with a contig N50 of 13.19 Mb. An additional 116.4 Gb of Bionano and 77.4 Gb of Hi-C data were applied to assemble contigs into scaffolds and further into 29 chromosomes, resulting in a 738.9-Mb genome with a scaffold N50 of 28.04 Mb. A total of 22,965 protein-coding genes were predicted from the genome with 22,519 (98.06%) genes functionally annotated. Comparative genomic and transcriptomic analyses revealed a rod-dominated visual system which was responsible for scotopic vision. The absence of cone opsins SWS1 and SWS2 resulted in the lack of ultraviolet and blue violet sensitivity. Mutations at key amino acid sites of RH1.1, RH1.2 and RH2 resulted in spectral tuning good for dim light vision and narrow colour vision. A higher expression level of rod phototransduction genes than that of cone genes and higher rod-to-cone ratio led to higher optical sensitivity under dim light conditions. In addition, analysis of the genes involved in eye morphogenesis and development revealed the loss of some conserved noncoding elements, which might be associated with the small eyes in catfish. Together, our study provides important clues for the adaptation of the catfish visual system to the nocturnal and benthic lifestyles. The draft genome of S. meridionalis represents a valuable resource for studies of the molecular mechanisms of ecological adaptation.
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Affiliation(s)
- Shuqing Zheng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Zhilong Liu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Juan Long
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Xiaoshuang Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Shuai Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Qingyuan Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Karen L Carleton
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Li Jin
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Zhijian Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Yaoguang Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
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15
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Vaux F, Bohn S, Hyde JR, O'Malley KG. Adaptive markers distinguish North and South Pacific Albacore amid low population differentiation. Evol Appl 2021; 14:1343-1364. [PMID: 34025772 PMCID: PMC8127716 DOI: 10.1111/eva.13202] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/19/2022] Open
Abstract
Albacore (Thunnus alalunga) support an economically valuable global fishery, but surprisingly little is known about the population structure of this highly migratory species. Physical tagging data suggest that Albacore from the North and South Pacific Ocean are separate stocks, but results from previous genetic studies did not support this two stock hypothesis. In addition, observed biological differences among juveniles suggest that there may be population substructure in the North Pacific. We used double-digest restriction site-associated DNA sequencing to assess population structure among 308 Albacore caught in 12 sample areas across the Pacific Ocean (10 North, 2 South). Since Albacore are highly migratory and spawning areas are unknown, sample groups were not assumed to be equivalent to populations and the genetic data were analyzed iteratively. We tested for putatively adaptive differences among groups and for genetic variation associated with sex. Results indicated that Albacore in the North and South Pacific can be distinguished using 84 putatively adaptive loci, but not using the remaining 12,788 presumed neutral sites. However, two individuals likely represent F1 hybrids between the North and South Pacific populations, and 43 Albacore potentially exhibit lower degrees of mixed ancestry. In addition, four or five cross-hemisphere migrants were potentially identified. No genetic evidence was found for population substructure within the North Pacific, and no loci appeared to distinguish males from females. Potential functions for the putatively adaptive loci were identified, but an annotated Albacore genome is required for further exploration. Future research should try to locate spawning areas so that life history, demography, and genetic population structure can be linked and spatiotemporal patterns can be investigated.
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Affiliation(s)
- Felix Vaux
- State Fisheries Genomics LabCoastal Oregon Marine Experiment StationDepartment of Fisheries and WildlifeHatfield Marine Science CenterOregon State UniversityNewportORUSA
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | - Sandra Bohn
- State Fisheries Genomics LabCoastal Oregon Marine Experiment StationDepartment of Fisheries and WildlifeHatfield Marine Science CenterOregon State UniversityNewportORUSA
| | - John R. Hyde
- Southwest Fisheries Science CenterNational Marine Fisheries ServiceLa JollaCAUSA
| | - Kathleen G. O'Malley
- State Fisheries Genomics LabCoastal Oregon Marine Experiment StationDepartment of Fisheries and WildlifeHatfield Marine Science CenterOregon State UniversityNewportORUSA
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16
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Sato I, Kasagi S, Takahashi A, Mizusawa K. Expression dynamics of visual opsin genes in marbled sole Pseudopleuronectes yokohamae during metamorphosis from the larval to the juvenile stage. Gene 2021; 787:145622. [PMID: 33798679 DOI: 10.1016/j.gene.2021.145622] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/24/2021] [Accepted: 03/26/2021] [Indexed: 11/29/2022]
Abstract
We clarified the properties of visual opsin genes in the marbled sole (Pseudopleuronectes yokohamae) by cDNA sequencing, quantification of the opsin gene expression from the larval to the juvenile stage, and measurement of the maximum absorption spectra (λmax) using photopigment reconstitution. In the marbled sole eye, at least eight visual opsin genes, lws, rh2-a, rh2-b, rh2-c, sws2a, sws2b, sws1, and rh1, were expressed. Quantitative RT-PCR analysis revealed that the expression of opsin genes increased (lws, rh2-c, sws2a, and rh1) or decreased (rh2-a, rh2-b, sws2b, and sws1) from the larval to the juvenile stage. Notably, rh2-a expression was observed only in pre- to mid-metamorphic stage larvae and disappeared after metamorphosis. Thus, pre-metamorphism-specific expression of rh2-a in the marbled sole suggests that its function is restricted to the developmental stage. The reconstituted RH2-A opsin λmax was 470 nm, which is typical of acanthopterygian species. These results strongly suggest that mid-wavelength-sensitive rh2-a expression was diminished drastically in the marbled sole, probably resulting in a shift of spectral sensitivity during its metamorphosis from the larval to the juvenile stage.
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Affiliation(s)
- Iku Sato
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
| | - Satoshi Kasagi
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan.
| | - Akiyoshi Takahashi
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
| | - Kanta Mizusawa
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
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17
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Liu Y, Wang Y, Ling X, Yan Z, Wu D, Liu J, Lu G. Effects of Nanoplastics and Butyl Methoxydibenzoylmethane on Early Zebrafish Embryos Identified by Single-Cell RNA Sequencing. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:1885-1896. [PMID: 33445878 DOI: 10.1021/acs.est.0c06479] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Nanoplastics with small particle sizes and high surface area/volume ratios easily absorb environmental pollutants and affect their bioavailability. In this study, polystyrene nanoplastic beads (PS-NPBs) with a particle size of 100 nm and butyl methoxydibenzoylmethane (BMDBM) sunscreen in personal-care products were chosen as target pollutants to study their developmental toxicity and interactive effects on zebrafish embryos. The exposure period was set from 2 to 12 h postfertilization (hpf). BMDBM and PS-NPBs significantly upregulated genes related to antioxidant enzymes and downregulated the gene expression of aromatase and DNA methyltransferases, but the influenced genes were not exactly the same. The combined exposure reduced the adverse effects on the expression of all genes. With the help of the single-cell RNA sequencing technology, neural mid cells were identified as the target cells of both pollutants, and brain development, head development, and the notch signaling pathway were the functions they commonly altered. The key genes and functions that are specifically affected by BMDBM and/or PS-NPBs were identified. BMDBM mainly affects the differentiation and fate of neurons in the central nervous system through the regulation of her5, her6, her11, lfng, pax2a, and fgfr4. The PS-NPBs regulate the expression of olig2, foxg1a, fzd8b, six3a, rx1, lhx2b, nkx2.1a, and sfrp5 to alter nervous system development, retinal development, and stem cell differentiation. The phenotypic responses of zebrafish larvae at 120 hpf were tested, and significant inhibition of locomotor activity was found, indicating that early effects on the central nervous system would have a sustained impact on the behavior of zebrafish.
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Affiliation(s)
- Yuxuan Liu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Yonghua Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Xin Ling
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Zhenhua Yan
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Donghai Wu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Jianchao Liu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Guanghua Lu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
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18
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Marisaldi L, Basili D, Gioacchini G, Canapa A, Carnevali O. De novo transcriptome assembly, functional annotation and characterization of the Atlantic bluefin tuna (Thunnus thynnus) larval stage. Mar Genomics 2020; 58:100834. [PMID: 33371994 DOI: 10.1016/j.margen.2020.100834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 10/22/2022]
Abstract
In the present work, we assembled and characterized a de novo larval transcriptome of the Atlantic bluefin tuna Thunnus thynnus by taking advantage of publicly available databases with the goal of better understanding its larval development. The assembled transcriptome comprised 37,117 protein-coding transcripts, of which 13,633 full-length (>80% coverage), with an Ex90N50 of 3061 bp and 76% of complete and single-copy core vertebrate genes orthologues. Of these transcripts, 34,980 had a hit against the EggNOG database and 14,983 with the KEGG database. Codon usage bias was identified in processes such as translation and muscle development. By comparing our data with a set of representative fish species, 87.1% of tuna transcripts were included in orthogroups with other species and 5.1% in assembly-specific orthogroups, which were enriched in terms related to muscle and bone development, visual system and ion transport. Following this comparative approach, protein families related to myosin, extracellular matrix and immune system resulted significantly expanded in the Atlantic bluefin tuna. Altogether, these results provide a glimpse of how the Atlantic bluefin tuna might have achieved early physical advantages over competing species in the pelagic environment. The information generated lays the foundation for future research on the more detailed exploration of physiological responses at the molecular level in different larval stages and paves the way to evolutionary studies on the Atlantic bluefin tuna.
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Affiliation(s)
- Luca Marisaldi
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona 60131, Italy
| | - Danilo Basili
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona 60131, Italy; Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Giorgia Gioacchini
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona 60131, Italy
| | - Adriana Canapa
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona 60131, Italy
| | - Oliana Carnevali
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona 60131, Italy.
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19
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Genomes of major fishes in world fisheries and aquaculture: Status, application and perspective. AQUACULTURE AND FISHERIES 2020. [DOI: 10.1016/j.aaf.2020.05.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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20
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Escobar-Camacho D, Carleton KL, Narain DW, Pierotti MER. Visual pigment evolution in Characiformes: The dynamic interplay of teleost whole-genome duplication, surviving opsins and spectral tuning. Mol Ecol 2020; 29:2234-2253. [PMID: 32421918 DOI: 10.1111/mec.15474] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 05/09/2020] [Accepted: 05/11/2020] [Indexed: 01/06/2023]
Abstract
Vision represents an excellent model for studying adaptation, given the genotype-to-phenotype map that has been characterized in a number of taxa. Fish possess a diverse range of visual sensitivities and adaptations to underwater light, making them an excellent group to study visual system evolution. In particular, some speciose but understudied lineages can provide a unique opportunity to better understand aspects of visual system evolution such as opsin gene duplication and neofunctionalization. In this study, we showcase the visual system evolution of neotropical Characiformes and the spectral tuning mechanisms they exhibit to modulate their visual sensitivities. Such mechanisms include gene duplications and losses, gene conversion, opsin amino acid sequence and expression variation, and A1 /A2 -chromophore shifts. The Characiforms we studied utilize three cone opsin classes (SWS2, RH2, LWS) and a rod opsin (RH1). However, the characiform's entire opsin gene repertoire is a product of dynamic evolution by opsin gene loss (SWS1, RH2) and duplication (LWS, RH1). The LWS- and RH1-duplicates originated from a teleost specific whole-genome duplication as well as characiform-specific duplication events. Both LWS-opsins exhibit gene conversion and, through substitutions in key tuning sites, one of the LWS-paralogues has acquired spectral sensitivity to green light. These sequence changes suggest reversion and parallel evolution of key tuning sites. Furthermore, characiforms' colour vision is based on the expression of both LWS-paralogues and SWS2. Finally, we found interspecific and intraspecific variation in A1 /A2 -chromophores proportions, correlating with the light environment. These multiple mechanisms may be a result of the diverse visual environments where Characiformes have evolved.
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Affiliation(s)
| | - Karen L Carleton
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Devika W Narain
- Environmental Sciences, Anton de Kom University of Suriname, Paramaribo, Suriname
| | - Michele E R Pierotti
- Naos Marine Laboratories, Smithsonian Tropical Research Institute, Panama, Republic of Panama
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21
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Natsidis P, Tsakogiannis A, Pavlidis P, Tsigenopoulos CS, Manousaki T. Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling. Commun Biol 2019; 2:400. [PMID: 31701028 PMCID: PMC6825128 DOI: 10.1038/s42003-019-0654-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 10/08/2019] [Indexed: 12/29/2022] Open
Abstract
Sparidae (Teleostei: Spariformes) are a family of fish constituted by approximately 150 species with high popularity and commercial value, such as porgies and seabreams. Although the phylogeny of this family has been investigated multiple times, its position among other teleost groups remains ambiguous. Most studies have used a single or few genes to decipher the phylogenetic relationships of sparids. Here, we conducted a thorough phylogenomic analysis using five recently available Sparidae gene-sets and 26 high-quality, genome-predicted teleost proteomes. Our analysis suggested that Tetraodontiformes (puffer fish, sunfish) are the closest relatives to sparids than all other groups used. By analytically comparing this result to our own previous contradicting finding, we show that this discordance is not due to different orthology assignment algorithms; on the contrary, we prove that it is caused by the increased taxon sampling of the present study, outlining the great importance of this aspect in phylogenomic analyses in general.
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Affiliation(s)
- Paschalis Natsidis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
- School of Medicine, University of Crete, Heraklion, Greece
| | - Alexandros Tsakogiannis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology, Heraklion, Greece
| | - Costas S. Tsigenopoulos
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Tereza Manousaki
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
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22
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Identification of tuna species Thunnus albacares and Katsuwonus pelamis in canned products by real-time PCR method. ACTA VET BRNO 2019. [DOI: 10.2754/avb201988030323] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Tuna species are a popular food among consumers. They are mostly sold as heat-processed canned products on the market. Different quality and price of tuna species can lead the producer to the adulteration of food products. The main difficulties in developing a method for species identification in these fish is the high similarity of DNA sequences among close relative fish species. All complete mitochondrial DNA sequences of skipjack tuna (Katsuwonus pelamis) and yellowfin tuna (Thunnus albacares) were compared to all other mitochondrial DNA sequences of tuna fish deposited in the GenBank. The most variable regions within species were determined and primers and probes were designed in this region for the species-specific DNA amplification of skipjack tuna and yellowfin tuna. Moreover, to check the content of amplifiable DNA of fish (namely tuna) in the sample, primers and a probe of mitochondrial12SrRNAgene in the region of conservative sequence were designed. Real time PCR methods were verified by investigating 51 samples of canned tuna with the declared content of tuna species from the market; the species was confirmed in all tested samples. This method was designed to be suitable for the determination of DNA sequences especially in highly heat treated products.
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23
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Improvement of the Pacific bluefin tuna (Thunnus orientalis) reference genome and development of male-specific DNA markers. Sci Rep 2019; 9:14450. [PMID: 31595011 PMCID: PMC6783451 DOI: 10.1038/s41598-019-50978-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 09/17/2019] [Indexed: 12/30/2022] Open
Abstract
The Pacific bluefin tuna, Thunnus orientalis, is a highly migratory species that is widely distributed in the North Pacific Ocean. Like other marine species, T. orientalis has no external sexual dimorphism; thus, identifying sex-specific variants from whole genome sequence data is a useful approach to develop an effective sex identification method. Here, we report an improved draft genome of T. orientalis and male-specific DNA markers. Combining PacBio long reads and Illumina short reads sufficiently improved genome assembly, with a 38-fold increase in scaffold contiguity (to 444 scaffolds) compared to the first published draft genome. Through analysing re-sequence data of 15 males and 16 females, 250 male-specific SNPs were identified from more than 30 million polymorphisms. All male-specific variants were male-heterozygous, suggesting that T. orientalis has a male heterogametic sex-determination system. The largest linkage disequilibrium block (3,174 bp on scaffold_064) contained 51 male-specific variants. PCR primers and a PCR-based sex identification assay were developed using these male-specific variants. The sex of 115 individuals (56 males and 59 females; sex was diagnosed by visual examination of the gonads) was identified with high accuracy using the assay. This easy, accurate, and practical technique facilitates the control of sex ratios in tuna farms. Furthermore, this method could be used to estimate the sex ratio and/or the sex-specific growth rate of natural populations.
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24
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Targeted mutagenesis of the ryanodine receptor by Platinum TALENs causes slow swimming behaviour in Pacific bluefin tuna (Thunnus orientalis). Sci Rep 2019; 9:13871. [PMID: 31554877 PMCID: PMC6761128 DOI: 10.1038/s41598-019-50418-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 09/05/2019] [Indexed: 11/08/2022] Open
Abstract
In bluefin tuna aquaculture, high mortalities of hatchery-reared juveniles occur in sea cages owing to wall collisions that are caused by high-speed swimming in panic due to changes in illuminance. Here, we report that targeted gene mutagenesis of the ryanodine receptor (RyR1b), which allows the sarcoplasmic reticulum to release Ca2+ in fast skeletal muscle, using highly active Platinum TALENs caused slow swimming behaviour in response to external stimuli in Pacific bluefin tuna (PBT) larvae. This characteristic would be a useful trait to prevent wall collisions in aquaculture production. A pair of Platinum TALENs targeting exons 2 and 43 of the PBT ryr1b gene induced deletions in each TALEN target site of the injected embryos with extremely high efficiency. In addition, ryr1b expression was significantly decreased in the mutated G0 larvae at 7 days after hatching (DAH). A touch-evoked escape behaviour assay revealed that the ryr1b-mutated PBT larvae swam away much less efficiently in response to mechanosensory stimulation at 7 DAH than did the wild-type larvae. Our results demonstrate that genome editing technologies are effective tools for determining the functional characterization of genes in a comparatively short period, and create avenues for facilitating genetic studies and breeding of bluefin tuna species.
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25
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Divergence, evolution and adaptation in ray-finned fish genomes. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1003-1018. [PMID: 31098893 DOI: 10.1007/s11427-018-9499-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 02/12/2019] [Indexed: 02/06/2023]
Abstract
With the rapid development of next-generation sequencing technologies and bioinformatics, over 50 ray-finned fish genomes by far have been sequenced with high quality. The genomic work provides abundant genetic resources for deep understanding of divergence, evolution and adaptation in the fish genomes. They are also instructive for identification of candidate genes for functional verification, molecular breeding, and development of novel marine drugs. As an example of other omics data, the Fish-T1K project generated a big database of fish transcriptomes to integrate with these published fish genomes for potential applications. In this review, we highlight the above-mentioned recent investigations and core topics on the ray-finned fish genome research, with a main goal to obtain a deeper understanding of fish biology for theoretical and practical applications.
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26
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Chang CH, Yan HY. Plasticity of opsin gene expression in the adult red shiner (Cyprinella lutrensis) in response to turbid habitats. PLoS One 2019; 14:e0215376. [PMID: 30978235 PMCID: PMC6461250 DOI: 10.1371/journal.pone.0215376] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 04/01/2019] [Indexed: 11/30/2022] Open
Abstract
Vision is very important to fish as it is required for foraging food, fighting competitors, fleeing from predators, and finding potential mates. Vertebrates express opsin genes in photoreceptor cells to receive visual signals, and the variety of light levels in aquatic habits has driven fish to evolve multiple opsin genes with expression profiles that are highly plastic. In this study, red shiners (Cyprinella lutrensis) were exposed to four water turbidity treatments and their opsin genes were cloned to elucidate how opsin gene expression could be modulated by ambient light conditions. Opsin gene cloning revealed that these fish have single RH1, SWS1, SWS2 and LWS genes and two RH2 genes. Phylogenetic analysis also indicated that these two RH2 opsin genes-RH2A and RH2B -are in-paralogous. Using quantitative PCR, we found evidence that opsin expression is plastic in adults. Elevated proportional expression of LWS in the cone under ambient light and turbid treatment indicated that the red shiner's visual spectrum displays a red shift in response to increased turbidity.
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Affiliation(s)
- Chia-Hao Chang
- Department of Life Science, Tunghai University, Taichung City, Taiwan
- Center for Ecology and Environment, Tunghai University, Taichung City, Taiwan
| | - Hong Young Yan
- National Museum of Marine Biology & Aquarium, Checheng, Pingtung, Taiwan
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27
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Machado AM, Tørresen OK, Kabeya N, Couto A, Petersen B, Felício M, Campos PF, Fonseca E, Bandarra N, Lopes-Marques M, Ferraz R, Ruivo R, Fonseca MM, Jentoft S, Monroig Ó, da Fonseca RR, C Castro LF. " Out of the Can": A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus. Genes (Basel) 2018; 9:E485. [PMID: 30304855 PMCID: PMC6210256 DOI: 10.3390/genes9100485] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/01/2018] [Accepted: 10/02/2018] [Indexed: 12/30/2022] Open
Abstract
Clupeiformes, such as sardines and herrings, represent an important share of worldwide fisheries. Among those, the European sardine (Sardina pilchardus, Walbaum 1792) exhibits significant commercial relevance. While the last decade showed a steady and sharp decline in capture levels, recent advances in culture husbandry represent promising research avenues. Yet, the complete absence of genomic resources from sardine imposes a severe bottleneck to understand its physiological and ecological requirements. We generated 69 Gbp of paired-end reads using Illumina HiSeq X Ten and assembled a draft genome assembly with an N50 scaffold length of 25,579 bp and BUSCO completeness of 82.1% (Actinopterygii). The estimated size of the genome ranges between 655 and 850 Mb. Additionally, we generated a relatively high-level liver transcriptome. To deliver a proof of principle of the value of this dataset, we established the presence and function of enzymes (Elovl2, Elovl5, and Fads2) that have pivotal roles in the biosynthesis of long chain polyunsaturated fatty acids, essential nutrients particularly abundant in oily fish such as sardines. Our study provides the first omics dataset from a valuable economic marine teleost species, the European sardine, representing an essential resource for their effective conservation, management, and sustainable exploitation.
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Affiliation(s)
- André M Machado
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
| | - Ole K Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway.
| | - Naoki Kabeya
- Department of Aquatic Bioscience, The University of Tokyo, Tokyo 113-8654, Japan.
| | - Alvarina Couto
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Bent Petersen
- Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
- Centre of Excellence for Omics-Driven Computational Biodiscovery, Faculty of Applied Sciences, Asian Institute of Medicine, Science and Technology, Kedah 08000, Malaysia.
| | - Mónica Felício
- Portuguese Institute for the Sea and Atmosphere, (IPMA), 1749-077 Lisbon, Portugal.
| | - Paula F Campos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Elza Fonseca
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, 4099-022 Porto, Portugal.
| | - Narcisa Bandarra
- Portuguese Institute for the Sea and Atmosphere, (IPMA), 1749-077 Lisbon, Portugal.
| | - Mónica Lopes-Marques
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
| | - Renato Ferraz
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4099-022 Porto, Portugal.
| | - Raquel Ruivo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
| | - Miguel M Fonseca
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway.
- Centre for Coastal Research, Department of Natural Sciences, University of Agder, 4630 Kristiansand, Norway.
| | - Óscar Monroig
- Instituto de Acuicultura Torre de la Sal, Consejo Superior de Investigaciones Científicas (IATS-CSIC), 12595 Ribera de Cabanes, Spain.
| | - Rute R da Fonseca
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
- Center for Macroecology, Evolution, and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark.
| | - L Filipe C Castro
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, 4099-022 Porto, Portugal.
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28
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Yasuike M, Iwasaki Y, Nishiki I, Nakamura Y, Matsuura A, Yoshida K, Noda T, Andoh T, Fujiwara A. The yellowtail (Seriola quinqueradiata) genome and transcriptome atlas of the digestive tract. DNA Res 2018; 25:547-560. [PMID: 30329019 PMCID: PMC6191305 DOI: 10.1093/dnares/dsy024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 06/28/2018] [Indexed: 12/30/2022] Open
Abstract
Seriola quinqueradiata (yellowtail) is the most widely farmed and economically important fish in aquaculture in Japan. In this study, we used the genome of haploid yellowtail fish larvae for de novo assembly of whole-genome sequences, and built a high-quality draft genome for the yellowtail. The total length of the assembled sequences was 627.3 Mb, consisting of 1,394 scaffold sequences (>2 kb) with an N50 length of 1.43 Mb. A total of 27,693 protein-coding genes were predicted for the draft genome, and among these, 25,832 predicted genes (93.3%) were functionally annotated. Given our lack of knowledge of the yellowtail digestive system, and using the annotated draft genome as a reference, we conducted an RNA-Seq analysis of its three digestive organs (stomach, intestine and rectum). The RNA-Seq results highlighted the importance of certain genes in encoding proteolytic enzymes necessary for digestion and absorption in the yellowtail gastrointestinal tract, and this finding will accelerate development of formulated feeds for this species. Since this study offers comprehensive annotation of predicted protein-coding genes, it has potential broad application to our understanding of yellowtail biology and aquaculture.
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Affiliation(s)
- Motoshige Yasuike
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Yuki Iwasaki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Issei Nishiki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Yoji Nakamura
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Aiko Matsuura
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Kazunori Yoshida
- Goto Laboratory, Stock Enhancement and Aquaculture Division, Seikai National Fisheries Research Institute Japan Fisheries Research and Education Agency, Tamanoura-cho, Goto, Nagasaki, Japan
| | - Tsutomu Noda
- Goto Laboratory, Stock Enhancement and Aquaculture Division, Seikai National Fisheries Research Institute Japan Fisheries Research and Education Agency, Tamanoura-cho, Goto, Nagasaki, Japan
| | - Tadashi Andoh
- Stock Enhancement and Aquaculture Division, Seikai National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Nagasaki, Japan
| | - Atushi Fujiwara
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
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29
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Visual pigment genes and absorbance spectra in the Japanese sardine Sardinops melanostictus (Teleostei: Clupeiformes). Comp Biochem Physiol B Biochem Mol Biol 2018; 218:54-63. [DOI: 10.1016/j.cbpb.2018.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 02/17/2018] [Accepted: 02/23/2018] [Indexed: 11/20/2022]
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30
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Marcionetti A, Rossier V, Bertrand JAM, Litsios G, Salamin N. First draft genome of an iconic clownfish species (Amphiprion frenatus). Mol Ecol Resour 2018; 18:1092-1101. [PMID: 29455459 DOI: 10.1111/1755-0998.12772] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 01/29/2018] [Accepted: 02/06/2018] [Indexed: 11/30/2022]
Abstract
Clownfishes (or anemonefishes) form an iconic group of coral reef fishes, principally known for their mutualistic interaction with sea anemones. They are characterized by particular life history traits, such as a complex social structure and mating system involving sequential hermaphroditism, coupled with an exceptionally long lifespan. Additionally, clownfishes are considered to be one of the rare groups to have experienced an adaptive radiation in the marine environment. Here, we assembled and annotated the first genome of a clownfish species, the tomato clownfish (Amphiprion frenatus). We obtained 17,801 assembled scaffolds, containing a total of 26,917 genes. The completeness of the assembly and annotation was satisfying, with 96.5% of the Actinopterygii Benchmarking Universal Single-Copy Orthologs (BUSCOs) being retrieved in A. frenatus assembly. The quality of the resulting assembly is comparable to other bony fish assemblies. This resource is valuable for advancing studies of the particular life history traits of clownfishes, as well as being useful for population genetic studies and the development of new phylogenetic markers. It will also open the way to comparative genomics. Indeed, future genomic comparison among closely related fishes may provide means to identify genes related to the unique adaptations to different sea anemone hosts, as well as better characterize the genomic signatures of an adaptive radiation.
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Affiliation(s)
- Anna Marcionetti
- Department of Computational Biology, Biophore, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Victor Rossier
- Department of Computational Biology, Biophore, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joris A M Bertrand
- Department of Computational Biology, Biophore, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Glenn Litsios
- Department of Computational Biology, Biophore, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicolas Salamin
- Department of Computational Biology, Biophore, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Yuan Z, Liu S, Zhou T, Tian C, Bao L, Dunham R, Liu Z. Comparative genome analysis of 52 fish species suggests differential associations of repetitive elements with their living aquatic environments. BMC Genomics 2018; 19:141. [PMID: 29439662 PMCID: PMC5811955 DOI: 10.1186/s12864-018-4516-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 01/31/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Repetitive elements make up significant proportions of genomes. However, their roles in evolution remain largely unknown. To provide insights into the roles of repetitive elements in fish genomes, we conducted a comparative analysis of repetitive elements of 52 fish species in 22 orders in relation to their living aquatic environments. RESULTS The proportions of repetitive elements in various genomes were found to be positively correlated with genome sizes, with a few exceptions. More importantly, there appeared to be specific enrichment between some repetitive element categories with species habitat. Specifically, class II transposons appear to be more abundant in freshwater bony fish than in marine bony fish when phylogenetic relationship is not considered. In contrast, marine bony fish harbor more tandem repeats than freshwater species. In addition, class I transposons appear to be more abundant in primitive species such as cartilaginous fish and lamprey than in bony fish. CONCLUSIONS The enriched association of specific categories of repetitive elements with fish habitats suggests the importance of repetitive elements in genome evolution and their potential roles in fish adaptation to their living environments. However, due to the restriction of the limited sequenced species, further analysis needs to be done to alleviate the phylogenetic biases.
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Affiliation(s)
- Zihao Yuan
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849 USA
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849 USA
| | - Tao Zhou
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849 USA
| | - Changxu Tian
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849 USA
| | - Lisui Bao
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849 USA
| | - Rex Dunham
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849 USA
| | - Zhanjiang Liu
- Department of Biology, College of Art and Sciences, Syracuse University, Syracuse, NY 13244 USA
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Kasagi S, Mizusawa K, Takahashi A. Green-shifting of SWS2A opsin sensitivity and loss of function of RH2-A opsin in flounders, genus Verasper. Ecol Evol 2017; 8:1399-1410. [PMID: 29375806 PMCID: PMC5773313 DOI: 10.1002/ece3.3745] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 08/29/2017] [Accepted: 11/22/2017] [Indexed: 11/11/2022] Open
Abstract
We identified visual opsin genes for three flounder species, including the spotted halibut (Verasper variegatus), slime flounder (Microstomus achne), and Japanese flounder (Paralichthys olivaceus). Structure and function of opsins for the three species were characterized together with those of the barfin flounder (V. moseri) that we previously reported. All four flounder species possessed five basic opsin genes, including lws, sws1, sws2, rh1, and rh2. Specific features were observed in rh2 and sws2. The rh2-a, one of the three subtypes of rh2, was absent in the genome of V. variegatus and pseudogenized in V. moseri. Moreover, rh2-a mRNA was not detected in M. achne and P. olivaceus, despite the presence of a functional reading frame. Analyses of the maximum absorption spectra (λmax) estimated by in vitro reconstitution indicated that SWS2A of M. achne (451.9 nm) and P. olivaceus (465.6 nm) were blue-sensitive, whereas in V. variegatus (485.4 nm), it was green-sensitive and comparable to V. moseri (482.3 nm). Our results indicate that although the four flounder species possess a similar opsin gene repertoire, the SWS2A opsin of the genus Verasper is functionally green-sensitive, while its overall structure remains conserved as a blue-sensitive opsin. Further, the rh2-a function seems to have been reduced during the evolution of flounders. λmax values of predicted ancestral SWS2A of Pleuronectiformes and Pleuronectidae was 465.4 and 462.4 nm, respectively, indicating that these were blue-sensitive. Thus, the green-sensitive SWS2A is estimated to be arisen in ancestral Verasper genus. It is suggested that the sensitivity shift of SWS2A from blue to green may have compensated functional reduction in RH2-A.
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Affiliation(s)
- Satoshi Kasagi
- School of Marine Biosciences Kitasato University Kitasato Minami-ku Sagamihara Kanagawa Japan
| | - Kanta Mizusawa
- School of Marine Biosciences Kitasato University Kitasato Minami-ku Sagamihara Kanagawa Japan
| | - Akiyoshi Takahashi
- School of Marine Biosciences Kitasato University Kitasato Minami-ku Sagamihara Kanagawa Japan
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Lin JJ, Wang FY, Li WH, Wang TY. The rises and falls of opsin genes in 59 ray-finned fish genomes and their implications for environmental adaptation. Sci Rep 2017; 7:15568. [PMID: 29138475 PMCID: PMC5686071 DOI: 10.1038/s41598-017-15868-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 11/03/2017] [Indexed: 01/25/2023] Open
Abstract
We studied the evolution of opsin genes in 59 ray-finned fish genomes. We identified the opsin genes and adjacent genes (syntenies) in each genome. Then we inferred the changes in gene copy number (N), syntenies, and tuning sites along each phylogenetic branch during evolution. The Exorh (rod opsin) gene has been retained in 56 genomes. Rh1, the intronless rod opsin gene, first emerged in ancestral Actinopterygii, and N increased to 2 by the teleost-specific whole genome duplication, but then decreased to 1 in the ancestor of Neoteleostei fishes. For cone opsin genes, the rhodopsin-like (Rh2) and long-wave-sensitive (LWS) genes showed great variation in N among species, ranging from 0 to 5 and from 0 to 4, respectively. The two short-wave-sensitive genes, SWS1 and SWS2, were lost in 23 and 6 species, respectively. The syntenies involving LWS, SWS2 and Rh2 underwent complex changes, while the evolution of the other opsin gene syntenies was much simpler. Evolutionary adaptation in tuning sites under different living environments was discussed. Our study provides a detailed view of opsin gene gains and losses, synteny changes and tuning site changes during ray-finned fish evolution.
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Affiliation(s)
- Jinn-Jy Lin
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan.,Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Nankang, Taipei, 11529, Taiwan.,Biodiversity Research Center, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Feng-Yu Wang
- Taiwan Ocean Research Institute, National Applied Research Laboratories, Kaohsiung, 852, Taiwan
| | - Wen-Hsiung Li
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan. .,Biodiversity Research Center, Academia Sinica, Nankang, Taipei, 11529, Taiwan. .,Department of Ecology and Evolution, University of Chicago, Chicago, 60637, USA.
| | - Tzi-Yuan Wang
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, 11529, Taiwan.
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Nakamura Y, Yasuike M, Mekuchi M, Iwasaki Y, Ojima N, Fujiwara A, Chow S, Saitoh K. Rhodopsin gene copies in Japanese eel originated in a teleost-specific genome duplication. ZOOLOGICAL LETTERS 2017; 3:18. [PMID: 29075512 PMCID: PMC5645911 DOI: 10.1186/s40851-017-0079-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/11/2017] [Indexed: 06/16/2023]
Abstract
BACKGROUND Gene duplication is considered important to increasing the genetic diversity in animals. In fish, visual pigment genes are often independently duplicated, and the evolutionary significance of such duplications has long been of interest. Eels have two rhodopsin genes (rho), one of which (freshwater type, fw-rho) functions in freshwater and the other (deep-sea type, ds-rho) in marine environments. Hence, switching of rho expression in retinal cells is tightly linked with eels' unique life cycle, in which they migrate from rivers or lakes to the sea. These rho genes are apparently paralogous, but the timing of their duplication is unclear due to the deep-branching phylogeny. The aim of the present study is to elucidate the evolutionary origin of the two rho copies in eels using comparative genomics methods. RESULTS In the present study, we sequenced the genome of Japanese eel Anguilla japonica and reconstructed two regions containing rho by de novo assembly. We found a single corresponding region in a non-teleostean primitive ray-finned fish (spotted gar) and two regions in a primitive teleost (Asian arowana). The order of ds-rho and the neighboring genes was highly conserved among the three species. With respect to fw-rho, which was lost in Asian arowana, the neighboring genes were also syntenic between Japanese eel and Asian arowana. In particular, the pattern of gene losses in ds-rho and fw-rho regions was the same as that in Asian arowana, and no discrepancy was found in any of the teleost genomes examined. Phylogenetic analysis supports mutual monophyly of these two teleostean synteny groups, which correspond to the ds-rho and fw-rho regions. CONCLUSIONS Syntenic and phylogenetic analyses suggest that the duplication of rhodopsin gene in Japanese eel predated the divergence of eel (Elopomorpha) and arowana (Osteoglossomorpha). Thus, based on the principle of parsimony, it is most likely that the rhodopsin paralogs were generated through a whole genome duplication in the ancestor of teleosts, and have remained till the present in eels with distinct functional roles. Our result indicates, for the first time, that teleost-specific genome duplication may have contributed to a gene innovation involved in eel-specific migratory life cycle.
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Affiliation(s)
- Yoji Nakamura
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
| | - Motoshige Yasuike
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
| | - Miyuki Mekuchi
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
| | - Yuki Iwasaki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
- Present address: National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540 Japan
| | - Nobuhiko Ojima
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
- Present address: Japan Fisheries Research and Education Agency, 2-3-3 Minatomirai, Nishi, Yokohama, Kanagawa 220-6115 Japan
| | - Atushi Fujiwara
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
| | - Seinen Chow
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
| | - Kenji Saitoh
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
- Present address: Tohoku National Fisheries Research Institute, Japan Fisheries Research and Education Agency, 3-27-5 Shinhama, Shiogama, Miyagi 985-0001 Japan
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35
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Hahn C, Genner MJ, Turner GF, Joyce DA. The genomic basis of cichlid fish adaptation within the deepwater "twilight zone" of Lake Malawi. Evol Lett 2017; 1:184-198. [PMID: 30283648 PMCID: PMC6124600 DOI: 10.1002/evl3.20] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 06/01/2017] [Accepted: 07/11/2017] [Indexed: 12/21/2022] Open
Abstract
Deepwater environments are characterized by low levels of available light at narrow spectra, great hydrostatic pressure, and low levels of dissolved oxygen—conditions predicted to exert highly specific selection pressures. In Lake Malawi over 800 cichlid species have evolved, and this adaptive radiation extends into the “twilight zone” below 50 m. We use population‐level RAD‐seq data to investigate whether four endemic deepwater species (Diplotaxodon spp.) have experienced divergent selection within this environment. We identify candidate genes including regulators of photoreceptor function, photopigments, lens morphology, and haemoglobin, many not previously implicated in cichlid adaptive radiations. Colocalization of functionally linked genes suggests coadapted “supergene” complexes. Comparisons of Diplotaxodon to the broader Lake Malawi radiation using genome resequencing data revealed functional substitutions and signatures of positive selection in candidate genes. Our data provide unique insights into genomic adaptation within deepwater habitats, and suggest genome‐level specialization for life at depth as an important process in cichlid radiation.
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Affiliation(s)
- Christoph Hahn
- Evolutionary and Environmental Genomics Group (@EvoHull), School of Environmental Sciences University of Hull Hull HU5 7RX United Kingdom.,Institute of Zoology University of Graz A-8010 Graz Austria
| | - Martin J Genner
- School of Biological Sciences University of Bristol Bristol Life Sciences Building, 24 Tyndall Avenue Bristol BS8 1TQ United Kingdom
| | - George F Turner
- School of Biological Sciences Bangor University Bangor Gwynedd LL57 2UW Wales United Kingdom
| | - Domino A Joyce
- Evolutionary and Environmental Genomics Group (@EvoHull), School of Environmental Sciences University of Hull Hull HU5 7RX United Kingdom
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36
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DiBattista JD, Saenz-Agudelo P, Piatek MJ, Wang X, Aranda M, Berumen ML. Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish. Mol Ecol Resour 2017; 17:1330-1341. [PMID: 28236665 DOI: 10.1111/1755-0998.12662] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 02/11/2017] [Accepted: 02/16/2017] [Indexed: 01/07/2023]
Abstract
Data from a large-scale restriction site-associated DNA sequencing (RAD-Seq) study of nine butterflyfish species in the Red Sea and Arabian Sea provided a means to test the utility of a recently published draft genome (Chaetodon austriacus) and assess apparent bias in this method of isolating nuclear loci. We here processed double-digest restriction site-associated DNA (ddRAD) sequencing data to identify single nucleotide polymorphism (SNP) markers and their associated function with and without our reference genome to see whether it improves the quality of RAD-Seq. Our analyses indicate (i) a modest gap between the number of nonannotated versus annotated SNPs across all species, (ii) an advantage of using genomic resources for closely related but not distantly related butterflyfish species based on the ability to assign putative gene function to SNPs and (iii) an enrichment of genes among sister butterflyfish taxa related to calcium transmembrane transport and binding. The latter result highlights the potential for this approach to reveal insights into adaptive mechanisms in populations inhabiting challenging coral reef environments such as the Red Sea, Arabian Sea and Arabian Gulf with further study.
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Affiliation(s)
- Joseph D DiBattista
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.,Department of Environment and Agriculture, Curtin University, PO Box U1987, Perth, WA, 6845, Australia
| | - Pablo Saenz-Agudelo
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.,Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, 5090000, Chile
| | - Marek J Piatek
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xin Wang
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Manuel Aranda
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Michael L Berumen
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
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37
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Barth JMI, Damerau M, Matschiner M, Jentoft S, Hanel R. Genomic Differentiation and Demographic Histories of Atlantic and Indo-Pacific Yellowfin Tuna (Thunnus albacares) Populations. Genome Biol Evol 2017; 9:1084-1098. [PMID: 28419285 PMCID: PMC5408087 DOI: 10.1093/gbe/evx067] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2017] [Indexed: 12/30/2022] Open
Abstract
Recent developments in the field of genomics have provided new and powerful insights into population structure and dynamics that are essential for the conservation of biological diversity. As a commercially highly valuable species, the yellowfin tuna (Thunnus albacares) is intensely exploited throughout its distribution in tropical oceans around the world, and is currently classified as near threatened. However, conservation efforts for this species have so far been hampered by limited knowledge of its population structure, due to incongruent results of previous investigations. Here, we use whole-genome sequencing in concert with a draft genome assembly to decipher the global population structure of the yellowfin tuna, and to investigate its demographic history. We detect significant differentiation of Atlantic and Indo-Pacific yellowfin tuna populations as well as the possibility of a third diverged yellowfin tuna group in the Arabian Sea. We further observe evidence for past population expansion as well as asymmetric gene flow from the Indo-Pacific to the Atlantic.
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Affiliation(s)
- Julia M I Barth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Malte Damerau
- Institute of Fisheries Ecology, Johann Heinrich von Thünen Institute, Federal Research Institute for Rural Areas, Forestry and Fisheries, Hamburg, Germany
| | - Michael Matschiner
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.,Centre for Coastal Research, Department of Natural Sciences, University of Agder, Kristiansand, Norway
| | - Reinhold Hanel
- Institute of Fisheries Ecology, Johann Heinrich von Thünen Institute, Federal Research Institute for Rural Areas, Forestry and Fisheries, Hamburg, Germany
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Stieb SM, Cortesi F, Sueess L, Carleton KL, Salzburger W, Marshall NJ. Why UV vision and red vision are important for damselfish (Pomacentridae): structural and expression variation in opsin genes. Mol Ecol 2017; 26:1323-1342. [PMID: 27997050 DOI: 10.1111/mec.13968] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 11/29/2016] [Accepted: 12/05/2016] [Indexed: 12/15/2022]
Abstract
Coral reefs belong to the most diverse ecosystems on our planet. The diversity in coloration and lifestyles of coral reef fishes makes them a particularly promising system to study the role of visual communication and adaptation. Here, we investigated the evolution of visual pigment genes (opsins) in damselfish (Pomacentridae) and examined whether structural and expression variation of opsins can be linked to ecology. Using DNA sequence data of a phylogenetically representative set of 31 damselfish species, we show that all but one visual opsin are evolving under positive selection. In addition, selection on opsin tuning sites, including cases of divergent, parallel, convergent and reversed evolution, has been strong throughout the radiation of damselfish, emphasizing the importance of visual tuning for this group. The highest functional variation in opsin protein sequences was observed in the short- followed by the long-wavelength end of the visual spectrum. Comparative gene expression analyses of a subset of the same species revealed that with SWS1, RH2B and RH2A always being expressed, damselfish use an overall short-wavelength shifted expression profile. Interestingly, not only did all species express SWS1 - a UV-sensitive opsin - and possess UV-transmitting lenses, most species also feature UV-reflective body parts. This suggests that damsels might benefit from a close-range UV-based 'private' communication channel, which is likely to be hidden from 'UV-blind' predators. Finally, we found that LWS expression is highly correlated to feeding strategy in damsels with herbivorous feeders having an increased LWS expression, possibly enhancing the detection of benthic algae.
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Affiliation(s)
- Sara M Stieb
- Sensory Neurobiology Group, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.,Zoological Institute, University of Basel, Basel, 4051, Switzerland
| | - Fabio Cortesi
- Sensory Neurobiology Group, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.,Zoological Institute, University of Basel, Basel, 4051, Switzerland
| | - Lorenz Sueess
- Sensory Neurobiology Group, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Karen L Carleton
- Department of Biology, The University of Maryland, College Park, MD, 20742, USA
| | | | - N J Marshall
- Sensory Neurobiology Group, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
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XU W, CHEN S. Genomics and genetic breeding in aquatic animals: progress and prospects. FRONTIERS OF AGRICULTURAL SCIENCE AND ENGINEERING 2017; 4:305. [DOI: 10.15302/j-fase-2017154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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40
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The genome of the Gulf pipefish enables understanding of evolutionary innovations. Genome Biol 2016; 17:258. [PMID: 27993155 PMCID: PMC5168715 DOI: 10.1186/s13059-016-1126-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 12/05/2016] [Indexed: 11/10/2022] Open
Abstract
Background Evolutionary origins of derived morphologies ultimately stem from changes in protein structure, gene regulation, and gene content. A well-assembled, annotated reference genome is a central resource for pursuing these molecular phenomena underlying phenotypic evolution. We explored the genome of the Gulf pipefish (Syngnathus scovelli), which belongs to family Syngnathidae (pipefishes, seahorses, and seadragons). These fishes have dramatically derived bodies and a remarkable novelty among vertebrates, the male brood pouch. Results We produce a reference genome, condensed into chromosomes, for the Gulf pipefish. Gene losses and other changes have occurred in pipefish hox and dlx clusters and in the tbx and pitx gene families, candidate mechanisms for the evolution of syngnathid traits, including an elongated axis and the loss of ribs, pelvic fins, and teeth. We measure gene expression changes in pregnant versus non-pregnant brood pouch tissue and characterize the genomic organization of duplicated metalloprotease genes (patristacins) recruited into the function of this novel structure. Phylogenetic inference using ultraconserved sequences provides an alternative hypothesis for the relationship between orders Syngnathiformes and Scombriformes. Comparisons of chromosome structure among percomorphs show that chromosome number in a pipefish ancestor became reduced via chromosomal fusions. Conclusions The collected findings from this first syngnathid reference genome open a window into the genomic underpinnings of highly derived morphologies, demonstrating that de novo production of high quality and useful reference genomes is within reach of even small research groups. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1126-6) contains supplementary material, which is available to authorized users.
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41
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Boughman JW, Svanbäck R. Synergistic selection between ecological niche and mate preference primes diversification. Evolution 2016; 71:6-22. [DOI: 10.1111/evo.13089] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 10/03/2016] [Accepted: 10/05/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Janette W. Boughman
- Department of Integrative Biology Michigan State University East Lansing Michigan 48824
| | - Richard Svanbäck
- Ecology, Evolutionary Biology & Behavior program; Animal Ecology, Department of Ecology and Genetics Uppsala University Norbyvägen 18D SE‐752 36 Uppsala Sweden
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DiBattista JD, Wang X, Saenz-Agudelo P, Piatek MJ, Aranda M, Berumen ML. Draft genome of an iconic Red Sea reef fish, the blacktail butterflyfish (Chaetodon austriacus): current status and its characteristics. Mol Ecol Resour 2016; 18:347-355. [DOI: 10.1111/1755-0998.12588] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 07/05/2016] [Accepted: 07/19/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Joseph D. DiBattista
- Division of Biological and Environmental Sciences and Engineering; Red Sea Research Center; King Abdullah University of Science and Technology; Thuwal 23955 Saudi Arabia
- Department of Environment and Agriculture; Curtin University; PO Box U1987 Perth WA 6845 Australia
| | - Xin Wang
- Division of Biological and Environmental Sciences and Engineering; Red Sea Research Center; King Abdullah University of Science and Technology; Thuwal 23955 Saudi Arabia
| | - Pablo Saenz-Agudelo
- Division of Biological and Environmental Sciences and Engineering; Red Sea Research Center; King Abdullah University of Science and Technology; Thuwal 23955 Saudi Arabia
- Instituto de Ciencias Ambientales y Evolutivas; Universidad Austral de Chile; Valdivia 5090000 Chile
| | - Marek J. Piatek
- Computational Bioscience Research Center; King Abdullah University of Science and Technology; Thuwal 23955 Saudi Arabia
| | - Manuel Aranda
- Division of Biological and Environmental Sciences and Engineering; Red Sea Research Center; King Abdullah University of Science and Technology; Thuwal 23955 Saudi Arabia
| | - Michael L. Berumen
- Division of Biological and Environmental Sciences and Engineering; Red Sea Research Center; King Abdullah University of Science and Technology; Thuwal 23955 Saudi Arabia
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Stieb SM, Carleton KL, Cortesi F, Marshall NJ, Salzburger W. Depth-dependent plasticity in opsin gene expression varies between damselfish (Pomacentridae) species. Mol Ecol 2016; 25:3645-61. [DOI: 10.1111/mec.13712] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 05/10/2016] [Accepted: 05/31/2016] [Indexed: 01/02/2023]
Affiliation(s)
- Sara M. Stieb
- Zoological Institute; University of Basel; Basel 4051 Switzerland
- Queensland Brain Institute; The University of Queensland; Brisbane QLD 4072 Australia
| | - Karen L. Carleton
- Department of Biology; University of Maryland; College Park MD 20742 USA
| | - Fabio Cortesi
- Zoological Institute; University of Basel; Basel 4051 Switzerland
- Queensland Brain Institute; The University of Queensland; Brisbane QLD 4072 Australia
| | - N. Justin Marshall
- Queensland Brain Institute; The University of Queensland; Brisbane QLD 4072 Australia
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Takahashi A, Kasagi S, Murakami N, Furufuji S, Kikuchi S, Mizusawa K, Andoh T. Chronic effects of light irradiated from LED on the growth performance and endocrine properties of barfin flounder Verasper moseri. Gen Comp Endocrinol 2016; 232:101-8. [PMID: 26795919 DOI: 10.1016/j.ygcen.2016.01.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Revised: 01/03/2016] [Accepted: 01/11/2016] [Indexed: 01/07/2023]
Abstract
We investigated the effects of specific wavelengths of light on the growth of barfin flounder. The fish, reared in white tanks in a dark room, were irradiated with light from light-emitting diodes (LEDs) with peak wavelengths of 464nm (blue), 518nm (green), and 635nm (red) under a controlled photoperiod (10.5:13.5, light-dark cycle; 06:00-16:30, light). Fish were reared for four weeks in three independent experiments at three different water temperatures (averages of 14.9°C, 8.6°C, and 6.6°C). The fish irradiated with blue and green light had higher specific growth rates (% body weight⋅day(-1)) than fish irradiated with red light. Notably, green light had the greatest effect on growth among the three light wavelengths at 6.6°C. In the brains of fish reared at 6.6°C, the amounts of melanin-concentrating hormone 1 mRNA under green light were lower than those under red light, and amounts of proopiomelanocortin-C mRNA under blue and green light were higher than those under red light. No differences were observed for other neuropeptides tested. In the pituitary, no difference was observed in growth hormone mRNA content. In plasma, higher levels of insulin and insulin-like growth factor-I were observed in fish under green light than those of fish under red light. These results suggest that the endocrine systems of barfin flounder are modulated by a specific wavelength of light that stimulates somatic growth.
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Affiliation(s)
- Akiyoshi Takahashi
- School of Marine Biosciences, Kitasato University, Kanagawa 252-0373, Japan.
| | - Satoshi Kasagi
- School of Marine Biosciences, Kitasato University, Kanagawa 252-0373, Japan
| | - Naoto Murakami
- Hokkaido National Fisheries Research Institute, Fisheries Research Agency, Hokkaido 088-1108, Japan
| | | | | | - Kanta Mizusawa
- School of Marine Biosciences, Kitasato University, Kanagawa 252-0373, Japan
| | - Tadashi Andoh
- Seikai National Fisheries Research Institute, Fisheries Research Agency, Nagasaki 851-2213, Japan
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Jang JC, Choi MJ, Yang YS, Lee HB, Yu YM, Kim JM. Dim-light photoreceptor of chub mackerel Scomber japonicus and the photoresponse upon illumination with LEDs of different wavelengths. FISH PHYSIOLOGY AND BIOCHEMISTRY 2016; 42:1015-1025. [PMID: 26746848 DOI: 10.1007/s10695-015-0193-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/28/2015] [Indexed: 06/05/2023]
Abstract
To study the absorption characteristics of rhodopsin, a dim-light photoreceptor, in chub mackerel (Scomber japonicus) and the relationship between light wavelengths on the photoresponse, the rod opsin gene was cloned into an expression vector, pMT4. Recombinant opsin was transiently expressed in COS-1 cells and reconstituted with 11-cis-retinal. Cells containing the regenerated rhodopsin were solubilized and subjected to UV/Vis spectroscopic analysis in the dark and upon illumination. Difference spectra from the lysates indicated an absorption maximum of mackerel rhodopsin around 500 nm. Four types of light-emitting diode (LED) modules with different wavelengths (red, peak 627 nm; cyan, 505 nm; blue, 442 nm; white, 447 + 560 nm) were constructed to examine their effects on the photoresponse in chub mackerel. Behavioral responses of the mackerels, including speed and frequencies acclimated in the dark and upon LED illumination, were analyzed using an underwater acoustic camera. Compared to an average speed of 22.25 ± 1.57 cm/s of mackerel movement in the dark, speed increased to 22.97 ± 0.29, 24.66 ± 1.06, 26.28 ± 2.28, and 25.19 ± 1.91 cm/s upon exposure to red, blue, cyan, and white LEDs, respectively. There were increases of 103.48 ± 1.58, 109.37 ± 5.29, 118.48 ± 10.82, and 109.43 ± 3.92 %, respectively, in the relative speed of the fishes upon illumination with red, blue, cyan, and white LEDs compared with that in the dark (set at 100 %). Similar rate of wavelength-dependent responses was observed in a frequency analysis. These results indicate that an LED emitting a peak wavelength close to an absorption maximum of rhodopsin is more effective at eliciting a response to light.
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Affiliation(s)
- Jun-Chul Jang
- Department of Fisheries Biology, Pukyong National University, 45 Yongso-ro, Nam-gu, Busan, 608-737, Korea
- LED-Marine Convergence Technology R&BD Center, Pukyong National University, 365 Sinseon-ro, Nam-gu, Busan, 608-739, Korea
| | - Mi-Jin Choi
- Department of Fisheries Biology, Pukyong National University, 45 Yongso-ro, Nam-gu, Busan, 608-737, Korea
| | - Yong-Soo Yang
- Fisheries System Engineering Division, National Institute of Fisheries Science, Gijang, Busan, 46083, Korea
| | - Hyung-Been Lee
- Fisheries System Engineering Division, National Institute of Fisheries Science, Gijang, Busan, 46083, Korea
| | - Young-Moon Yu
- LED-Marine Convergence Technology R&BD Center, Pukyong National University, 365 Sinseon-ro, Nam-gu, Busan, 608-739, Korea
| | - Jong-Myoung Kim
- Department of Fisheries Biology, Pukyong National University, 45 Yongso-ro, Nam-gu, Busan, 608-737, Korea.
- Dept. of Marine BioMaterials & Aquaculture, Pukyong National University, 45 Yongso-ro, Nam-gu, Busan, 608-737, Korea.
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Bar I, Cummins S, Elizur A. Transcriptome analysis reveals differentially expressed genes associated with germ cell and gonad development in the Southern bluefin tuna (Thunnus maccoyii). BMC Genomics 2016; 17:217. [PMID: 26965070 PMCID: PMC4785667 DOI: 10.1186/s12864-016-2397-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 01/14/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Controlling and managing the breeding of bluefin tuna (Thunnus spp.) in captivity is an imperative step towards obtaining a sustainable supply of these fish in aquaculture production systems. Germ cell transplantation (GCT) is an innovative technology for the production of inter-species surrogates, by transplanting undifferentiated germ cells derived from a donor species into larvae of a host species. The transplanted surrogates will then grow and mature to produce donor-derived seed, thus providing a simpler alternative to maintaining large-bodied broodstock such as the bluefin tuna. Implementation of GCT for new species requires the development of molecular tools to follow the fate of the transplanted germ cells. These tools are based on key reproductive and germ cell-specific genes. RNA-Sequencing (RNA-Seq) provides a rapid, cost-effective method for high throughput gene identification in non-model species. This study utilized RNA-Seq to identify key genes expressed in the gonads of Southern bluefin tuna (Thunnus maccoyii, SBT) and their specific expression patterns in male and female gonad cells. RESULTS Key genes involved in the reproductive molecular pathway and specifically, germ cell development in gonads, were identified using analysis of RNA-Seq transcriptomes of male and female SBT gonad cells. Expression profiles of transcripts from ovary and testis cells were compared, as well as testis germ cell-enriched fraction prepared with Percoll gradient, as used in GCT studies. Ovary cells demonstrated over-expression of genes related to stem cell maintenance, while in testis cells, transcripts encoding for reproduction-associated receptors, sex steroids and hormone synthesis and signaling genes were over-expressed. Within the testis cells, the Percoll-enriched fraction showed over-expression of genes that are related to post-meiosis germ cell populations. CONCLUSIONS Gonad development and germ cell related genes were identified from SBT gonads and their expression patterns in ovary and testis cells were determined. These expression patterns correlate with the reproductive developmental stage of the sampled fish. The majority of the genes described in this study were sequenced for the first time in T. maccoyii. The wealth of SBT gonadal and germ cell-related gene sequences made publicly available by this study provides an extensive resource for further GCT and reproductive molecular biology studies of this commercially valuable fish.
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Affiliation(s)
- Ido Bar
- Genecology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, 4558 Maroochydore DC, Queensland, Australia
| | - Scott Cummins
- Genecology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, 4558 Maroochydore DC, Queensland, Australia
| | - Abigail Elizur
- Genecology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, 4558 Maroochydore DC, Queensland, Australia
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Shibata M, Mekuchi M, Mori K, Muta S, Chowdhury VS, Nakamura Y, Ojima N, Saitoh K, Kobayashi T, Wada T, Inouye K, Kuhara S, Tashiro K. Transcriptomic features associated with energy production in the muscles of Pacific bluefin tuna and Pacific cod. Biosci Biotechnol Biochem 2016; 80:1114-24. [PMID: 26924100 DOI: 10.1080/09168451.2016.1151341] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Bluefin tuna are high-performance swimmers and top predators in the open ocean. Their swimming is grounded by unique features including an exceptional glycolytic potential in white muscle, which is supported by high enzymatic activities. Here we performed high-throughput RNA sequencing (RNA-Seq) in muscles of the Pacific bluefin tuna (Thunnus orientalis) and Pacific cod (Gadus macrocephalus) and conducted a comparative transcriptomic analysis of genes related to energy production. We found that the total expression of glycolytic genes was much higher in the white muscle of tuna than in the other muscles, and that the expression of only six genes for glycolytic enzymes accounted for 83.4% of the total. These expression patterns were in good agreement with the patterns of enzyme activity previously reported. The findings suggest that the mRNA expression of glycolytic genes may contribute directly to the enzymatic activities in the muscles of tuna.
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Affiliation(s)
- Mami Shibata
- a Graduate School of Bioresource and Bioenvironmental Sciences , Kyushu University , Fukuoka , Japan
| | - Miyuki Mekuchi
- b Research Center for Aquatic Genomics, National Research Institute of Fisheries Science , Fisheries Research Agency , Yokohama , Japan
| | - Kazuki Mori
- c Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST) , Tokyo , Japan
| | - Shigeru Muta
- d Laboratory of Molecular Gene Techniques, Division of Molecular Biosciences, Department of Bioscience and Biotechnology, Faculty of Agriculture , Kyushu University , Fukuoka , Japan
| | - Vishwajit Sur Chowdhury
- e Division for Experimental Natural Science, Faculty of Arts and Science , Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University , Fukuoka , Japan
| | - Yoji Nakamura
- b Research Center for Aquatic Genomics, National Research Institute of Fisheries Science , Fisheries Research Agency , Yokohama , Japan
| | - Nobuhiko Ojima
- b Research Center for Aquatic Genomics, National Research Institute of Fisheries Science , Fisheries Research Agency , Yokohama , Japan
| | - Kenji Saitoh
- b Research Center for Aquatic Genomics, National Research Institute of Fisheries Science , Fisheries Research Agency , Yokohama , Japan
| | | | - Tokio Wada
- f Fisheries Research Agency , Yokohama , Japan
| | - Kiyoshi Inouye
- g Japan Fisheries Science and Technology Association , Tokyo , Japan
| | - Satoru Kuhara
- d Laboratory of Molecular Gene Techniques, Division of Molecular Biosciences, Department of Bioscience and Biotechnology, Faculty of Agriculture , Kyushu University , Fukuoka , Japan
| | - Kosuke Tashiro
- d Laboratory of Molecular Gene Techniques, Division of Molecular Biosciences, Department of Bioscience and Biotechnology, Faculty of Agriculture , Kyushu University , Fukuoka , Japan
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The genome of the miiuy croaker reveals well-developed innate immune and sensory systems. Sci Rep 2016; 6:21902. [PMID: 26902509 PMCID: PMC4763219 DOI: 10.1038/srep21902] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 01/27/2016] [Indexed: 01/08/2023] Open
Abstract
The miiuy croaker, Miichthys miiuy, is a representative Sciaenidae known for its exceptionally large otoliths. This species mainly inhabits turbid aquatic environments with mud to sandy mud bottoms. However, the characteristics of the immune system of this organism and its specific aquatic environment adaptations are poorly understood. Thus, we present a high-quality draft genome of miiuy croaker. The expansions of several gene families which are critical for the fish innate immune system were identified. Compared with the genomes of other fishes, some changes have occurred in the miiuy croaker sensory system including modification of vision and expansion of taste and olfaction receptors. These changes allow miiuy croaker to adapt to the environment during the long-term natural selection. The genome of miiuy croaker may elucidate its relatively well-developed immune defense and provide an adaptation model of the species thriving in turbid deep aquatic environments.
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Uchino T, Nakamura Y, Sekino M, Kai W, Fujiwara A, Yasuike M, Sugaya T, Fukuda H, Sano M, Sakamoto T. Constructing Genetic Linkage Maps Using the Whole Genome Sequence of Pacific Bluefin Tuna (<i>Thunnus orientalis</i>) and a Comparison of Chromosome Structure among Teleost Species. ACTA ACUST UNITED AC 2016. [DOI: 10.4236/abb.2016.72010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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50
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Pecoraro C, Babbucci M, Villamor A, Franch R, Papetti C, Leroy B, Ortega-Garcia S, Muir J, Rooker J, Arocha F, Murua H, Zudaire I, Chassot E, Bodin N, Tinti F, Bargelloni L, Cariani A. Methodological assessment of 2b-RAD genotyping technique for population structure inferences in yellowfin tuna (Thunnus albacares). Mar Genomics 2015; 25:43-48. [PMID: 26711352 DOI: 10.1016/j.margen.2015.12.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 12/01/2015] [Accepted: 12/08/2015] [Indexed: 12/18/2022]
Abstract
Global population genetic structure of yellowfin tuna (Thunnus albacares) is still poorly understood despite its relevance for the tuna fishery industry. Low levels of genetic differentiation among oceans speak in favour of the existence of a single panmictic population worldwide of this highly migratory fish. However, recent studies indicated genetic structuring at a much smaller geographic scales than previously considered, pointing out that YFT population genetic structure has not been properly assessed so far. In this study, we demonstrated for the first time, the utility of 2b-RAD genotyping technique for investigating population genetic diversity and differentiation in high gene-flow species. Running de novo pipeline in Stacks, a total of 6772 high-quality genome-wide SNPs were identified across Atlantic, Indian and Pacific population samples representing all major distribution areas. Preliminary analyses showed shallow but significant population structure among oceans (FST=0.0273; P-value<0.01). Discriminant Analysis of Principal Components endorsed the presence of genetically discrete yellowfin tuna populations among three oceanic pools. Although such evidence needs to be corroborated by increasing sample size, these results showed the efficiency of this genotyping technique in assessing genetic divergence in a marine fish with high dispersal potential.
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Affiliation(s)
- Carlo Pecoraro
- Dept. Biological, Geological and Environmental Sciences (BIGEA), University of Bologna, Via Selmi 3, 40126 Bologna, Italy; Institut de Recherche pour le Développement (IRD), UMR MARBEC (IRD/Ifremer/UM2/CNRS) SFA, Fishing Port, BP570 Victoria, Seychelles.
| | - Massimiliano Babbucci
- Comparative Biomedicine and Food Science, University of Padova, viale dell'Università 16, 35020 Legnaro, PD, Italy.
| | - Adriana Villamor
- Dept. Biological, Geological and Environmental Sciences (BIGEA), University of Bologna, Via Selmi 3, 40126 Bologna, Italy.
| | - Rafaella Franch
- Comparative Biomedicine and Food Science, University of Padova, viale dell'Università 16, 35020 Legnaro, PD, Italy.
| | - Chiara Papetti
- Section of Integrative Ecophysiology, Alfred-Wegener-Institute for Polar and Marine Research, Am Handelshafen 12, Bremerhaven 27570, Germany.
| | - Bruno Leroy
- Secretariat of the Pacific Community, Oceanic Fishery Programme, BP D5, 98848 Noumea, New Caledonia.
| | - Sofia Ortega-Garcia
- Departamento de Pesquerias, Instituto Politécnico Nacional-CICIMAR, Avenida IPN s/n, La Paz, BCS, Mexico.
| | - Jeff Muir
- Pelagic Fisheries Research Program, University of Hawaii, Marine Science Building 312, Honolulu, HI 96822, USA.
| | - Jay Rooker
- Department of Marine Biology, Texas A&M University, 1001 Texas Clipper Road, Galveston, TX 77553, USA.
| | - Freddy Arocha
- Instituto Oceanográfico de Venezuela, Universidad de Oriente, Avda. Universidad Cerro Colorado, Cumana 6101, Venezuela.
| | - Hilario Murua
- Marine Research Division, AZTI, Herrera Kaia-Portualdea z/g, Pasaia, 20110, Gipuzkoa, Spain.
| | - Iker Zudaire
- Ikerbasque Fundazioa, Maria Diaz de Haro, 3-6°, Bilbao, 48013, Bizkaia, Spain; Institut de Recherche pour le Développement (IRD), UMR MARBEC (IRD/Ifremer/UM2/CNRS) SFA, Fishing Port, BP570 Victoria, Seychelles
| | - Emmanuel Chassot
- Institut de Recherche pour le Développement (IRD), UMR MARBEC (IRD/Ifremer/UM2/CNRS) SFA, Fishing Port, BP570 Victoria, Seychelles.
| | - Nathalie Bodin
- Institut de Recherche pour le Développement (IRD), UMR MARBEC (IRD/Ifremer/UM2/CNRS) SFA, Fishing Port, BP570 Victoria, Seychelles.
| | - Fausto Tinti
- Dept. Biological, Geological and Environmental Sciences (BIGEA), University of Bologna, Via Selmi 3, 40126 Bologna, Italy.
| | - Luca Bargelloni
- Comparative Biomedicine and Food Science, University of Padova, viale dell'Università 16, 35020 Legnaro, PD, Italy.
| | - Alessia Cariani
- Dept. Biological, Geological and Environmental Sciences (BIGEA), University of Bologna, Via Selmi 3, 40126 Bologna, Italy.
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