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Liu Q, Naganuma T. Metabolomics in sturgeon research: a mini-review. FISH PHYSIOLOGY AND BIOCHEMISTRY 2024; 50:1895-1910. [PMID: 38980504 PMCID: PMC11286732 DOI: 10.1007/s10695-024-01377-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 07/02/2024] [Indexed: 07/10/2024]
Abstract
Sturgeons are ancient fish, with 27 species distributed in the Northern Hemisphere. This review first touches upon the significance of sturgeons in the context of their biological, ecological, and economic importance, highlighting their status as "living fossils" and the challenges they face in genomic research due to their diverse chromosome numbers. This review then discusses how omics technologies (genomics, transcriptomics, proteomics, and metabolomics) have been used in sturgeon research, which so far has only been done on Acipenser species. It focuses on metabolomics as a way to better understand how sturgeons work and how they react to their environment. Specific studies in sturgeon metabolomics are cited, showing how metabolomics has been used to investigate various aspects of sturgeon biology, such as growth, reproduction, stress responses, and nutrition. These studies demonstrate the potential of metabolomics in improving sturgeon aquaculture practices and conservation efforts. Overall, the review suggests that metabolomics, as a relatively new scientific tool, has the potential to enhance our understanding of sturgeon biology and aid in their conservation and sustainable aquaculture, contributing to global food security efforts.
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Affiliation(s)
- Qi Liu
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
| | - Takeshi Naganuma
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan.
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2
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Ding Y, Zou M, Guo B. Genomic signatures associated with recurrent scale loss in cyprinid fish. Integr Zool 2024. [PMID: 38816909 DOI: 10.1111/1749-4877.12851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Scale morphology represents a fundamental feature of fish and a key evolutionary trait underlying fish diversification. Despite frequent and recurrent scale loss throughout fish diversification, comprehensive genome-wide analyses of the genomic signatures associated with scale loss in divergent fish lineages remain scarce. In the current study, we investigated genome-wide signatures, specifically convergent protein-coding gene loss, amino acid substitutions, and cis-regulatory sequence changes, associated with recurrent scale loss in two divergent Cypriniformes lineages based on large-scale genomic, transcriptomic, and epigenetic data. Results demonstrated convergent changes in many genes related to scale formation in divergent scaleless fish lineages, including loss of P/Q-rich scpp genes (e.g. scpp6 and scpp7), accelerated evolution of non-coding elements adjacent to the fgf and fgfr genes, and convergent amino acid changes in genes (e.g. snap29) under relaxed selection. Collectively, these findings highlight the existence of a shared genetic architecture underlying recurrent scale loss in divergent fish lineages, suggesting that evolutionary outcomes may be genetically repeatable and predictable in the convergence of scale loss in fish.
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Affiliation(s)
- Yongli Ding
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ming Zou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Baocheng Guo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, China
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3
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Fodor E, Okendo J, Szabó N, Szabó K, Czimer D, Tarján-Rácz A, Szeverényi I, Low BW, Liew JH, Koren S, Rhie A, Orbán L, Miklósi Á, Varga M, Burgess SM. The reference genome of Macropodus opercularis (the paradise fish). Sci Data 2024; 11:540. [PMID: 38796485 PMCID: PMC11127978 DOI: 10.1038/s41597-024-03277-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 04/18/2024] [Indexed: 05/28/2024] Open
Abstract
Amongst fishes, zebrafish (Danio rerio) has gained popularity as a model system over most other species and while their value as a model is well documented, their usefulness is limited in certain fields of research such as behavior. By embracing other, less conventional experimental organisms, opportunities arise to gain broader insights into evolution and development, as well as studying behavioral aspects not available in current popular model systems. The anabantoid paradise fish (Macropodus opercularis), an "air-breather" species has a highly complex behavioral repertoire and has been the subject of many ethological investigations but lacks genomic resources. Here we report the reference genome assembly of M. opercularis using long-read sequences at 150-fold coverage. The final assembly consisted of 483,077,705 base pairs (~483 Mb) on 152 contigs. Within the assembled genome we identified and annotated 20,157 protein coding genes and assigned ~90% of them to orthogroups.
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Affiliation(s)
- Erika Fodor
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Javan Okendo
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Nóra Szabó
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Kata Szabó
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Dávid Czimer
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Anita Tarján-Rácz
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Ildikó Szeverényi
- Frontline Fish Genomics Research Group, Department of Applied Fish Biology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Georgikon Campus, Keszthely, Hungary
| | - Bi Wei Low
- Science Unit, Lingnan University, Hong Kong, China
| | | | - Sergey Koren
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Arang Rhie
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - László Orbán
- Frontline Fish Genomics Research Group, Department of Applied Fish Biology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Georgikon Campus, Keszthely, Hungary
| | - Ádám Miklósi
- Department of Ethology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Máté Varga
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary.
| | - Shawn M Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA.
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4
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Wang B, Wu B, Liu X, Hu Y, Ming Y, Bai M, Liu J, Xiao K, Zeng Q, Yang J, Wang H, Guo B, Tan C, Hu Z, Zhao X, Li Y, Yue Z, Mei J, Jiang W, Yang Y, Li Z, Gao Y, Chen L, Jian J, Du H. Whole-genome Sequencing Reveals Autooctoploidy in Chinese Sturgeon and Its Evolutionary Trajectories. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzad002. [PMID: 38862424 DOI: 10.1093/gpbjnl/qzad002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 09/12/2023] [Accepted: 09/20/2023] [Indexed: 06/13/2024]
Abstract
The order Acipenseriformes, which includes sturgeons and paddlefishes, represents "living fossils" with complex genomes that are good models for understanding whole-genome duplication (WGD) and ploidy evolution in fishes. Here, we sequenced and assembled the first high-quality chromosome-level genome for the complex octoploid Acipenser sinensis (Chinese sturgeon), a critically endangered species that also represents a poorly understood ploidy group in Acipenseriformes. Our results show that A. sinensis is a complex autooctoploid species containing four kinds of octovalents (8n), a hexavalent (6n), two tetravalents (4n), and a divalent (2n). An analysis taking into account delayed rediploidization reveals that the octoploid genome composition of Chinese sturgeon results from two rounds of homologous WGDs, and further provides insights into the timing of its ploidy evolution. This study provides the first octoploid genome resource of Acipenseriformes for understanding ploidy compositions and evolutionary trajectories of polyploid fishes.
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Affiliation(s)
- Binzhong Wang
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
| | - Bin Wu
- BGI-Shenzhen, Shenzhen 518083, China
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Xueqing Liu
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
| | - Yacheng Hu
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
| | - Yao Ming
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Mingzhou Bai
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby 2800, Denmark
| | - Juanjuan Liu
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
| | - Kan Xiao
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
| | - Qingkai Zeng
- River Basin Complex Administration Center, China Three Gorges Corporation, Yichang 443100, China
| | - Jing Yang
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
| | - Hongqi Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Baifu Guo
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
| | - Chun Tan
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
| | - Zixuan Hu
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
| | - Xun Zhao
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
| | - Yanhong Li
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhen Yue
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
| | - Junpu Mei
- BGI-Shenzhen, Shenzhen 518083, China
- BGI-Sanya, BGI-Shenzhen, Sanya 572025, China
| | - Wei Jiang
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
| | - Yuanjin Yang
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
| | - Zhiyuan Li
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
| | - Yong Gao
- Yangtze Eco-Environment Engineering Research Center, China Three Gorges Corporation, Beijing 100038, China
| | - Lei Chen
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- River Basin Complex Administration Center, China Three Gorges Corporation, Yichang 443100, China
| | - Jianbo Jian
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby 2800, Denmark
| | - Hejun Du
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
- Yangtze River Biodiversity Research Center, China Three Gorges Corporation, Wuhan 430014, China
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5
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Kato A, Pipil S, Ota C, Kusakabe M, Watanabe T, Nagashima A, Chen AP, Islam Z, Hayashi N, Wong MKS, Komada M, Romero MF, Takei Y. Convergent gene losses and pseudogenizations in multiple lineages of stomachless fishes. Commun Biol 2024; 7:408. [PMID: 38570609 PMCID: PMC10991444 DOI: 10.1038/s42003-024-06103-x] [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: 04/03/2023] [Accepted: 03/25/2024] [Indexed: 04/05/2024] Open
Abstract
The regressive evolution of independent lineages often results in convergent phenotypes. Several teleost groups display secondary loss of the stomach, and four gastric genes, atp4a, atp4b, pgc, and pga2 have been co-deleted in agastric (stomachless) fish. Analyses of genotypic convergence among agastric fishes showed that four genes, slc26a9, kcne2, cldn18a, and vsig1, were co-deleted or pseudogenized in most agastric fishes of the four major groups. kcne2 and vsig1 were also deleted or pseudogenized in the agastric monotreme echidna and platypus, respectively. In the stomachs of sticklebacks, these genes are expressed in gastric gland cells or surface epithelial cells. An ohnolog of cldn18 was retained in some agastric teleosts but exhibited an increased non-synonymous substitution when compared with gastric species. These results revealed novel convergent gene losses at multiple loci among the four major groups of agastric fish, as well as a single gene loss in the echidna and platypus.
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Affiliation(s)
- Akira Kato
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.
- Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, Japan.
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, Japan.
- Department of Physiology & Biomedical Engineering, Mayo Clinic College of Medicine & Science, Rochester, MN, USA.
| | - Supriya Pipil
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Chihiro Ota
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Makoto Kusakabe
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
- Department of Biological Sciences, Faculty of Science, Shizuoka University, Shizuoka, Japan
| | - Taro Watanabe
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Ayumi Nagashima
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - An-Ping Chen
- Department of Physiology & Biomedical Engineering, Mayo Clinic College of Medicine & Science, Rochester, MN, USA
| | - Zinia Islam
- Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, Japan
| | - Naoko Hayashi
- Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, Japan
| | - Marty Kwok-Shing Wong
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
- Department of Biomolecular Science, Toho University, Funabashi, Japan
| | - Masayuki Komada
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Michael F Romero
- Department of Physiology & Biomedical Engineering, Mayo Clinic College of Medicine & Science, Rochester, MN, USA
- Department of Nephrology & Hypertension, Mayo Clinic College of Medicine & Science, Rochester, MN, USA
| | - Yoshio Takei
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
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6
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Bian C, Huang Y, Li R, Xu P, You X, Lv Y, Ruan Z, Chen J, Xu J, Shi Q. Genomics comparisons of three chromosome-level mudskipper genome assemblies reveal molecular clues for water-to-land evolution and adaptation. J Adv Res 2024; 58:93-104. [PMID: 37220853 PMCID: PMC10982859 DOI: 10.1016/j.jare.2023.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 04/19/2023] [Accepted: 05/18/2023] [Indexed: 05/25/2023] Open
Abstract
INTRODUCTION Mudskippers are a large group of amphibious fishes that have developed many morphological and physiological capacities to live on land. Genomics comparisons of chromosome-level genome assemblies of three representative mudskippers, Boleophthalmus pectinirostris (BP), Periophthalmus magnuspinnatus (PM) and P. modestus (PMO), may be able to provide novel insights into the water-to-land evolution and adaptation. METHODS Two chromosome-level genome assemblies for BP and PM were respectively sequenced by an integration of PacBio, Nanopore and Hi-C sequencing. A series of standard assembly and annotation pipelines were subsequently performed for both mudskippers. We also re-annotated the PMO genome, downloaded from NCBI, to obtain a redundancy-reduced annotation. Three-way comparative analyses of the three mudskipper genomes in a large scale were carried out to discover detailed genomic differences, such as different gene sizes, and potential chromosomal fission and fusion events. Comparisons of several representative gene families among the three amphibious mudskippers and some other teleosts were also performed to find some molecular clues for terrestrial adaptation. RESULTS We obtained two high-quality haplotype genome assemblies with 23 and 25 chromosomes for BP and PM respectively. We also found two specific chromosome fission events in PM. Ancestor chromosome analysis has discovered a common fusion event in mudskipper ancestor. This fusion was then retained in all the three mudskipper species. A loss of some SCPP (secretory calcium-binding phosphoprotein) genes were identified in the three mudskipper genomes, which could lead to reduction of scales for a part-time terrestrial residence. The loss of aanat1a gene, encoding an important enzyme (arylalkylamine N-acetyltransferase 1a, AANAT1a) for dopamine metabolism and melatonin biosynthesis, was confirmed in PM but not in PMO (as previously reported existence in BP), suggesting a better air vision of PM than both PMO and BP. Such a tiny variation within the genus Periophthalmus exemplifies to prove a step-by-step evolution for the mudskippers' water-to-land adaptation. CONCLUSION These high-quality mudskipper genome assemblies will become valuable genetic resources for in-depth discovery of genomic evolution for the terrestrial adaptation of amphibious fishes.
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Affiliation(s)
- Chao Bian
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen 518081, China; Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Sciences, Neijiang Normal University, Neijiang 641100, China.
| | - Yu Huang
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen 518081, China
| | - Ruihan 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, Shenzhen 518081, China
| | - Pengwei 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, Shenzhen 518081, 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, Shenzhen 518081, China; Applied Research Institute for Modern Fishery Industry, Guangdong Dabaihui Marine Technology Group Co. Ltd., Huizhou 516357, China
| | - Yunyun Lv
- Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Sciences, Neijiang Normal University, Neijiang 641100, China
| | - Zhiqiang Ruan
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen 518081, China; Applied Research Institute for Modern Fishery Industry, Guangdong Dabaihui Marine Technology Group Co. Ltd., Huizhou 516357, China
| | - Jieming Chen
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen 518081, China; Applied Research Institute for Modern Fishery Industry, Guangdong Dabaihui Marine Technology Group Co. Ltd., Huizhou 516357, 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, Shenzhen 518081, China; Applied Research Institute for Modern Fishery Industry, Guangdong Dabaihui Marine Technology Group Co. Ltd., Huizhou 516357, China
| | - Qiong Shi
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen 518081, China; Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Sciences, Neijiang Normal University, Neijiang 641100, China; Applied Research Institute for Modern Fishery Industry, Guangdong Dabaihui Marine Technology Group Co. Ltd., Huizhou 516357, China.
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7
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Minařík M, Modrell MS, Gillis JA, Campbell AS, Fuller I, Lyne R, Micklem G, Gela D, Pšenička M, Baker CVH. Identification of multiple transcription factor genes potentially involved in the development of electrosensory versus mechanosensory lateral line organs. Front Cell Dev Biol 2024; 12:1327924. [PMID: 38562141 PMCID: PMC10982350 DOI: 10.3389/fcell.2024.1327924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/19/2024] [Indexed: 04/04/2024] Open
Abstract
In electroreceptive jawed vertebrates, embryonic lateral line placodes give rise to electrosensory ampullary organs as well as mechanosensory neuromasts. Previous reports of shared gene expression suggest that conserved mechanisms underlie electroreceptor and mechanosensory hair cell development and that electroreceptors evolved as a transcriptionally related "sister cell type" to hair cells. We previously identified only one transcription factor gene, Neurod4, as ampullary organ-restricted in the developing lateral line system of a chondrostean ray-finned fish, the Mississippi paddlefish (Polyodon spathula). The other 16 transcription factor genes we previously validated in paddlefish were expressed in both ampullary organs and neuromasts. Here, we used our published lateral line organ-enriched gene-set (arising from differential bulk RNA-seq in late-larval paddlefish), together with a candidate gene approach, to identify 25 transcription factor genes expressed in the developing lateral line system of a more experimentally tractable chondrostean, the sterlet (Acipenser ruthenus, a small sturgeon), and/or that of paddlefish. Thirteen are expressed in both ampullary organs and neuromasts, consistent with conservation of molecular mechanisms. Seven are electrosensory-restricted on the head (Irx5, Irx3, Insm1, Sp5, Satb2, Mafa and Rorc), and five are the first-reported mechanosensory-restricted transcription factor genes (Foxg1, Sox8, Isl1, Hmx2 and Rorb). However, as previously reported, Sox8 is expressed in ampullary organs as well as neuromasts in a catshark (Scyliorhinus canicula), suggesting the existence of lineage-specific differences between cartilaginous and ray-finned fishes. Overall, our results support the hypothesis that ampullary organs and neuromasts develop via largely conserved transcriptional mechanisms, and identify multiple transcription factors potentially involved in the formation of electrosensory versus mechanosensory lateral line organs.
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Affiliation(s)
- Martin Minařík
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Melinda S. Modrell
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - J. Andrew Gillis
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Alexander S. Campbell
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Isobel Fuller
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Rachel Lyne
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Gos Micklem
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - David Gela
- Faculty of Fisheries and Protection of Waters, Research Institute of Fish Culture and Hydrobiology, University of South Bohemia in České Budějovice, Vodňany, Czechia
| | - Martin Pšenička
- Faculty of Fisheries and Protection of Waters, Research Institute of Fish Culture and Hydrobiology, University of South Bohemia in České Budějovice, Vodňany, Czechia
| | - Clare V. H. Baker
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
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8
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Ruan R, Li Y, Yue H, Ye H, Jin J, Wu J, Du H, Li C. Transcriptome Analyses Reveal Expression Profiles of Morphologically Undifferentiated and Differentiated Gonads of Yangtze Sturgeon Acipenser dabryanus. Genes (Basel) 2023; 14:2058. [PMID: 38003000 PMCID: PMC10671670 DOI: 10.3390/genes14112058] [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: 10/01/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Sturgeon is known as a primitive fish with the ZZ/ZW sex determination system and is highly prized for its valuable caviar. Exploring the molecular mechanisms underlying gonadal differentiation would contribute to broadening our knowledge on the genetic regulation of sex differentiation of fish, enabling improved artificial breeding and management of sturgeons. However, the mechanisms are still poorly understood in sturgeons. This study aimed to profile expression patterns between female and male gonads at morphologically undifferentiated and early differentiated stages and identify vital genes involved in gonadal sex differentiation of sturgeons. The sexes of Yangtze sturgeon (Acipenser dabryanus) juveniles were identified via the sex-specific DNA marker and histological observation. Transcriptome analyses were carried out on female and male gonads at 30, 80 and 180 days post-hatching. The results showed that there was a total of 17 overlapped DEGs in the comparison groups of between female and male gonads at the three developmental stages, in which there were three DEGs related to ovarian steroidogenesis, including hsd17b1, foxl2 and cyp19a1. The three DEGs were highly expressed in the female gonads, of which the expression levels were gradually increased with the number of days after hatching. No well-known testis-related genes were found in the overlapped DEGs. Additionally, the expression levels of hsd17b1 and cyp19a1 mRNA were decreased with the knockdown of foxl2 mRNA via siRNA. The results further suggested that foxl2 should play a crucial role in the ovarian differentiation of sturgeons. In conclusion, this study showed that more genes involved in ovarian development than testis development emerged with sexually dimorphic expression during early gonadal sex differentiation, and it provided a preliminary understanding of the molecular regulation on gonadal differentiation of sturgeons.
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Affiliation(s)
- Rui Ruan
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (R.R.); (Y.L.); (H.Y.); (H.Y.); (J.J.); (J.W.)
| | - Ying Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (R.R.); (Y.L.); (H.Y.); (H.Y.); (J.J.); (J.W.)
| | - Huamei Yue
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (R.R.); (Y.L.); (H.Y.); (H.Y.); (J.J.); (J.W.)
| | - Huan Ye
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (R.R.); (Y.L.); (H.Y.); (H.Y.); (J.J.); (J.W.)
| | - Jiali Jin
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (R.R.); (Y.L.); (H.Y.); (H.Y.); (J.J.); (J.W.)
| | - Jinping Wu
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (R.R.); (Y.L.); (H.Y.); (H.Y.); (J.J.); (J.W.)
| | - Hao Du
- Laboratory of Freshwater Fish Germplasm Resources and Biotechnology, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Chuangju Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (R.R.); (Y.L.); (H.Y.); (H.Y.); (J.J.); (J.W.)
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9
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Kawasaki K, Sasagawa I, Mikami M, Nakatomi M, Ishiyama M. Ganoin and acrodin formation on scales and teeth in spotted gar: A vital role of enamelin in the unique process of enamel mineralization. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:455-468. [PMID: 36464775 PMCID: PMC10239528 DOI: 10.1002/jez.b.23183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/12/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022]
Abstract
Gars and bichirs develop scales and teeth with ancient actinopterygian characteristics. Their scale surface and tooth collar are covered with enamel, also known as ganoin, whereas the tooth cap is equipped with an enamel-like tissue, acrodin. Here, we investigated the formation and mineralization of the ganoin and acrodin matrices in spotted gar, and the evolution of the scpp5, ameloblastin (ambn), and enamelin (enam) genes, which encode matrix proteins of ganoin. Results suggest that, in bichirs and gars, all these genes retain structural characteristics of their orthologs in stem actinopterygians, presumably reflecting the presence of ganoin on scales and teeth. During scale formation, Scpp5 and Enam were initially found in the incipient ganoin matrix and the underlying collagen matrix, whereas Ambn was detected mostly in a surface region of the well-developed ganoin matrix. Although collagen is the principal acrodin matrix protein, Scpp5 was detected within the matrix. Similarities in timings of mineralization and the secretion of Scpp5 suggest that acrodin evolved by the loss of the matrix secretory stage of ganoin formation: dentin formation is immediately followed by the maturation stage. The late onset of Ambn secretion during ganoin formation implies that Ambn is not essential for mineral ribbon formation, the hallmark of the enamel matrix. Furthermore, Scpp5 resembles amelogenin that is not important for the initial formation of mineral ribbons in mammals. It is thus likely that the evolution of ENAM was vital to the origin of the unique mineralization process of the enamel matrix.
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Affiliation(s)
- Kazuhiko Kawasaki
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Ichiro Sasagawa
- Advanced Research Center, School of Life Dentistry at Niigata the Nippon Dental University, Niigata, Japan
| | - Masato Mikami
- Department of Microbiology, School of Life Dentistry at Niigata the Nippon Dental University, Niigata, Japan
| | - Mitsushiro Nakatomi
- Department of Human, Information and Life Sciences, School of Health Sciences, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Mikio Ishiyama
- Department of Histology, School of Life Dentistry at Niigata the Nippon Dental University, Niigata, Japan
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10
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Thorstensen MJ, Weinrauch AM, Bugg WS, Jeffries KM, Anderson WG. Tissue-specific transcriptomes reveal potential mechanisms of microbiome heterogeneity in an ancient fish. Database (Oxford) 2023; 2023:baad055. [PMID: 37590163 PMCID: PMC10434735 DOI: 10.1093/database/baad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 06/16/2023] [Accepted: 07/23/2023] [Indexed: 08/19/2023]
Abstract
The lake sturgeon (Acipenser fulvescens) is an ancient, octoploid fish faced with conservation challenges across its range in North America, but a lack of genomic resources has hindered molecular research in the species. To support such research, we created a transcriptomic database from 13 tissues: brain, esophagus, gill, head kidney, heart, white muscle, liver, glandular stomach, muscular stomach, anterior intestine, pyloric cecum, spiral valve and rectum. The transcriptomes for each tissue were sequenced and assembled individually from a mean of 98.3 million (±38.9 million SD) reads each. In addition, an overall transcriptome was assembled and annotated with all data used for each tissue-specific transcriptome. All assembled transcriptomes and their annotations were made publicly available as a scientific resource. The non-gut transcriptomes provide important resources for many research avenues. However, we focused our analysis on messenger ribonucleic acid (mRNA) observations in the gut because the gut represents a compartmentalized organ system with compartmentalized functions, and seven of the sequenced tissues were from each of these portions. These gut-specific analyses were used to probe evidence of microbiome regulation by studying heterogeneity in microbial genes and genera identified from mRNA annotations. Gene set enrichment analyses were used to reveal the presence of photoperiod and circadian-related transcripts in the pyloric cecum, which may support periodicity in lake sturgeon digestion. Similar analyses were used to identify different types of innate immune regulation across the gut, while analyses of unique transcripts annotated to microbes revealed heterogeneous genera and genes among different gut tissues. The present results provide a scientific resource and information about the mechanisms of compartmentalized function across gut tissues in a phylogenetically ancient vertebrate. Database URL: https://figshare.com/projects/Lake_Sturgeon_Transcriptomes/133143.
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Affiliation(s)
- Matt J Thorstensen
- Department of Biological Sciences, University of Manitoba, 212B Biological Sciences Building, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - Alyssa M Weinrauch
- Department of Biological Sciences, University of Manitoba, 212B Biological Sciences Building, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - William S Bugg
- Department of Biological Sciences, University of Manitoba, 212B Biological Sciences Building, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - Ken M Jeffries
- Department of Biological Sciences, University of Manitoba, 212B Biological Sciences Building, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - W Gary Anderson
- Department of Biological Sciences, University of Manitoba, 212B Biological Sciences Building, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
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11
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Fodor E, Okendo J, Szabó N, Szabó K, Czimer D, Tarján-Rácz A, Szeverényi I, Low BW, Liew JH, Koren S, Rhie A, Orbán L, Miklósi Á, Varga M, Burgess SM. The reference genome of the paradise fish ( Macropodus opercularis). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552018. [PMID: 37609174 PMCID: PMC10441432 DOI: 10.1101/2023.08.10.552018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Over the decades, a small number of model species, each representative of a larger taxa, have dominated the field of biological research. Amongst fishes, zebrafish (Danio rerio) has gained popularity over most other species and while their value as a model is well documented, their usefulness is limited in certain fields of research such as behavior. By embracing other, less conventional experimental organisms, opportunities arise to gain broader insights into evolution and development, as well as studying behavioral aspects not available in current popular model systems. The anabantoid paradise fish (Macropodus opercularis), an "air-breather" species from Southeast Asia, has a highly complex behavioral repertoire and has been the subject of many ethological investigations, but lacks genomic resources. Here we report the reference genome assembly of Macropodus opercularis using long-read sequences at 150-fold coverage. The final assembly consisted of ≈483 Mb on 152 contigs. Within the assembled genome we identified and annotated 20,157 protein coding genes and assigned ≈90% of them to orthogroups. Completeness analysis showed that 98.5% of the Actinopterygii core gene set (ODB10) was present as a complete ortholog in our reference genome with a further 1.2 % being present in a fragmented form. Additionally, we cloned multiple genes important during early development and using newly developed in situ hybridization protocols, we showed that they have conserved expression patterns.
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Affiliation(s)
- Erika Fodor
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Javan Okendo
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Nóra Szabó
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Kata Szabó
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Dávid Czimer
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Anita Tarján-Rácz
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Ildikó Szeverényi
- Department of Ethology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Bi Wei Low
- Science Unit, Lingnan University, Hong Kong, China
| | | | - Sergey Koren
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Arang Rhie
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - László Orbán
- Frontline Fish Genomics Research Group, Department of Applied Fish Biology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Georgikon Campus, Keszthely, Hungary
| | - Ádám Miklósi
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Máté Varga
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Shawn M. Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
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12
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Umu SU, Paynter VM, Trondsen H, Buschmann T, Rounge TB, Peterson KJ, Fromm B. Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine. CELL GENOMICS 2023; 3:100348. [PMID: 37601971 PMCID: PMC10435380 DOI: 10.1016/j.xgen.2023.100348] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/15/2023] [Accepted: 05/26/2023] [Indexed: 08/22/2023]
Abstract
The annotation of microRNAs depends on the availability of transcriptomics data and expert knowledge. This has led to a gap between the availability of novel genomes and high-quality microRNA complements. Using >16,000 microRNAs from the manually curated microRNA gene database MirGeneDB, we generated trained covariance models for all conserved microRNA families. These models are available in our tool MirMachine, which annotates conserved microRNAs within genomes. We successfully applied MirMachine to a range of animal species, including those with large genomes and genome duplications and extinct species, where small RNA sequencing is hard to achieve. We further describe a microRNA score of expected microRNAs that can be used to assess the completeness of genome assemblies. MirMachine closes a long-persisting gap in the microRNA field by facilitating automated genome annotation pipelines and deeper studies into the evolution of genome regulation, even in extinct organisms.
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Affiliation(s)
- Sinan Uğur Umu
- Department of Pathology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Vanessa M. Paynter
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Håvard Trondsen
- Department of Pathology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Trine B. Rounge
- Department of Research, Cancer Registry of Norway, Oslo, Norway
- Centre for Bioinformatics, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Kevin J. Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Bastian Fromm
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, Tromsø, Norway
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13
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Zhou W, Furey NM, Soisook P, Thong VD, Lim BK, Rossiter SJ, Mao X. Diversification and introgression in four chromosomal taxa of the Pearson's horseshoe bat (Rhinolophus pearsoni) group. Mol Phylogenet Evol 2023; 183:107784. [PMID: 37040825 DOI: 10.1016/j.ympev.2023.107784] [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: 12/09/2022] [Revised: 03/11/2023] [Accepted: 04/07/2023] [Indexed: 04/13/2023]
Abstract
Chromosomal variation among closely related taxa is common in both plants and animals, and can reduce rates of introgression as well as promote reproductive isolation and speciation. In mammals, studies relating introgression to chromosomal variation have tended to focus on a few model systems and typically characterized levels of introgression using small numbers of loci. Here we took a genome-wide approach to examine how introgression rates vary among four closely related horseshoe bats (Rhinolophus pearsoni group) that possess different diploid chromosome numbers (2n = 42, 44, 46, and 60) resulting from Robertsonian (Rb) changes (fissions/fusions). Using a sequence capture we obtained orthologous loci for thousands of nuclear loci, as well as mitogenomes, and performed phylogenetic and population genetic analyses. We found that the taxon with 2n = 60 was the first to diverge in this group, and that the relationships among the three other taxa (2n = 42, 44 and 46) showed discordance across our different analyses. Our results revealed signatures of multiple ancient introgression events between the four taxa, with evidence of mitonuclar discordance in phylogenetic trees and reticulation events in their evolutionary history. Despite this, we found no evidence of recent and/or ongoing introgression between taxa. Overall, our results indicate that the effects of Rb changes on the reduction of introgression are complicated and that these may contribute to reproductive isolation and speciation in concert with other factors (e.g. phenotypic and genic divergence).
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Affiliation(s)
- Weiwei Zhou
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, China
| | - Neil M Furey
- Fauna & Flora International (Cambodia), PO Box 1380, No. 19, Street 360, Boeng Keng Kong 1, Phnom Penh 12000, Cambodia
| | - Pipat Soisook
- Princess Maha Chakri Sirindhorn Natural History Museum, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Vu D Thong
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet Road, Cau Giay District, Hanoi, Viet Nam; Graduate University of Science and Technology, VAST, Viet Nam
| | - Burton K Lim
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario M5S 2C6, Canada
| | - Stephen J Rossiter
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK.
| | - Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, China.
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14
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Redmond AK, Casey D, Gundappa MK, Macqueen DJ, McLysaght A. Independent rediploidization masks shared whole genome duplication in the sturgeon-paddlefish ancestor. Nat Commun 2023; 14:2879. [PMID: 37208359 DOI: 10.1038/s41467-023-38714-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 05/12/2023] [Indexed: 05/21/2023] Open
Abstract
Whole genome duplication (WGD) is a dramatic evolutionary event generating many new genes and which may play a role in survival through mass extinctions. Paddlefish and sturgeon are sister lineages that both show genomic evidence for ancient WGD. Until now this has been interpreted as two independent WGD events due to a preponderance of duplicate genes with independent histories. Here we show that although there is indeed a plurality of apparently independent gene duplications, these derive from a shared genome duplication event occurring well over 200 million years ago, likely close to the Permian-Triassic mass extinction period. This was followed by a prolonged process of reversion to stable diploid inheritance (rediploidization), that may have promoted survival during the Triassic-Jurassic mass extinction. We show that the sharing of this WGD is masked by the fact that paddlefish and sturgeon lineage divergence occurred before rediploidization had proceeded even half-way. Thus, for most genes the resolution to diploidy was lineage-specific. Because genes are only truly duplicated once diploid inheritance is established, the paddlefish and sturgeon genomes are thus a mosaic of shared and non-shared gene duplications resulting from a shared genome duplication event.
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Affiliation(s)
- Anthony K Redmond
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Dearbhaile Casey
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Manu Kumar Gundappa
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Daniel J Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Aoife McLysaght
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.
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15
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Long X, Charlesworth D, Qi J, Wu R, Chen M, Wang Z, Xu L, Fu H, Zhang X, Chen X, He L, Zheng L, Huang Z, Zhou Q. Independent Evolution of Sex Chromosomes and Male Pregnancy-Related Genes in Two Seahorse Species. Mol Biol Evol 2022; 40:6964685. [PMID: 36578180 PMCID: PMC9851323 DOI: 10.1093/molbev/msac279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/14/2022] [Accepted: 12/22/2022] [Indexed: 12/30/2022] Open
Abstract
Unlike birds and mammals, many teleosts have homomorphic sex chromosomes, and changes in the chromosome carrying the sex-determining locus, termed "turnovers", are common. Recent turnovers allow studies of several interesting questions. One question is whether the new sex-determining regions evolve to become completely non-recombining, and if so, how and why. Another is whether (as predicted) evolutionary changes that benefit one sex accumulate in the newly sex-linked region. To study these questions, we analyzed the genome sequences of two seahorse species of the Syngnathidae, a fish group in which many species evolved a unique structure, the male brood pouch. We find that both seahorse species have XY sex chromosome systems, but their sex chromosome pairs are not homologs, implying that at least one turnover event has occurred. The Y-linked regions occupy 63.9% and 95.1% of the entire sex chromosome of the two species and do not exhibit extensive sequence divergence with their X-linked homologs. We find evidence for occasional recombination between the extant sex chromosomes that may account for their homomorphism. We argue that these Y-linked regions did not evolve by recombination suppression after the turnover, but by the ancestral nature of the low crossover rates in these chromosome regions. With such an ancestral crossover landscape, a turnover can instantly create an extensive Y-linked region. Finally, we test for adaptive evolution of male pouch-related genes after they became Y-linked in the seahorse.
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Affiliation(s)
- Xin Long
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China,Research Center for Intelligent Computing Platforms, Zhejiang Lab, Hangzhou 311100, China
| | - Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh EH9 3LF, UK
| | - Jianfei Qi
- Department of Aquaculture, Fisheries Research Institute of Fujian, Xiamen 361013, China
| | - Ruiqiong Wu
- Fujian Key Laboratory of Developmental and Neural Biology & Southern Center for Biomedical Research, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China
| | - Meiling Chen
- Fujian Key Laboratory of Developmental and Neural Biology & Southern Center for Biomedical Research, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China
| | - Zongji Wang
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Luohao Xu
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Honggao Fu
- Fujian Key Laboratory of Developmental and Neural Biology & Southern Center for Biomedical Research, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China
| | - Xueping Zhang
- Fujian Key Laboratory of Developmental and Neural Biology & Southern Center for Biomedical Research, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China
| | - Xinxin Chen
- Department of Aquaculture, Fisheries Research Institute of Fujian, Xiamen 361013, China
| | - Libin He
- Department of Aquaculture, Fisheries Research Institute of Fujian, Xiamen 361013, China
| | | | | | - Qi Zhou
- Corresponding authors: E-mails: ; ;
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16
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Dores RM, McKinley G, Meyers A, Martin M, Shaughnessy CA. Structure/Function Studies on the Activation Motif of Two Non-Mammalian Mrap1 Orthologs, and Observations on the Phylogeny of Mrap1, Including a Novel Characterization of an Mrap1 from the Chondrostean Fish, Polyodon spathula. Biomolecules 2022; 12:1681. [PMID: 36421695 PMCID: PMC9688151 DOI: 10.3390/biom12111681] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 08/12/2023] Open
Abstract
In derived bony vertebrates, activation of the melanocortin-2 receptor (Mc2r) by its ACTH ligand requires chaperoning by the Mc2r accessory protein (Mrap1). The N-terminal domain of the non-mammalian tetrapod MRAP1 from chicken (c; Gallus gallus) has the putative activation motif, W18D19Y20I21, and the N-terminal domain in the neopterygian ray-finned fish Mrap1 from bowfin (bf; Amia calva) has the putative activation motif, Y18D19Y20I21. The current study used an alanine-substitution paradigm to test the hypothesis that only the Y20 position in the Mrap1 ortholog of these non-mammalian vertebrates is required for activation of the respective Mc2r ortholog. Instead, we found that for cMRAP1, single alanine-substitution resulted in a gradient of inhibition of activation (Y20 >> D19 = W18 > I21). For bfMrap1, single alanine-substitution also resulted in a gradient of inhibition of activation (Y20 >> D19 > I21 > Y18). This study also included an analysis of Mc2r activation in an older lineage of ray-finned fish, the paddlefish (p), Polyodon spathula (subclass Chondronstei). Currently no mrap1 gene has been found in the paddlefish genome. When pmc2r was expressed alone in our CHO cell/cAMP reporter gene assay, no activation was observed following stimulation with ACTH. However, when pmc2r was co-expressed with either cmrap1 or bfmrap1 robust dose response curves were generated. These results indicate that the formation of an Mc2r/Mrap1 heterodimer emerged early in the radiation of the bony vertebrates.
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Affiliation(s)
- Robert M. Dores
- Department of Biological Sciences, University of Denver, Denver, CO 80210, USA
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17
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Zhang X, Wu W, Zhou J, Li L, Jiang H, Chen J. MiR-34b/c play a role in early sex differentiation of Amur sturgeon, Acipenser schrenckii. Front Zool 2022; 19:23. [PMID: 36163040 PMCID: PMC9511750 DOI: 10.1186/s12983-022-00469-6] [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: 05/16/2022] [Accepted: 09/16/2022] [Indexed: 12/03/2022] Open
Abstract
Background Sex differentiation can be viewed as a controlled regulatory balance between sex differentiation-related mRNAs and post-transcriptional mechanisms mediated by non-coding RNAs. In mammals, increasing evidence has been reported regarding the importance of gonad-specific microRNAs (miRNAs) in sex differentiation. Although many fishes express a large number of gonadal miRNAs, the effects of these sex-biased miRNAs on sex differentiation in teleost fish remain unknown. Previous studies have shown the exclusive and sexually dimorphic expression of miR-34b/c in the gonads of the Amur sturgeon (Acipenser schrenckii), suggesting its potential role in the sex differentiation process. Results Using quantitative real-time PCR (qPCR), we observed that miR-34b/c showed consistent spatiotemporal expression patterns; the expression levels significantly increased during early sex differentiation. Using in situ hybridization, miR-34c was found to be located in the germ cells. In primary germ cells in vitro, the group subjected to overexpression and inhibition of miR-34c showed significantly higher proliferation ability and lower apoptosis, respectively, compared to the corresponding control group. Luciferase reporter assays using the ar-3′UTR-psiCHECK-2 luciferase vector suggested a targeted regulatory interaction between miR-34b/c and the 3′UTR of the androgen receptor (ar) mRNA. Furthermore, miR-34b/c and ar showed negative expression patterns during early sex differentiation. Additionally, a negative feedback regulation pattern was observed between foxl2 expression in the ovaries and amh and sox9 expression in the testes during early sex differentiation. Conclusions This study sheds new light on the roles of miR-34b/c in gonad development of Amur sturgeon, and provides the first comprehensive evidence that the gonad-predominant microRNAs may have a major role in sex differentiation in teleost fish. Supplementary Information The online version contains supplementary material available at 10.1186/s12983-022-00469-6.
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Affiliation(s)
- Xiujuan Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Wenhua Wu
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Jiabin Zhou
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Linmiao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Haiying Jiang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China.
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18
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Lu J, Huang P, Sun J, Liu J. DupScan: predicting and visualizing vertebrate genome duplication database. Nucleic Acids Res 2022; 51:D906-D912. [PMID: 36018807 PMCID: PMC9825427 DOI: 10.1093/nar/gkac718] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 07/24/2022] [Accepted: 08/10/2022] [Indexed: 01/30/2023] Open
Abstract
Duplicated genes prevail in vertebrates and are important in the acquisition of new genes and novelties. Whole genome duplication (WGD) is one of the sources of duplicated genes. It can provide raw materials for natural selection by increasing the flexibility and complexity of the genome. WGDs are the driving force for the evolution of vertebrates and contribute greatly to their species diversity, especially in fish species with complicated WGD patterns. Here, we constructed the DupScan database (https://dupscan.sysumeg.com/) by integrating 106 chromosomal-level genomes, which can analyze and visualize synteny at both the gene and genome scales, visualize the Ka, Ks, and 4DTV values, and browse genomes. DupScan was used to perform functional adaptation for the intricate WGD investigation based on synteny matching. DupScan supports the analysis of five WGD rounds (R): VGD2 (vertebrate genome duplication 2), Ars3R (Acipenser-ruthenus-specific 3R), Pss3R (Polyodon-spathula-specific 3R), Ts3R (teleost-specific duplication 3R), Ss4R (salmonid-specific 4R), and Cs4R (carp-specific 4R). DupScan serves as one-stop analysis platform for synteny and WGD research in which users can analyze and predict synteny and WGD patterns across 106 species of whole genome sequences. This further aided us in elucidating genome evolutionary patterns across over 60,000 vertebrate species with synteny and WGD events.
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Affiliation(s)
- Jianguo Lu
- To whom correspondence should be addressed. Tel: +86 756 3668927; Fax: +86 756 3668927;
| | - Peilin Huang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai 519082, China
| | - Jialiang Sun
- College of Computer Science, Nankai University, Tianjin 300350, China
| | - Jian Liu
- Correspondence may also be addressed to Jian Liu.
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Zhang X, Li G, Zhou J, Lv M, Li L, Chen J. Full-length gonad transcriptome analysis of Amur sturgeon Dmrt family genes: identification, characterization, and expression patterns during gonadal differentiation. FISH PHYSIOLOGY AND BIOCHEMISTRY 2022; 48:839-852. [PMID: 35650309 DOI: 10.1007/s10695-022-01087-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
The regulatory mechanisms that govern sex differentiation in sturgeon are still poorly understood. The doublesex and Mab-3-related transcription factor (Dmrt) gene family is known for its extensive roles in sex determination and differentiation across vertebrates. This study aimed to identify new members of sturgeon Dmrt family genes and core actors in the gonadal differentiation of Amur sturgeon. A full-length gonad transcriptome database was exploited to identify Dmrt gene orthologs. Analyses of phylogenetic relationships and selection pressure were performed, and tissue expression profiles and spatiotemporal expression patterns in gonads were then analyzed using real-time PCR. In total, five Dmrt family genes were identified from the full-length gonad transcriptome, including Dmrt2, DmrtA1, DmrtA2, DmrtB1a, and DmrtB1b. Phylogenetic analysis showed that these genes were clustered into clades corresponding to the doublesex/Mav-3 (DM) genes of vertebrates. Furthermore, the analysis of evolutionary selective pressure indicated that DmrtB1a and DmrtB1b were subject to positive selection, suggesting the existence of adaptive evolution in sturgeon. The extensive tissue expression profiling of each Dmrt family gene revealed typical characteristics. Remarkably, according to a spatiotemporal expression pattern analysis, in later stages, DmrtB1b expression increased in testes and was significantly higher in testes than in ovaries at 24 months after hatching (M) and 36 M. This study provides a genetic resource of full-length Dmrt family genes and increases the understanding of Dmrt functions in sex differentiation in sturgeon.
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Affiliation(s)
- Xiujuan Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Guanyu Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Jiabin Zhou
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Mei Lv
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Linmiao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China.
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20
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Huang Y, Li J, Bian C, Li R, You X, Shi Q. Evolutionary Genomics Reveals Multiple Functions of Arylalkylamine N-Acetyltransferase in Fish. Front Genet 2022; 13:820442. [PMID: 35664299 PMCID: PMC9160868 DOI: 10.3389/fgene.2022.820442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 04/15/2022] [Indexed: 11/21/2022] Open
Abstract
As an important hormone, melatonin participates in endocrine regulation of diverse functions in vertebrates. Its biosynthesis is catalyzed by four cascaded enzymes, among them, arylalkylamine N-acetyltransferase (AANAT) is the most critical one. Although only single aanat gene has been identified in most groups of vertebrates, researchers including us have determined that fish have the most diverse of aanat genes (aanat1a, aanat1b, and aanat2), playing various potential roles such as seasonal migration, amphibious aerial vision, and cave or deep-sea adaptation. With the rapid development of genome and transcriptome sequencing, more and more putative sequences of fish aanat genes are going to be available. Related phylogeny and functional investigations will enrich our understanding of AANAT functions in various fish species.
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Affiliation(s)
- 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, Shenzhen, China
- *Correspondence: Yu Huang, ; Qiong Shi,
| | - Jia Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB-Ugent Center for Plant Systems Biology, Ghent, Belgium
| | - 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, Shenzhen, China
- BGI Education Center, College of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, China
| | - Ruihan 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, Shenzhen, China
- BGI Education Center, College of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, 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, Shenzhen, 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, Shenzhen, China
- BGI Education Center, College of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, China
- *Correspondence: Yu Huang, ; Qiong Shi,
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21
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Leurs N, Martinand-Mari C, Marcellini S, Debiais-Thibaud M. Parallel evolution of ameloblastic scpp genes in bony and cartilaginous vertebrates. Mol Biol Evol 2022; 39:6582990. [PMID: 35535508 PMCID: PMC9122587 DOI: 10.1093/molbev/msac099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
In bony vertebrates, skeletal mineralization relies on the secretory calcium-binding phosphoproteins (Scpp) family whose members are acidic extracellular proteins posttranslationally regulated by the Fam20°C kinase. As scpp genes are absent from the elephant shark genome, they are currently thought to be specific to bony fishes (osteichthyans). Here, we report a scpp gene present in elasmobranchs (sharks and rays) that evolved from local tandem duplication of sparc-L 5′ exons and show that both genes experienced recent gene conversion in sharks. The elasmobranch scpp is remarkably similar to the osteichthyan scpp members as they share syntenic and gene structure features, code for a conserved signal peptide, tyrosine-rich and aspartate/glutamate-rich regions, and harbor putative Fam20°C phosphorylation sites. In addition, the catshark scpp is coexpressed with sparc-L and fam20°C in tooth and scale ameloblasts, similarly to some osteichthyan scpp genes. Despite these strong similarities, molecular clock and phylogenetic data demonstrate that the elasmobranch scpp gene originated independently from the osteichthyan scpp gene family. Our study reveals convergent events at the sparc-L locus in the two sister clades of jawed vertebrates, leading to parallel diversification of the skeletal biomineralization toolkit. The molecular evolution of sparc-L and its coexpression with fam20°C in catshark ameloblasts provides a unifying genetic basis that suggests that all convergent scpp duplicates inherited similar features from their sparc-L precursor. This conclusion supports a single origin for the hypermineralized outer odontode layer as produced by an ancestral developmental process performed by Sparc-L, implying the homology of the enamel and enameloid tissues in all vertebrates.
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Affiliation(s)
- Nicolas Leurs
- Institut des Sciences de l'Evolution de Montpellier, ISEM, Univ Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Camille Martinand-Mari
- Institut des Sciences de l'Evolution de Montpellier, ISEM, Univ Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Sylvain Marcellini
- Departamento de Biología Celular, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
| | - Mélanie Debiais-Thibaud
- Institut des Sciences de l'Evolution de Montpellier, ISEM, Univ Montpellier, CNRS, IRD, EPHE, Montpellier, France
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22
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Ritchie AM, Hua X, Bromham L. Diversification Rate is Associated with Rate of Molecular Evolution in Ray-Finned Fish (Actinopterygii). J Mol Evol 2022; 90:200-214. [PMID: 35262772 PMCID: PMC8975766 DOI: 10.1007/s00239-022-10052-6] [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: 06/08/2021] [Accepted: 02/24/2022] [Indexed: 10/27/2022]
Abstract
Understanding the factors that drive diversification of taxa across the tree of life is a key focus of macroevolutionary research. While the effects of life history, ecology, climate and geography on diversity have been studied for many taxa, the relationship between molecular evolution and diversification has received less attention. However, correlations between rates of molecular evolution and diversification rate have been detected in a range of taxa, including reptiles, plants and birds. A correlation between rates of molecular evolution and diversification rate is a prediction of several evolutionary theories, including the evolutionary speed hypothesis which links variation in mutation rates to differences in speciation rates. If it is widespread, such correlations could also have significant practical impacts, if they are not adequately accounted for in phylogenetic inference of evolutionary rates and timescales. Ray-finned fish (Actinopterygii) offer a prime target to test for this relationship due to their extreme variation in clade size suggesting a wide range of diversification rates. We employ both a sister-pairs approach and a whole-tree approach to test for correlations between substitution rate and net diversification. We also collect life history and ecological trait data and account for potential confounding factors including body size, latitude, max depth and reef association. We find evidence to support a relationship between diversification and synonymous rates of nuclear evolution across two published backbone phylogenies, as well as weak evidence for a relationship between mitochondrial nonsynonymous rates and diversification at the genus level.
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Affiliation(s)
- Andrew M Ritchie
- Research School of Biological Sciences, Australian National University, Canberra, ACT 2600, Australia. .,Research School of Biological Sciences, Australian National University, Robertson Building, 134 Linnaeus Way, Canberra, ACT 2600, Australia.
| | - Xia Hua
- Research School of Biological Sciences, Australian National University, Canberra, ACT 2600, Australia.,Mathematical Sciences Institute, Australian National University, Canberra, ACT 2600, Australia
| | - Lindell Bromham
- Research School of Biological Sciences, Australian National University, Canberra, ACT 2600, Australia
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23
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Convergent losses of SCPP genes and ganoid scales among non-teleost actinopterygians. Gene 2022; 811:146091. [PMID: 34864098 DOI: 10.1016/j.gene.2021.146091] [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: 08/03/2021] [Revised: 10/25/2021] [Accepted: 11/23/2021] [Indexed: 12/25/2022]
Abstract
Various secretory calcium-binding phosphoprotein (SCPP) genes are expressed in the skin and jaw during the formation of bone, teeth, and scales in osteichthyans (bony vertebrates). Among these mineralized skeletal units is the ganoid scale, found in many fossil actinopterygians (ray-finned fish) but confirmed only in Polypteriformes (bichirs, reedfish) and Lepisosteiformes (gars) among extant clades. Here, we examined SCPP genes in the genome of seven non-teleost actinopterygian species that possess or do not possess ganoid scales. As a result, 39-43 SCPP genes were identified in Polypteriformes and Lepisosteiformes, whereas 22-24 SCPP genes were found in Acipenseriformes (sturgeons, paddlefish) and Amiiformes (bowfin). Most of these genes form two clusters in the genome of Polypteriformes, Lepisosteiformes, and Amiiformes, and these two clusters are duplicated in Acipenseriformes. Despite their distant phylogenetic relationship, Polypteriformes and Lepisosteiformes retain many orthologous SCPP genes. These results imply that common ancestors of extant actinopterygians possessed a large repertoire of SCPP genes, and that many SCPP genes were lost independently in Acipenseriformes and Amiiformes. Notably, most SCPP genes originally located in one of the two SCPP gene clusters are retained in Polypteriformes and Lepisosteiformes but were secondarily lost in Acipenseriformes and Amiiformes. In Lepisosteiformes, orthologs of these lost genes show high or detectable expression levels in the skin but not in the jaw. We thus hypothesize that many SCPP genes located in this cluster are involved in the formation of ganoid scales in Polypteriformes and Lepisosteiformes, and that their orthologs and ganoid scales were convergently lost in Acipenseriformes and Amiiformes.
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24
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Atake OJ, Eames BF. Mineralized Cartilage and Bone-Like Tissues in Chondrichthyans Offer Potential Insights Into the Evolution and Development of Mineralized Tissues in the Vertebrate Endoskeleton. Front Genet 2022; 12:762042. [PMID: 35003210 PMCID: PMC8727550 DOI: 10.3389/fgene.2021.762042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/30/2021] [Indexed: 11/25/2022] Open
Abstract
The impregnation of biominerals into the extracellular matrix of living organisms, a process termed biomineralization, gives rise to diverse mineralized (or calcified) tissues in vertebrates. Preservation of mineralized tissues in the fossil record has provided insights into the evolutionary history of vertebrates and their skeletons. However, current understanding of the vertebrate skeleton and of the processes underlying its formation is biased towards biomedical models such as the tetrapods mouse and chick. Chondrichthyans (sharks, skates, rays, and chimaeras) and osteichthyans are the only vertebrate groups with extant (living) representatives that have a mineralized skeleton, but the basal phylogenetic position of chondrichthyans could potentially offer unique insights into skeletal evolution. For example, bone is a vertebrate novelty, but the internal supporting skeleton (endoskeleton) of extant chondrichthyans is commonly described as lacking bone. The molecular and developmental basis for this assertion is yet to be tested. Subperichondral tissues in the endoskeleton of some chondrichthyans display mineralization patterns and histological and molecular features of bone, thereby challenging the notion that extant chondrichthyans lack endoskeletal bone. Additionally, the chondrichthyan endoskeleton demonstrates some unique features and others that are potentially homologous with other vertebrates, including a polygonal mineralization pattern, a trabecular mineralization pattern, and an unconstricted perichordal sheath. Because of the basal phylogenetic position of chondrichthyans among all other extant vertebrates with a mineralized skeleton, developmental and molecular studies of chondrichthyans are critical to flesh out the evolution of vertebrate skeletal tissues, but only a handful of such studies have been carried out to date. This review discusses morphological and molecular features of chondrichthyan endoskeletal tissues and cell types, ultimately emphasizing how comparative embryology and transcriptomics can reveal homology of mineralized skeletal tissues (and their cell types) between chondrichthyans and other vertebrates.
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Affiliation(s)
- Oghenevwogaga J Atake
- Department of Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, SK, Canada
| | - B Frank Eames
- Department of Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, SK, Canada
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25
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Maugars G, Mauvois X, Martin P, Aroua S, Rousseau K, Dufour S. New Insights Into the Evolution of Corticotropin-Releasing Hormone Family With a Special Focus on Teleosts. Front Endocrinol (Lausanne) 2022; 13:937218. [PMID: 35937826 PMCID: PMC9353778 DOI: 10.3389/fendo.2022.937218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 06/09/2022] [Indexed: 11/30/2022] Open
Abstract
Corticotropin-releasing hormone (CRH) was discovered for its role as a brain neurohormone controlling the corticotropic axis in vertebrates. An additional crh gene, crh2, paralog of crh (crh1), and likely resulting from the second round (2R) of vertebrate whole genome duplication (WGD), was identified in a holocephalan chondrichthyan, in basal mammals, various sauropsids and a non-teleost actinopterygian holostean. It was suggested that crh2 has been recurrently lost in some vertebrate groups including teleosts. We further investigated the fate of crh1 and crh2 in vertebrates with a special focus on teleosts. Phylogenetic and synteny analyses showed the presence of duplicated crh1 paralogs, crh1a and crh1b, in most teleosts, resulting from the teleost-specific WGD (3R). Crh1b is conserved in all teleosts studied, while crh1a has been lost independently in some species. Additional crh1 paralogs are present in carps and salmonids, resulting from specific WGD in these lineages. We identified crh2 gene in additional vertebrate groups such as chondrichthyan elasmobranchs, sarcopterygians including dipnoans and amphibians, and basal actinoperygians, Polypteridae and Chondrostei. We also revealed the presence of crh2 in teleosts, including elopomorphs, osteoglossomorphs, clupeiforms, and ostariophysians, while it would have been lost in Euteleostei along with some other groups. To get some insights on the functional evolution of the crh paralogs, we compared their primary and 3D structure, and by qPCR their tissue distribution, in two representative species, the European eel, which possesses three crh paralogs (crh1a, crh1b, crh2), and the Atlantic salmon, which possesses four crh paralogs of the crh1-type. All peptides conserved the structural characteristics of human CRH. Eel crh1b and both salmon crh1b genes were mainly expressed in the brain, supporting the major role of crh1b paralogs in controlling the corticotropic axis in teleosts. In contrast, crh1a paralogs were mainly expressed in peripheral tissues such as muscle and heart, in eel and salmon, reflecting a striking subfunctionalization between crh1a and b paralogs. Eel crh2 was weakly expressed in the brain and peripheral tissues. These results revisit the repertoire of crh in teleosts and highlight functional divergences that may have contributed to the differential conservation of various crh paralogs in teleosts.
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Affiliation(s)
- Gersende Maugars
- Muséum National d’Histoire Naturelle, Unité Mixte de Recherche Biologie des Organismes et Ecosystèmes Aquatiques (UMR BOREA), Biology of Aquatic Organisms and Ecosystems, Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Sorbonne Université, Paris, France
- Université Le Havre Normandie - Stress Environnementaux et Biosurveillance des milieux aquatiques UMR-I 02SEBIO -FR CNRS 3730 SCALE, Le Havre, France
- *Correspondence: Gersende Maugars,
| | - Xavier Mauvois
- Muséum National d’Histoire Naturelle, Unité Mixte de Recherche Biologie des Organismes et Ecosystèmes Aquatiques (UMR BOREA), Biology of Aquatic Organisms and Ecosystems, Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Sorbonne Université, Paris, France
| | - Patrick Martin
- Conservatoire National du Saumon Sauvage (CNSS), Chanteuges, France
| | - Salima Aroua
- Université Le Havre Normandie - Stress Environnementaux et Biosurveillance des milieux aquatiques UMR-I 02SEBIO -FR CNRS 3730 SCALE, Le Havre, France
| | - Karine Rousseau
- Muséum National d’Histoire Naturelle, Unité Mixte de Recherche Biologie des Organismes et Ecosystèmes Aquatiques (UMR BOREA), Biology of Aquatic Organisms and Ecosystems, Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Sorbonne Université, Paris, France
| | - Sylvie Dufour
- Muséum National d’Histoire Naturelle, Unité Mixte de Recherche Biologie des Organismes et Ecosystèmes Aquatiques (UMR BOREA), Biology of Aquatic Organisms and Ecosystems, Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Sorbonne Université, Paris, France
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Bachvaroff TR, McDonald RC, Plough LV, Chung JS. Chromosome-level genome assembly of the blue crab, Callinectes sapidus. G3-GENES GENOMES GENETICS 2021; 11:6304867. [PMID: 34544121 PMCID: PMC8496215 DOI: 10.1093/g3journal/jkab212] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/15/2021] [Indexed: 11/14/2022]
Abstract
The blue crab, Callinectes sapidus (Rathbun, 1896) is an economically, culturally, and ecologically important species found across the temperate and tropical North and South American Atlantic coast. A reference genome will enable research for this high-value species. Initial assembly combined 200× coverage Illumina paired-end reads, a 60× 8 kb mate-paired library, and 50× PacBio data using the MaSuRCA assembler resulting in a 985 Mb assembly with a scaffold N50 of 153 kb. Dovetail Chicago and HiC sequencing with the 3d DNA assembler and Juicebox assembly tools were then used for chromosome scaffolding. The 50 largest scaffolds span 810 Mb are 1.5-37 Mb long and have a repeat content of 36%. The 190 Mb unplaced sequence is in 3921 sequences over 10 kb with a repeat content of 68%. The final assembly N50 is 18.9 Mb for scaffolds and 9317 bases for contigs. Of arthropod BUSCO, ∼88% (888/1013) were complete and single copies. Using 309 million RNAseq read pairs from 12 different tissues and developmental stages, 25,249 protein-coding genes were predicted. Between C. sapidus and Portunus trituberculatus genomes, 41 of 50 large scaffolds had high nucleotide identity and protein-coding synteny, but 9 scaffolds in both assemblies were not clear matches. The protein-coding genes included 9423 one-to-one putative orthologs, of which 7165 were syntenic between the two crab species. Overall, the two crab genome assemblies show strong similarities at the nucleotide, protein, and chromosome level and verify the blue crab genome as an excellent reference for this important seafood species.
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Affiliation(s)
- Tsvetan R Bachvaroff
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
| | - Ryan C McDonald
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
| | - Louis V Plough
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Horn Point, MD 21613, USA
| | - J Sook Chung
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA
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27
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Thompson AW, Hawkins MB, Parey E, Wcisel DJ, Ota T, Kawasaki K, Funk E, Losilla M, Fitch OE, Pan Q, Feron R, Louis A, Montfort J, Milhes M, Racicot BL, Childs KL, Fontenot Q, Ferrara A, David SR, McCune AR, Dornburg A, Yoder JA, Guiguen Y, Roest Crollius H, Berthelot C, Harris MP, Braasch I. The bowfin genome illuminates the developmental evolution of ray-finned fishes. Nat Genet 2021; 53:1373-1384. [PMID: 34462605 PMCID: PMC8423624 DOI: 10.1038/s41588-021-00914-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 07/13/2021] [Indexed: 02/07/2023]
Abstract
The bowfin (Amia calva) is a ray-finned fish that possesses a unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. The phylogenetic position of bowfin as a representative of neopterygian fishes, its archetypical body plan and its unduplicated and slowly evolving genome make bowfin a central species for the genomic exploration of ray-finned fishes. Here we present a chromosome-level genome assembly for bowfin that enables gene-order analyses, settling long-debated neopterygian phylogenetic relationships. We examine chromatin accessibility and gene expression through bowfin development to investigate the evolution of immune, scale, respiratory and fin skeletal systems and identify hundreds of gene-regulatory loci conserved across vertebrates. These resources connect developmental evolution among bony fishes, further highlighting the bowfin's importance for illuminating vertebrate biology and diversity in the genomic era.
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Affiliation(s)
- Andrew W Thompson
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Ecology, Evolution & Behavior Program, Michigan State University, East Lansing, MI, USA
| | - M Brent Hawkins
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Orthopedic Research, Boston Children's Hospital, Boston, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Elise Parey
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Dustin J Wcisel
- Department of Molecular Biomedical Sciences, NC State University, Raleigh, NC, USA
| | - Tatsuya Ota
- Department of Evolutionary Studies of Biosystems, SOKENDAI (the Graduate University for Advanced Studies), Hayama, Japan
| | - Kazuhiko Kawasaki
- Department of Anthropology, Pennsylvania State University, University Park, PA, USA
| | - Emily Funk
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
- Animal Science Department, University of California Davis, Davis, CA, USA
| | - Mauricio Losilla
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Ecology, Evolution & Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Olivia E Fitch
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Ecology, Evolution & Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Qiaowei Pan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Romain Feron
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Alexandra Louis
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | | | - Marine Milhes
- GeT-PlaGe, INRAE, Genotoul, Castanet-Tolosan, France
| | - Brett L Racicot
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Quenton Fontenot
- Department of Biological Sciences, Nicholls State University, Thibodaux, LA, USA
| | - Allyse Ferrara
- Department of Biological Sciences, Nicholls State University, Thibodaux, LA, USA
| | - Solomon R David
- Department of Biological Sciences, Nicholls State University, Thibodaux, LA, USA
| | - Amy R McCune
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, NC State University, Raleigh, NC, USA
- Comparative Medicine Institute, NC State University, Raleigh, NC, USA
- Center for Human Health and the Environment, NC State University, Raleigh, NC, USA
| | | | - Hugues Roest Crollius
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Camille Berthelot
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Matthew P Harris
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Orthopedic Research, Boston Children's Hospital, Boston, MA, USA
| | - Ingo Braasch
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA.
- Ecology, Evolution & Behavior Program, Michigan State University, East Lansing, MI, USA.
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28
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Stöck M, Kratochvíl L, Kuhl H, Rovatsos M, Evans BJ, Suh A, Valenzuela N, Veyrunes F, Zhou Q, Gamble T, Capel B, Schartl M, Guiguen Y. A brief review of vertebrate sex evolution with a pledge for integrative research: towards ' sexomics'. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200426. [PMID: 34247497 PMCID: PMC8293304 DOI: 10.1098/rstb.2020.0426] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2021] [Indexed: 02/07/2023] Open
Abstract
Triggers and biological processes controlling male or female gonadal differentiation vary in vertebrates, with sex determination (SD) governed by environmental factors or simple to complex genetic mechanisms that evolved repeatedly and independently in various groups. Here, we review sex evolution across major clades of vertebrates with information on SD, sexual development and reproductive modes. We offer an up-to-date review of divergence times, species diversity, genomic resources, genome size, occurrence and nature of polyploids, SD systems, sex chromosomes, SD genes, dosage compensation and sex-biased gene expression. Advances in sequencing technologies now enable us to study the evolution of SD at broader evolutionary scales, and we now hope to pursue a sexomics integrative research initiative across vertebrates. The vertebrate sexome comprises interdisciplinary and integrated information on sexual differentiation, development and reproduction at all biological levels, from genomes, transcriptomes and proteomes, to the organs involved in sexual and sex-specific processes, including gonads, secondary sex organs and those with transcriptional sex-bias. The sexome also includes ontogenetic and behavioural aspects of sexual differentiation, including malfunction and impairment of SD, sexual differentiation and fertility. Starting from data generated by high-throughput approaches, we encourage others to contribute expertise to building understanding of the sexomes of many key vertebrate species. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)'.
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Affiliation(s)
- Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries—IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Prague, Czech Republic
| | - Heiner Kuhl
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries—IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
| | - Michail Rovatsos
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Ben J. Evans
- Department of Biology, McMaster University, Life Sciences Building Room 328, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK
- Department of Organismal Biology—Systematic Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Frédéric Veyrunes
- Institut des Sciences de l'Evolution de Montpellier, ISEM UMR 5554 (CNRS/Université de Montpellier/IRD/EPHE), Montpellier, France
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
- Department of Neuroscience and Developmental Biology, University of Vienna, A-1090 Vienna, Austria
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
| | - Blanche Capel
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Würzburg, 97074 Würzburg, Germany
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
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29
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Ocampo Daza D, Bergqvist CA, Larhammar D. The Evolution of Oxytocin and Vasotocin Receptor Genes in Jawed Vertebrates: A Clear Case for Gene Duplications Through Ancestral Whole-Genome Duplications. Front Endocrinol (Lausanne) 2021; 12:792644. [PMID: 35185783 PMCID: PMC8851675 DOI: 10.3389/fendo.2021.792644] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 11/22/2021] [Indexed: 12/02/2022] Open
Abstract
The neuronal and neuroendocrine peptides oxytocin (OT) and vasotocin (VT), including vasopressins, have six cognate receptors encoded by six receptor subtype genes in jawed vertebrates. The peptides elicit a broad range of responses that are specifically mediated by the receptor subtypes including neuronal functions regulating behavior and hormonal actions on reproduction and water/electrolyte balance. Previously, we have demonstrated that these six receptor subtype genes, which we designated VTR1A, VTR1B, OTR, VTR2A, VTR2B and VTR2C, arose from a syntenic ancestral gene pair, one VTR1/OTR ancestor and one VTR2 ancestor, through the early vertebrate whole-genome duplications (WGD) called 1R and 2R. This was supported by both phylogenetic and chromosomal conserved synteny data. More recently, other studies have focused on confounding factors, such as the OTR/VTR orthologs in cyclostomes, to question this scenario for the origin of the OTR/VTR gene family; proposing instead less parsimonious interpretations involving only one WGD followed by complex series of chromosomal or segmental duplications. Here, we have updated the phylogeny of the OTR/VTR gene family, including a larger number of vertebrate species, and revisited seven representative neighboring gene families from our previous conserved synteny analyses, adding chromosomal information from newer high-coverage genome assemblies from species that occupy key phylogenetic positions: the polypteriform fish reedfish (Erpetoichthys calabaricus), the cartilaginous fish thorny skate (Amblyraja radiata) and a more recent high-quality assembly of the Western clawed frog (Xenopus tropicalis) genome. Our analyses once again add strong support for four-fold symmetry, i.e., chromosome quadruplication in the same time window as the WGD events early in vertebrate evolution, prior to the jawed vertebrate radiation. Thus, the evolution of the OTR/VTR gene family can be most parsimoniously explained by two WGD events giving rise to the six ancestral genes, followed by differential gene losses of VTR2 genes in different lineages. We also argue for more coherence and clarity in the nomenclature of OT/VT receptors, based on the most parsimonious scenario.
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Affiliation(s)
- Daniel Ocampo Daza
- Subdepartment of Evolution and Development, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
- Department of Molecular and Cell Biology, University of California Merced, Merced, CA, United States
| | - Christina A. Bergqvist
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Dan Larhammar
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- *Correspondence: Dan Larhammar,
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