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Cheng Y, Shang D, Luo M, Huang C, Lai F, Wang X, Xu X, Ying R, Wang L, Zhao Y, Zhang L, Long M, Cheng H, Zhou R. Whole genome-wide chromosome fusion and new gene birth in the Monopterus albus genome. Cell Biosci 2020; 10:67. [PMID: 32477490 PMCID: PMC7240998 DOI: 10.1186/s13578-020-00432-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/13/2020] [Indexed: 12/11/2022] Open
Abstract
Background Teleost fishes account for over half of extant vertebrate species. A core question in biology is how genomic changes drive phenotypic diversity that relates to the origin of teleost fishes. Results Here, we used comparative genomic analyses with chromosome assemblies of diverse lineages of vertebrates and reconstructed an ancestral vertebrate genome, which revealed phylogenomic trajectories in vertebrates. We found that the whole-genome-wide chromosome fission/fusions took place in the Monopterus albus lineage after the 3-round whole-genome duplication. Four times of genomic fission/fusions events resulted in the whole genome-wide chromosome fusions in the genomic history of the lineage. In addition, abundant recently evolved new genes for reproduction emerged in the Monopterus albus after separated from medaka. Notably, we described evolutionary trajectories of conserved blocks related to sex determination genes in teleosts. Conclusions These data pave the way for a better understanding of genomic evolution in extant teleosts.
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Affiliation(s)
- Yibin Cheng
- 1Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072 People's Republic of China
| | - Dantong Shang
- 1Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072 People's Republic of China
| | - Majing Luo
- 1Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072 People's Republic of China
| | - Chunhua Huang
- 1Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072 People's Republic of China
| | - Fengling Lai
- 1Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072 People's Republic of China
| | - Xin Wang
- 1Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072 People's Republic of China
| | - Xu Xu
- 1Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072 People's Republic of China
| | - Ruhong Ying
- 1Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072 People's Republic of China
| | - Lingling Wang
- 1Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072 People's Republic of China
| | - Yu Zhao
- 1Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072 People's Republic of China
| | - Li Zhang
- 2Department of Ecology and Evolution, University of Chicago, Chicago, 60637 USA
| | - Manyuan Long
- 2Department of Ecology and Evolution, University of Chicago, Chicago, 60637 USA
| | - Hanhua Cheng
- 1Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072 People's Republic of China
| | - Rongjia Zhou
- 1Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072 People's Republic of China
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da Silva M, Matoso DA, Artoni RF, Feldberg E. Karyotypic Diversity and Evolutionary Trends in Neotropical Electric Fish of the Genus Gymnotus (Gymnotiformes: Gymnotidae). Zebrafish 2019; 16:308-320. [PMID: 31045488 DOI: 10.1089/zeb.2018.1716] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Electric fish of the order Gymnotiformes are endemic to the Neotropical region, and their highest diversity is observed in the Amazon region. The family Gymnotidae, which consists of the genera Electrophorus and Gymnotus, is a natural group and is located at the base of the phylogeny of the order. Gymnotus is a widely distributed and specious genus with high karyotypic diversity, especially concerning to the diploid number and the locations of repetitive sequences. Our karyotyping results in five species of the family Gymnotidae (Gymnotus ucamara, Gymnotus cf. stenoleucus, Gymnotus cf. pedanopterus, Gymnotus mamiraua, and Gymnotus carapo "Maranhão") corroborate the proposal of plasticity of the diploid number in this group. Moreover, in this study, we propose that the 5S ribosomal DNA (rDNA) sequences were species-specific markers that act as a potential biogeographical marker for the genus. Besides, the sequence's location, particularly in G. mamiraua from Central Amazon, shows a close relationship with 5S of the Gymnotus species, with 54 chromosomes, from the Paraná-Paraguay basin in the Center-South of Brazil. Considering that the ancestral diploid number for Gymnotidae is 52 chromosomes, we also suggest that the trend in the family is toward a decrease in the chromosome number. However, the carapo clade stands out in this regard, with an increase and a decrease in chromosome number; this pattern may be reinforced with the ecologic behaviors and the geodispersal patterns of this clade.
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Affiliation(s)
- Maelin da Silva
- 1 Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | - Daniele Aparecida Matoso
- 2 Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Brazil
| | - Roberto Ferreira Artoni
- 1 Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | - Eliana Feldberg
- 3 Programa de Pós Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
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Inferring Diversity and Evolution in Fish by Means of Integrative Molecular Cytogenetics. ScientificWorldJournal 2015; 2015:365787. [PMID: 26345638 PMCID: PMC4546756 DOI: 10.1155/2015/365787] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Revised: 07/20/2015] [Accepted: 07/22/2015] [Indexed: 11/23/2022] Open
Abstract
Fish constitute a paraphyletic and profusely diversified group that has historically puzzled ichthyologists. Hard efforts are necessary to better understand this group, due to its extensive diversity. New species are often identified and it leads to questions about their phylogenetic aspects. Cytogenetics is becoming an important biodiversity-detection tool also used to measure biodiversity evolutionary aspects. Molecular cytogenetics by fluorescence in situ hybridization (FISH) allowed integrating quantitative and qualitative data from DNA sequences and their physical location in chromosomes and genomes. Although there is no intention on presenting a broader review, the current study presents some evidences on the need of integrating molecular cytogenetic data to other evolutionary biology tools to more precisely infer cryptic species detection, population structuring in marine environments, intra- and interspecific karyoevolutionary aspects of freshwater groups, evolutionary dynamics of marine fish chromosomes, and the origin and differentiation of sexual and B chromosomes. The new cytogenetic field, called cytogenomics, is spreading due to its capacity to give resolute answers to countless questions that cannot be answered by traditional methodologies. Indeed, the association between chromosomal markers and DNA sequencing as well as between biological diversity analysis methodologies and phylogenetics triggers the will to search for answers about fish evolutionary, taxonomic, and structural features.
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Almeida JS, Migues VH, Diniz D, Affonso PRAM. A Unique Sex Chromosome System in the Knifefish Gymnotus bahianus with Inferences About Chromosomal Evolution of Gymnotidae. J Hered 2015; 106:177-83. [DOI: 10.1093/jhered/esu087] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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da Silva M, Matoso DA, Artoni RF, Feldberg E. New Approach Data in Electric Fish (Teleostei: Gymnotus): Sex Chromosome Evolution and Repetitive DNA. Zebrafish 2014; 11:528-35. [DOI: 10.1089/zeb.2013.0966] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Maelin da Silva
- Programa de Pós Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Daniele Aparecida Matoso
- Departamento de Biologia, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | - Roberto Ferreira Artoni
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | - Eliana Feldberg
- Programa de Pós Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
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Evolutionary dynamics of rRNA gene clusters in cichlid fish. BMC Evol Biol 2012; 12:198. [PMID: 23035959 PMCID: PMC3503869 DOI: 10.1186/1471-2148-12-198] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 09/25/2012] [Indexed: 11/30/2022] Open
Abstract
Background Among multigene families, ribosomal RNA (rRNA) genes are the most frequently studied and have been explored as cytogenetic markers to study the evolutionary history of karyotypes among animals and plants. In this report, we applied cytogenetic and genomic methods to investigate the organization of rRNA genes among cichlid fishes. Cichlids are a group of fishes that are of increasing scientific interest due to their rapid and convergent adaptive radiation, which has led to extensive ecological diversity. Results The present paper reports the cytogenetic mapping of the 5S rRNA genes from 18 South American, 22 African and one Asian species and the 18S rRNA genes from 3 African species. The data obtained were comparatively analyzed with previously published information related to the mapping of rRNA genes in cichlids. The number of 5S rRNA clusters per diploid genome ranged from 2 to 15, with the most common pattern being the presence of 2 chromosomes bearing a 5S rDNA cluster. Regarding 18S rDNA mapping, the number of sites ranged from 2 to 6, with the most common pattern being the presence of 2 sites per diploid genome. Furthermore, searching the Oreochromis niloticus genome database led to the identification of a total of 59 copies of 5S rRNA and 38 copies of 18S rRNA genes that were distributed in several genomic scaffolds. The rRNA genes were frequently flanked by transposable elements (TEs) and spread throughout the genome, complementing the FISH analysis that detect only clustered copies of rRNA genes. Conclusions The organization of rRNA gene clusters seems to reflect their intense and particular evolutionary pathway and not the evolutionary history of the associated taxa. The possible role of TEs as one source of rRNA gene movement, that could generates the spreading of ribosomal clusters/copies, is discussed. The present paper reinforces the notion that the integration of cytogenetic data and genomic analysis provides a more complete picture for understanding the organization of repeated sequences in the genome.
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