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Zhang R, Li C, Yu M, Huang X, Zhang M, Liu S, Pan S, Xue W, Wang C, Mao C, Zhang H, Fan G. Chromosome-level genome assembly of the humpback puffer, Tetraodon palembangensis. GIGABYTE 2021; 2021:gigabyte17. [PMID: 36824331 PMCID: PMC9632004 DOI: 10.46471/gigabyte.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/31/2021] [Indexed: 11/09/2022] Open
Abstract
The humpback puffer, Tetraodon palembangensis, is a poisonous freshwater pufferfish species mainly distributed in Southeast Asia (Thailand, Laos, Malaysia and Indonesia). The humpback puffer has many interesting biological features, such as inactivity, tetrodotoxin production and body expansion. Here, we report the first chromosome-level genome assembly of the humpback puffer. The genome size is 362 Mb, with a contig N50 value of ∼1.78 Mb and a scaffold N50 value of ∼15.8 Mb. Based on this genome assembly, ∼61.5 Mb (18.11%) repeat sequences were identified, 19,925 genes were annotated, and the function of 90.01% of these genes could be predicted. Finally, a phylogenetic tree of ten teleost fish species was constructed. This analysis suggests that the humpback puffer and T. nigroviridis share a common ancestor 18.1 million years ago (MYA), and diverged from T. rubripes 45.8 MYA. The humpback puffer genome will be a valuable genomic resource to illustrate possible mechanisms of tetrodotoxin synthesis and tolerance.
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Affiliation(s)
- Rui Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Chang Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Mengjun Yu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | | | - Mengqi Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Shanshan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Shanshan Pan
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Weizhen Xue
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Congyan Wang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Chunyan Mao
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - He Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China,Department of Biology, Hong Kong Baptist University, Hong Kong, China, Corresponding authors. E-mail: ;
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China, Corresponding authors. E-mail: ;
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Martinez PA, Jacobina UP, Molina WF. Comparative cytogenetics and heterochromatic patterns in two species of the genus Acanthostracion (Ostraciidae: Tetraodontiformes). Mar Genomics 2011; 4:215-20. [PMID: 21867974 DOI: 10.1016/j.margen.2011.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Revised: 06/01/2011] [Accepted: 06/04/2011] [Indexed: 10/18/2022]
Abstract
Some groups of fish, such as those belonging to the Order Tetraodontiformes, may differ significantly in the amount and location of heterochromatin in the chromosomes. There is a marked variation in DNA content of more than seven-fold among the families of this Order. However, the karyoevolutionary mechanisms responsible for this variation are essentially unknown. The largest genomic contents are present in species of the family Ostraciidae (2.20-2.60pg). The present study cytogenetically characterized two species of the family Ostraciidae, Acanthostracion polygonius and A. quadricornis, using conventional staining, C-bandings, Ag-NOR, CMA(3)/DAPI, AluI, PstI, EcoRI, TaqI and HinfI restriction enzymes (REs) and double FISH with 18S and 5S rDNA probes. The karyotypes of both species showed 2n=52 acrocentric chromosomes (FN=52; chromosome arms) and pronounced conserved structural characteristics. A significant heterochromatic content was observed equilocally distributed in pericentromeric position in all the chromosome pairs. This condition is unusual in relation to the karyotypes of other families of Tetraodontiformes and probability is the cause of the higher DNA content in Ostraciidae. Given the role played by repetitive sequences in the genomic reorganization of this Order, it is suggested that the conspicuous heterochromatic blocks, present in the same chromosomal position and with apparently similar composition, may have arisen or undergo evolutionary changes in concert providing clues about the chromosomal mechanisms which led to extensive variation in genomic content of different Tetraodontiformes families.
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Affiliation(s)
- Pablo Ariel Martinez
- Universidade Federal do Rio Grande do Norte (UFRN), Departamento de Biologia Celular e Genética, Centro de Biociências, Lagoa Nova s/n, CEP 59078-970, Natal, Rio Grande do Norte, Brazil.
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de Lima LCB, Martinez PA, Molina WF. Cytogenetic characterization of three Balistoidea fish species from the Atlantic with inferences on chromosomal evolution in the families Monacanthidae and Balistidae. COMPARATIVE CYTOGENETICS 2011; 5:61-69. [PMID: 24260619 PMCID: PMC3833730 DOI: 10.3897/compcytogen.v5i1.1141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Accepted: 03/23/2010] [Indexed: 06/02/2023]
Abstract
The Tetraodontiformes are the most derived group of teleostean fish. Among other apomorphies, they are characterized by a high degree of fusions or significant bone loss in the head and body. In the early phylogenetic proposals presented for this order, the families Balistidae and Monacanthidae have been unanimously considered to be closely related. Although they have moderate species diversity, they are scarcely known in cytogenetic aspect and chromosomal pattern comparisons between these groups have yet to be established. The species Cantherhines macrocerus (Hollard,1853), Cantherhines pullus (Ranzani, 1842) (Monacanthidae) and Melichthys niger (Bloch, 1786) (Balistidae) were cytogenetically analyzed using conventional (Ag-impregnation, C-banding, CMA3- and DAPI-fluorescence) and molecular (FISH with an 18S rDNA probe) cytogenetic protocols. The karyotypes of all three species were very similar possessing diploid chromosome numbers 2n = 40 and composed exclusively of acrocentric chromosomes. Single NOR-bearing pair as well as positive heterochromatic blocks at pericentromeric regions were identified in the karyotypes of the three species studied. NOR-bearing sites were positively labeled after Ag-impregnation, C-banding, CMA3-fluorescence and FISH with an 18S rDNA probe but were negative after DAPI-fluorescence. Such remarkable shared conspicuous chromosomal characters corroborate either close phylogenetic relationship of these families, previously established by morphological and molecular data, or rather conservative nature of karyotype differentiation processes. The later hypothesis, however, appears less probable due to centric or in tandem fusions documented for another Balistoidea species.
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Affiliation(s)
- Lorena Corina Bezerra de Lima
- />Department of Cell Biology and Genetics, Centro de Biociências, Universidade Federal do io Grande do Norte, Campus Universitário, 59078 – 970 Natal, RN, Brazil
| | - Pablo Ariel Martinez
- />Department of Cell Biology and Genetics, Centro de Biociências, Universidade Federal do io Grande do Norte, Campus Universitário, 59078 – 970 Natal, RN, Brazil
| | - Wagner Franco Molina
- />Department of Cell Biology and Genetics, Centro de Biociências, Universidade Federal do io Grande do Norte, Campus Universitário, 59078 – 970 Natal, RN, Brazil
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Martinez PA, de Araujo WC, Molina WF. Derived cytogenetic traits, multiple NORs and B chromosomes in the compact karyotype of Canthigaster figueiredoi (Tetraodontiformes). Mar Genomics 2010; 3:85-9. [DOI: 10.1016/j.margen.2010.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Revised: 07/21/2010] [Accepted: 07/22/2010] [Indexed: 10/19/2022]
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Fischer C, Bouneau L, Coutanceau JP, Weissenbach J, Volff JN, Ozouf-Costaz C. Global heterochromatic colocalization of transposable elements with minisatellites in the compact genome of the pufferfish Tetraodon nigroviridis. Gene 2004; 336:175-83. [PMID: 15246529 DOI: 10.1016/j.gene.2004.04.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2004] [Revised: 03/31/2004] [Accepted: 04/13/2004] [Indexed: 11/24/2022]
Abstract
Because of its unusual high degree of compaction and paucity of repetitive sequences, the genome of the smooth pufferfish Tetraodon nigroviridis is the subject of a well-advanced sequencing project. An astonishing diversity of transposable elements not found in the human and the mouse has been observed in the genome of T. nigroviridis. Due to the difficulty of assembling repeat-rich regions, the whole genome shotgun sequencing approach will probably fail to reveal the general organisation of this compact vertebrate genome. Therefore, in order to gain new insights into the global distribution pattern of repeated DNA in the genome of T. nigroviridis, we have reconstructed partial/complete repetitive sequences from data generated by the genome project and performed double-colour fluorescent in situ hybridization (FISH) analysis for representatives of three major categories of repeated sequences including two minisatellites (ms100 and ms104), two DNA transposons (Tol2 and Buffy1) and two non-long terminal repeat (LTR) retrotransposons (Rex3 and Babar). We show that DNA transposons and retroelements very frequently colocalize with minisatellites and mostly accumulate within heterochromatic regions. These results, which have not been reported so far for the fugu Takifugu rubripes, show that repeated elements are generally excluded from gene-rich regions in T. nigroviridis and underline the extreme degree of compartmentalization of this compact genome. The genome organization of the pufferfish is clearly different from that observed in humans, where repeated sequences make up an important fraction of euchromatic DNA, and is more similar to that observed in the fruit fly Drosophila melanogaster.
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Affiliation(s)
- Cécile Fischer
- Genoscope/Centre National de Séquençage and CNRS-UMR 8030, F-91057, Evry Cedex 06, France
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Mandrioli M, Manicardi GC. Cytogenetic and molecular analysis of the pufferfish Tetraodon fluviatilis (Osteichthyes). Genetica 2002; 111:433-8. [PMID: 11841187 DOI: 10.1023/a:1013787230829] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In view of their compact genome, pufferfish (Tetraodontiformes) have been proposed as model animal for the study of the vertebrate genome. Despite such interest, cytogenetic information about puffers is still scanty. To fill this gap, a cytogenetic analysis of T. fluviatilis has been performed using both classical and molecular techniques. C-banding, followed by DAPI staining, evidenced that in T. fluviatilis, like all other puffer species so far examined, heterochromatin is essentially AT-rich and it is located at centromeres, whereas staining with CMA3, silver staining and FISH with a 28S ribosomal RNA gene DNA probe showed 2-4 nucleolar organizing regions (NORs) located in heterochromatic regions in the considered puffer species. FISH with the 5S probe put in evidence both in T. fluviatilis and in T. nigroviridis only a 5S cluster per haploid genome that is physically unlinked with the major ribosomal RNA genes including the 28S rRNA genes. Hybridization with the (TTAGGG)n probe showed in all the puffers brightly fluorescent signals uniform both in size and intensity at the end of all the chromosomes. Finally, mariner-like elements (MLEs) have been identified in T. fluviatilis and they have located into the NOR-associated heterochromatin.
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Affiliation(s)
- M Mandrioli
- Dipartimento di Biologia Animale, Università degli Studi di Modena e Reggio Emilia, Modena, Italy.
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