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Kong S, Zhou Z, Zhou T, Zhao J, Chen L, Lin H, Pu F, Ke Q, Bai H, Xu P. Genome-Wide Association Study of Body Shape-Related Traits in Large Yellow Croaker (Larimichthys crocea). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:631-643. [PMID: 32666363 DOI: 10.1007/s10126-020-09983-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/05/2020] [Indexed: 06/11/2023]
Abstract
Large yellow croaker (Larimichthys crocea) is one of the most important cultured marine fish on the southeast coast of China. Its body shape is important for the aquaculture industry since it affects the behavior such as swimming, ingesting, and evading, as well as customer preference. Due to the greater consumer demand of small head, slender body large yellow croaker, selecting and breeding of slender individuals with the assistance of genetic markers will benefit the industry quickly. In this study, several traits were employed to represent body shape, including body depth/body length (BD/BL), body thickness/body length (BT/BL), caudal peduncle depth/caudal peduncle length (CPDLR), tail length/body length (TL/BL), and body area/head area (BA/HA). Genome-wide association study was conducted with a panmictic population of 280 individuals to identify SNP and genes potentially associated with body shape. A set of 20 SNPs on 12 chromosomes were identified to be significantly associated with body shape-related traits. Besides, 5 SNPs were identified to be suggestive associated with CPDLR and BT/BL. Surrounding these SNPs, we found some body shape-related candidate genes, including fabp1, acrv1, bcor, mstn, bambi, and neo1, which involved in lipid metabolism, TGF-β signaling, and BMP pathway and other important regulatory pathways. These results will be useful for the understanding of the genetic basis of body shape formation and helpful for body shape controlling of large yellow croaker by using marker-assisted selection.
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Affiliation(s)
- Shengnan Kong
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Zhixiong Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Tao Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Ji Zhao
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Lin Chen
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Huanling Lin
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Fei Pu
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China
| | - Qiaozhen Ke
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Huaqiang Bai
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Peng Xu
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China.
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
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Comparative transcriptome analysis reveals potential evolutionary differences in adaptation of temperature and body shape among four Percidae species. PLoS One 2019; 14:e0215933. [PMID: 31063465 PMCID: PMC6504104 DOI: 10.1371/journal.pone.0215933] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 04/10/2019] [Indexed: 12/18/2022] Open
Abstract
Considering the divergent temperature habitats and morphological traits of four Percidae species: yellow perch (Perca flavescens), Eurasian perch (Perca fluviatilis), pike perch (Sander lucioperca), and ruffe (Gymnocephalus cernua), we stepped into the transcriptome level to discover genes and mechanisms that drive adaptation to different temperature environments and evolution in body shape. Based on 93,566 to 181,246 annotated unigenes of the four species, we identified 1,117 one-to-one orthologous genes and subsequently constructed the phylogenetic trees that are consistent with previous studies. Together with the tree, the ratios of nonsynonymous to synonymous substitutions presented decreased evolutionary rates from the D. rerio branch to the sub-branch clustered by P. flavescens and P. fluviatilis. The specific 93 fast-evolving genes and 57 positively selected genes in P. flavescens, compared with 22 shared fast-evolving genes among P. fluviatilis, G. cernua, and S. lucioperca, showed an intrinsic foundation that ensure its adaptation to the warmer Great Lakes and farther south, especially in functional terms like “Cul4-RING E3 ubiquitin ligase complex.” Meanwhile, the specific 78 fast-evolving genes and 41 positively selected genes in S. lucioperca drew a clear picture of how it evolved to a large and elongated body with camera-type eyes and muscle strength so that it could occupy the highest position in the food web. Overall, our results uncover genetic basis that support evolutionary adaptation of temperature and body shape in four Percid species, and could furthermore assist studies on environmental adaptation in fishes.
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Dong L, Han Z, Fang M, Xiao S, Wang Z. Genome-wide association study identifies loci for body shape in the large yellow croaker (Larimichthys crocea). AQUACULTURE AND FISHERIES 2019. [DOI: 10.1016/j.aaf.2018.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Kikko T, Ishizaki D, Kuwamura K, Okamoto H, Ujiie M, Ide A, Saegusa J, Kai Y, Nakayama K, Fujioka Y. Juvenile migration of the exclusively pelagic cyprinid, Gnathopogon caerulescens (Honmoroko) in Lake Biwa, Central Japan. JOURNAL OF FISH BIOLOGY 2018; 92:1590-1603. [PMID: 29624686 DOI: 10.1111/jfb.13616] [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: 12/02/2017] [Accepted: 03/05/2018] [Indexed: 06/08/2023]
Abstract
Migration of wild and cultivated juvenile honmoroko Gnathopogon caerulescens of from the spawning and nursery areas in Lake Biwa were investigated, both in the Ibanaiko Lagoon and its outlet to Daido River, using beam-trawl surveys in 2013 and 2014. The study demonstrated migration of G. caerulescens from a nursery lagoon toward Lake Biwa after the juvenile stage. These findings appear to be the first direct evidence for migration of an exclusively pelagic cyprinid species from a littoral nursery to a pelagic adult habitat in a large deep lake.
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Affiliation(s)
- T Kikko
- Shiga Prefectural Fisheries Experimental Station, 2138-3, Hassaka, Hikone, Shiga, 522-0057, Japan
| | - D Ishizaki
- Shiga Prefectural Fisheries Experimental Station, 2138-3, Hassaka, Hikone, Shiga, 522-0057, Japan
| | - K Kuwamura
- Shiga Prefectural Fisheries Experimental Station, 2138-3, Hassaka, Hikone, Shiga, 522-0057, Japan
| | - H Okamoto
- Shiga Prefectural Fisheries Experimental Station, 2138-3, Hassaka, Hikone, Shiga, 522-0057, Japan
| | - M Ujiie
- Shiga Prefectural Fisheries Experimental Station, 2138-3, Hassaka, Hikone, Shiga, 522-0057, Japan
| | - A Ide
- Shiga Prefectural Fisheries Experimental Station, 2138-3, Hassaka, Hikone, Shiga, 522-0057, Japan
| | - J Saegusa
- Shiga Prefectural Fisheries Experimental Station, 2138-3, Hassaka, Hikone, Shiga, 522-0057, Japan
| | - Y Kai
- Maizuru Fisheries Research Station, Field Science Education and Research Center, Kyoto University, Nagahama, Maizuru, Kyoto, 625-0086, Japan
| | - K Nakayama
- Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Y Fujioka
- Shiga Prefectural Fisheries Experimental Station, 2138-3, Hassaka, Hikone, Shiga, 522-0057, Japan
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Reynolds HT, Vijayakumar V, Gluck-Thaler E, Korotkin HB, Matheny PB, Slot JC. Horizontal gene cluster transfer increased hallucinogenic mushroom diversity. Evol Lett 2018; 2:88-101. [PMID: 30283667 PMCID: PMC6121855 DOI: 10.1002/evl3.42] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 11/29/2017] [Accepted: 01/23/2018] [Indexed: 12/24/2022] Open
Abstract
Secondary metabolites are a heterogeneous class of chemicals that often mediate interactions between species. The tryptophan‐derived secondary metabolite, psilocin, is a serotonin receptor agonist that induces altered states of consciousness. A phylogenetically disjunct group of mushroom‐forming fungi in the Agaricales produce the psilocin prodrug, psilocybin. Spotty phylogenetic distributions of fungal compounds are sometimes explained by horizontal transfer of metabolic gene clusters among unrelated fungi with overlapping niches. We report the discovery of a psilocybin gene cluster in three hallucinogenic mushroom genomes, and evidence for its horizontal transfer between fungal lineages. Patterns of gene distribution and transmission suggest that synthesis of psilocybin may have provided a fitness advantage in the dung and late wood‐decay fungal niches, which may serve as reservoirs of fungal indole‐based metabolites that alter behavior of mycophagous and wood‐eating invertebrates. These hallucinogenic mushroom genomes will serve as models in neurochemical ecology, advancing the (bio)prospecting and synthetic biology of novel neuropharmaceuticals.
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Affiliation(s)
- Hannah T Reynolds
- Department of Plant Pathology The Ohio State University 2021 Coffey Road Columbus Ohio 43210.,Department of Biological & Environmental Sciences Western Connecticut State University 181 White St. Danbury Connecticut 06810-6826
| | - Vinod Vijayakumar
- Department of Plant Pathology The Ohio State University 2021 Coffey Road Columbus Ohio 43210
| | - Emile Gluck-Thaler
- Department of Plant Pathology The Ohio State University 2021 Coffey Road Columbus Ohio 43210
| | - Hailee Brynn Korotkin
- Ecology & Evolutionary Biology University of Tennessee 334 Hesler Biology Building Knoxville Tennessee 37996-1610
| | - Patrick Brandon Matheny
- Ecology & Evolutionary Biology University of Tennessee 334 Hesler Biology Building Knoxville Tennessee 37996-1610
| | - Jason C Slot
- Department of Plant Pathology The Ohio State University 2021 Coffey Road Columbus Ohio 43210
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Mokodongan DF, Montenegro J, Mochida K, Fujimoto S, Ishikawa A, Kakioka R, Yong L, Mulis, Hadiaty RK, Mandagi IF, Masengi KW, Wachi N, Hashiguchi Y, Kitano J, Yamahira K. Phylogenomics reveals habitat-associated body shape divergence in Oryzias woworae species group (Teleostei: Adrianichthyidae). Mol Phylogenet Evol 2018; 118:194-203. [DOI: 10.1016/j.ympev.2017.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 09/11/2017] [Accepted: 10/04/2017] [Indexed: 12/24/2022]
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Outomuro D, Johansson F. A potential pitfall in studies of biological shape: Does size matter? J Anim Ecol 2017; 86:1447-1457. [PMID: 28699246 DOI: 10.1111/1365-2656.12732] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/21/2017] [Indexed: 01/26/2023]
Abstract
The number of published studies using geometric morphometrics (GM) for analysing biological shape has increased steadily since the beginning of the 1990s, covering multiple research areas such as ecology, evolution, development, taxonomy and palaeontology. Unfortunately, we have observed that many published studies using GM do not evaluate the potential allometric effects of size on shape, which normally require consideration or assessment. This might lead to misinterpretations and flawed conclusions in certain cases, especially when size effects explain a large part of the shape variation. We assessed, for the first time and in a systematic manner, how often published studies that have applied GM consider the potential effects of allometry on shape. We reviewed the 300 most recent published papers that used GM for studying biological shape. We also estimated how much of the shape variation was explained by allometric effects in the reviewed papers. More than one-third (38%) of the reviewed studies did not consider the allometric component of shape variation. In studies where the allometric component was taken into account, it was significant in 88% of the cases, explaining up to 87.3% of total shape variation. We believe that one reason that may cause the observed results is a misunderstanding of the process that superimposes landmark configurations, i.e. the Generalized Procrustes Analysis, which removes isometric effects of size on shape, but not allometric effects. Allometry can be a crucial component of shape variation. We urge authors to address, and report, size effects in studies of biological shape. However, we do not propose to always remove size effects, but rather to evaluate the research question with and without the allometric component of shape variation. This approach can certainly provide a thorough understanding of how much size contributes to the observed shaped variation.
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Affiliation(s)
- David Outomuro
- Section for Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Frank Johansson
- Section for Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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Nakazawa T, Liu SYV, Sakai Y, Araki KS, Tsai CH, Okuda N. Spatial genetic structure and body size divergence in endangered Gymnogobius isaza in ancient Lake Biwa. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:756-764. [PMID: 28745537 DOI: 10.1080/24701394.2017.1357708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Gymnogobius isaza is a freshwater goby endemic to ancient Lake Biwa, the largest lake in Japan. The species is now listed as 'Critically Endangered' in the Red Data Book of Japan. Nevertheless, it remains subject to fishing without any specific management strategies. Previous studies using mitochondrial DNA markers showed that this fish species has two cryptic lineages. However, little is known about spatial genetic structure and ecological differences across the broad lakescape. In this study, we collected fish samples at nine locations along the lakeshore during the breeding season and tested for the presence of spatial heterogeneity in the lineage's composition while measuring body size as the most fundamental biological trait. The results showed that the major lineage dominated all the sampling locations whereas the minor lineage consisted of only 11% (16/143) of samples. Furthermore, although their spatial distributions overlapped (i.e. the two lineages may be well mixed), we found it possible that the minor lineage may have a potentially narrower distribution than the major lineage. In addition, we found that the two lineages differ in body size; specifically, the minor lineage is smaller in size. From the viewpoint of genetic diversity conservation and sustainable resource use, this fish should be managed as two genetic stocks and spatial and/or body size-based fishery management is desirable, with particular attention to the minor (smaller sized) lineage.
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Affiliation(s)
- Takefumi Nakazawa
- a Department of Life Sciences , National Cheng Kung University , Tainan , Taiwan
| | - Shang-Yin Vanson Liu
- b Department of Marine Biotechnology and Resources , National Sun Yat-Sen University , Kaohsiung , Taiwan
| | - Yoichiro Sakai
- c Lake Biwa Environmental Research Institute , Shiga , Japan
| | - Kiwako S Araki
- d Faculty of Life Sciences , Ristumeikan University , Shiga , Japan
| | - Cheng-Han Tsai
- e Australian Institute of Marine Science, School of Marine and Tropical Biology , James Cook University , Australia
| | - Noboru Okuda
- f Research Institute for Humanity and Nature , Kyoto , Japan
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Quantitative trait locus analysis of body shape divergence in nine-spined sticklebacks based on high-density SNP-panel. Sci Rep 2016; 6:26632. [PMID: 27226078 PMCID: PMC4880927 DOI: 10.1038/srep26632] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 05/06/2016] [Indexed: 12/26/2022] Open
Abstract
Heritable phenotypic differences between populations, caused by the selective effects of distinct environmental conditions, are of commonplace occurrence in nature. However, the actual genomic targets of this kind of selection are still poorly understood. We conducted a quantitative trait locus (QTL) mapping study to identify genomic regions responsible for morphometric differentiation between genetically and phenotypically divergent marine and freshwater nine-spined stickleback (Pungitius pungitius) populations. Using a dense panel of SNP-markers obtained by restriction site associated DNA sequencing of an F2 recombinant cross, we found 22 QTL that explained 3.5-12.9% of phenotypic variance in the traits under investigation. We detected one fairly large-effect (PVE = 9.6%) QTL for caudal peduncle length-a trait with a well-established adaptive function showing clear differentiation among marine and freshwater populations. We also identified two large-effect QTL for lateral plate numbers, which are different from the lateral plate QTL reported in earlier studies of this and related species. Hence, apart from identifying several large-effect QTL in shape traits showing adaptive differentiation in response to different environmental conditions, the results suggest intra- and interspecific heterogeneity in the genomic basis of lateral plate number variation.
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Tabata R, Kakioka R, Tominaga K, Komiya T, Watanabe K. Phylogeny and historical demography of endemic fishes in Lake Biwa: the ancient lake as a promoter of evolution and diversification of freshwater fishes in western Japan. Ecol Evol 2016; 6:2601-23. [PMID: 27066244 PMCID: PMC4798153 DOI: 10.1002/ece3.2070] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/16/2016] [Accepted: 02/22/2016] [Indexed: 01/21/2023] Open
Abstract
To elucidate the origins of the endemic fish of Lake Biwa, an ancient lake in Japan, and the role of the lake in the diversification of freshwater fish in western Japan, we established a molecular phylogenetic framework with an absolute time scale and inferred the historical demography of a large set of fish species in and around the lake. We used mtDNA sequences obtained from a total of 190 specimens, including 11 endemic species of Lake Biwa and their related species, for phylogenetic analyses with divergence time estimations and from a total of 2319 specimens of 42 species (including 14 endemics) occurring in the lake for population genetic analyses. Phylogenetic analysis suggested that some of the endemic species diverged from their closest relatives earlier (1.3–13.0 Ma) than the period in which the present environmental characteristics of the lake started to develop (ca. 0.4 Ma), whereas others diverged more recently (after 0.4 Ma). In contrast, historical demographic parameters suggested that almost all species, including endemic and nonendemic ones, expanded their populations after the development of the present lake environment. In phylogeographic analyses, common or very close haplotypes of some species were obtained from Lake Biwa and other regions of western Japan. The phylogenetic and historical demographic evidence suggests that there was a time lag between phylogenetic divergence and population establishment and that phenotypic adaptation of some endemic species to the limnetic environment occurred much later than the divergences of those endemic lineages. Population structure and phylogeographic patterns suggest that Lake Biwa has functioned not only as the center of adaptive evolution but also as a reservoir for fish diversity in western Japan.
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Affiliation(s)
- Ryoichi Tabata
- Graduate School of Science Kyoto University Kitashirakawa-Oiwakecho Sakyo Kyoto 606-8502 Japan
| | - Ryo Kakioka
- Graduate School of Science Kyoto University Kitashirakawa-Oiwakecho Sakyo Kyoto 606-8502 Japan; Research Institute for Humanity and Nature 457-4 Kamigamo-Motoyama Kita-ku Kyoto 603-8047 Japan
| | - Koji Tominaga
- Graduate School of Science Kyoto University Kitashirakawa-Oiwakecho Sakyo Kyoto606-8502 Japan; Kwansei Gakuin Senior High School 1-155 Uegahara-ichibancho Nishinomiya Hyogo 662-8501 Japan
| | - Takefumi Komiya
- Graduate School of Science Kyoto University Kitashirakawa-Oiwakecho Sakyo Kyoto 606-8502 Japan
| | - Katsutoshi Watanabe
- Graduate School of Science Kyoto University Kitashirakawa-Oiwakecho Sakyo Kyoto 606-8502 Japan
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