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Yang X, Song Y, Zhang R, Yu M, Guo X, Guo H, Du X, Sun S, Li C, Mao X, Fan G, Liu X. Unravelling the genomic features, phylogeny and genetic basis of tooth ontogenesis in Characiformes through analysis of four genomes. DNA Res 2023; 30:dsad022. [PMID: 37788574 PMCID: PMC10590162 DOI: 10.1093/dnares/dsad022] [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: 03/25/2023] [Revised: 09/27/2023] [Accepted: 10/02/2023] [Indexed: 10/05/2023] Open
Abstract
Characiformes is a diverse and evolutionarily significant order of freshwater fish encompassing over 2,300 species. Despite its diversity, our understanding of Characiformes' evolutionary relationships and adaptive mechanisms is limited due to insufficient genome sequences. In this study, we sequenced and assembled the genomes of four Characiformes species, three of which were chromosome-level assemblies. Our analyses revealed dynamic changes in gene family evolution, repeat sequences and variations in chromosomal collinearity within these genomes. With the assembled genomes, we were not only able to elucidate the evolutionary relationship of the four main orders in Otophysi but also indicated Characiformes as the paraphyletic group. Comparative genomic analysis with other available fish genomes shed light on the evolution of genes related to tooth development in Characiformes. Notably, variations in the copy number of secretory calcium-binding phosphoproteins (SCPP) genes were observed among different orders of Otophysi, indicating their potential contribution to the diversity of tooth types. Our study offers invaluable genome sequences and novel insights into Characiformes' evolution, paving the way for further genomic and evolutionary research in fish.
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Affiliation(s)
- Xianwei Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue Song
- BGI Research, Qingdao 266555, China
| | | | | | | | | | - Xiao Du
- BGI Research, Qingdao 266555, China
- BGI Research, Shenzhen 518083, China
| | - Shuai Sun
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Qingdao 266555, China
| | | | | | - Guangyi Fan
- BGI Research, Qingdao 266555, China
- BGI Research, Shenzhen 518083, China
| | - Xin Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Shenzhen 518083, China
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Nguinkal JA, Brunner RM, Verleih M, Rebl A, de Los Ríos-Pérez L, Schäfer N, Hadlich F, Stüeken M, Wittenburg D, Goldammer T. The First Highly Contiguous Genome Assembly of Pikeperch ( Sander lucioperca), an Emerging Aquaculture Species in Europe. Genes (Basel) 2019; 10:E708. [PMID: 31540274 PMCID: PMC6770990 DOI: 10.3390/genes10090708] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/27/2019] [Accepted: 09/08/2019] [Indexed: 01/14/2023] Open
Abstract
The pikeperch (Sander lucioperca) is a fresh and brackish water Percid fish natively inhabiting the northern hemisphere. This species is emerging as a promising candidate for intensive aquaculture production in Europe. Specific traits like cannibalism, growth rate and meat quality require genomics based understanding, for an optimal husbandry and domestication process. Still, the aquaculture community is lacking an annotated genome sequence to facilitate genome-wide studies on pikeperch. Here, we report the first highly contiguous draft genome assembly of Sander lucioperca. In total, 413 and 66 giga base pairs of DNA sequencing raw data were generated with the Illumina platform and PacBio Sequel System, respectively. The PacBio data were assembled into a final assembly size of ~900 Mb covering 89% of the 1,014 Mb estimated genome size. The draft genome consisted of 1966 contigs ordered into 1,313 scaffolds. The contig and scaffold N50 lengths are 3.0 Mb and 4.9 Mb, respectively. The identified repetitive structures accounted for 39% of the genome. We utilized homologies to other ray-finned fishes, and ab initio gene prediction methods to predict 21,249 protein-coding genes in the Sander lucioperca genome, of which 88% were functionally annotated by either sequence homology or protein domains and signatures search. The assembled genome spans 97.6% and 96.3% of Vertebrate and Actinopterygii single-copy orthologs, respectively. The outstanding mapping rate (99.9%) of genomic PE-reads on the assembly suggests an accurate and nearly complete genome reconstruction. This draft genome sequence is the first genomic resource for this promising aquaculture species. It will provide an impetus for genomic-based breeding studies targeting phenotypic and performance traits of captive pikeperch.
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Affiliation(s)
- Julien Alban Nguinkal
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Ronald Marco Brunner
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Marieke Verleih
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Alexander Rebl
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Lidia de Los Ríos-Pérez
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Nadine Schäfer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Frieder Hadlich
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Marcus Stüeken
- State Research Center of Agriculture and Fisheries M-V, 17194 Hohen Wangelin, Germany.
| | - Dörte Wittenburg
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
| | - Tom Goldammer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
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PATHAK AJEYKUMAR, SARKAR UTTAMKUMAR, DAYAL RAJESH, SINGH SRIPRAKASH. UPFBase—A freshwater fish diversity database of Uttar Pradesh, India. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2019. [DOI: 10.56093/ijans.v89i3.88103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Worldwide, global databases on fishes lack fish diversity information at regional scale of a country, which has fascinated many fishery workers to know the regional scale fish diversity. Databases are essential part of the biodiversity science and have been used widely in the biological research. The present study discusses development, services and utility of the database application (UPFBase) providing information on the freshwater fish biodiversity of Uttar Pradesh. To develop UPFBase, data on the fish biodiversity of this region was compiled from different sources that include primary data generated from different projects and secondary data from published literatures. The collected data were screened and then digitized. Microsoft ACCESS relational database and Visual Basic language technologies were used for designing and implementing the standalone database application with the data management capability. Presently, UPFBase provides taxonomy, synonyms, local name, common name, morphology, biology, distribution, habitat, economic importance, conservation status and other fishery information on 129 fishes belonging to 11 orders and 27 families. UPFBase is user friendly and provides ease in working through search, query and action command button tools. It can easily be deployed on the mobile storages devices like CD-ROM, Pen drive, PCMCIA etc and can be installed on any Windows based Intel x86 machines. This version of UPFBase was built for countries, where computational hardware and software resources are in scare and it is expected that it might play imperious role in knowing and managing the indigenous fish diversity for decision making and posterity.
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Symonová R, Howell WM. Vertebrate Genome Evolution in the Light of Fish Cytogenomics and rDNAomics. Genes (Basel) 2018; 9:genes9020096. [PMID: 29443947 PMCID: PMC5852592 DOI: 10.3390/genes9020096] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/25/2018] [Accepted: 01/29/2018] [Indexed: 12/19/2022] Open
Abstract
To understand the cytogenomic evolution of vertebrates, we must first unravel the complex genomes of fishes, which were the first vertebrates to evolve and were ancestors to all other vertebrates. We must not forget the immense time span during which the fish genomes had to evolve. Fish cytogenomics is endowed with unique features which offer irreplaceable insights into the evolution of the vertebrate genome. Due to the general DNA base compositional homogeneity of fish genomes, fish cytogenomics is largely based on mapping DNA repeats that still represent serious obstacles in genome sequencing and assembling, even in model species. Localization of repeats on chromosomes of hundreds of fish species and populations originating from diversified environments have revealed the biological importance of this genomic fraction. Ribosomal genes (rDNA) belong to the most informative repeats and in fish, they are subject to a more relaxed regulation than in higher vertebrates. This can result in formation of a literal 'rDNAome' consisting of more than 20,000 copies with their high proportion employed in extra-coding functions. Because rDNA has high rates of transcription and recombination, it contributes to genome diversification and can form reproductive barrier. Our overall knowledge of fish cytogenomics grows rapidly by a continuously increasing number of fish genomes sequenced and by use of novel sequencing methods improving genome assembly. The recently revealed exceptional compositional heterogeneity in an ancient fish lineage (gars) sheds new light on the compositional genome evolution in vertebrates generally. We highlight the power of synergy of cytogenetics and genomics in fish cytogenomics, its potential to understand the complexity of genome evolution in vertebrates, which is also linked to clinical applications and the chromosomal backgrounds of speciation. We also summarize the current knowledge on fish cytogenomics and outline its main future avenues.
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Affiliation(s)
- Radka Symonová
- Faculty of Science, Department of Biology, University of Hradec Králové, 500 03 Hradec Králové, Czech Republic.
| | - W Mike Howell
- Department of Biological and Environmental Sciences, Samford University, Birmingham, AL 35229, USA.
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H 2S Donor NaHS Changes the Production of Endogenous H 2S and NO in D-Galactose-Induced Accelerated Ageing. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:5707830. [PMID: 28512525 PMCID: PMC5420433 DOI: 10.1155/2017/5707830] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 03/06/2017] [Accepted: 03/13/2017] [Indexed: 01/08/2023]
Abstract
Aims. The study was designed to explore whether hydrogen sulphide (H2S) and nitric oxide (NO) generation changed in D-galactose- (D-gal-) induced ageing, the possible effects of exogenous H2S supplementation, and related mechanisms. Results. In D-gal-induced senescent mice, both H2S and NO levels in the heart, liver, and kidney tissues were decreased significantly. A similar trend was observed in D-gal-challenged human umbilical vein endothelial cells (HUVECs). Sustained H2S donor (NaHS) treatment for 2 months elevated H2S and NO levels in these mice, and during this period, the D-gal-induced senescent phenotype was reversed. The protective effect of NaHS is associated with a decrease in reactive oxygen species levels and an increase in antioxidants, such as glutathione, and superoxide dismutase and glutathione peroxidase activities. Increased expression of the H2S-producing enzymes cystathionine γ-lyase (CSE) and cystathionine-β-synthase (CBS) in the heart, liver, and kidney tissues was observed in the NaHS-treated groups. NaHS supplementation also significantly postponed D-gal-induced HUVEC senescence. Conclusions. Endogenous hydrogen sulphide production in both ageing mice and endothelial cells is insufficient. Exogenous H2S can partially rescue ageing-related dysfunction by inducing endogenous H2S and NO production and reducing oxidative stress. Restoring endogenous H2S production may contribute to healthy ageing, and H2S may have antiageing effects.
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Rashid I, Nagpure NS, Srivastava P, Kumar R, Pathak AK, Singh M, Kushwaha B. HRGFish: A database of hypoxia responsive genes in fishes. Sci Rep 2017; 7:42346. [PMID: 28205556 PMCID: PMC5304231 DOI: 10.1038/srep42346] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/04/2017] [Indexed: 11/09/2022] Open
Abstract
Several studies have highlighted the changes in the gene expression due to the hypoxia response in fishes, but the systematic organization of the information and the analytical platform for such genes are lacking. In the present study, an attempt was made to develop a database of hypoxia responsive genes in fishes (HRGFish), integrated with analytical tools, using LAMPP technology. Genes reported in hypoxia response for fishes were compiled through literature survey and the database presently covers 818 gene sequences and 35 gene types from 38 fishes. The upstream fragments (3,000 bp), covered in this database, enables to compute CG dinucleotides frequencies, motif finding of the hypoxia response element, identification of CpG island and mapping with the reference promoter of zebrafish. The database also includes functional annotation of genes and provides tools for analyzing sequences and designing primers for selected gene fragments. This may be the first database on the hypoxia response genes in fishes that provides a workbench to the scientific community involved in studying the evolution and ecological adaptation of the fish species in relation to hypoxia.
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Affiliation(s)
- Iliyas Rashid
- Molecular Biology and Biotechnology Division, ICAR- National Bureau of Fish Genetic Resources, Lucknow- 226002, Uttar Pradesh, India.,AMITY Institute of Biotechnology, AMITY University Uttar Pradesh, Lucknow-226028, Uttar Pradesh, India
| | - Naresh Sahebrao Nagpure
- Fish Genetics and Biotechnology Division, ICAR- Central Institute of Fisheries Education, Mumbai-400 061, Maharashtra, India
| | - Prachi Srivastava
- AMITY Institute of Biotechnology, AMITY University Uttar Pradesh, Lucknow-226028, Uttar Pradesh, India
| | - Ravindra Kumar
- Molecular Biology and Biotechnology Division, ICAR- National Bureau of Fish Genetic Resources, Lucknow- 226002, Uttar Pradesh, India
| | - Ajey Kumar Pathak
- Molecular Biology and Biotechnology Division, ICAR- National Bureau of Fish Genetic Resources, Lucknow- 226002, Uttar Pradesh, India
| | - Mahender Singh
- Molecular Biology and Biotechnology Division, ICAR- National Bureau of Fish Genetic Resources, Lucknow- 226002, Uttar Pradesh, India
| | - Basdeo Kushwaha
- Molecular Biology and Biotechnology Division, ICAR- National Bureau of Fish Genetic Resources, Lucknow- 226002, Uttar Pradesh, India
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