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Madrigal G, Minhas BF, Catchen J. Klumpy: A tool to evaluate the integrity of long-read genome assemblies and illusive sequence motifs. Mol Ecol Resour 2024:e13982. [PMID: 38800997 DOI: 10.1111/1755-0998.13982] [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] [Received: 03/28/2024] [Accepted: 05/13/2024] [Indexed: 05/29/2024]
Abstract
The improvement and decreasing costs of third-generation sequencing technologies has widened the scope of biological questions researchers can address with de novo genome assemblies. With the increasing number of reference genomes, validating their integrity with minimal overhead is vital for establishing confident results in their applications. Here, we present Klumpy, a tool for detecting and visualizing both misassembled regions in a genome assembly and genetic elements (e.g. genes) of interest in a set of sequences. By leveraging the initial raw reads in combination with their respective genome assembly, we illustrate Klumpy's utility by investigating antifreeze glycoprotein (afgp) loci across two icefishes, by searching for a reported absent gene in the northern snakehead fish, and by scanning the reference genomes of a mudskipper and bumblebee for misassembled regions. In the two former cases, we were able to provide support for the noncanonical placement of an afgp locus in the icefishes and locate the missing snakehead gene. Furthermore, our genome scans were able identify an unmappable locus in the mudskipper reference genome and identify a putative repetitive element shared among several species of bees.
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Affiliation(s)
- Giovanni Madrigal
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Bushra Fazal Minhas
- Informatics Program, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Julian Catchen
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Informatics Program, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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Wang Y, Zhang X, Wang J, Wang C, Xiong F, Qian Y, Meng M, Zhou M, Chen W, Ding Z, Yu D, Liu Y, Chang Y, He S, Yang L. Genomic insights into the seawater adaptation in Cyprinidae. BMC Biol 2024; 22:87. [PMID: 38637780 PMCID: PMC11027309 DOI: 10.1186/s12915-024-01885-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/11/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Cyprinidae, the largest fish family, encompasses approximately 367 genera and 3006 species. While they exhibit remarkable adaptability to diverse aquatic environments, it is exceptionally rare to find them in seawater, with the Far Eastern daces being of few exceptions. Therefore, the Far Eastern daces serve as a valuable model for studying the genetic mechanisms underlying seawater adaptation in Cyprinidae. RESULTS Here, we sequenced the chromosome-level genomes of two Far Eastern daces (Pseudaspius brandtii and P. hakonensis), the two known cyprinid fishes found in seawater, and performed comparative genomic analyses to investigate their genetic mechanism of seawater adaptation. Demographic history reconstruction of the two species reveals that their population dynamics are correlated with the glacial-interglacial cycles and sea level changes. Genomic analyses identified Pseudaspius-specific genetic innovations related to seawater adaptation, including positively selected genes, rapidly evolving genes, and conserved non-coding elements (CNEs). Functional assays of Pseudaspius-specific variants of the prolactin (prl) gene showed enhanced cell adaptation to greater osmolarity. Functional assays of Pseudaspius specific CNEs near atg7 and usp45 genes suggest that they exhibit higher promoter activity and significantly induced at high osmolarity. CONCLUSIONS Our results reveal the genome-wide evidence for the evolutionary adaptation of cyprinid fishes to seawater, offering valuable insights into the molecular mechanisms supporting the survival of migratory fish in marine environments. These findings are significant as they contribute to our understanding of how cyprinid fishes navigate and thrive in diverse aquatic habitats, providing useful implications for the conservation and management of marine ecosystems.
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Affiliation(s)
- Ying Wang
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, 430056, China.
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China.
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, BS81TQ, UK.
| | - Xuejing Zhang
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, 430056, China
| | - Jing Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Cheng Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fei Xiong
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, 430056, China
| | - Yuting Qian
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Minghui Meng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Min Zhou
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, 430056, China
| | - Wenjun Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zufa Ding
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dan Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yumei Chang
- National and Local Joint Engineering Laboratory for Freshwater Fish Breeding, Heilongjiang Province's Key Laboratory of Fish Stress Resistance Breeding and Germplasm Characteristics On Special Habitats, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, Heilongjiang, China
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China.
| | - Liandong Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China.
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, BS81TQ, UK.
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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: 0] [Impact Index Per Article: 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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Lü Z, Yu Z, Luo W, Liu T, Wang Y, Liu Y, Liu J, Liu B, Gong L, Liu L, Li Y. Chromosome-level genome assembly and annotation of eel goby (Odontamblyopus rebecca). Sci Data 2024; 11:160. [PMID: 38307872 PMCID: PMC10837429 DOI: 10.1038/s41597-024-02997-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/25/2024] [Indexed: 02/04/2024] Open
Abstract
The eel gobies fascinate researchers with many important features, including its unique body structure, benthic lifestyle, and degenerated eyes. However, genome assembly and exploration of the unique genomic composition of the eel gobies are still in their infancy. This has severely limited research progress on gobies. In this study, multi-platform sequencing data were generated and used to assemble and annotate the genome of O. rebecca at the chromosome-level. The assembled genome size of O. rebecca is 918.57 Mbp, which is similar to the estimated genome size (903.03 Mbp) using 17-mer. The scaffold N50 is 41.67 Mbp, and 23 chromosomes were assembled using Hi-C technology with a mounting rate of 99.96%. Genome annotation indicates that 53.29% of the genome is repetitive sequences, and 22,999 protein-coding genes are predicted, of which 21,855 have functional annotations. The chromosome-level genome of O. rebecca will not only provide important genomic resources for comparative genomic studies of gobies, but also expand our knowledge of the genetic origin of their unique features fascinating researchers for decades.
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Affiliation(s)
- Zhenming Lü
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Ziwei Yu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Wenkai Luo
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Tianwei Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Yuzheng Wang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Yantang Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Jing Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Liqin Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Yongxin Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China.
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Han FY, Wu RX, Miao BB, Niu SF, Wang QH, Liang ZB. Whole-Genome Sequencing Analyses Reveal the Whip-like Tail Formation, Innate Immune Evolution, and DNA Repair Mechanisms of Eupleurogrammus muticus. Animals (Basel) 2024; 14:434. [PMID: 38338077 PMCID: PMC10854985 DOI: 10.3390/ani14030434] [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] [Received: 11/15/2023] [Revised: 01/19/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Smallhead hairtail (Eupleurogrammus muticus) is an important marine economic fish distributed along the northern Indian Ocean and the northwest Pacific coast; however, little is known about the mechanism of its genetic evolution. This study generated the first genome assembly of E. muticus at the chromosomal level using a combination of PacBio SMRT, Illumina Nova-Seq, and Hi-C technologies. The final assembled genome size was 709.27 Mb, with a contig N50 of 25.07 Mb, GC content of 40.81%, heterozygosity rate of 1.18%, and repetitive sequence rate of 35.43%. E. muticus genome contained 21,949 protein-coding genes (97.92% of the genes were functionally annotated) and 24 chromosomes. There were 143 expansion gene families, 708 contraction gene families, and 4888 positively selected genes in the genome. Based on the comparative genomic analyses, we screened several candidate genes and pathways related to whip-like tail formation, innate immunity, and DNA repair in E. muticus. These findings preliminarily reveal some molecular evolutionary mechanisms of E. muticus at the genomic level and provide important reference genomic data for the genetic studies of other trichiurids.
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Affiliation(s)
- Fang-Yuan Han
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (F.-Y.H.); (S.-F.N.); (Z.-B.L.)
| | - Ren-Xie Wu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (F.-Y.H.); (S.-F.N.); (Z.-B.L.)
| | - Ben-Ben Miao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China;
| | - Su-Fang Niu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (F.-Y.H.); (S.-F.N.); (Z.-B.L.)
| | - Qing-Hua Wang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, China;
| | - Zhen-Bang Liang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (F.-Y.H.); (S.-F.N.); (Z.-B.L.)
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Kato S, Arakaki S, Nagano AJ, Kikuchi K, Hirase S. Genomic landscape of introgression from the ghost lineage in a gobiid fish uncovers the generality of forces shaping hybrid genomes. Mol Ecol 2023. [PMID: 38047388 DOI: 10.1111/mec.17216] [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] [Received: 07/14/2023] [Revised: 09/23/2023] [Accepted: 10/26/2023] [Indexed: 12/05/2023]
Abstract
Extinct lineages can leave legacies in the genomes of extant lineages through ancient introgressive hybridization. The patterns of genomic survival of these extinct lineages provide insight into the role of extinct lineages in current biodiversity. However, our understanding on the genomic landscape of introgression from extinct lineages remains limited due to challenges associated with locating the traces of unsampled 'ghost' extinct lineages without ancient genomes. Herein, we conducted population genomic analyses on the East China Sea (ECS) lineage of Chaenogobius annularis, which was suspected to have originated from ghost introgression, with the aim of elucidating its genomic origins and characterizing its landscape of introgression. By combining phylogeographic analysis and demographic modelling, we demonstrated that the ECS lineage originated from ancient hybridization with an extinct ghost lineage. Forward simulations based on the estimated demography indicated that the statistic γ of the HyDe analysis can be used to distinguish the differences in local introgression rates in our data. Consistent with introgression between extant organisms, we found reduced introgression from extinct lineage in regions with low recombination rates and with functional importance, thereby suggesting a role of linked selection that has eliminated the extinct lineage in shaping the hybrid genome. Moreover, we identified enrichment of repetitive elements in regions associated with ghost introgression, which was hitherto little known but was also observed in the re-analysis of published data on introgression between extant organisms. Overall, our findings underscore the unexpected similarities in the characteristics of introgression landscapes across different taxa, even in cases of ghost introgression.
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Affiliation(s)
- Shuya Kato
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Hamamatsu, Shizuoka, Japan
| | - Seiji Arakaki
- Amakusa Marine Biological Laboratory, Kyushu University, Amakusa, Kumamoto, Japan
| | - Atsushi J Nagano
- Department of Life Sciences, Faculty of Agriculture, Ryukoku University, Ōtsu, Shiga, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Kiyoshi Kikuchi
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Hamamatsu, Shizuoka, Japan
| | - Shotaro Hirase
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Hamamatsu, Shizuoka, Japan
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Chen H, Wang L, Wang L, Zhang H, Wang H, Song L. Synergistic modulation of neuroendocrine-inflammation pathway by microRNAs facilitates intertidal adaptation of molluscs. FISH & SHELLFISH IMMUNOLOGY 2023; 142:109165. [PMID: 37839542 DOI: 10.1016/j.fsi.2023.109165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/17/2023]
Abstract
Neuroendocrine-immune system is an evolution-conserved regulatory network in maintaining the homeostasis of animals. While knowledge on the roles of neuroendocrine-immune system in the disease and stress responses of organisms is growing, the ecological roles of neuroendocrine-immune system, especially how it shapes the unique lifestyle of organisms remain insufficiently investigated. As an endemic and dominant mollusc in intertidal region, oysters have evolved with a primitive neuroendocrine-immune system and with a sessile lifestyle. Recently, a novel neuroendocrine-immune pathway, Ca2+/calmodulin (CaM)-nitrite oxide synthase (NOS)/nitrite oxide (NO)-tumor necrosis factor (TNF) pathway, is identified in oysters and found altered dynamically during aerial exposure, one common but challenging stresses for intertidal organisms and a decisive factor shaping their habitat. Since the pathway proves fatal in prolonged aerial exposure, we hypothesized that the activation/deactivation of pathway could be strictly modulated in adaptation to the sessile lifestyle of oysters. Here, a synergistic modulation on the Ca2+/CaM-NOS/NO-TNF pathway by four members of miR-92 family and two oyster-specific miRNAs was identified, which further hallmarks the resilience and survival strategy of oysters to aerial exposure. Briefly, these six miRNAs were down-regulating CgCaM24243 post-transcriptionally and deactivating the pathway during the early-stage of stress. However, a robust recession of these miRNAs occurred at the late-stage of stress, resulting in the reactivation of pathway and overwhelming accumulation of cytokines. These results demonstrated a complicated interaction between miRNAs and ancient neuroendocrine-immune system, which facilitates the environmental adaptation of intertidal oysters and provides novel insight on the function and evolution of neuroendocrine-immune system in ecological context.
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Affiliation(s)
- Hao Chen
- Center of Deep Sea Research, and CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Lin Wang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China.
| | - Huan Zhang
- Center of Deep Sea Research, and CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Hao Wang
- Center of Deep Sea Research, and CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Laoshan Laboratory, Qingdao, 266235, China.
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Rao A, Lyu B, Jahan I, Lubertozzi A, Zhou G, Tedeschi F, Jankowsky E, Kang J, Carstens B, Poss KD, Baskin K, Goldman JA. The translation initiation factor homolog eif4e1c regulates cardiomyocyte metabolism and proliferation during heart regeneration. Development 2023; 150:dev201376. [PMID: 37306388 PMCID: PMC10281269 DOI: 10.1242/dev.201376] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 04/28/2023] [Indexed: 05/25/2023]
Abstract
The eIF4E family of translation initiation factors bind 5' methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability, yet other related eIF4E families exist and are utilized in specific contexts or tissues. Here, we describe a family called Eif4e1c, for which we find roles during heart development and regeneration in zebrafish. The Eif4e1c family is present in all aquatic vertebrates but is lost in all terrestrial species. A core group of amino acids shared over 500 million years of evolution forms an interface along the protein surface, suggesting that Eif4e1c functions in a novel pathway. Deletion of eif4e1c in zebrafish caused growth deficits and impaired survival in juveniles. Mutants surviving to adulthood had fewer cardiomyocytes and reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although eif4e1c is broadly expressed, its disruption had most notable impact on the heart and at juvenile stages. Our findings reveal context-dependent requirements for translation initiation regulators during heart regeneration.
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Affiliation(s)
- Anupama Rao
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Baken Lyu
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Ishrat Jahan
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Anna Lubertozzi
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Gao Zhou
- Center for RNA Molecular Biology, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106USA
| | - Frank Tedeschi
- Center for RNA Molecular Biology, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106USA
| | - Eckhard Jankowsky
- Center for RNA Molecular Biology, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Bryan Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Kenneth D. Poss
- Department of Cell Biology, Duke Regeneration Center, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kedryn Baskin
- Department of Cell Biology and Physiology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Joseph Aaron Goldman
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
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Carlson KB, Nguyen C, Wcisel DJ, Yoder JA, Dornburg A. Ancient fish lineages illuminate toll-like receptor diversification in early vertebrate evolution. Immunogenetics 2023; 75:465-478. [PMID: 37555888 DOI: 10.1007/s00251-023-01315-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/28/2023] [Indexed: 08/10/2023]
Abstract
Since its initial discovery over 50 years ago, understanding the evolution of the vertebrate RAG- mediated adaptive immune response has been a major area of research focus for comparative geneticists. However, how the evolutionary novelty of an adaptive immune response impacted the diversity of receptors associated with the innate immune response has received considerably less attention until recently. Here, we investigate the diversification of vertebrate toll-like receptors (TLRs), one of the most ancient and well conserved innate immune receptor families found across the Tree of Life, integrating genomic data that represent all major vertebrate lineages with new transcriptomic data from Polypteriformes, the earliest diverging ray-finned fish lineage. Our analyses reveal TLR sequences that reflect the 6 major TLR subfamilies, TLR1, TLR3, TLR4, TLR5, TLR7, and TLR11, and also currently unnamed, yet phylogenetically distinct TLR clades. We additionally recover evidence for a pulse of gene gain coincident with the rise of the RAG-mediated adaptive immune response in jawed vertebrates, followed by a period of rapid gene loss during the Cretaceous. These gene losses are primarily concentrated in marine teleost fish and synchronous with the mid Cretaceous anoxic event, a period of rapid extinction for marine species. Finally, we reveal a mismatch between phylogenetic placement and gene nomenclature for up to 50% of TLRs found in clades such as ray-finned fishes, cyclostomes, amphibians, and elasmobranchs. Collectively, these results provide an unparalleled perspective of TLR diversity and offer a ready framework for testing gene annotations in non-model species.
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Affiliation(s)
- Kara B Carlson
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
- Genetics and Genomics Academy, North Carolina State University, Raleigh, NC, USA
| | - Cameron Nguyen
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Dustin J Wcisel
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, USA
- Genetics and Genomics Academy, North Carolina State University, Raleigh, NC, USA
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA.
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Liu Y, Liu T, Wang Y, Liu J, Liu B, Gong L, Lü Z, Liu L. Genome Sequencing Provides Novel Insights into Mudflat Burrowing Adaptations in Eel Goby Taenioides sp. (Teleost: Amblyopinae). Int J Mol Sci 2023; 24:12892. [PMID: 37629073 PMCID: PMC10454203 DOI: 10.3390/ijms241612892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Amblyopinae is one of the lineage of bony fish that preserves amphibious traits living in tidal mudflat habitats. In contrast to other active amphibious fish, Amblyopinae species adopt a seemly more passive lifestyle by living in deep burrows of mudflat to circumvent the typical negative effects associated with terrestriality. However, little is known about the genetic origin of these mudflat deep-burrowing adaptations in Amblyopinae. Here we sequenced the first genome of Amblyopinae species, Taenioides sp., to elucidate their mudflat deep-burrowing adaptations. Our results revealed an assembled genome size of 774.06 Mb with 23 pseudochromosomes anchored, which predicted 22,399 protein-coding genes. Phylogenetic analyses indicated that Taenioides sp. diverged from the active amphibious fish of mudskipper approximately 28.3 Ma ago. In addition, 185 and 977 putative gene families were identified to be under expansion, contraction and 172 genes were undergone positive selection in Taenioides sp., respectively. Enrichment categories of top candidate genes under significant expansion and selection were mainly associated with hematopoiesis or angiogenesis, DNA repairs and the immune response, possibly suggesting their involvement in the adaptation to the hypoxia and diverse pathogens typically observed in mudflat burrowing environments. Some carbohydrate/lipid metabolism, and insulin signaling genes were also remarkably alterated, illustrating physiological remolding associated with nutrient-limited subterranean environments. Interestingly, several genes related to visual perception (e.g., crystallins) have undergone apparent gene losses, pointing to their role in the small vestigial eyes development in Taenioides sp. Our work provide valuable resources for understanding the molecular mechanisms underlying mudflat deep-burrowing adaptations in Amblyopinae, as well as in other tidal burrowing teleosts.
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Affiliation(s)
- Yantao Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China
| | - Tianwei Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China
| | - Yuzhen Wang
- National Engineering Research Center for Facilitated Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Jing Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China
| | - Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China
| | - Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China
| | - Zhenming Lü
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China
| | - Liqin Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China
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11
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Zhou H, Donatelli CM, Laneuville O, Standen EM. Skeletal anatomy of the pectoral fin in mudskipper species from terrestrial and aquatic habitats. J Morphol 2023; 284:e21612. [PMID: 37458082 DOI: 10.1002/jmor.21612] [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] [Received: 03/10/2023] [Revised: 05/24/2023] [Accepted: 06/09/2023] [Indexed: 07/18/2023]
Abstract
Mudskippers are a group of amphibious fishes in the family Oxudercidae, whose species inhabit a range of habitats from mostly aquatic to mostly terrestrial. Most of our understanding about habitat preference comes from natural history observations, particularly where they are collected (i.e., low intertidal vs. high intertidal regions). Mudskippers have undergone several morphological changes to accommodate a terrestrial life, including major changes to the pectoral and pelvic girdles. These changes result in a novel crutching gait, which mudskippers use to move over land. Though the appendicular morphology and crutching gait of mudskippers have been described in some species, few studies have compared skeletal structures across the family. In our study, we use microcomputed tomography (µCT) scans to compare the skeletal anatomy of 16 species of aquatic and terrestrial mudskippers. Linear discriminant analysis is used to analyze measurements obtained through geometric morphometrics (landmarks). We found bone structures of the pectoral region in the terrestrial group were significantly longer and wider than those in the aquatic group. Furthermore, a significant difference in anatomy is shown between terrestrial and aquatic genera with both axial and appendicular elements contributing to the separation between groups. This work describes the differences in skeletal morphology associated with terrestriality in mudskippers and provides valuable insights into specific anatomical characteristics contributing to their adaptation to novel environments.
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Affiliation(s)
- Haodong Zhou
- Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Odette Laneuville
- Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Ontario, Canada
| | - Emily M Standen
- Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Ontario, Canada
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12
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Mao Y, Peng T, Shao F, Zhao Q, Peng Z. Molecular evolution of the hemoglobin gene family across vertebrates. Genetica 2023:10.1007/s10709-023-00187-9. [PMID: 37069365 DOI: 10.1007/s10709-023-00187-9] [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] [Received: 09/02/2022] [Accepted: 04/11/2023] [Indexed: 04/19/2023]
Abstract
Adaptation to various altitudes and oxygen levels is a major aspect of vertebrate evolution. Hemoglobin is an erythrocyte protein belonging to the globin superfamily, and the α-, β-globin genes of jawed vertebrates encode tetrameric ((α2β2) hemoglobin, which contributes to aerobic metabolism by delivering oxygen from the respiratory exchange surfaces into cells. However, there are various gaps in knowledge regarding hemoglobin gene evolution, including patterns in cartilaginous fish and the roles of gene conversion in various taxa. Hence, we evaluated the evolutionary history of the vertebrate hemoglobin gene family by analyses of 97 species representing all classes of vertebrates. By genome-wide analyses, we extracted 879 hemoglobin sequences. Members of the hemoglobin gene family were conserved in birds and reptiles but variable in mammals, amphibians, and teleosts. Gene motifs, structures, and synteny were relatively well-conserved among vertebrates. Our results revealed that purifying selection contributed substantially to the evolution of all vertebrate hemoglobin genes, with mean dN/dS (ω) values ranging from 0.057 in teleosts to 0.359 in reptiles. In general, after the fish-specific genome duplication, the teleost hemoglobin genes showed variation in rates of evolution, and the β-globin genes showed relatively high ω values after a gene transposition event in amniotes. We also observed that the frequency of gene conversion was high in amniotes, with fewer hemoglobin genes and higher rates of evolution. Collectively, our findings provide detail insight into complex evolutionary processes shaping the vertebrate hemoglobin gene family, involving gene duplication, gene loss, purifying selection, and gene conversion.
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Affiliation(s)
- Yang Mao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, 400715, China
- Clinical Research Center, The Second Affiliated Hospital, Army Medical University, Chongqing, 400037, China
| | - Taotao Peng
- Department of Anesthesiology, Second Affiliated Hospital, Army Medical University, Chongqing, 400037, China
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, 400715, China
| | - Qingyuan Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, 400715, China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, 400715, China.
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Ma H, Hong WS, Chen SX. A progestin regulates the prostaglandin pathway in the neuroendocrine system in female mudskipper Boleophthalmus pectinirostris. J Steroid Biochem Mol Biol 2023; 231:106300. [PMID: 36990161 DOI: 10.1016/j.jsbmb.2023.106300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 02/02/2023] [Accepted: 02/23/2023] [Indexed: 03/30/2023]
Abstract
Sex hormones regulate the reproductive cycle through brain-pituitary axis, but the molecular mechanism is still enigmatic. In the reproductive season, the mudskipper Boleophthalmus pectinirostris possesses a semilunar periodicity spawning rhythm, which coincides with the semilunar periodicity variations in 17α-hydroxyprogesterone, the precursor of 17α,20β-dihydroxy-4-pregnen-3-one (DHP), a sexual progestin in teleosts. In the present study, we investigated in vitro the brain transcriptional differences between DHP-treated tissues and control groups using RNA-seq. Differential expression analysis revealed that 2700 genes significantly differentially expressed, including 1532 up-regulated and 1168 down-regulated genes. The majority of prostaglandin pathway-related genes were dramatically up-regulated, especially the prostaglandin receptor 6 (ptger6). Tissue distribution analysis revealed that ptger6 gene was ubiquitously expressed. In situ hybridization results showed that ptger6, nuclear progestin receptor (pgr), and DHP-induced c-fos mRNA were co-expressed in the ventral telencephalic area, the ventral nucleus of ventral telencephalic area, the anterior part of parvocellular preoptic nucleus, the magnocellular part of magnocellular preoptic nucleus, the ventral zone of periventricular hypothalamus, the anterior tubercular nucleus, the periventricular nucleus of posterior tuberculum, and the torus longitudinalis. DHP significantly enhanced promoter activities of ptger6 via Pgr. Together, this study suggested that DHP regulates the prostaglandin pathway in the neuroendocrine system of teleost fish.
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Affiliation(s)
- He Ma
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Wang Shu Hong
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China; State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, 361102, China
| | - Shi Xi Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China; State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, 361102, China.
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14
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Amblyopinae Mitogenomes Provide Novel Insights into the Paraphyletic Origin of Their Adaptation to Mudflat Habitats. Int J Mol Sci 2023; 24:ijms24054362. [PMID: 36901796 PMCID: PMC10001788 DOI: 10.3390/ijms24054362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/10/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
The water-to-land transition is one of the most important events in evolutionary history of vertebrates. However, the genetic basis underlying many of the adaptations during this transition remains unclear. Mud-dwelling gobies in the subfamily Amblyopinae are one of the teleosts lineages that show terrestriality and provide a useful system for clarifying the genetic changes underlying adaptations to terrestrial life. Here, we sequenced the mitogenome of six species in the subfamily Amblyopinae. Our results revealed a paraphyletic origin of Amblyopinae with respect to Oxudercinae, which are the most terrestrial fishes and lead an amphibious life in mudflats. This partly explains the terrestriality of Amblyopinae. We also detected unique tandemly repeated sequences in the mitochondrial control region in Amblyopinae, as well as in Oxudercinae, which mitigate oxidative DNA damage stemming from terrestrial environmental stress. Several genes, such as ND2, ND4, ND6 and COIII, have experienced positive selection, suggesting their important roles in enhancing the efficiency of ATP production to cope with the increased energy requirements for life in terrestrial environments. These results strongly suggest that the adaptive evolution of mitochondrial genes has played a key role in terrestrial adaptions in Amblyopinae, as well as in Oxudercinae, and provide new insights into the molecular mechanisms underlying the water-to-land transition in vertebrates.
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15
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The gastric proton pump in gobiid and mudskipper fishes. Evidence of stomach loss? Comp Biochem Physiol A Mol Integr Physiol 2022; 274:111300. [PMID: 36031062 DOI: 10.1016/j.cbpa.2022.111300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 08/20/2022] [Accepted: 08/21/2022] [Indexed: 01/01/2023]
Abstract
Stomach loss has occurred independently multiple times during gnathostome evolution with notable frequency within the Teleostei. Significantly, this loss of acid-peptic digestion has been found to correlate with the secondary genomic loss of the gastric proton pump subunits (atp4a, atp4b) and pepsinogens/pepsins (pga, pgc). Gastric glands produce gastric juice containing the acid and pepsin and thus their presence is a hallmark feature of a digestive system capable of acid-peptic digestion. However, in gobiid fishes although oesogaster and gastric glands have been identified histologically, their functional significance has been questioned. In the present study we address whether the gastric proton pump is present and expressed in gastric glands of the goby Neogobius species (Gobiidae) and in members of the family Oxudercidae, a group of amphibious gobiid fishes commonly known as mudskippers (genera: Periophthalmus, Boleophthalmus, Periophthalmodon and Scartelaos). We confirmed the presence of gastric glands and have immunohistochemically localized gastric proton pump expression to these glands in Neogobius fluviatilis and Periophthalmus novemradiatus, Periophthalmus barbarus and Boleophthalmus boddarti. Genome analysis in Neogobius melanostomus, Periophthalmus magnuspinnatus, Scartelaos histophorus, Boleophthalmus pectinirostris, and Periophthalmodon schlosseri revealed the presence of both atp4a and atp4b subunit orthologues in all species in a conserved genomic loci organization. Moreover, it was possible to deduce that the complete open reading frame and the key functional amino acid residues are present. The conserved expression of the gastric proton pump provides clear evidence of the potential for gastric acid secretion indicating that acid digestion is retained in these gobiid fishes and not lost.
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Corush JB, Zhang J. One size does not fit all: Variation in anatomical traits associated with emersion behavior in mudskippers (Gobiidae: Oxudercinae). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.967067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Life histories involving transitions between differing habitats (i.e., aquatic to terrestrial or marine to freshwater) require numerous anatomical, physiological, and behavioral changes. Often, the traits associated with these changes are thought to come in suites, but all traits thought to be associated with particular life histories may not be required. While some traits are found in all species with a particular habitat transition, a grab bag approach may apply to other traits in that any trait may be sufficient for successful habitat transitions. We examine patterns of morphological traits associated with prolonged emersion in mudskipper, an amphibious fishes clade, where prolonged emersion appears twice. We test the evolutionary history of multiple characteristics associated with cutaneous respiration. We find most traits thought to be key for prolonged emersion show no phylogenetic signal and no tight correlation with prolonged emersion. Such traits appear in species with prolonged emersion but also non-emerging species. Only capillary density, which, when increased, allows for increased oxygen absorption, shows strong phylogenetic signal and correlation with prolonged emersion. Further experimental, functional genomics, and observational studies are needed to fully understand the mechanisms associated with each of these traits. With respect to traits associated with other particular behaviors, a comparative framework can be helpful in identifying evolutionary correlates.
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Expression of Antimicrobic Peptide Piscidin1 in Gills Mast Cells of Giant Mudskipper Periophthalmodon schlosseri (Pallas, 1770). Int J Mol Sci 2022; 23:ijms232213707. [PMID: 36430187 PMCID: PMC9692400 DOI: 10.3390/ijms232213707] [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: 09/29/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022] Open
Abstract
The amphibious teleost Giant mudskipper (Periophthalmodon schlosseri, Pallas 1770) inhabit muddy plains and Asian mangrove forests. It spends more than 90% of its life outside of the water, using its skin, gills, and buccal-pharyngeal cavity mucosa to breathe in oxygen from the surrounding air. All vertebrates have been found to have mast cells (MCs), which are part of the innate immune system. These cells are mostly found in the mucous membranes of the organs that come in contact with the outside environment. According to their morphology, MCs have distinctive cytoplasmic granules that are released during the degranulation process. Additionally, these cells have antimicrobial peptides (AMPs) that fight a variety of infections. Piscidins, hepcidins, defensins, cathelicidins, and histonic peptides are examples of fish AMPs. Confocal microscopy was used in this study to assess Piscidin1 expression in Giant Mudskipper branchial MCs. Our results demonstrated the presence of MCs in the gills is highly positive for Piscidin1. Additionally, colocalized MCs labeled with TLR2/5-HT and Piscidin1/5-HT supported our data. The expression of Piscidin1 in giant mudskipper MCs highlights the involvement of this peptide in the orchestration of teleost immunity, advancing the knowledge of the defense system of this fish.
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Zhao X, Huang Y, Bian C, You X, Zhang X, Chen J, Wang M, Hu C, Xu Y, Xu J, Shi Q. Whole genome sequencing of the fast-swimming Southern bluefin tuna (Thunnus maccoyii). Front Genet 2022; 13:1020017. [DOI: 10.3389/fgene.2022.1020017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
The economically important Southern bluefin tuna (Thunnus maccoyii) is a world-famous fast-swimming fish, but its genomic information is limited. Here, we performed whole genome sequencing and assembled a draft genome for Southern bluefin tuna, aiming to generate useful genetic data for comparative functional prediction. The final genome assembly is 806.54 Mb, with scaffold and contig N50 values of 3.31 Mb and 67.38 kb, respectively. Genome completeness was evaluated to be 95.8%. The assembled genome contained 23,403 protein-coding genes and 236.1 Mb of repeat sequences (accounting for 29.27% of the entire assembly). Comparative genomics analyses of this fast-swimming tuna revealed that it had more than twice as many hemoglobin genes (18) as other relatively slow-moving fishes (such as seahorse, sunfish, and tongue sole). These hemoglobin genes are mainly localized in two big clusters (termed as “MNˮ and “LAˮ respectively), which is consistent with other reported fishes. However, Thr39 of beta-hemoglobin in the MN cluster, conserved in other fishes, was mutated as cysteine in tunas including the Southern bluefin tuna. Since hemoglobins are reported to transport oxygen efficiently for aerobic respiration, our genomic data suggest that both high copy numbers of hemoglobin genes and an adjusted function of the beta-hemoglobin may support the fast-swimming activity of tunas. In summary, we produced a primary genome assembly and predicted hemoglobin-related roles for the fast-swimming Southern bluefin tuna.
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Zhao X, Liu Y, Du X, Ma S, Song N, Zhao L. Whole-Genome Survey Analyses Provide a New Perspective for the Evolutionary Biology of Shimofuri Goby, Tridentiger bifasciatus. Animals (Basel) 2022; 12:ani12151914. [PMID: 35953903 PMCID: PMC9367431 DOI: 10.3390/ani12151914] [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: 06/08/2022] [Revised: 07/12/2022] [Accepted: 07/20/2022] [Indexed: 11/16/2022] Open
Abstract
The shimofuri goby (Tridentiger bifasciatus) is a small and highly adaptable goby, distributed along the coasts of China, the Sea of Japan, and the west coastal and estuarine areas of the Northwest Pacific. Next-generation sequencing was used to generate genome-wide survey data to provide essential characterization of the shimofuri goby genome and for the further mining of genomic information. The genome size of the shimofuri goby was estimated to be approximately 887.60 Mb through K-mer analysis, with a heterozygosity ratio and repeat sequence ratio of 0.47% and 32.60%, respectively. The assembled genome was used to identify microsatellite motifs (Simple Sequence Repeats, SSRs), extract single-copy homologous genes and assemble the mitochondrial genome. A total of 288,730 SSRs were identified. The most frequent SSRs were dinucleotide repeats (with a frequency of 61.15%), followed by trinucleotide (29.87%), tetranucleotide (6.19%), pentanucleotide (1.13%), and hexanucleotide repeats (1.66%). The results of the phylogenetic analysis based on single-copy homologous genes showed that the shimofuri goby and Rhinogobius similis can be clustered into one branch. The shimofuri goby was originally thought to be the same as the chameleon goby (Tridentiger trigonocephalus) due to their close morphological resemblance. However, a complete mitochondrial genome was assembled and the results of the phylogenetic analysis support the inclusion of the shimofuri goby as a separate species. PSMC analysis indicated that the shimofuri goby experienced a bottleneck event during the Pleistocene Glacial Epoch, in which its population size decreased massively, and then it began to recover gradually after the Last Glacial Maximum. This study provides a reference for the further assembly of the complete genome map of the shimofuri goby, and is a valuable genomic resource for the study of its evolutionary biology.
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Affiliation(s)
- Xiang Zhao
- The Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao 266003, China; (X.Z.); (X.D.); (S.M.); (N.S.)
| | - Yaxian Liu
- Yantai Laishan Marine Fisheries Supervision and Monitoring Brigade, Yantai 264000, China;
| | - Xueqing Du
- The Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao 266003, China; (X.Z.); (X.D.); (S.M.); (N.S.)
| | - Siyu Ma
- The Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao 266003, China; (X.Z.); (X.D.); (S.M.); (N.S.)
| | - Na Song
- The Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao 266003, China; (X.Z.); (X.D.); (S.M.); (N.S.)
| | - Linlin Zhao
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
- Marine Ecology and Environmental Science Laboratory, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Correspondence:
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Abstract
An explosive volcanic eruption occurred in the Ogasawara Islands on 13-15 August 2021, bringing unprecedented amounts of floating pumice to the coast of Okinawa Island in the Ryukyu Archipelago, 1300 km west of the volcano, approximately 2 months later. The coast of Okinawa Island, especially along the northern part, is home to many typical subtropical seascapes, including coral reefs and mangrove forests, so the possible impact of the large amount of pumice is attracting attention. Here, we report early evidence of ecosystem changes as a result of large-scale pumice stranding on coastal beaches, in estuaries and mangrove forests and passage across fringing coral reefs. Massive pumice drifts are major obstacles to fishing activities and ship traffic, but short and long-term changes in coastal ecosystems can also occur. The phenomena observed on Okinawa Island can be a preview of coastal impacts for the Kyushu, Shikoku, Honshu Islands, where pumice has subsequently washed ashore.
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A chromosome-level genome assembly of the jade perch (Scortum barcoo). Sci Data 2022; 9:408. [PMID: 35840598 PMCID: PMC9287455 DOI: 10.1038/s41597-022-01523-y] [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: 04/28/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Endemic to Australia, jade perch (Scortum barcoo) is a highly profitable freshwater bass species. It has extraordinarily high levels of omega-3 polyunsaturated fatty acids (PUFAs), which detailed genes involved in are largely unclear. Meanwhile, there were four chromosome-level bass species have been previous sequenced, while the bass ancestor genome karyotypes have not been estimated. Therefore, we sequenced, assembled and annotated a genome of jade perch to characterize the detailed genes for biosynthesis of omega-3 PUFAs and to deduce the bass ancestor genome karyotypes. We constructed a chromosome-level genome assembly with 24 pairs of chromosomes, 657.7 Mb in total length, and the contig and the scaffold N50 of 4.8 Mb and 28.6 Mb respectively. We also identified repetitive elements (accounting for 19.7% of the genome assembly) and predicted 26,905 protein-coding genes. Meanwhile, we performed genome-wide localization and characterization of several important genes encoding some key enzymes in the biosynthesis pathway of PUFAs. These genes may contribute to the high concentration of omega-3 in jade perch. Moreover, we conducted a series of comparative genomic analyses among four representative bass species at a chromosome level, resulting in a series of sequences of a deductive bass ancestor genome. Measurement(s) | whole genome sequencing | Technology Type(s) | Illumina Sequencing • Oxford Nanopore Sequencing |
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22
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Tang SL, Liang XF, Li L, Wu J, Lu K. Genome-wide identification and expression patterns of opsin genes during larval development in Chinese perch (Siniperca chuatsi). Gene X 2022; 825:146434. [PMID: 35304240 DOI: 10.1016/j.gene.2022.146434] [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: 08/31/2021] [Revised: 02/01/2022] [Accepted: 03/11/2022] [Indexed: 11/16/2022] Open
Abstract
Vision is important for fish to forage food and fishes express opsin genes to receive visual signals. Chinese perch (Siniperca chuatsi) larvae prey on other fish species larvae at firstfeeding but donoteat any zooplankton, the expression of opsin genes in S. chuatsilarvae is unknown. In this study, we conducted a whole-genome analysis and demonstrated that S. chuatsihave5cone opsin genes (sws1, sws2Aα, sws2Aβ, rh2and lws)and 2 rod opsin genes (rh1and rh1-exorh). The syntenicanalysisshowedthe flanking genes ofall opsin genes were conserved during fish evolution, but the ancestorof S. chuatsimightlost some opsin gene copies duringtheevolution.The phylogeneticanalysisshowed sws1of S. chuatsiwas closest to those of Lates calcariferwhich had a truncated sws1gene; the sws2Aα, sws2Aβ,lws,rh2,rh1 andrh1-exorh of S. chuatsihad a closer relationship with those of Percomorpha fishes.Importantly, results of in situhybridization showed the sws1 opsingene,which is related to forage zooplankton,had extremely low levelexpression in retinaat early stages.Surprisingly, the rh2 opsin gene had a high level expression at firstfeeding stage. The sws2Aα, sws2Aβand lwshad a little expression at early stages but the lwsshowed a increasing trend with larval development, rh1 opsin gene expression appeared at15 dph. In thisstudy, we found a specialpattern of visual opsin genes expression in S. chuatsi, it might influence the larval first feeding and feeding habit.
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Affiliation(s)
- Shu-Lin Tang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan 430070, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
| | - Xu-Fang Liang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan 430070, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China.
| | - Ling Li
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan 430070, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
| | - Jiaqi Wu
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan 430070, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
| | - Ke Lu
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan 430070, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
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23
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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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24
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Hu W, Mu Y, Lin F, Li X, Zhang J. New Insight Into Visual Adaptation in the Mudskipper Cornea: From Morphology to the Cornea-Related COL8A2 Gene. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.871370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Much research has focused on visual system evolution in bony fishes. The capacity of visual systems to perceive and respond to external signals is integral to evolutionary success. However, integrated research on the mechanisms of adaptive evolution based on corneal structure and related genes remains limited. In this study, scanning electron microscopy (SEM) was used to assess the microstructure and adaptation of corneal epithelial cells. Then, the evolution of the cornea-related COL8A2 gene was investigated. We found various projections (microridges, microplicae, microholes, and microvilli) on the corneal epithelial cells of amphibious mudskippers. Compared with those of fully aquatic fishes, these microstructures were considered adaptations to the variable environments experienced by amphibious mudskippers, as they can resist dryness in terrestrial environments and infection in aquatic environments. Moreover, strong purifying selection was detected for COL8A2. In addition, some specific amino acid substitution sites were also identified in the COL8A2 sequence in mudskippers. Interestingly, the evolutionary rate of the COL8A2 gene was significantly and positively correlated with maximum diving depth in our dataset. Specifically, with increasing diving depth, the evolutionary rate of the COL8A2 gene seemed to gradually accelerate. The results indicated that the cornea of bony fishes has evolved through adaptation to cope with the different diving depths encountered during the evolutionary process, with the corneal evolution of the amphibious mudskipper group showing a unique pattern.
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25
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Thacker CE, Shelley JJ, McCraney WT, Adams M, Hammer MP, Unmack PJ. Phylogeny, diversification, and biogeography of a hemiclonal hybrid system of native Australian freshwater fishes (Gobiiformes: Gobioidei: Eleotridae: Hypseleotris). BMC Ecol Evol 2022; 22:22. [PMID: 35236294 PMCID: PMC8892812 DOI: 10.1186/s12862-022-01981-3] [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] [Received: 10/03/2021] [Accepted: 02/21/2022] [Indexed: 11/10/2022] Open
Abstract
Background Carp gudgeons (genus Hypseleotris) are a prominent part of the Australian freshwater fish fauna, with species distributed around the western, northern, and eastern reaches of the continent. We infer a calibrated phylogeny of the genus based on nuclear ultraconserved element (UCE) sequences and using Bayesian estimation of divergence times, and use this phylogeny to investigate geographic patterns of diversification with GeoSSE. The southeastern species have hybridized to form hemiclonal lineages, and we also resolve relationships of hemiclones and compare their phylogenetic placement in the UCE phylogeny with a hypothesis based on complete mitochondrial genomes. We then use phased SNPs extracted from the UCE sequences for population structure analysis among the southeastern species and hemiclones. Results Hypseleotris cyprinoides, a widespread euryhaline species known from throughout the Indo-Pacific, is resolved outside the remainder of the species. Two Australian radiations comprise the bulk of Hypseleotris, one primarily in the northwestern coastal rivers and a second inhabiting the southeastern region including the Murray–Darling, Bulloo-Bancannia and Lake Eyre basins, plus coastal rivers east of the Great Dividing Range. Our phylogenetic results reveal cytonuclear discordance between the UCE and mitochondrial hypotheses, place hemiclone hybrids among their parental taxa, and indicate that the genus Kimberleyeleotris is nested within the northwestern Hypseleotris radiation along with three undescribed species. We infer a crown age for Hypseleotris of 17.3 Ma, date the radiation of Australian species at roughly 10.1 Ma, and recover the crown ages of the northwestern (excluding H. compressa) and southeastern radiations at 5.9 and 7.2 Ma, respectively. Range-dependent diversification analyses using GeoSSE indicate that speciation and extinction rates have been steady between the northwestern and southeastern Australian radiations and between smaller radiations of species in the Kimberley region and the Arnhem Plateau. Analysis of phased SNPs confirms inheritance patterns and reveals high levels of heterozygosity among the hemiclones. Conclusions The northwestern species have restricted ranges and likely speciated in allopatry, while the southeastern species are known from much larger areas, consistent with peripatric speciation or allopatric speciation followed by secondary contact. Species in the northwestern Kimberley region differ in shape from those in the southeast, with the Kimberley species notably more elongate and slender than the stocky southeastern species, likely due to the different topographies and flow regimes of the rivers they inhabit.
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Affiliation(s)
- Christine E Thacker
- Vertebrate Zoology, Santa Barbara Museum of Natural History, 2559 Puesta del Sol, Santa Barbara, CA, 93105, USA. .,Research and Collections, Department of Ichthyology, Natural History Museum of Los Angeles County, 900 Exposition Blvd., Los Angeles, CA, 90007, USA.
| | - James J Shelley
- School of BioSciences, University of Melbourne, Melbourne, VIC, 3010, Australia.,Department of Environment, Land, Water and Planning, Arthur Rylah Institute for Environmental Research, 123 Brown Street, Heidelberg, VIC, 3084, Australia
| | - W Tyler McCraney
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 612 Charles E. Young Drive South, Box 957246, Los Angeles, CA, 90095-7246, USA
| | - Mark Adams
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, SA, 5000, Australia.,School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Michael P Hammer
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, SA, 5000, Australia.,Museum and Art Gallery of the Northern Territory, GPO Box 4646, Darwin, NT, 0801, Australia
| | - Peter J Unmack
- Centre for Applied Water Science, Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2617, Australia
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26
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Epigenomic and Proteomic Changes in Fetal Spleens Persistently Infected with Bovine Viral Diarrhea Virus: Repercussions for the Developing Immune System, Bone, Brain, and Heart. Viruses 2022; 14:v14030506. [PMID: 35336913 PMCID: PMC8949278 DOI: 10.3390/v14030506] [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: 02/04/2022] [Revised: 02/18/2022] [Accepted: 02/20/2022] [Indexed: 12/10/2022] Open
Abstract
Bovine viral diarrhea virus (BVDV) infection during early gestation results in persistently infected (PI) immunotolerant calves that are the primary reservoirs of the virus. Pathologies observed in PI cattle include congenital defects of the brain, heart, and bone as well as marked functional defects in their immune system. It was hypothesized that fetal BVDV infection alters T cell activation and signaling genes by epigenetic mechanisms. To test this, PI and control fetal splenic tissues were collected on day 245 of gestation, 170 days post maternal infection. DNA was isolated for reduced representation bisulfite sequencing, protein was isolated for proteomics, both were analyzed with appropriate bioinformatic methods. Within set parameters, 1951 hypermethylated and 691 hypomethylated DNA regions were identified in PI compared to control fetuses. Pathways associated with immune system, neural, cardiac, and bone development were associated with heavily methylated DNA. The proteomic analysis revealed 12 differentially expressed proteins in PI vs. control animals. Upregulated proteins were associated with protein processing, whereas downregulated proteins were associated with lymphocyte migration and development in PI compared to control fetal spleens. The epigenetic changes in DNA may explain the immune dysfunctions, abnormal bone formation, and brain and heart defects observed in PI animals.
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27
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Steppan SJ, Meyer AA, Barrow LN, Alhajeri BH, S Y Al-Zaidan A, Gignac PM, Erickson GM. Phylogenetics And The Evolution Of Terrestriality In Mudskippers (Gobiidae: Oxudercinae). Mol Phylogenet Evol 2022; 169:107416. [PMID: 35032645 DOI: 10.1016/j.ympev.2022.107416] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/30/2021] [Accepted: 12/08/2021] [Indexed: 01/23/2023]
Abstract
The initial vertebrate conquest of land by stegocephalians (Sarcopterygia) allowed access to new resources and exploitation of untapped niches precipitating a major phylogenetic diversification. However, a paucity of fossils has left considerable uncertainties about phylogenetic relationships and the eco-morphological stages in this key transition in Earth history. Among extant actinopterygians, three genera of mudskippers (Gobiidae: Oxudercinae), Boleophthalmus, Periophthalmus and Periophthalmodon are the most terrestrialized, with vertebral, appendicular, locomotory, respiratory, and epithelial specializations enabling overland excursions up to 14 hours. Unlike early stegocephalians, the ecologies and morphologies of the 45 species of oxudercines are well known, making them viable analogs for the initial vertebrate conquest of land. Nevertheless, they have received little phylogenetic attention. We compiled the largest molecular dataset to date, with 29 oxudercine species, and 5 nuclear and mitochondrial loci. Phylogenetic and comparative analyses revealed strong support for two independent terrestrial transitions, and a complex suit of ecomorphological forms in estuarine environments. Furthermore, neither Oxudercinae nor their presumed sister-group the eel gobies (Amblyopinae, a group of elongated gobies) were monophyletic with respect to each other, requiring a merging of these two subfamilies and revealing an expansion of phenotypic variation within the "mudskipper" clade. We did not find support for the expected linear model of ecomorphological and locomotory transition from fully aquatic, to mudswimming, to pectoral-aided mudswimming, to lobe-finned terrestrial locomotion proposed by earlier morphological studies. This high degree of convergent or parallel transitions to terrestriality, and apparent divergent directions of estuarine adaptation, promises even greater potential for this clade to illuminate the conquest of land. Future work should focus on these less-studied species with "transitional" and other mud-habitat specializations to fully resolve the dynamics of this diversification.
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Affiliation(s)
- Scott J Steppan
- Department of Biological Science, 327 Stadium Dr., Florida State University, Tallahassee Florida, 32306-4295, USA.
| | - Anna A Meyer
- Department of Biological Science, 327 Stadium Dr., Florida State University, Tallahassee Florida, 32306-4295, USA
| | - Lisa N Barrow
- Department of Biological Science, 327 Stadium Dr., Florida State University, Tallahassee Florida, 32306-4295, USA; Department of Biology, University of New Mexico, Albuquerque, NM 87131-0001, USA
| | - Bader H Alhajeri
- Department of Biological Sciences, Kuwait University, Safat, 13060, Kuwait
| | | | - Paul M Gignac
- Department of Anatomy and Cell Biology, Oklahoma State University Center for Health Sciences, Tulsa Oklahoma 74107-1898, USA
| | - Gregory M Erickson
- Department of Biological Science, 327 Stadium Dr., Florida State University, Tallahassee Florida, 32306-4295, USA
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28
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Yang Y, Yoo JY, Baek SH, Song HY, Jo S, Jung SH, Choi JH. Chromosome-level genome assembly of the shuttles hoppfish, Periophthalmus modestus. Gigascience 2022; 11:6505119. [PMID: 35022698 PMCID: PMC8756193 DOI: 10.1093/gigascience/giab089] [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] [Received: 08/04/2021] [Revised: 11/08/2021] [Accepted: 12/05/2021] [Indexed: 11/28/2022] Open
Abstract
Background The shuttles hoppfish (mudskipper), Periophthalmus modestus, is one of the mudskippers, which are the largest group of amphibious teleost fishes, which are uniquely adapted to live on mudflats. Because mudskippers can survive on land for extended periods by breathing through their skin and through the lining of the mouth and throat, they were evaluated as a model for the evolutionary sea-land transition of Devonian protoamphibians, ancestors of all present tetrapods. Results A total of 39.6, 80.2, 52.9, and 33.3 Gb of Illumina, Pacific Biosciences, 10X linked, and Hi-C data, respectively, was assembled into 1,419 scaffolds with an N50 length of 33 Mb and BUSCO score of 96.6%. The assembly covered 117% of the estimated genome size (729 Mb) and included 23 pseudo-chromosomes anchored by a Hi-C contact map, which corresponded to the top 23 longest scaffolds above 20 Mb and close to the estimated one. Of the genome, 43.8% were various repetitive elements such as DNAs, tandem repeats, long interspersed nuclear elements, and simple repeats. Ab initio and homology-based gene prediction identified 30,505 genes, of which 94% had homology to the 14 Actinopterygii transcriptomes and 89% and 85% to Pfam familes and InterPro domains, respectively. Comparative genomics with 15 Actinopterygii species identified 59,448 gene families of which 12% were only in P. modestus. Conclusions We present the high quality of the first genome assembly and gene annotation of the shuttles hoppfish. It will provide a valuable resource for further studies on sea-land transition, bimodal respiration, nitrogen excretion, osmoregulation, thermoregulation, vision, and mechanoreception.
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Affiliation(s)
- Youngik Yang
- Department of Applied Research, National Marine Biodiversity Institute of Korea, Seocheon 33662, South Korea
| | - Ji Yong Yoo
- Marine Bio-Resources and Information Center, National Marine Biodiversity Institute of Korea, Seocheon 33662, South Korea
| | - Sang Ho Baek
- Marine Bio-Resources and Information Center, National Marine Biodiversity Institute of Korea, Seocheon 33662, South Korea
| | - Ha Yeun Song
- Division of Bioresources Bank, Honam National Institute of Biological Resources, Mokpo 58762, South Korea
| | - Seonmi Jo
- Department of Applied Research, National Marine Biodiversity Institute of Korea, Seocheon 33662, South Korea
| | - Seung-Hyun Jung
- Department of Applied Research, National Marine Biodiversity Institute of Korea, Seocheon 33662, South Korea
| | - Jeong-Hyeon Choi
- Department of Applied Research, National Marine Biodiversity Institute of Korea, Seocheon 33662, South Korea
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29
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Ma H, Yang MS, Zhang YT, Qiu HT, You XX, Chen SX, Hong WS. Expressions of melanopsins in telencephalon imply their function in synchronizing semilunar spawning rhythm in the mudskipper Boleophthalmus pectinirostris. Gen Comp Endocrinol 2022; 315:113926. [PMID: 34653434 DOI: 10.1016/j.ygcen.2021.113926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 09/22/2021] [Accepted: 10/09/2021] [Indexed: 11/04/2022]
Abstract
The mudskipper Boleophthalmus pectinirostris inhabits intertidal mudflats, exhibiting semilunar reproductive rhythms. To investigate whether melanopsin is possibly involved in the synchronization of the semilunar spawning rhythm in the female mudskipper, we first cloned all four melanopsin subtypes (opn4m1, opn4m3, opn4x1, opn4x2) in B. pectinirostris. Results from RTq-PCR showed that significantly higher transcription levels of all four melanopsin subtypes were observed in the eyes rather than other tissues. In brain, all four melanopsin subtypes were also detectable in different regions, including the telencephalon, in which the expression of melanopsin has not been reported in other teleosts. The transcription levels of opn4m3 and opn4x1 in the telencephalon exhibited a daily fluctuation pattern. When females entered the spawning season, opn4m1 and opn4x1 transcript levels increased significantly in the telencephalon. During the spawning season, the transcript levels of opn4m3 and opn4x1 in the telencephalon appeared to have a cyclic pattern associated with semilunar periodicity, exhibiting two cycles with a peak around the first or the last lunar quarters. Results from ISH showed that, opn4x1 mRNA was localized in the medial of dorsal telencephalic area, dorsal nucleus of ventral telencephalic area (Vd), ventral nucleus of ventral telencephalic area (Vv), anterior part of parvocellular preoptic nucleus, magnocellular part of the magnocellular preoptic nucleus (PMmc), habenular and ventral zone of hypothalamus. Intriguingly, gnrh3 mRNA was also located in Vd, Vv and PMmc. Taken together, our results suggested that melanopsins, e.g. opn4x1, expressed in the telencephalon might mediate semilunar spawning activity in the female mudskipper.
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Affiliation(s)
- He Ma
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Ming Shu Yang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Yu Ting Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Heng Tong Qiu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Xin Xin You
- Shenzhen Key Laboratory of Marine Genomics, Marine and Fisheries Institute, BGI-Shenzhen, Shenzhen 518083, China
| | - Shi Xi Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen 361102, China.
| | - Wan Shu Hong
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen 361102, China.
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30
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Xu P, Zhao C, You X, Yang F, Chen J, Ruan Z, Gu R, Xu J, Bian C, Shi Q. Draft Genome of the Mirrorwing Flyingfish ( Hirundichthys speculiger). Front Genet 2021; 12:695700. [PMID: 34306036 PMCID: PMC8294118 DOI: 10.3389/fgene.2021.695700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/03/2021] [Indexed: 12/04/2022] Open
Affiliation(s)
- Pengwei Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chenxi Zhao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xinxin You
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 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, BGI, Shenzhen, China
| | - Fan Yang
- Marine Geological Department, Marine Geological Survey Institute of Hainan Province, Haikou, China
| | - Jieming Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 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, BGI, Shenzhen, China
| | - Zhiqiang Ruan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 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, BGI, Shenzhen, China
| | - Ruobo Gu
- 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
| | - Junmin Xu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Chao Bian
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 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, BGI, Shenzhen, China
| | - Qiong Shi
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 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, BGI, Shenzhen, China
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31
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Li J, Bian C, Yi Y, Yu H, You X, Shi Q. Temporal dynamics of teleost populations during the Pleistocene: a report from publicly available genome data. BMC Genomics 2021; 22:490. [PMID: 34193045 PMCID: PMC8247217 DOI: 10.1186/s12864-021-07816-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 06/14/2021] [Indexed: 12/04/2022] Open
Abstract
Background Global climate oscillation, as a selection dynamic, is an ecologically important element resulting in global biodiversity. During the glacial geological periods, most organisms suffered detrimental selection pressures (such as food shortage and habitat loss) and went through population declines. However, during the mild interglacial periods, many species re-flourished. These temporal dynamics of effective population sizes (Ne) provide essential information for understanding and predicting evolutionary outcomes during historical and ongoing global climate changes. Results Using high-quality genome assemblies and corresponding sequencing data, we applied the Pairwise Sequentially Markovian Coalescent (PSMC) method to quantify Ne changes of twelve representative teleost species from approximately 10 million years ago (mya) to 10 thousand years ago (kya). These results revealed multiple rounds of population contraction and expansion in most of the examined teleost species during the Neogene and the Quaternary periods. We observed that 83% (10/12) of the examined teleosts had experienced a drastic decline in Ne before the last glacial period (LGP, 110–12 kya), slightly earlier than the reported pattern of Ne changes in 38 avian species. In comparison with the peaks, almost all of the examined teleosts maintained long-term lower Ne values during the last few million years. This is consistent with increasingly dramatic glaciation during this period. Conclusion In summary, these findings provide a more comprehensive understanding of the historical Ne changes in teleosts. Results presented here could lead to the development of appropriate strategies to protect species in light of ongoing global climate changes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07816-7.
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Affiliation(s)
- Jia Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, Guangdong, China.
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, Guangdong, China.,Center of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau, China
| | - Yunhai Yi
- 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, Guangdong, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, China
| | - Hui Yu
- 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, Guangdong, 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, Guangdong, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 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, Guangdong, China. .,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong, China. .,Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China.
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32
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Liu Q, Mishra M, Saxena AS, Wu H, Qiu Y, Zhang X, You X, Ding S, Miyamoto MM. Balancing selection maintains ancient polymorphisms at conserved enhancers for the olfactory receptor genes of a Chinese marine fish. Mol Ecol 2021; 30:4023-4038. [PMID: 34107131 DOI: 10.1111/mec.16016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 05/10/2021] [Accepted: 06/01/2021] [Indexed: 12/22/2022]
Abstract
The study of balancing selection, as a selective force maintaining adaptive genetic variation in gene pools longer than expected by drift, is currently experiencing renewed interest due to the increased availability of new data, methods of analysis, and case studies. In this investigation, evidence of balancing selection operating on conserved enhancers of the olfactory receptor (OR) genes is presented for the Chinese sleeper (Bostrychus sinensis), a coastal marine fish that is emerging as a model species for evolutionary studies in the Northwest Pacific marginal seas. Coupled with tests for Gene Ontology enrichment and transcription factor binding, population genomic data allow for the identification of an OR cluster in the sleeper with a downstream flanking region containing three enhancers that are conserved with human and other fish species. Phylogenetic and population genetic analyses indicate that the enhancers are under balancing selection as evidenced by their translineage polymorphisms, excess common alleles, and increased within-group diversities. Age comparisons between the translineage polymorphisms and most recent common ancestors of neutral genealogies substantiate that the former are old, and thus, due to ancient balancing selection. The survival and reproduction of vertebrates depend on their sense of smell, and thereby, on their ORs. In addition to locus duplication and allelic variation of structural genes, this study highlights a third mechanism by which receptor diversity can be achieved for detecting and responding to the huge variety of environmental odorants (i.e., by balancing selection acting on OR gene expression through their enhancer variability).
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Affiliation(s)
- Qiaohong Liu
- Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Mrinal Mishra
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Ayush S Saxena
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Haohao Wu
- Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ying Qiu
- Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Laboratory of Molecular Breeding in Marine Economic Animals, BGI Academy of Sciences, BGI Marine, Shenzhen, China
| | - Xinhui Zhang
- Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Laboratory of Molecular Breeding in Marine Economic Animals, BGI Academy of Sciences, BGI Marine, Shenzhen, China
| | - Xinxin You
- Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Laboratory of Molecular Breeding in Marine Economic Animals, BGI Academy of Sciences, BGI Marine, Shenzhen, China
| | - Shaoxiong Ding
- Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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33
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Ding W, Zhang X, Zhao X, Jing W, Cao Z, Li J, Huang Y, You X, Wang M, Shi Q, Bing X. A Chromosome-Level Genome Assembly of the Mandarin Fish ( Siniperca chuatsi). Front Genet 2021; 12:671650. [PMID: 34249093 PMCID: PMC8262678 DOI: 10.3389/fgene.2021.671650] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/07/2021] [Indexed: 11/13/2022] Open
Abstract
The mandarin fish, Siniperca chuatsi, is an economically important perciform species with widespread aquaculture practices in China. Its special feeding habit, acceptance of only live prey fishes, contributes to its delicious meat. However, little is currently known about related genetic mechanisms. Here, we performed whole-genome sequencing and assembled a 758.78 Mb genome assembly of the mandarin fish, with the scaffold and contig N50 values reaching 2.64 Mb and 46.11 Kb, respectively. Approximately 92.8% of the scaffolds were ordered onto 24 chromosomes (Chrs) with the assistance of a previously established genetic linkage map. The chromosome-level genome contained 19,904 protein-coding genes, of which 19,059 (95.75%) genes were functionally annotated. The special feeding behavior of mandarin fish could be attributable to the interaction of a variety of sense organs (such as vision, smell, and endocrine organs). Through comparative genomics analysis, some interesting results were found. For example, olfactory receptor (OR) genes (especially the beta and delta types) underwent a significant expansion, and endocrinology/vision related npy, spexin, and opsin genes presented various functional mutations. These may contribute to the special feeding habit of the mandarin fish by strengthening the olfactory and visual systems. Meanwhile, previously identified sex-related genes and quantitative trait locis (QTLs) were localized on the Chr14 and Chr17, respectively. 155 toxin proteins were predicted from mandarin fish genome. In summary, the high-quality genome assembly of the mandarin fish provides novel insights into the feeding habit of live prey and offers a valuable genetic resource for the quality improvement of this freshwater fish.
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Affiliation(s)
- Weidong Ding
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Xinhui Zhang
- 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, China
| | - Xiaomeng Zhao
- 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, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Wu Jing
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Zheming Cao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Jia Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, China
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, China
- BGI Education Center, 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, Shenzhen, China
| | - Min Wang
- BGI Zhenjiang Institute of Hydrobiology, Zhenjiang, 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, Shenzhen, China
| | - Xuwen Bing
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
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34
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Moreno Santillán DD, Lama TM, Gutierrez Guerrero YT, Brown AM, Donat P, Zhao H, Rossiter SJ, Yohe LR, Potter JH, Teeling EC, Vernes SC, Davies KTJ, Myers E, Hughes GM, Huang Z, Hoffmann F, Corthals AP, Ray DA, Dávalos LM. Large-scale genome sampling reveals unique immunity and metabolic adaptations in bats. Mol Ecol 2021; 30:6449-6467. [PMID: 34146369 DOI: 10.1111/mec.16027] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 05/27/2021] [Accepted: 06/03/2021] [Indexed: 11/28/2022]
Abstract
Comprising more than 1,400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species, one generated in this study, encompassing a large number of lineages, with a particular emphasis on multi-gene family evolution across immune and metabolic genes. In agreement with previous analyses, we found lineage-specific expansions of the APOBEC3 and MHC-I gene families, and loss of the proinflammatory PYHIN gene family. We inferred more than 1,000 gene losses unique to bats, including genes involved in the regulation of inflammasome pathways such as epithelial defence receptors, the natural killer gene complex and the interferon-gamma induced pathway. Gene set enrichment analyses revealed genes lost in bats are involved in defence response against pathogen-associated molecular patterns and damage-associated molecular patterns. Gene family evolution and selection analyses indicate bats have evolved fundamental functional differences compared to other mammals in both innate and adaptive immune system, with the potential to enhance antiviral immune response while dampening inflammatory signalling. In addition, metabolic genes have experienced repeated expansions related to convergent shifts to plant-based diets. Our analyses support the hypothesis that, in tandem with flight, ancestral bats had evolved a unique set of immune adaptations whose functional implications remain to be explored.
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Affiliation(s)
| | - Tanya M Lama
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
| | - Yocelyn T Gutierrez Guerrero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, Mexico City, Mexico
| | - Alexis M Brown
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
| | - Paul Donat
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
| | - Huabin Zhao
- Department of Ecology, Tibetan Centre for Ecology and Conservation at WHU-TU, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Laurel R Yohe
- Department of Earth & Planetary Science, Yale University, New Haven, Connecticut, USA
| | - Joshua H Potter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Sonja C Vernes
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.,School of Biology, The University of St Andrews, Fife, UK
| | - Kalina T J Davies
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Eugene Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Graham M Hughes
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Zixia Huang
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Federico Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, USA
| | - Angelique P Corthals
- Department of Sciences, John Jay College of Criminal Justice, New York, New York, USA
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA.,Consortium for Inter- Disciplinary Environmental Research, Stony Brook University, Stony Brook, New York, USA
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35
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Liu D, Wang X, Guo H, Zhang X, Zhang M, Tang W. Chromosome-level genome assembly of the endangered humphead wrasse Cheilinus undulatus: Insight into the expansion of opsin genes in fishes. Mol Ecol Resour 2021; 21:2388-2406. [PMID: 34003602 DOI: 10.1111/1755-0998.13429] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 04/30/2021] [Accepted: 05/10/2021] [Indexed: 11/26/2022]
Abstract
Wrasses are dominant components of major coral reef systems. Among wrasses, Cheilinus undulatus is an endangered species with high economic and ecological value that exhibits sex reversal of females to males, while sexual selection occurs in breeding aggregations. However, the molecular-associated mechanism underlying this remains unclear. Opsin gene diversification is regarded as a potent force in sexual selection. Here we present a genome assembly of C. undulatus, using Illumina, Nanopore and Hi-C sequencing. The 1.17 Gb genome was generated from 328 contigs with an N50 length of 16.5 Mb and anchored to 24 chromosomes. In total, 22,218 genes were functionally annotated, and 96.36% of BUSCO genes were fully represented. Transcriptomic analyses showed that 96.79% of the predicted genes were expressed. Transposons were most abundant, accounting for 39.88% of the genome, with low divergence, owing to their evolution with close species ~60.53 million years ago. In total, 567/1,826 gene families were expanded and contracted in the reconstructed phylogeny, respectively. Forty-six genes were under positive selection. Comparative genomic analyses with other fish revealed expansion of opsin SWS2B, LWS1 and Rh2. The elevated duplicates of SWS2B were generated by gene conversions via transposition of transposons followed by nonallelic homologous recombination. Amino acid substitutions of opsin paralogues occurred at key tuning sites, causing a spectral shift in maximal absorbance of visual pigment to capture functional changes. Among these opsin genes, SWS2B-3 and 4 and Rh1 are expressed in the retina. The genome sequence of C. undulatus provides valuable resources for future investigation of the conservation, evolution and behaviour of fishes.
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Affiliation(s)
- Dong Liu
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Xinyang Wang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Hongyi Guo
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Xuguang Zhang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Ming Zhang
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, GA, USA
| | - Wenqiao Tang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
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36
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Fuiten AM, Cresko WA. Evolutionary divergence of a Hoxa2b hindbrain enhancer in syngnathids mimics results of functional assays. Dev Genes Evol 2021; 231:57-71. [PMID: 34003345 DOI: 10.1007/s00427-021-00676-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: 12/28/2020] [Accepted: 04/29/2021] [Indexed: 10/21/2022]
Abstract
Hoxa2 genes provide critical patterning signals during development, and their regulation and function have been extensively studied. We report a previously uncharacterized significant sequence divergence of a highly conserved hindbrain hoxa2b enhancer element in the family syngnathidae (pipefishes, seahorses, pipehorses, seadragons). We compared the hox cis-regulatory element variation in the Gulf pipefish and two species of seahorse against eight other species of fish, as well as human and mouse. We annotated the hoxa2b enhancer element binding sites across three species of seahorse, four species of pipefish, and one species of ghost pipefish. Finally, we performed in situ hybridization analysis of hoxa2b expression in Gulf pipefish embryos. We found that all syngnathid fish examined share a modified rhombomere 4 hoxa2b enhancer element, despite the fact that this element has been found to be highly conserved across all vertebrates examined previously. Binding element sequence motifs and spacing between binding elements have been modified for the hoxa2b enhancer in several species of pipefish and seahorse, and that the loss of the Prep/Meis binding site and further space shortening happened after ghost pipefish split from the rest of the syngnathid clade. We showed that expression of this gene in rhombomere 4 is lower relative to the surrounding rhombomeres in developing Gulf pipefish embryos, reflecting previously published functional tests for this enhancer. Our findings highlight the benefits of studying highly derived, diverse taxa for understanding of gene regulatory evolution and support the hypothesis that natural mutations can occur in deeply conserved pathways in ways potentially related to phenotypic diversity.
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Affiliation(s)
- Allison M Fuiten
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
- Present address: Department of Dermatology, Oregon Health and Science University, Portland, OR, 97239, USA
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA.
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37
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Zhang K, Huang Y, Shi Q. Genome-wide identification and characterization of 14-3-3 genes in fishes. Gene 2021; 791:145721. [PMID: 34010706 DOI: 10.1016/j.gene.2021.145721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 11/13/2022]
Abstract
The 14-3-3 family genes are highly conserved regulatory factors in eukaryotes with involvement in multiple important cellular processes. However, detailed investigations of this family in fishes are very limited. Here, a comparative genomic and transcriptomic survey were performed to investigate the 14-3-3 family in fishes. We confirmed that the numbers of 14-3-3 genes ranged from 5 to 7 in non-teleost fishes, as well as additional 14-3-3 genes (9 to 11) in teleost fishes. In addition, some special teleost fishes possess 17 to 25 14-3-3s, which undergone the fourth whole-genome duplication (WGD). We also found that six pairs of fish 14-3-3 genes were clustered with mammalian ε, γ, ς, η, τand β isotypes, respectively, while σ was absent with a potential specificity within mammals, on the basis of their phylogenetic and synteny analyses. According to our results, we inferred that the diversity of 14-3-3 genes in fishes seems to be generated from a combination of WGD and gene loss. Comparative transcriptomic analysis revealed that there are differences in tissue distribution, and we speculated that 14-3-3 genes may contribute to terrestrial adaptations in mudskippers. In addition, protein sequence alignments of 14-3-3s supported their differential roles in fishes. In summary, our present comparative genomic and transcriptomic survey will benefit for further functional investigations of these fish genes.
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Affiliation(s)
- Kai Zhang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China.
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, 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 518083, China; Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
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38
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Mu Y, Bian C, Liu R, Wang Y, Shao G, Li J, Qiu Y, He T, Li W, Ao J, Shi Q, Chen X. Whole genome sequencing of a snailfish from the Yap Trench (~7,000 m) clarifies the molecular mechanisms underlying adaptation to the deep sea. PLoS Genet 2021; 17:e1009530. [PMID: 33983934 PMCID: PMC8118300 DOI: 10.1371/journal.pgen.1009530] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 04/05/2021] [Indexed: 11/25/2022] Open
Abstract
Hadal environments (depths below 6,000 m) are characterized by extremely high hydrostatic pressures, low temperatures, a scarce food supply, and little light. The evolutionary adaptations that allow vertebrates to survive in this extreme environment are poorly understood. Here, we constructed a high-quality reference genome for Yap hadal snailfish (YHS), which was captured at a depth of ~7,000 m in the Yap Trench. The final YHS genome assembly was 731.75 Mb, with a contig N50 of 0.75 Mb and a scaffold N50 of 1.26 Mb. We predicted 24,329 protein-coding genes in the YHS genome, and 24,265 of these genes were successfully functionally annotated. Phylogenetic analyses suggested that YHS diverged from a Mariana Trench snailfish approximately 0.92 million years ago. Many genes associated with DNA repair show evidence of positive selection and have expanded copy numbers in the YHS genome, possibly helping to maintain the integrity of DNA under increased hydrostatic pressure. The levels of trimethylamine N-oxide (TMAO), a potent protein stabilizer, are much higher in the muscles of YHS than in those of shallow-water fish. This difference is perhaps due to the five copies of the TMAO-generating enzyme flavin-containing monooxygenase-3 gene (fmo3) in the YHS genome and the abundance of trimethylamine (TMA)-generating bacteria in the YHS gut. Thus, the high TMAO content might help YHS adapt to high hydrostatic pressure by improving protein stability. Additionally, the evolutionary features of the YHS genes encoding sensory-related proteins are consistent with the scarce food supply and darkness in the hadal environments. These results clarify the molecular mechanisms underlying the adaptation of hadal organisms to the deep-sea environment and provide valuable genomic resources for in-depth investigations of hadal biology. Hadal environments (depths below 6,000 m) are characterized by extremely high hydrostatic pressures, low temperatures, a scarce food supply, and little light. Fish are the only vertebrates inhabiting the hadal zone, and hadal snailfishes have been found in at least five geographically separated marine trenches. However, the genetic mechanisms that allow vertebrates to live in such extreme conditions are not well understood. Here, we constructed a high-quality reference genome for Yap hadal snailfish (YHS) captured at a depth of ~7,000 m in the Yap Trench, using long reads obtained by Pacific Biosciences Sequel sequencing. Comparative genomic analyses revealed that many genes associated with DNA repair show evidence of positive selection and have expanded copy numbers in the YHS genome, which potentially reflect the difficulty of maintaining DNA integrity under high hydrostatic pressure. Moreover, the five copies of the trimethylamine N-oxide (TMAO)-generating enzyme flavin-containing monooxygenase-3 gene (fmo3) and the abundance of trimethylamine (TMA)-generating bacteria in the YHS gut could provide enough TMAO to improve protein stability under hadal conditions. In addition, characteristics of the YHS sensory system genes were consistent with the scarce food supply and darkness in the hadal zone. Our results provide new insights into the molecular mechanisms underlying the adaptation of hadal organisms to the deep-sea environment and valuable genomic resources that will help further clarify hadal adaptations.
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Affiliation(s)
- Yinnan Mu
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong, China
| | - Ruoyu Liu
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yuguang Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Guangming Shao
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Jia Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong, China
| | - Ying Qiu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong, China
| | - Tianliang He
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Wanru Li
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Jingqun Ao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong, China
- * E-mail: (QS); (XC)
| | - Xinhua Chen
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
- * E-mail: (QS); (XC)
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Deng Y, Meng M, Fang J, Jiang H, Sun N, Lv W, Lei Y, Wang C, Bo J, Liu C, Wang Y, Yang L, He S. Genome of the butterfly hillstream loach provides insights into adaptations to torrential mountain stream life. Mol Ecol Resour 2021; 21:1922-1935. [PMID: 33893720 DOI: 10.1111/1755-0998.13400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 03/25/2021] [Accepted: 04/13/2021] [Indexed: 11/27/2022]
Abstract
Butterfly hillstream loach (Beaufortia kweichowensis), a benthic fish in the torrential mountain streams, possesses a totally flat ventrum, flattened craniofacial and body skeletons, and enlarged paired fins covered by substantially small keratinous structures. However, little is known about the genetic basis of these specialized morphological adaptations. Here we present a 448.52-Mb genome assembly with contig N50 length of 5.53 Mb by integrating Illumina short-read sequencing, Nanopore long-read sequencing and HiC-based chromatin map. Demographic history reconstruction of the butterfly hillstream loach reveals that the population dynamics is correlated with the different stages of uplifting of the Tibetan Plateau. Comparative genomic analysis finds evidence of six keratin genes in butterfly hillstream loach evolving under positive selection. Within these genes, two keratin genes exhibit species-specific and divergent amino acid changes, suggesting a role in the formation of the unculi. Additionally, a series of positively selected genes, rapid evolving genes, specific variant genes and expanded gene families are found, including genes related to Hedgehog, Notch and BMP pathways, which may be involved in craniofacial development. These findings may have important implications for understanding the genetic basis of phenotypic adaptation to torrential mountain stream life.
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Affiliation(s)
- Yu Deng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Minghui Meng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jian Fang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Haifeng Jiang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ning Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenqi Lv
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yi Lei
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Cheng Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jing Bo
- University of Chinese Academy of Sciences, Beijing, China.,Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Chun Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Ying Wang
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, China
| | - Liandong Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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40
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Genomic characteristics and profile of microsatellite primers for Acanthogobius ommaturus by genome survey sequencing. Biosci Rep 2021; 40:226786. [PMID: 33111957 PMCID: PMC7670571 DOI: 10.1042/bsr20201295] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 10/27/2020] [Accepted: 10/27/2020] [Indexed: 11/17/2022] Open
Abstract
Acanthogobius ommaturus is one of the suitable species to study the genetic mechanism of adaptive evolution, but there are few reports on its genetics. In the present study, the genomic survey sequencing method was used to analyze the genome characters of A. ommaturus. A total of 50.50 G high-quality sequence data were obtained in the present study. From the 19-mer distribution frequency, the estimated genome size was 928.01 Mb. The calculated sequence repeat rate was about 38.31%, the heterozygosity was approximately 0.17%, and the GC% content was approximately 40.88%. Moreover, 475,724 simple sequence repeats (SSRs) were identified. Among them, dinucleotide repeats were the most (53.70% of the total SSRs), followed by tri- (35.36%), hexa- (4.59%), tetra- (4.57%) and penta- (1.77%) nucleotide repeats type. This is the first genome-wide feature of this species to be reported.
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41
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Genetic Adaptations in Mudskipper and Tetrapod Give Insights into Their Convergent Water-to-Land Transition. Animals (Basel) 2021; 11:ani11020584. [PMID: 33672418 PMCID: PMC7926366 DOI: 10.3390/ani11020584] [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: 01/15/2021] [Revised: 02/13/2021] [Accepted: 02/20/2021] [Indexed: 11/17/2022] Open
Abstract
Water-to-land transition has been independently evolved in multiple vertebrate lineages including the most recent common ancestor of tetrapod and multiple fish clades, and among them, mudskippers uniquely adapted to the mudflat. Even though physiological and morphological adaptation of mudskippers is thought to resemble that of the ancestral tetrapod, it is unclear if they share genome-wide evolutionary signatures. To detect potential signatures of positive selection in mudskipper and tetrapods, we analyzed 4118 singleton orthologues of terrestrial tetrapods, coelacanth, mudskipper, and fully aquatic fishes. Among positively selected genes identified in mudskipper and tetrapod lineages, genes involved in immune responses, mitochondrial oxidative phosphorylation, and kidney development were detected. On the other hand, tetrapod-specific and mudskipper-specific positively selected genes were functionally enriched for DNA repair processes, which could be associated with higher exposure to UV light. We also performed gene family analysis and discovered convergent contraction of eight gene families, including βγ-crystallin coding genes in both tetrapod and mudskipper lineages. Findings of this study suggest the similar genetic adaptation against environmental constraints between the ancient tetrapod and mudskippers for their land adaptation.
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42
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Dong YW, Blanchard TS, Noll A, Vasquez P, Schmitz J, Kelly SP, Wright PA, Whitehead A. Genomic and physiological mechanisms underlying skin plasticity during water to air transition in an amphibious fish. J Exp Biol 2021; 224:jeb235515. [PMID: 33328287 PMCID: PMC7860121 DOI: 10.1242/jeb.235515] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/09/2020] [Indexed: 12/24/2022]
Abstract
The terrestrial radiation of vertebrates required changes in skin that resolved the dual demands of maintaining a mechanical and physiological barrier while also facilitating ion and gas transport. Using the amphibious killifish Kryptolebias marmoratus, we found that transcriptional regulation of skin morphogenesis was quickly activated upon air exposure (1 h). Rapid regulation of cell-cell adhesion complexes and pathways that regulate stratum corneum formation was consistent with barrier function and mechanical reinforcement. Unique blood vessel architecture and regulation of angiogenesis likely supported cutaneous respiration. Differences in ionoregulatory transcripts and ionocyte morphology were correlated with differences in salinity acclimation and resilience to air exposure. Evolutionary analyses reinforced the adaptive importance of these mechanisms. We conclude that rapid plasticity of barrier, respiratory and ionoregulatory functions in skin evolved to support the amphibious lifestyle of K. marmoratus; similar processes may have facilitated the terrestrial radiation of other contemporary and ancient fishes.
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Affiliation(s)
- Yun-Wei Dong
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao, People's Republic of China
| | - Tessa S Blanchard
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada, N1G 2W1
| | - Angela Noll
- Primate Genetics Laboratory, German Primate Center (DPZ), Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Picasso Vasquez
- Department of Environmental Toxicology, University of California Davis, Davis, CA 95616, USA
| | - Juergen Schmitz
- Institute of Experimental Pathology, Center for Molecular Biology of Inflammation (ZMBE), University of Münster, 48149 Münster, Germany
| | - Scott P Kelly
- Department of Biology, York University, Toronto, ON, Canada, M3J 1P3
| | - Patricia A Wright
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada, N1G 2W1
| | - Andrew Whitehead
- Department of Environmental Toxicology, Center for Population Biology, Coastal and Marine Sciences Institute, University of California Davis, Davis, CA 95616, USA
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43
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Kushwaha B, Pandey M, Das P, Joshi CG, Nagpure NS, Kumar R, Kumar D, Agarwal S, Srivastava S, Singh M, Sahoo L, Jayasankar P, Meher PK, Shah TM, Hinsu AT, Patel N, Koringa PG, Das SP, Patnaik S, Bit A, Iquebal MA, Jaiswal S, Jena J. The genome of walking catfish Clarias magur (Hamilton, 1822) unveils the genetic basis that may have facilitated the development of environmental and terrestrial adaptation systems in air-breathing catfishes. DNA Res 2021; 28:6070145. [PMID: 33416875 PMCID: PMC7934567 DOI: 10.1093/dnares/dsaa031] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/21/2020] [Indexed: 11/14/2022] Open
Abstract
The walking catfish Clarias magur (Hamilton, 1822) (magur) is an important catfish species inhabiting the Indian subcontinent. It is considered as a highly nutritious food fish and has the capability to walk to some distance, and survive a considerable period without water. Assembly, scaffolding and several rounds of iterations resulted in 3,484 scaffolds covering ∼94% of estimated genome with 9.88 Mb largest scaffold, and N50 1.31 Mb. The genome possessed 23,748 predicted protein encoding genes with annotation of 19,279 orthologous genes. A total of 166 orthologous groups represented by 222 genes were found to be unique for this species. The Computational Analysis of gene Family Evolution (CAFE) analysis revealed expansion of 207 gene families and 100 gene families have rapidly evolved. Genes specific to important environmental and terrestrial adaptation, viz. urea cycle, vision, locomotion, olfactory and vomeronasal receptors, immune system, anti-microbial properties, mucus, thermoregulation, osmoregulation, air-breathing, detoxification, etc. were identified and critically analysed. The analysis clearly indicated that C. magur genome possessed several unique and duplicate genes similar to that of terrestrial or amphibians’ counterparts in comparison to other teleostean species. The genome information will be useful in conservation genetics, not only for this species but will also be very helpful in such studies in other catfishes.
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Affiliation(s)
- Basdeo Kushwaha
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Manmohan Pandey
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Paramananda Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Naresh S Nagpure
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Ravindra Kumar
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Suyash Agarwal
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Shreya Srivastava
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Mahender Singh
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Lakshman Sahoo
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Pallipuram Jayasankar
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Prem K Meher
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Tejas M Shah
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Ankit T Hinsu
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Namrata Patel
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Prakash G Koringa
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Sofia P Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Siddhi Patnaik
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Amrita Bit
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Mir A Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Joykrushna Jena
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
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44
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Abstract
The innate immune system acts rapidly in an identical and nonspecific way every time the body is exposed to pathogens. As such, it cannot build and maintain immunological memory to help prevent reinfection. Researchers contend that trained immunity is influenced by intracellular metabolic pathways and epigenetic remodeling. The purpose of this review was to explore the topic of trained innate immunity based on the results of relevant previous studies. This systematic review entailed identifying articles related to trained innate immunity. The sources were obtained from PubMed using different search terms that included "trained innate immunity," "trained immunity," "trained," "innate," "immunity," and "immune system." Boolean operators were used to combine terms and phrases. A review of previous study results revealed that little is currently known about the molecular and cellular processes that mediate or induce a trained immune response in animals. However, it is believed that alterations in the phenotypes of cell populations and the numbers of specific cells may play a critical role in mediating the trained immune response. Increasing evidence shows that the protective processes and actions that occur during a secondary infection are not entirely linked to the adaptive immune system. Instead, these events also involve heightened activation of innate immune cells. While trained innate immune cells may have a shorter memory, they assist in the fight against pathogens and provide cross-protection. Identification of the mechanisms and molecules that underlie trained innate immunity has highlighted important features of the human immune response. Such advances continue to open doors for future research on how the body responds to disease-causing pathogens.
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Affiliation(s)
- Borros Arneth
- Institute for Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Justus Liebig University Giessen, Hospital of the Universities of Giessen and Marburg, UKGM, Feulgenstr 12, 35339, Giessen, Germany.
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45
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Cai L, Liu G, Wei Y, Zhu Y, Li J, Miao Z, Chen M, Yue Z, Yu L, Dong Z, Ye H, Sun W, Huang R. Whole-genome sequencing reveals sex determination and liver high-fat storage mechanisms of yellowstripe goby (Mugilogobius chulae). Commun Biol 2021; 4:15. [PMID: 33398077 PMCID: PMC7782490 DOI: 10.1038/s42003-020-01541-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 12/01/2020] [Indexed: 01/29/2023] Open
Abstract
As a promising novel marine fish model for future research on marine ecotoxicology as well as an animal model of human disease, the genome information of yellowstripe goby (Mugilogobius chulae) remains unknown. Here we report the first annotated chromosome-level reference genome assembly for yellowstripe goby. A 20.67-cM sex determination region was discovered on chromosome 5 and seven potential sex-determining genes were identified. Based on combined genome and transcriptome data, we identified three key lipid metabolic pathways for high-fat accumulation in the liver of yellowstripe goby. The changes in the expression patterns of MGLL and CPT1 at different development stage of the liver, and the expansion of the ABCA1 gene, innate immune gene TLR23, and TRIM family genes may help in balancing high-fat storage in hepatocytes and steatohepatitis. These results may provide insights into understanding the molecular mechanisms of sex determination and high-fat storage in the liver of marine fishes.
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Affiliation(s)
- Lei Cai
- grid.464317.3Guangdong Provincial Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Guocheng Liu
- grid.21155.320000 0001 2034 1839BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yuanzheng Wei
- grid.464317.3Guangdong Provincial Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Yabing Zhu
- grid.21155.320000 0001 2034 1839BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Jianjun Li
- grid.464317.3Guangdong Provincial Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Zongyu Miao
- grid.464317.3Guangdong Provincial Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Meili Chen
- grid.464317.3Guangdong Provincial Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Zhen Yue
- grid.21155.320000 0001 2034 1839BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Lujun Yu
- grid.464317.3Guangdong Provincial Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Zhensheng Dong
- grid.21155.320000 0001 2034 1839BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Huixin Ye
- grid.464317.3Guangdong Provincial Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Wenjing Sun
- grid.21155.320000 0001 2034 1839BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Ren Huang
- grid.464317.3Guangdong Provincial Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
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46
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Byrne HM, Green JAM, Balbus SA, Ahlberg PE. Tides: A key environmental driver of osteichthyan evolution and the fish-tetrapod transition? Proc Math Phys Eng Sci 2020; 476:20200355. [PMID: 33223936 DOI: 10.1098/rspa.2020.0355] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/24/2020] [Indexed: 12/12/2022] Open
Abstract
Tides are a major component of the interaction between the marine and terrestrial environments, and thus play an important part in shaping the environmental context for the evolution of shallow marine and coastal organisms. Here, we use a dedicated tidal model and palaeogeographic reconstructions from the Late Silurian to early Late Devonian (420 Ma, 400 Ma and 380 Ma, Ma = millions of years ago) to explore the potential significance of tides for the evolution of osteichthyans (bony fish) and tetrapods (land vertebrates). The earliest members of the osteichthyan crown-group date to the Late Silurian, approximately 425 Ma, while the earliest evidence for tetrapods is provided by trackways from the Middle Devonian, dated to approximately 393 Ma, and the oldest tetrapod body fossils are Late Devonian, approximately 373 Ma. Large tidal ranges could have fostered both the evolution of air-breathing organs in osteichthyans to facilitate breathing in oxygen-depleted tidal pools, and the development of weight-bearing tetrapod limbs to aid navigation within the intertidal zones. We find that tidal ranges over 4 m were present around areas of evolutionary significance for the origin of osteichthyans and the fish-tetrapod transition, highlighting the possible importance of tidal dynamics as a driver for these evolutionary processes.
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Affiliation(s)
- H M Byrne
- School of Ocean Sciences, Bangor University, Menai Bridge, UK.,Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - J A M Green
- School of Ocean Sciences, Bangor University, Menai Bridge, UK
| | - S A Balbus
- Department of Physics, University of Oxford, Oxford, UK
| | - P E Ahlberg
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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47
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Tunnah L, Robertson CE, Turko AJ, Wright PA. Acclimation to prolonged aquatic hypercarbia or air enhances hemoglobin‑oxygen affinity in an amphibious fish. Comp Biochem Physiol A Mol Integr Physiol 2020; 252:110848. [PMID: 33217558 DOI: 10.1016/j.cbpa.2020.110848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/12/2020] [Accepted: 11/12/2020] [Indexed: 10/23/2022]
Abstract
When the amphibious mangrove rivulus (Kryptolebias marmoratus) leaves water for extended periods, hemoglobin-O2 binding affinity increases. We tested the hypothesis that the change in affinity was a consequence of hemoglobin isoform switching driven by exposure to environments associated with increased internal CO2 levels. We exposed K. marmoratus to either water (control, pH 8.1), air, aquatic hypercarbia (5.1 kPa CO2, pH 6.6-6.8), or aquatic acid (isocarbic control, pH 6.6-6.8), for 7 days, and measured hemoglobin-O2 affinity spectrophotometrically. We found that mangrove rivulus compensated for elevated CO2 and aquatic acid exposure by shifting hemoglobin-O2 affinity back to aquatic (control) levels when measured at an ecologically-relevant high CO2 level that would be experienced in vivo. Using proteomics, we found that the hemoglobin subunits present in the blood did not change between treatments, but air and aquatic acid exposure altered the abundance of cathodic hemoglobin subunits. We therefore conclude that hemoglobin isoform switching is not a primary strategy used by mangrove rivulus to adjust P50 under these conditions. Abundances of other RBC proteins also differed between treatment groups relative to control fish (e.g. Rhesus protein type A, band 3 anion exchanger). Overall, our data indicate that both aquatic hypercarbia and aquatic acidosis create similar changes in hemoglobin-O2 affinity as air exposure. However, the protein-level consequences differ between these groups, indicating that the red blood cell response of mangrove rivulus can be modulated depending on the environmental cue received.
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Affiliation(s)
- Louise Tunnah
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
| | - Cayleih E Robertson
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
| | - Andy J Turko
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada; Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Patricia A Wright
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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48
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Cannicci S, Fratini S, Meriggi N, Bacci G, Iannucci A, Mengoni A, Cavalieri D. To the Land and Beyond: Crab Microbiomes as a Paradigm for the Evolution of Terrestrialization. Front Microbiol 2020; 11:575372. [PMID: 33117320 PMCID: PMC7575764 DOI: 10.3389/fmicb.2020.575372] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/15/2020] [Indexed: 11/13/2022] Open
Abstract
The transition to terrestrial environments by formerly aquatic species has occurred repeatedly in many animal phyla and lead to the vast diversity of extant terrestrial species. The differences between aquatic and terrestrial habitats are enormous and involved remarkable morphological and physiological changes. Convergent evolution of various traits is evident among phylogenetically distant taxa, but almost no information is available about the role of symbiotic microbiota in such transition. Here, we suggest that intertidal and terrestrial brachyuran crabs are a perfect model to study the evolutionary pathways and the ecological role of animal-microbiome symbioses, since their transition to land is happening right now, through a number of independent lineages. The microorganisms colonizing the gut of intertidal and terrestrial crabs are expected to play a major role to conquer the land, by reducing water losses and permitting the utilization of novel food sources. Indeed, it has been shown that the microbiomes hosted in the digestive system of terrestrial isopods has been critical to digest plant items, but nothing is known about the microbiomes present in the gut of truly terrestrial crabs. Other important physiological regulations that could be facilitated by microbiomes are nitrogen excretion and osmoregulation in the new environment. We also advocate for advances in comparative and functional genomics to uncover physiological aspects of these ongoing evolutionary processes. We think that the multidisciplinary study of microorganisms associated with terrestrial crabs will shed a completely new light on the biological and physiological processes involved in the sea-land transition.
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Affiliation(s)
- Stefano Cannicci
- Swire Institute of Marine Science and Division of Ecology and Biodiversity, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Biology, University of Florence, Florence, Italy
| | - Sara Fratini
- Department of Biology, University of Florence, Florence, Italy
| | - Niccolò Meriggi
- Department of Biology, University of Florence, Florence, Italy
| | - Giovanni Bacci
- Department of Biology, University of Florence, Florence, Italy
| | | | - Alessio Mengoni
- Department of Biology, University of Florence, Florence, Italy
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49
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Shen HY, Zhou Y, Zhou QJ, Li MY, Chen J. Mudskipper interleukin-34 modulates the functions of monocytes/macrophages via the colony-stimulating factor-1 receptor 1. Zool Res 2020; 41:123-137. [PMID: 32150792 PMCID: PMC7109011 DOI: 10.24272/j.issn.2095-8137.2020.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Interleukin-34 (IL-34) is a novel cytokine that plays an important role in innate immunity and inflammatory processes by binding to the colony-stimulating factor-1 receptor (CSF-1R). However, information on the function of IL-34 in fish remains limited. In the present study, we identified an IL-34 homolog from mudskippers (Boleophthalmus pectinirostris). In silico analysis showed that the mudskipper IL-34 (BpIL-34) was similar to other known IL-34 variants in sequence and structure and was most closely related to an orange-spotted grouper (Epinephelus coioides) homolog. BpIL-34 transcripts were constitutively expressed in various tissues, with the highest level of expression found in the brain. Edwardsiella tarda infection significantly up-regulated the mRNA expression of BpIL-34 in the mudskipper tissues. The recombinant mature BpIL-34 peptide (rBpIL-34) was purified and used to produce anti-rBpIL-34 IgG. Western blot analysis combined with PNGase F digestion revealed that native BpIL-34 in monocytes/macrophages (MOs/MФs) was N-glycosylated. In vitro, rBpIL-34 treatment enhanced the phagocytotic and bactericidal activity of mudskipper MOs/MФs, as well as the mRNA expression of pro-inflammatory cytokines like tumor necrosis factor α (BpTNF-α) and BpIL-1β in these cells. Furthermore, the knockdown of mudskipper CSF-1R1 (BpCSF-1R1), but not mudskipper BpCSF-1R2, significantly inhibited the rBpIL-34-mediated enhanced effect on MO/MФ function. In conclusion, our results indicate that mudskipper BpIL-34 modulates the functions of MOs/MФs via BpCSF-1R1.
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Affiliation(s)
- Hai-Yu Shen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315832, China
| | - Yan Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315832, China
| | - Qian-Jin Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China. E-mail: .,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315832, China.,Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, Zhejiang 315832, China
| | - Ming-Yun Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315832, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315832, China.,Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, Zhejiang 315832, China E-mail: jchen1975@ 163.com
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50
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Soo HJ, Sam KK, Chong J, Lau NS, Ting SY, Kuah MK, Kwang SY, Ranjani M, Shu-Chien AC. Functional characterisation of fatty acyl desaturase, Fads2, and elongase, Elovl5, in the Boddart's goggle-eyed goby Boleophthalmus boddarti (Gobiidae) suggests an incapacity for long-chain polyunsaturated fatty acid biosynthesis. JOURNAL OF FISH BIOLOGY 2020; 97:83-99. [PMID: 32222967 DOI: 10.1111/jfb.14328] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 03/15/2020] [Accepted: 03/17/2020] [Indexed: 06/10/2023]
Abstract
The biosynthesis of long-chain polyunsaturated fatty acids (LC-PUFA), a process to convert C18 polyunsaturated fatty acids into eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA) or arachidonic acid (ARA), requires the concerted activities of two enzymes, the fatty acyl desaturase (Fads) and elongase (Elovl). This study highlights the cloning, functional characterisation and tissue expression pattern of a Fads and an Elovl from the Boddart's goggle-eyed goby (Boleophthalmus boddarti), a mudskipper species widely distributed in the Indo-Pacific region. Phylogenetic analysis revealed that the cloned fads and elovl are clustered with other teleost orthologs, respectively. The investigation of the genome of several mudskipper species, namely Boleophthalmus pectinirostris, Periophthalmus schlosseri and Periophthalmus magnuspinnatus, revealed a single Fads2 and two elongases, Elovl5 and Elovl4 for each respective species. A heterologous yeast assay indicated that the B. boddarti Fads2 possessed low desaturation activity on C18 PUFA and no desaturation on C20 and C22 PUFA substrates. In comparison, the Elovl5 showed a wide range of substrate specificity, with a capacity to elongate C18, C20 and C22 PUFA substrates. An amino acid residue that affects the capacity to elongate C22:5n-3 was identified in the B. boddarti Elovl5. Both genes are highly expressed in brain tissue. Among all tissues, DHA is highly concentrated in neuron-rich tissues, whereas EPA is highly deposited in gills. Taken together, the results showed that due to the inability to perform desaturation steps, B. boddarti is unable to biosynthesise LC-PUFA, relying on dietary intake to acquire these nutrients.
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Affiliation(s)
- Han-Jie Soo
- School of Biological Sciences, Universiti Sains Malaysia, Minden, Malaysia
| | - Ka Kei Sam
- Centre for Chemical Biology, Sains@USM, Bayan Lepas, Malaysia
| | - Joey Chong
- School of Biological Sciences, Universiti Sains Malaysia, Minden, Malaysia
| | - Nyok-Sean Lau
- Centre for Chemical Biology, Sains@USM, Bayan Lepas, Malaysia
| | - Seng Yeat Ting
- Centre for Chemical Biology, Sains@USM, Bayan Lepas, Malaysia
| | - Meng-Kiat Kuah
- Centre for Chemical Biology, Sains@USM, Bayan Lepas, Malaysia
| | - Sim Yee Kwang
- Center for Marine and Coastal Studies, Universiti Sains Malaysia, Minden, Malaysia
| | | | - Alexander Chong Shu-Chien
- School of Biological Sciences, Universiti Sains Malaysia, Minden, Malaysia
- Centre for Chemical Biology, Sains@USM, Bayan Lepas, Malaysia
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