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Zhang K, Huang Y, Zhang Y, Liang R, Li Q, Li R, Zhao X, Bian C, Chen Y, Wu J, Shi Q, Lin L. A chromosome-level reference genome assembly of the Reeve's moray eel (Gymnothorax reevesii). Sci Data 2023; 10:501. [PMID: 37516767 PMCID: PMC10387071 DOI: 10.1038/s41597-023-02394-7] [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: 04/20/2023] [Accepted: 07/17/2023] [Indexed: 07/31/2023] Open
Abstract
Due to potentially hostile behaviors and elusive habitats, moray eels (Muraenidae) as one group of apex predators in coral reefs all across the globe have not been well investigated. Here, we constructed a chromosome-level genome assembly for the representative Reeve's moray eel (Gymnothorax reevesii). This haplotype genome assembly is 2.17 Gb in length, and 97.87% of the sequences are anchored into 21 chromosomes. It contains 56.34% repetitive sequences and 23,812 protein-coding genes, of which 96.77% are functionally annotated. This sequenced marine species in Anguilliformes makes a good complement to the genetic resource of eel genomes. It not only provides a genetic resource for in-depth studies of the Reeve's moray eel, but also enables deep-going genomic comparisons among various eels.
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Affiliation(s)
- Kai Zhang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou, 510225, 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, 518081, China
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Yuxuan Zhang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou, 510225, China
| | - Rishen Liang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou, 510225, China
| | - Qingqing Li
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou, 510225, 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
| | - 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, 518081, 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, Shenzhen, 518081, China
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Yongnan Chen
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou, 510225, China
| | - Jinhui Wu
- Agro-Tech Extension Center of Guangdong Province, Guangzhou, 510225, 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, 518081, China.
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
| | - Li Lin
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China.
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou, 510225, China.
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Kornfield IL, Ritte U, Richler C, Wahrman J. BIOCHEMICAL AND CYTOLOGICAL DIFFERENTIATION AMONG CICHLID FISHES OF THE SEA OF GALILEE. Evolution 2017; 33:1-14. [DOI: 10.1111/j.1558-5646.1979.tb04657.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/1977] [Revised: 06/09/1978] [Indexed: 11/27/2022]
Affiliation(s)
- I. L. Kornfield
- Department of Genetics; The Hebrew University of Jerusalem; Israel
| | - U. Ritte
- Department of Genetics; The Hebrew University of Jerusalem; Israel
| | - C. Richler
- Department of Genetics; The Hebrew University of Jerusalem; Israel
| | - J. Wahrman
- Department of Genetics; The Hebrew University of Jerusalem; Israel
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Kai W, Nomura K, Fujiwara A, Nakamura Y, Yasuike M, Ojima N, Masaoka T, Ozaki A, Kazeto Y, Gen K, Nagao J, Tanaka H, Kobayashi T, Ototake M. A ddRAD-based genetic map and its integration with the genome assembly of Japanese eel (Anguilla japonica) provides insights into genome evolution after the teleost-specific genome duplication. BMC Genomics 2014; 15:233. [PMID: 24669946 PMCID: PMC3986909 DOI: 10.1186/1471-2164-15-233] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 03/17/2014] [Indexed: 12/30/2022] Open
Abstract
Background Recent advancements in next-generation sequencing technology have enabled cost-effective sequencing of whole or partial genomes, permitting the discovery and characterization of molecular polymorphisms. Double-digest restriction-site associated DNA sequencing (ddRAD-seq) is a powerful and inexpensive approach to developing numerous single nucleotide polymorphism (SNP) markers and constructing a high-density genetic map. To enrich genomic resources for Japanese eel (Anguilla japonica), we constructed a ddRAD-based genetic map using an Ion Torrent Personal Genome Machine and anchored scaffolds of the current genome assembly to 19 linkage groups of the Japanese eel. Furthermore, we compared the Japanese eel genome with genomes of model fishes to infer the history of genome evolution after the teleost-specific genome duplication. Results We generated the ddRAD-based linkage map of the Japanese eel, where the maps for female and male spanned 1748.8 cM and 1294.5 cM, respectively, and were arranged into 19 linkage groups. A total of 2,672 SNP markers and 115 Simple Sequence Repeat markers provide anchor points to 1,252 scaffolds covering 151 Mb (13%) of the current genome assembly of the Japanese eel. Comparisons among the Japanese eel, medaka, zebrafish and spotted gar genomes showed highly conserved synteny among teleosts and revealed part of the eight major chromosomal rearrangement events that occurred soon after the teleost-specific genome duplication. Conclusions The ddRAD-seq approach combined with the Ion Torrent Personal Genome Machine sequencing allowed us to conduct efficient and flexible SNP genotyping. The integration of the genetic map and the assembled sequence provides a valuable resource for fine mapping and positional cloning of quantitative trait loci associated with economically important traits and for investigating comparative genomics of the Japanese eel.
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Affiliation(s)
| | | | - Atushi Fujiwara
- National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama-shi, Kanagawa 236-8648, Japan.
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Guo B, Gan X, He S. Hox genes of the Japanese eel Anguilla japonica and Hox cluster evolution in teleosts. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2010; 314:135-47. [PMID: 19670462 DOI: 10.1002/jez.b.21318] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Compared with other diploid teleosts (2n=48), anguilloid fish have a specialized karyotype (2n=38) and remarkable morphological variation, and represent one basal group species of teleosts. To investigate the Hox gene/cluster inventory in basal teleosts, a PCR-based survey of Hox genes in the Japanese eel (Anguilla japonica) was conducted with both gene-specific and homeobox-targeted degenerate primers. Our data provide evidence that at least 34 distinct Hox genes exist in the Japanese eel genome and that they represent eight Hox clusters. Duplication of Hox genes in the Japanese eel appears to be the result of the fish-specific genome duplication (FSGD) event. The Japanese eel shared the FSGD event with other teleosts such as zebrafish and pufferfish. A member of Hox paralog group one (HoxA1b) was preserved in the Japanese eel but was lost in other teleosts. Available Hox data revealed that the Hox cluster evolved distinctly in different teleost lineages. All duplicated Hox clusters were retained after the FSGD event in basal teleosts like in the Japanese eel, whereas crown teleosts lost one cluster (HoxCb or HoxDb). Based on current teleostean phylogeny, the HoxDb cluster was lost independently in the teleost lineages Otocephala and Euteleostei.
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Affiliation(s)
- Baocheng Guo
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, P.R. China
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Cardinaud B, Sugamori KS, Coudouel S, Vincent JD, Niznik HB, Vernier P. Early emergence of three dopamine D1 receptor subtypes in vertebrates. Molecular phylogenetic, pharmacological, and functional criteria defining D1A, D1B, and D1C receptors in European eel Anguilla anguilla. J Biol Chem 1997; 272:2778-87. [PMID: 9006917 DOI: 10.1074/jbc.272.5.2778] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The existence of dopamine D1C and D1D receptors in Xenopus and chicken, respectively, challenged the established duality (D1A and D1B) of the dopamine D1 receptor class in vertebrates. To ascertain the molecular diversity of this gene family in early diverging vertebrates, we isolated four receptor-encoding sequences from the European eel Anguilla anguilla. Molecular phylogeny assigned two receptor sequences (D1A1 and D1A2) to the D1A subtype, and a third receptor to the D1B subtype. Additional sequence was orthologous to the Xenopus D1C receptor and to several other previously unclassified fish D1-like receptors. When expressed in COS-7 cells, eel D1A and D1B receptors display affinity profiles for dopaminergic ligands similar to those of other known vertebrate homologues. The D1C receptor exhibits pharmacological characteristics virtually identical to its Xenopus homologue. Functionally, while all eel D1 receptors stimulate adenylate cyclase, the eel D1B receptor exhibits greater constitutive activity than either D1A or D1C receptors. Semiquantitative reverse transcription-polymerase chain reaction reveals the differential distribution of D1A1, D1A2, D1B, and D1C receptor mRNA within the hypothalamic-pituitary axis of the eel brain. Taken together, these data suggest that the D1A, D1B, and D1C receptors arose prior to the evolutionary divergence of fish and tetrapods and exhibit molecular, pharmacological, and functional attributes that unambiguously allow for their classification as distinct D1 receptor subtypes in the vertebrate phylum.
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MESH Headings
- Adenylyl Cyclases/metabolism
- Amino Acid Sequence
- Anguilla
- Animals
- Base Sequence
- Benzazepines/metabolism
- Binding, Competitive
- Brain/metabolism
- COS Cells
- Chickens
- Cloning, Molecular
- DNA Primers
- Evolution, Molecular
- Genetic Variation
- Humans
- Kinetics
- Molecular Sequence Data
- Multigene Family
- Phylogeny
- Polymerase Chain Reaction
- RNA, Messenger/analysis
- RNA, Messenger/biosynthesis
- Receptors, Dopamine D1/chemistry
- Receptors, Dopamine D1/genetics
- Receptors, Dopamine D1/metabolism
- Receptors, Dopamine D5
- Recombinant Proteins/biosynthesis
- Recombinant Proteins/chemistry
- Recombinant Proteins/metabolism
- Sequence Homology, Amino Acid
- Transcription, Genetic
- Transfection
- Vertebrates
- Xenopus
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Affiliation(s)
- B Cardinaud
- Institut Alfred Fessard, UPR2212, CNRS, 91198 Gif-sur-Yvette cedex, France
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Kishida M, Hirano T, Kubota J, Hasegawa S, Kawauchi H, Yamaguchi K, Shirahata K. Isolation of two forms of growth hormone secreted from eel pituitaries in vitro. Gen Comp Endocrinol 1987; 65:478-88. [PMID: 3549441 DOI: 10.1016/0016-6480(87)90134-1] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Two forms of growth hormone (GH) were purified by chromatofocusing of medium from cultured Japanese eel (Anguilla japonica) pituitaries. The pituitaries were organ-cultured in Eagle's minimum essential medium with Earle's salts. Following polyacrylamide gel electrophoresis of the medium at pH 9.5, two prominent bands were seen with Rf 0.36 and 0.29; they were designated as eGHI and eGHII, respectively. Seven-hundred fifty milliliters of medium, in which 260 pituitaries were cultured for 6-10 weeks, was concentrated by DIAFLO membrane (YM-5) and subjected to gel filtration on a Sephadex G-75 column and to chromatofocusing on a PBE-94 column. eGHI and II were finally purified by gel filtration on a Sephadex G-75 column, yielding 2.0 mg of eGHI and 1.3 mg of eGHII. Both eGHI and eGHII were equipotent to ovine GH in promoting growth of juvenile rainbow trout. The putative GH-producing cells in the proximal pars distalis of the eel pituitary were stained specifically with antisera raised against eGHI or eGHII; no cross-reactivity was seen in the follicular prolactin cells in the rostral pars distalis. As determined by gel isoelectric focusing, eGHI and eGHII have isoelectric points of 6.3 and 6.7, respectively. Identical molecular masses of 23,000 Da were determined by sodium dodecyl sulfate gel electrophoresis. Their amino acid compositions strongly resembled each other; comparison of the partial N-terminal amino acids indicates that sequence 1 to 36 of GHII is exactly the same as 4 to 39 of GHI.
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