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Macpherson ESB, Hauser FE, Van Nynatten A, Chang BSW, Lovejoy NR. Evolution of rhodopsin in flatfishes (Pleuronectiformes) is associated with depth and migratory behavior. JOURNAL OF FISH BIOLOGY 2024. [PMID: 38859571 DOI: 10.1111/jfb.15828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 04/06/2024] [Accepted: 05/17/2024] [Indexed: 06/12/2024]
Abstract
Visual signals are involved in many fitness-related tasks and are therefore essential for survival in many species. Aquatic organisms are ideal systems to study visual evolution, as the high diversity of spectral properties in aquatic environments generates great potential for adaptation to different light conditions. Flatfishes are an economically important group, with over 800 described species distributed globally, including halibut, flounder, sole, and turbot. The diversity of flatfish species and wide array of environments they occupy provides an excellent opportunity to understand how this variation translates to molecular adaptation of vision genes. Using models of molecular evolution, we investigated how the light environments inhabited by different flatfish lineages have shaped evolution in the rhodopsin gene, which is responsible for mediating dim-light visual transduction. We found strong evidence for positive selection in rhodopsin, and this was correlated with both migratory behavior and several fundamental aspects of habitat, including depth and freshwater/marine evolutionary transitions. We also identified several mutations that likely affect the wavelength of peak absorbance of rhodopsin, and outline how these shifts in absorbance correlate with the response to the light spectrum present in different habitats. This is the first study of rhodopsin evolution in flatfishes that considers their extensive diversity, and our results highlight how ecologically-driven molecular adaptation has occurred across this group in response to transitions to novel light environments.
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Affiliation(s)
- Esme S B Macpherson
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Frances E Hauser
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Alexander Van Nynatten
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Belinda S W Chang
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Nathan R Lovejoy
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
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2
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Wang Y, Zhang X, Wang J, Wang C, Xiong F, Qian Y, Meng M, Zhou M, Chen W, Ding Z, Yu D, Liu Y, Chang Y, He S, Yang L. Genomic insights into the seawater adaptation in Cyprinidae. BMC Biol 2024; 22:87. [PMID: 38637780 PMCID: PMC11027309 DOI: 10.1186/s12915-024-01885-2] [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: 12/11/2023] [Accepted: 04/11/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Cyprinidae, the largest fish family, encompasses approximately 367 genera and 3006 species. While they exhibit remarkable adaptability to diverse aquatic environments, it is exceptionally rare to find them in seawater, with the Far Eastern daces being of few exceptions. Therefore, the Far Eastern daces serve as a valuable model for studying the genetic mechanisms underlying seawater adaptation in Cyprinidae. RESULTS Here, we sequenced the chromosome-level genomes of two Far Eastern daces (Pseudaspius brandtii and P. hakonensis), the two known cyprinid fishes found in seawater, and performed comparative genomic analyses to investigate their genetic mechanism of seawater adaptation. Demographic history reconstruction of the two species reveals that their population dynamics are correlated with the glacial-interglacial cycles and sea level changes. Genomic analyses identified Pseudaspius-specific genetic innovations related to seawater adaptation, including positively selected genes, rapidly evolving genes, and conserved non-coding elements (CNEs). Functional assays of Pseudaspius-specific variants of the prolactin (prl) gene showed enhanced cell adaptation to greater osmolarity. Functional assays of Pseudaspius specific CNEs near atg7 and usp45 genes suggest that they exhibit higher promoter activity and significantly induced at high osmolarity. CONCLUSIONS Our results reveal the genome-wide evidence for the evolutionary adaptation of cyprinid fishes to seawater, offering valuable insights into the molecular mechanisms supporting the survival of migratory fish in marine environments. These findings are significant as they contribute to our understanding of how cyprinid fishes navigate and thrive in diverse aquatic habitats, providing useful implications for the conservation and management of marine ecosystems.
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Affiliation(s)
- Ying Wang
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, 430056, China.
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China.
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, BS81TQ, UK.
| | - Xuejing Zhang
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, 430056, China
| | - Jing Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Cheng Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fei Xiong
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, 430056, China
| | - Yuting Qian
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Minghui Meng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Min Zhou
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, 430056, China
| | - Wenjun Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zufa Ding
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dan Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yumei Chang
- National and Local Joint Engineering Laboratory for Freshwater Fish Breeding, Heilongjiang Province's Key Laboratory of Fish Stress Resistance Breeding and Germplasm Characteristics On Special Habitats, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, Heilongjiang, China
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China.
| | - Liandong Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China.
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, BS81TQ, UK.
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Lin YT, Hung WC, Yeh YF, Lu KM, Cherng DH, Han YS. Effects of Different LED Light Spectra on Growth and Immunity of the Japanese Eel ( Anguilla japonica) and Giant Mottled Eel ( A. marmorata). Zool Stud 2023; 62:e28. [PMID: 37671172 PMCID: PMC10475466 DOI: 10.6620/zs.2023.62-28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 04/28/2023] [Indexed: 09/07/2023]
Abstract
Indoor recirculating aquaculture systems make light control possible and enable the usage of specific coloured lights to promote the growth and immunity of aquaculture species. Five different LED wavelengths (white light [460 nm], red light [622 nm], green light [517 nm], blue light [467 nm], and the dark) were used in this study to evaluate growth and immunity in the glass eel stage of two high-valued anguillid species, Japanese eel (Anguilla japonica) and giant mottled eel (A. marmorata). There were no significant differences in growth of the Japanese eel among the groups after 12 weeks of feeding (p > 0.05); the survival rate of each group was over 95%. The giant mottled eel showed better growth in total length and body weight in the red light and dark groups (p < 0.05). Expression levels of immune-related genes were not significantly different between each group of the Japanese eel and the giant mottled eel (p > 0.05). The growth of the Japanese glass eel was not significantly sensitive to different LED wavelengths, while the giant mottled glass eel showed better growth under red light and dark environments. Neither eel species showed significant differences in innate immunity under different LED wavelengths.
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Affiliation(s)
- Yen-Ting Lin
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei 10617, Taiwan. E-mail: (Han); (Lin); (Hung)
| | - Wei-Chun Hung
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei 10617, Taiwan. E-mail: (Han); (Lin); (Hung)
| | - Yin-Fu Yeh
- Everlight Electronics Co., LTD. No.6-8, Zhonghua Rd., Shulin Dist., New Taipei City 23860, Taiwan. E-mail: (Yeh); (Cherng)
| | - Kuang-Mao Lu
- Everlight Electronics Co., LTD. No.6-8, Zhonghua Rd., Shulin Dist., New Taipei City 23860, Taiwan. E-mail: (Yeh); (Cherng)
| | - Ding-Hwa Cherng
- Everlight Electronics Co., LTD. No.6-8, Zhonghua Rd., Shulin Dist., New Taipei City 23860, Taiwan. E-mail: (Yeh); (Cherng)
| | - Yu-San Han
- Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei 10617, Taiwan. E-mail: (Han); (Lin); (Hung)
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Gao J, Xu G, Xu P. Whole-genome resequencing of three Coilia nasus population reveals genetic variations in genes related to immune, vision, migration, and osmoregulation. BMC Genomics 2021; 22:878. [PMID: 34872488 PMCID: PMC8647404 DOI: 10.1186/s12864-021-08182-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/17/2021] [Indexed: 11/17/2022] Open
Abstract
Background Coilia nasus is an important anadromous fish, widely distributed in China, Japan, and Korea. Based on morphological and ecological researches of C. nasus, two ecotypes were identified. One is the anadromous population (AP). The sexually mature fish run thousands of kilometers from marine to river for spawning. Another one is the resident population which cannot migrate. Based on their different habitats, they were classified into landlocked population (LP) and sea population (SP) which were resident in the freshwater lake and marine during the entire lifetime, respectively. However, they have never been systematically studied. Moreover, C. nasus is declining sharply due to overfishing and pollution recently. Therefore, further understandings of C. nasus populations are needed for germplasm protection. Results Whole-genome resequencing of AP, LP, and SP were performed to enrich the understanding of different populations of C. nasus. At the genome level, 3,176,204, 3,307,069, and 3,207,906 single nucleotide polymorphisms (SNPs) and 1,892,068, 2,002,912, and 1,922,168 insertion/deletion polymorphisms (InDels) were generated in AP, LP, and SP, respectively. Selective sweeping analysis showed that 1022 genes were selected in AP vs LP; 983 genes were selected in LP vs SP; 116 genes were selected in AP vs SP. Among them, selected genes related to immune, vision, migration, and osmoregulation were identified. Furthermore, their expression profiles were detected by quantitative real-time PCR. Expression levels of selected genes related to immune, and vision in LP were significantly lower than AP and SP. Selected genes related to migration in AP were expressed significantly more highly than LP. Expression levels of selected genes related to osmoregulation were also detected. The expression of NKAα and NKCC1 in LP were significantly lower than SP, while expression of NCC, SLC4A4, NHE3, and V-ATPase in LP was significantly higher than SP. Conclusions Combined to life history of C. nasus populations, our results revealed that the molecular mechanisms of their differences of immune, vision, migration, and osmoregulation. Our findings will provide a further understanding of different populations of C. nasus and will be beneficial for wild C. nasus protection. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08182-0.
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Affiliation(s)
- Jun Gao
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, Jiangsu, China
| | - Gangchun Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, Jiangsu, China. .,Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, Jiangsu, China.
| | - Pao Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, Jiangsu, China. .,Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, Jiangsu, China.
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5
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Chang CH, Catchen J, Moran RL, Rivera-Colón AG, Wang YC, Fuller RC. Sequence Analysis and Ontogenetic Expression Patterns of Cone Opsin Genes in the Bluefin Killifish (Lucania goodei). J Hered 2021; 112:357-366. [PMID: 33837393 DOI: 10.1093/jhered/esab017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Sensory systems allow for the transfer of environmental stimuli into internal cues that can alter physiology and behavior. Many studies of visual systems focus on opsins to compare spectral sensitivity among individuals, populations, and species living in different lighting environments. This requires an understanding of the cone opsins, which can be numerous. The bluefin killifish is a good model for studying the interaction between environments and visual systems as they are found in both clear springs and tannin-stained swamps. We conducted a genome-wide screening and demonstrated that the bluefin killifish has 9 cone opsins: 1 SWS1 (354 nm), 2 SWS2 (SWS2B: 359 nm, SWS2A: 448 nm), 2 RH2 (RH2-2: 476 nm, RH2-1: 537 nm), and 4 LWS (LWS-1: 569 nm, LWS-2: 524 nm, LWS-3: 569 nm, LWS-R: 560 or 569 nm). These 9 cone opsins were located on 4 scaffolds. One scaffold contained the 2 SWS2 and 3 of the 4 LWS opsins in the same syntenic order as found in other cyprinodontoid fishes. We also compared opsin expression in larval and adult killifish under clear water conditions, which mimic springs. Two of the newly discovered opsins (LWS-2 and LWS-3) were expressed at low levels (<0.2%). Whether these opsins make meaningful contributions to visual perception in other contexts (i.e., swamp conditions) is unclear. In contrast, there was an ontogenetic change from using LWS-R to LWS-1 opsin. Bluefin killifish adults may be slightly more sensitive to longer wavelengths, which might be related to sexual selection and/or foraging preferences.
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Affiliation(s)
- Chia-Hao Chang
- TIGP, Biodiversity Program, Tunghai University, Taiwan Boulevard, Taichung City, Taiwan
| | - Julian Catchen
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, South Goodwin, Urbana, IL
| | - Rachel L Moran
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN
| | - Angel G Rivera-Colón
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, South Goodwin, Urbana, IL
| | - Yu-Chun Wang
- Planning and Information Division, Fisheries Research Institute, Keelung City, Taiwan
| | - Rebecca C Fuller
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, 606 East Healey Street, Champaign, IL
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6
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Basili D, Gioacchini G, Todisco V, Candelma M, Marisaldi L, Pappalardo L, Carnevali O. Opsins and gonadal circadian rhythm in the swordfish (Xiphias gladius) ovary: Their potential roles in puberty and reproductive seasonality. Gen Comp Endocrinol 2021; 303:113707. [PMID: 33387470 DOI: 10.1016/j.ygcen.2020.113707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 12/07/2020] [Accepted: 12/28/2020] [Indexed: 01/02/2023]
Abstract
Circadian rhythm is well known to play a pivotal role in reproduction but the presence of a gonadal circadian rhythm is opening a lot of questions about a local regulation of reproduction. In the present study, we first set to identify the key genes driving circadian rhythmicity from the gonadal transcriptome of the swordfish, a commercially relevant species undergoing overfishing, and we then investigated whether their transcriptional activity was influenced by the maturation stage. Finally, we explored whether seasonality had the ability to modulate the expression of these genes. Interestingly, we identified a wide number of circadian rhythm related genes in the transcriptome of the swordfish gonad including, among the others, clock, bmal1, cry2 and per2, which have been found to be differentially expressed between sexually immature and mature individuals sampled during the breeding season. This differential modulation was also found for melatonin biosynthesis genes (mel1b, asmt and tph1) as well as opsin genes (opsin4, tmt opsin, parapinopsin, VA opsin, rho and sws), known to be the primary receptors of light stimuli. These differences were not observed between mature and immature individuals when considering the non-breeding season suggesting that, despite the molecular machinery of mature gonads is able to respond to signals driving ovarian maturation, these signals are not present hence highlighting the potential role of seasonality in modulating the gonadal circadian rhythm. These results confirm the presence of a gonadal circadian rhythm in the swordfish and open new interesting questions about its role in driving puberty onset.
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Affiliation(s)
- Danilo Basili
- Dipartimento di Scienze della Vita e dell'Ambiente, Universita' Politecnica delle Marche, Ancona, Italy
| | - Giorgia Gioacchini
- Dipartimento di Scienze della Vita e dell'Ambiente, Universita' Politecnica delle Marche, Ancona, Italy
| | - Vittoria Todisco
- Dipartimento di Scienze della Vita e dell'Ambiente, Universita' Politecnica delle Marche, Ancona, Italy
| | - Michela Candelma
- Dipartimento di Scienze della Vita e dell'Ambiente, Universita' Politecnica delle Marche, Ancona, Italy
| | - Luca Marisaldi
- Dipartimento di Scienze della Vita e dell'Ambiente, Universita' Politecnica delle Marche, Ancona, Italy
| | | | - Oliana Carnevali
- Dipartimento di Scienze della Vita e dell'Ambiente, Universita' Politecnica delle Marche, Ancona, Italy.
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7
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Chang CH, Wang YC, Shao YT, Liu SH. Phylogenetic analysis and ontogenetic changes in the cone opsins of the western mosquitofish (Gambusia affinis). PLoS One 2020; 15:e0240313. [PMID: 33048954 PMCID: PMC7553354 DOI: 10.1371/journal.pone.0240313] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/23/2020] [Indexed: 11/25/2022] Open
Abstract
To convert external light into internal neural signal, vertebrates rely on a special group of proteins, the visual opsins. Four of the five types of visual opsins—short-wavelength sensitive 1 (Sws1), short-wavelength sensitive 2 (Sws2), medium-wavelength sensitive (Rh2), and long-wavelength sensitive (Lws)—are expressed in cone cells for scotopic vision, with the fifth, rhodopsin (Rh1), being expressed in rod cells for photopic vision. Fish often display differing ontogenetic cone opsin expression profiles, which may be related to dietary and/or habitat ontogenetic shift. The western mosquitofish (Gambusia affinis) is an aggressive invader that has successfully colonized every continent except Antarctica. The strong invasiveness of this species may be linked to its visual acuity since it can inhabit turbid waters better than other fishes. By genome screening and transcriptome analysis, we identify seven cone opsin genes in the western mosquitofish, including one sws1, two sws2, one rh2, and three lws. The predicted maximal absorbance wavelength (λmax) values of the respective proteins are 353 nm for Sws1, 449 nm for Sws2a, 408 nm for Sws2b, 516 nm for Rh2-1, 571 nm for Lws-1, and 519 nm for Lws-3. Retention of an intron in the lws-r transcript likely renders this visual opsin gene non-functional. Our real-time quantitative PCR demonstrates that adult male and female western mosquitofish do not differ in their cone opsin expression profiles, but we do reveal an ontogenetic shift in cone opsin expression. Compared to adults, larvae express proportionally more sws1 and less lws-1, suggesting that the western mosquitofish is more sensitive to shorter wavelengths in the larval stage, but becomes more sensitive to longer wavelengths in adulthood.
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Affiliation(s)
- Chia-Hao Chang
- TIGP Biodiversity Program, Tunghai University, Taichung City, Taiwan
- Center for Ecology and Environment, Tunghai University, Taichung City, Taiwan
| | - Yu-Chun Wang
- Planning and Information Division, Fisheries Research Institute, Keelung City, Taiwan
| | - Yi Ta Shao
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, Taiwan
| | - Shih-Hui Liu
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung City, Taiwan
- * E-mail: ,
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8
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Huyen KT, Linh NQ. Phylogenetic analysis of Anguilla marmorata population in Thua Thien Hue, Vietnam based on the cytochrome C oxidase I (COI) gene fragments. AMB Express 2020; 10:122. [PMID: 32638238 PMCID: PMC7340690 DOI: 10.1186/s13568-020-01059-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 07/02/2020] [Indexed: 11/20/2022] Open
Abstract
The giant mottled eel is a species with high commercial value so overfishing, river management, and water pollution have negatively affected its movement and population numbers. Anguilla marmorata (eel) was listed in the Vietnam Red Data Book 2007 with a description of Vulnerability. This study used a barcode technique to analyze molecular characteristics and build genetic plants based on the cytochrome c oxidase I gene segment isolated from the mitochondrial genome of 48 individuals of A. marmorata collected in five different ecological regions of Thua Thien Hue, Vietnam. The isolated the cytochrome c oxidase I sequence has a length of 843 nucleotides, four base nucleotides of 30.03% Thymine, 25.15% Cytosine, 27.49% Adenine, and 17.43% Guanine. The percentage of Guanine + Cytosine content (42.58%) is acceptable, lower than the Adenine + Thymine content. The replacement capacity of Adenine and Guanine is 22.45% highest, the ratio between Thymine and Guanine; Cytosine and Guanine are the lowest at 2.72%. The establishment of genetically modified plants has shown the high genetic similarity of individuals in eel populations in Thua Thien Hue. The population of Anguilla marmorata eels in Thua Thien Hue, Vietnam is divided into two separate groups that are guided by the migration process and specific ecological. This is particularly important in building strategies to conserve and develop the gene for eel in Vietnam and Thua Thien Hue.
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9
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Byun JH, Hyeon JY, Kim ES, Kim BH, Miyanishi H, Kagawa H, Takeuchi Y, Kim SJ, Takemura A, Hur SP. Gene expression patterns of novel visual and non-visual opsin families in immature and mature Japanese eel males. PeerJ 2020; 8:e8326. [PMID: 32149019 PMCID: PMC7049458 DOI: 10.7717/peerj.8326] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 12/02/2019] [Indexed: 01/24/2023] Open
Abstract
This study was carried out to identify and estimate physiological function of a new type of opsin subfamily present in the retina and whole brain tissues of Japanese eel using RNA–Seq transcriptome method. A total of 18 opsin subfamilies were identified through RNA–seq. The visual opsin family included Rh2, SWS2, FWO, DSO, and Exo-Rhod. The non-visual opsin family included four types of melanopsin subfamily (Opn4x1, Opn4x2, Opn4m1, and Opn4m2), peropsin, two types of neuropsin subfamily (Opn5-like, Opn5), Opn3, three types of TMT opsin subfamily (TMT1, 2, 3), VA-opsin, and parapinopsin. In terms of changes in photoreceptor gene expression in the retina of sexually mature and immature male eels, DSO mRNA increased in the maturation group. Analysis of expression of opsin family gene in male eel brain before and after maturation revealed that DSO and SWS2 expression in terms of visual opsin mRNA increased in the sexually mature group. In terms of non-visual opsin mRNA, parapinopsin mRNA increased whereas that of TMT2 decreased in the fore-brain of the sexually mature group. The mRNA for parapinopsin increased in the mid-brain of the sexually mature group, whereas those of TMT1 and TMT3 increased in the hind-brain of the sexually mature group. DSO mRNA also increased in the retina after sexual maturation, and DSO and SWS2 mRNA increased in whole brain part, suggesting that DSO and SWS2 are closely related to sexual maturation.
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Affiliation(s)
- Jun-Hwan Byun
- Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Ji-Yeon Hyeon
- Jeju Research Institute, Korea Institute of Ocean Science & Technology, Jeju, Jeju, Republic of Korea.,Department of Biology, Jeju National University, Jeju, Jeju, Republic of Korea
| | - Eun-Su Kim
- Jeju Research Institute, Korea Institute of Ocean Science & Technology, Jeju, Jeju, Republic of Korea.,Department of Biology, Jeju National University, Jeju, Jeju, Republic of Korea
| | - Byeong-Hoon Kim
- Marine Science Institute, Jeju National University, Jeju, Jeju, Republic of Korea
| | - Hiroshi Miyanishi
- Department of Marine Biology and Environmental Sciences, Faculty of Agriculture, University of Miyazaki, Gakuen-Kibanadai-Nishi, Miyazaki, Japan
| | - Hirohiko Kagawa
- Department of Marine Biology and Environmental Sciences, Faculty of Agriculture, University of Miyazaki, Gakuen-Kibanadai-Nishi, Miyazaki, Japan
| | - Yuki Takeuchi
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Se-Jae Kim
- Department of Biology, Jeju National University, Jeju, Jeju, Republic of Korea
| | - Akihiro Takemura
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Sung-Pyo Hur
- Jeju Research Institute, Korea Institute of Ocean Science & Technology, Jeju, Jeju, Republic of Korea.,Department of Biology, Jeju National University, Jeju, Jeju, Republic of Korea
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Xu G, Bian C, Nie Z, Li J, Wang Y, Xu D, You X, Liu H, Gao J, Li H, Liu K, Yang J, Li Q, Shao N, Zhuang Y, Fang D, Jiang T, Lv Y, Huang Y, Gu R, Xu J, Ge W, Shi Q, Xu P. Genome and population sequencing of a chromosome-level genome assembly of the Chinese tapertail anchovy (Coilia nasus) provides novel insights into migratory adaptation. Gigascience 2020; 9:giz157. [PMID: 31895412 PMCID: PMC6939831 DOI: 10.1093/gigascience/giz157] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 09/28/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Seasonal migration is one of the most spectacular events in nature; however, the molecular mechanisms related to this phenomenon have not been investigated in detail. The Chinese tapertail, or Japanese grenadier anchovy, Coilia nasus, is a valuable migratory fish of high economic importance and special migratory dimorphism (with certain individuals as non-migratory residents). RESULTS In this study, an 870.0-Mb high-quality genome was assembled by the combination of Illumina and Pacific Biosciences sequencing. Approximately 812.1 Mb of scaffolds were linked to 24 chromosomes using a high-density genetic map from a family of 104 full siblings and their parents. In addition, population sequencing of 96 representative individuals from diverse areas along the putative migration path identified 150 candidate genes, which are mainly enriched in 3 Ca2+-related pathways. Based on integrative genomic and transcriptomic analyses, we determined that the 3 Ca2+-related pathways are critical for promotion of migratory adaption. A large number of molecular markers were also identified, which distinguished migratory individuals and non-migratory freshwater residents. CONCLUSIONS We assembled a chromosome-level genome for the Chinese tapertail anchovy. The genome provided a valuable genetic resource for understanding of migratory adaption and population genetics and will benefit the aquaculture and management of this economically important fish.
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Affiliation(s)
- Gangchun Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Binhu District, Wuxi 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Yantian District, Shenzhen 518083, China
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Zhijuan Nie
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Jia Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Yantian District, Shenzhen 518083, China
| | - Yuyu Wang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Dongpo Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Xinxin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Yantian District, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Yantian District, Shenzhen 518083, China
| | - Hongbo Liu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Jiancao Gao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Hongxia Li
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Kai Liu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Jian Yang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Quanjie Li
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Nailin Shao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Yanbing Zhuang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Dian Fang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Tao Jiang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Yunyun Lv
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Yantian District, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Yantian District, Shenzhen 518083, China
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Yantian District, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Yantian District, Shenzhen 518083, China
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - Ruobo Gu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
| | - Junmin Xu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Yantian District, Shenzhen 518083, China
| | - Wei Ge
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Yantian District, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Yantian District, Shenzhen 518083, China
| | - Pao Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Binhu District, Wuxi 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Binhu District, Wuxi, 214081, China
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11
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Liu DW, Wang FY, Lin JJ, Thompson A, Lu Y, Vo D, Yan HY, Zakon H. The Cone Opsin Repertoire of Osteoglossomorph Fishes: Gene Loss in Mormyrid Electric Fish and a Long Wavelength-Sensitive Cone Opsin That Survived 3R. Mol Biol Evol 2019; 36:447-457. [PMID: 30590689 DOI: 10.1093/molbev/msy241] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Vertebrates have four classes of cone opsin genes derived from two rounds of genome duplication. These are short wavelength sensitive 1(SWS1), short wavelength sensitive 2(SWS2), medium wavelength sensitive (RH2), and long wavelength sensitive (LWS). Teleosts had another genome duplication at their origin and it is believed that only one of each cone opsin survived the ancestral teleost duplication event. We tested this by examining the retinal cones of a basal teleost group, the osteoglossomorphs. Surprisingly, this lineage has lost the typical vertebrate green-sensitive RH2 opsin gene and, instead, has a duplicate of the LWS opsin that is green sensitive. This parallels the situation in mammalian evolution in which the RH2 opsin gene was lost in basal mammals and a green-sensitive opsin re-evolved in Old World, and independently in some New World, primates from an LWS opsin gene. Another group of fish, the characins, possess green-sensitive LWS cones. Phylogenetic analysis shows that the evolution of green-sensitive LWS opsins in these two teleost groups derives from a common ancestral LWS opsin that acquired green sensitivity. Additionally, the nocturnally active African weakly electric fish (Mormyroideae), which are osteoglossomorphs, show a loss of the SWS1 opsin gene. In comparison with the independently evolved nocturnally active South American weakly electric fish (Gymnotiformes) with a functionally monochromatic LWS opsin cone retina, the presence of SWS2, LWS, and LWS2 cone opsins in mormyrids suggests the possibility of color vision.
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Affiliation(s)
- Da-Wei Liu
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Feng-Yu Wang
- Taiwan Ocean Research Institute, National Applied Research Laboratories, Kaohsiung, Taiwan
| | - Jinn-Jy Lin
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Ammon Thompson
- Department of Integrative Biology, The University of Texas, Austin, TX
| | - Ying Lu
- Department of Integrative Biology, The University of Texas, Austin, TX.,Department of Neuroscience, The University of Texas, Austin, TX
| | - Derek Vo
- Department of Integrative Biology, The University of Texas, Austin, TX
| | - Hong Young Yan
- National Museum of Marine Biology and Aquarium, Chencheng, Pingtung, Taiwan
| | - Harold Zakon
- Department of Integrative Biology, The University of Texas, Austin, TX.,Department of Neuroscience, The University of Texas, Austin, TX
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12
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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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13
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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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