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Khensuwan S, de Menezes Cavalcante Sassi F, Rosa de Moraes RL, Rab P, Liehr T, Supiwong W, Seetapan K, Tanomtong A, Tantisuwichwong N, Arunsang S, Buasriyot P, Tongnunui S, Cioffi MDB. Chromosomes of Asian cyprinid fishes: Novel insight into the chromosomal evolution of Labeoninae (Teleostei, Cyprinidae). PLoS One 2024; 19:e0292689. [PMID: 38324533 PMCID: PMC10849230 DOI: 10.1371/journal.pone.0292689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/26/2023] [Indexed: 02/09/2024] Open
Abstract
The Labeoninae subfamily is a highly diversified but demonstrably monophyletic lineage of cyprinid fishes comprising five tribes and six incertae sedis genera. This widely distributed assemblage contains some 48 genera and around 480 recognized species distributed in freshwaters of Africa and Asia. In this study, the karyotypes and other chromosomal properties of five Labeoninae species found in Thailand Labeo chrysophekadion (Labeonini) and Epalzeorhynchos bicolor, Epalzeorhynchos munense, Henicorhynchus siamensis, Thynnichthys thynnoides (´Osteochilini´) were examined using conventional and molecular cytogenetic protocols. Our results confirmed a diploid chromosome number (2n) invariably 2n = 50, but the ratio of uni- and bi-armed chromosomes was highly variable among their karyotypes, indicating extensive structural chromosomal rearrangements. Karyotype of L. chrysophekadion contained 10m+6sm+20st+14a, 32m+10sm+8st for H. siamensis, 20m+12sm+10st+8a in E. bicolor, 20m+8sm+8st+14a in E. munense, and 18m+24sm+8st in T. thynnoides. Except for H. siamensis, which had four sites of 5S rDNA sites, other species under study had only one chromosome pair with those sites. In contrast, only one pair containing 18S rDNA sites were found in the karyotypes of three species, whereas two sites were found in that of E. bicolor. These cytogenetic patterns indicated that the cytogenomic divergence patterns of these labeonine species largely corresponded to the inferred phylogenetic tree. In spite of the 2n stability, diverse patterns of rDNA and microsatellite distribution as well as their various karyotype structures demonstrated significant evolutionary differentiation of Labeoninae genomes as exemplified in examined species. Labeoninae offers a traditional point of view on the evolutionary forces fostering biological diversity, and the recent findings add new pieces to comprehend the function of structural chromosomal rearrangements in adaption and speciation.
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Affiliation(s)
- Sudarat Khensuwan
- Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen, Thailand
| | | | - Renata Luiza Rosa de Moraes
- Departamento de Genética e Evolução, Laboratório de Citogenética de Peixes, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Petr Rab
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, Czech Academy of Sciences, Rumburská, Liběchov, Czech Republic
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | - Weerayuth Supiwong
- Faculty of Interdisciplinary Studies, Khon Kaen University, Nong Khai Campus, Muang, Nong Khai, Thailand
| | - Kriengkrai Seetapan
- School of Agriculture and Natural Resources, University of Phayao, Tumbol Maeka, Muang, Phayao, Thailand
| | - Alongklod Tanomtong
- Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen, Thailand
| | | | - Satit Arunsang
- Program in Animal Science, Faculty of Agricultural Technology and Agro-Industry, Rajamangala University of Technology Suvarnabhumi, Phra Nakhon Si Ayutthaya, Ayutthaya, Thailand
| | - Phichaya Buasriyot
- Faculty of Science and Technology, Rajamangala University of Technology Suvarnabhumi, Mueang Nonthaburi, Nonthaburi, Thailand
| | - Sampun Tongnunui
- Department of Conservation Biology, Mahidol University, Kanchanburi Campus, Sai Yok, Kanchanaburi Province, Thailand
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Laboratório de Citogenética de Peixes, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
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2
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Khensuwan S, Sassi FDMC, Moraes RLR, Jantarat S, Seetapan K, Phintong K, Thongnetr W, Kaewsri S, Jumrusthanasan S, Supiwong W, Rab P, Tanomtong A, Liehr T, Cioffi MB. Chromosomes of Asian Cyprinid Fishes: Genomic Differences in Conserved Karyotypes of 'Poropuntiinae' (Teleostei, Cyprinidae). Animals (Basel) 2023; 13:ani13081415. [PMID: 37106978 PMCID: PMC10135121 DOI: 10.3390/ani13081415] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/13/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
The representatives of cyprinid lineage 'Poropuntiinae' with 16 recognized genera and around 100 species form a significant part of Southeast Asian ichthyofauna. Cytogenetics are valuable when studying fish evolution, especially the dynamics of repetitive DNAs, such as ribosomal DNAs (5S and 18S) and microsatellites, that can vary between species. Here, karyotypes of seven 'poropuntiin' species, namely Cosmochilus harmandi, Cyclocheilichthys apogon, Hypsibarbus malcomi, H. wetmorei, Mystacoleucus chilopterus, M. ectypus, and Puntioplties proctozysron occurring in Thailand were examined using conventional and molecular cytogenetic protocols. Variable numbers of uni- and bi-armed chromosomes indicated widespread chromosome rearrangements with a stable diploid chromosome number (2n) of 50. Examination with fluorescence in situ hybridization using major and minor ribosomal probes showed that Cosmochilus harmandi, Cyclocheilichthys apogon, and Puntioplites proctozystron all had one chromosomal pair with 5S rDNA sites. However, more than two sites were found in Hypsibarbus malcolmi, H. wetmorei, Mystacoleucus chilopterus, and M. ectypus. The number of chromosomes with 18S rDNA sites varied amongst their karyotypes from one to three; additionally, comparative genomic hybridization and microsatellite patterns varied among species. Our results reinforce the trend of chromosomal evolution in cyprinifom fishes, with major chromosomal rearrangements, while conserving their 2n.
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Affiliation(s)
- Sudarat Khensuwan
- Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen 40002, Thailand
| | - Francisco de M C Sassi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos 13565-905, Brazil
| | - Renata L R Moraes
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos 13565-905, Brazil
| | - Sitthisak Jantarat
- Department of Science, Faculty of Science and Technology, Prince of Songkla University, Pattani 94000, Thailand
| | - Kriengkrai Seetapan
- School of Agriculture and Natural Resources, University of Phayao, Tumbol Maeka, Muang, Phayao 56000, Thailand
| | - Krit Phintong
- Department of Fundamental Science, Faculty of Science and Technology, Surindra Rajabhat University, Muang, Surin 32000, Thailand
| | - Weera Thongnetr
- Division of Biology, Department of Science, Faculty of Science and Technology, Rajamangala University of Technology Krungthep, Bangkok 10120, Thailand
| | - Sarawut Kaewsri
- Program in Biology, Faculty of Science, Buriram Rajabhat University, Muang, Buriram 31000, Thailand
| | - Sarun Jumrusthanasan
- Program in Biology, Faculty of Science, Buriram Rajabhat University, Muang, Buriram 31000, Thailand
| | - Weerayuth Supiwong
- Faculty of Applied Science and Engineering, Khon Kaen University, Nong Khai Campus, Muang, Nong Khai 43000, Thailand
| | - Petr Rab
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Alongklod Tanomtong
- Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen 40002, Thailand
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, 07747 Jena, Germany
| | - Marcelo B Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos 13565-905, Brazil
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3
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Prazdnikov DV. Chromosome complements of Channalucius and C.striata from Phu Quoc Island and karyotypic evolution in snakehead fishes (Actinopterygii, Channidae). COMPARATIVE CYTOGENETICS 2023; 17:1-12. [PMID: 36761446 PMCID: PMC9836404 DOI: 10.3897/compcytogen.v17.i1.94943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
Snakehead fishes of the family Channidae are obligatory air-breathers freshwater predators, the vast majority of which belong to the genus Channa Scopoli, 1777. Channa species are characterized by high karyotypic diversity due to various types of chromosomal rearrangements. It is assumed that, in addition to the lifestyle, fragmentation and isolation of snakehead populations contribute to an increase in karyotypic diversity. However, the chromosome complements of many isolated populations of widespread Channa species remain unknown, and the direction of karyotype transformations is poorly understood. This paper describes the previously unstudied karyotypes of Channalucius (Cuvier, 1831) and C.striata (Bloch, 1793) from Phu Quoc Island and analyzes the trends of karyotypic evolution in the genus Channa. In C.lucius, the karyotypes are differed in the number of chromosome arms (2n = 48, NF = 50 and 51), while in C.striata, the karyotypes are differed in the diploid chromosome number (2n = 44 and 43, NF = 48). A comparative cytogenetic analysis showed that the main trend of karyotypic evolution of Channa species is associated with a decrease in the number of chromosomes and an increase in the number of chromosome arms, mainly due to fusions and pericentric inversions. The data obtained support the assumption that fragmentation and isolation of populations, especially of continental islands, contribute to the karyotypic diversification of snakeheads and are of interest for further cytogenetic studies of Channidae.
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Affiliation(s)
- Denis V Prazdnikov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky pr. 33, Moscow, 119071, Russia Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Moscow Russia
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de Sousa RPC, Vasconcelos CP, Rosário NFD, Oliveira-Filho ABD, de Oliveira EHC, de Bello Cioffi M, Vallinoto M, Silva-Oliveira GC. Evolutionary Dynamics of Two Classes of Repetitive DNA in the Genomes of Two Species of Elopiformes (Teleostei, Elopomorpha). Zebrafish 2022; 19:24-31. [PMID: 35171711 DOI: 10.1089/zeb.2021.0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The order Elopiformes includes fish species of medium to large size with a circumglobal distribution, in both the open sea, coastal, and estuarine waters. The Elopiformes are considered an excellent model for evolutionary studies due to their ample adaptive capacity, which allow them to exploit a range of different ecological niches. In this study, we analyzed the karyotype structure and distribution of two classes of repetitive DNA (microsatellites and transposable elements) in two Elopiformes species (Elops smithi and Megalops atlanticus). The results showed that the microsatellite sequences had a very similar distribution in these species, primarily associated to heterochromatin (centromeres and telomeres), suggesting these sequences contribute to the chromosome structure. In contrast, specific signals detected throughout the euchromatic regions indicate that some of these sequences may play a role in the regulation of gene expression. By contrast, the transposable elements presented a distinct distribution in the two species, pointing to a possible interspecific difference in the function of these sequences in the genomes of the two species. Therefore, the comparative genome mapping provides new insights into the structure and organization of these repetitive sequences in the Elopiformes genome.
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Affiliation(s)
- Rodrigo Petry Corrêa de Sousa
- Instituto de Estudos Costeiros, Universidade Federal do Pará, Laboratório de Evolução, Bragança, Brazil.,Instituto de Ciências Biológicas and Universidade Federal do Pará, Belém, Brazil
| | | | - Nayara Furtado do Rosário
- Instituto de Estudos Costeiros, Universidade Federal do Pará, Laboratório de Evolução, Bragança, Brazil
| | | | - Edivaldo Herculano Corrêa de Oliveira
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil.,Laboratório de Culturas de Células e Citogenética, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Marcelo de Bello Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Evolução e Genética, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Marcelo Vallinoto
- Instituto de Estudos Costeiros, Universidade Federal do Pará, Laboratório de Evolução, Bragança, Brazil.,Research Center in Biodiversity and Genetic Resources, Associated Laboratory, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
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5
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Comparative cytogenomic analysis of Cardinal fishes (Perciformes, Apogonidae) from Thailand. THE NUCLEUS 2021. [DOI: 10.1007/s13237-021-00352-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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6
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Yeesin P, Buasriyot P, Ditcharoen S, Chaiyasan P, Suwannapoom C, Juntaree S, Jantarat S, Talumphai S, Cioffi MDB, Liehr T, Tanomtong A, Supiwong W. Comparative study of four Mystus species (Bagridae, Siluriformes) from Thailand: insights into their karyotypic diversity. COMPARATIVE CYTOGENETICS 2021; 15:119-136. [PMID: 33959235 PMCID: PMC8093182 DOI: 10.3897/compcytogen.v15i2.60649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/21/2021] [Indexed: 06/12/2023]
Abstract
Karyotypes of four catfishes of the genus Mystus Scopoli, 1777 (family Bagridae), M. atrifasciatus Fowler, 1937, M. mysticetus Roberts, 1992, M. singaringan (Bleeker, 1846) and M. wolffii (Bleeker, 1851), were analysed by conventional and Ag-NOR banding as well as fluorescence in situ hybridization (FISH) techniques. Microsatellite d(GC)15, d(CAA)10, d(CAT)10 and d(GAA)10 repeat probes were applied in FISH. The obtained data revealed that the four studied species have different chromosome complements. The diploid chromosome numbers (2n) and the fundamental numbers (NF) range between 52 and 102, 54 and 104, 56 and 98, or 58 and 108 in M. mysticetus, M. atrifasciatus, M. singaringan or M. wolffii, respectively. Karyotype formulae of M. mysticetus, M. atrifasciatus, M. singaringan and M. wolffii are 24m+26sm+4a, 26m+24sm+2a, 24m+18sm+14a and 30m+22sm+6a, respectively. A single pair of NORs was identified adjacent to the telomeres of the short arm of chromosome pairs 3 (metacentric) in M. atrifasciatus, 20 (submetacentric) in M. mysticetus, 15 (submetacentric) in M. singaringan, and 5 (metacentric) in M. wolffii. The d(GC)15, d(CAA)10, d(CAT)10 and d(GAA)10 repeats were abundantly distributed in species-specific patterns. Overall, we present a comparison of cytogenetic and molecular cytogenetic patterns of four species from genus Mystus providing insights into their karyotype diversity in the genus.
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Affiliation(s)
- Pun Yeesin
- Department of Technology and Industries, Faculty of Science and Technology, Prince of Songkla University, Pattani Campus, Muang, Pattani 94000, Thailand
| | - Phichaya Buasriyot
- Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen 40002, Thailand
| | - Sukhonthip Ditcharoen
- Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen 40002, Thailand
| | - Patcharaporn Chaiyasan
- Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen 40002, Thailand
| | - Chatmongkon Suwannapoom
- Department of Fishery, School of Agriculture and Natural Resources, University of Phayao, Muang, Phayao 56000, Thailand
| | - Sippakorn Juntaree
- Applied Science Program, Faculty of Interdisciplinary Studies, Nong Khai Campus, Khon Kaen University, Muang, Nong Khai 43000, Thailand
| | - Sitthisak Jantarat
- Department of Science, Faculty of Science and Technology, Prince of Songkla University, Pattani Campus, Mueng, Pattani 94000, Thailand
| | - Sucheela Talumphai
- Major Biology, Department of Science and Technology, Faculty of Liberal Arts and Science, Roi Et Rajabhat University, Roi Et 45120, Thailand
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Am Klinikum 1, D-07747, Jena, Germany
| | - Alongklod Tanomtong
- Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen 40002, Thailand
| | - Weerayuth Supiwong
- Applied Science Program, Faculty of Interdisciplinary Studies, Nong Khai Campus, Khon Kaen University, Muang, Nong Khai 43000, Thailand
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7
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Zhou J, Wang S, Yu L, Li N, Li S, Zhang Y, Qin R, Gao W, Deng C. Cloning and physical localization of male-biased repetitive DNA sequences in Spinacia oleracea (Amaranthaceae). COMPARATIVE CYTOGENETICS 2021; 15:101-118. [PMID: 33959234 PMCID: PMC8087614 DOI: 10.3897/compcytogen.v15i2.63061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/28/2021] [Indexed: 06/12/2023]
Abstract
Spinach (Spinacia oleracea Linnaeus, 1753) is an ideal material for studying molecular mechanisms of early-stage sex chromosome evolution in dioecious plants. Degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR) technique facilitates the retrotransposon-relevant studies by enriching specific repetitive DNA sequences from a micro-dissected single chromosome. We conducted genomic subtractive hybridization to screen sex-biased DNA sequences by using the DOP-PCR amplification products of micro-dissected spinach Y chromosome. The screening yielded 55 male-biased DNA sequences with 30 576 bp in length, of which, 32 DNA sequences (12 049 bp) contained repeat DNA sequences, including LTR/Copia, LTR/Gypsy, simple repeats, and DNA/CMC-EnSpm. Among these repetitive DNA sequences, four DNA sequences that contained a fragment of Ty3-gypsy retrotransposons (SP73, SP75, SP76, and SP77) were selected as fluorescence probes to hybridization on male and female spinach karyotypes. Fluorescence in situ hybridization (FISH) signals of SP73 and SP75 were captured mostly on the centromeres and their surrounding area for each homolog. Hybridization signals primarily appeared near the putative centromeres for each homologous chromosome pair by using SP76 and SP77 probes for FISH, and sporadic signals existed on the long arms. Results can be served as a basis to study the function of repetitive DNA sequences in sex chromosome evolution in spinach.
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Affiliation(s)
- Jian Zhou
- College of Life Sciences, Henan Normal University, Xinxiang 453007, ChinaHenan Normal UniversityXinxiangChina
| | - Shaojing Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, ChinaHenan Normal UniversityXinxiangChina
| | - Li’ang Yu
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USAUniversity of Illinois at Urbana-ChampaignUrbanaUnited States of America
| | - Ning Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, ChinaHenan Normal UniversityXinxiangChina
| | - Shufen Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, ChinaHenan Normal UniversityXinxiangChina
| | - Yulan Zhang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, ChinaHenan Normal UniversityXinxiangChina
| | - Ruiyun Qin
- College of Life Sciences, Henan Normal University, Xinxiang 453007, ChinaHenan Normal UniversityXinxiangChina
| | - Wujun Gao
- College of Life Sciences, Henan Normal University, Xinxiang 453007, ChinaHenan Normal UniversityXinxiangChina
| | - Chuanliang Deng
- College of Life Sciences, Henan Normal University, Xinxiang 453007, ChinaHenan Normal UniversityXinxiangChina
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8
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Sproul JS, Barton LM, Maddison DR. Repetitive DNA Profiles Reveal Evidence of Rapid Genome Evolution and Reflect Species Boundaries in Ground Beetles. Syst Biol 2021; 69:1137-1148. [PMID: 32267949 DOI: 10.1093/sysbio/syaa030] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 03/16/2020] [Accepted: 03/30/2020] [Indexed: 12/11/2022] Open
Abstract
Genome architecture is a complex, multidimensional property of an organism defined by the content and spatial organization of the genome's component parts. Comparative study of entire genome architecture in model organisms is shedding light on mechanisms underlying genome regulation, evolution, and diversification, but such studies require costly analytical approaches which make extensive comparative study impractical for most groups. However, lower-cost methods that measure a single architectural component (e.g., distribution of one class of repeats) have potential as a new data source for evolutionary studies insofar as that measure correlates with more complex biological phenomena, and for which it could serve as part of an explanatory framework. We investigated copy number variation (CNV) profiles in ribosomal DNA (rDNA) as a simple measure reflecting the distribution of rDNA subcomponents across the genome. We find that signatures present in rDNA CNV profiles strongly correlate with species boundaries in the breve species group of Bembidion, and vary across broader taxonomic sampling in Bembidion subgenus Plataphus. Profiles of several species show evidence of re-patterning of rDNA-like sequences throughout the genome, revealing evidence of rapid genome evolution (including among sister pairs) not evident from analysis of traditional data sources such as multigene data sets. Major re-patterning of rDNA-like sequences has occurred frequently within the evolutionary history of Plataphus. We confirm that CNV profiles represent an aspect of genomic architecture (i.e., the linear distribution of rDNA components across the genome) via fluorescence in-situ hybridization. In at least one species, novel rDNA-like elements are spread throughout all chromosomes. We discuss the potential of copy number profiles of rDNA, or other repeats, as a low-cost tool for incorporating signal of genomic architecture variation in studies of species delimitation and genome evolution. [Bembidion; Carabidae; copy number variation profiles; rapid genome evolution; ribosomal DNA; species delimitation.].
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Affiliation(s)
- John S Sproul
- Department of Integrative Biology, Oregon State University, 3029 Cordley Hall, Corvallis, OR 97331, USA.,Department of Biology, University of Rochester, 402 Hutchison Hall, PO Box 270211, Rochester, NY 14627, USA
| | - Lindsey M Barton
- Department of Integrative Biology, Oregon State University, 3029 Cordley Hall, Corvallis, OR 97331, USA
| | - David R Maddison
- Department of Integrative Biology, Oregon State University, 3029 Cordley Hall, Corvallis, OR 97331, USA
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9
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Ditcharoen S, Sassi FDMC, Bertollo LAC, Molina WF, Liehr T, Saenjundaeng P, Tanomtong A, Supiwong W, Suwannapoom C, Cioffi MDB. Comparative chromosomal mapping of microsatellite repeats reveals divergent patterns of accumulation in 12 Siluridae (Teleostei: Siluriformes) species. Genet Mol Biol 2020; 43:e20200091. [PMID: 33156890 PMCID: PMC7654372 DOI: 10.1590/1678-4685-gmb-2020-0091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 09/03/2020] [Indexed: 01/08/2023] Open
Abstract
The freshwater family Siluridae occurs in Eurasia and is especially speciose in South and Southeast Asia, representing an important aquaculture and fishery targets. However, despite the restricted cytogenetic data, a high diploid number variation (from 2n=40 to 92) characterizes this fish group. Considering the large genomic divergence among its species, silurid genomes have experienced an enormous diversification throughout their evolutionary history. Here, we aim to investigate the chromosomal distribution of several microsatellite repeats in 12 Siluridae species and infer about their possible roles in the karyotype evolution that occurred in this group. Our results indicate divergent patterns of microsatellite distribution and accumulation among the analyzed species. Indeed, they are especially present in significant chromosome locations, such as the centromeric and telomeric regions, precisely the ones associated with several kinds of chromosomal rearrangements. Our data provide pieces of evidence that repetitive DNAs played a direct role in fostering the chromosomal differentiation and biodiversity in this fish family.
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Affiliation(s)
- Sukhonthip Ditcharoen
- Khon Kaen UniversityKhon Kaen UniversityDepartment of BiologyMuangKhon KaenThailandKhon Kaen University, Faculty of Science, Department of
Biology, Toxic Substances in Livestock and Aquatic Animals Research Group, Muang, Khon Kaen,
Thailand.
| | - Francisco de Menezes Cavalcante Sassi
- Universidade Federal de São Carlos
(UFSCar)Universidade Federal de São Carlos (UFSCar)Departamento de Genética e
EvoluçãoSão CarlosSPBrazilUniversidade Federal de São Carlos (UFSCar),
Departamento de Genética e Evolução, São Carlos, SP,
Brazil.
| | - Luiz Antonio Carlos Bertollo
- Universidade Federal de São Carlos
(UFSCar)Universidade Federal de São Carlos (UFSCar)Departamento de Genética e
EvoluçãoSão CarlosSPBrazilUniversidade Federal de São Carlos (UFSCar),
Departamento de Genética e Evolução, São Carlos, SP,
Brazil.
| | - Wagner Franco Molina
- Universidade Federal do Rio Grande do NorteUniversidade Federal do Rio Grande do NorteDepartamento de Biologia Celular e GenéticaNatalRNBrazilUniversidade Federal do Rio Grande do Norte (UFRN), Centro de
Biociências, Departamento de Biologia Celular e Genética, Natal, RN,
Brazil.
| | - Thomas Liehr
- University Hospital JenaUniversity Hospital JenaInstitute of Human GeneticsJenaGermanyUniversity Hospital Jena, Institute of Human Genetics, Jena,
Germany.
| | - Pasakorn Saenjundaeng
- Khon Kaen UniversityKhon Kaen UniversityFaculty of Applied Science and EngineeringMuangNong KhaiThailandKhon Kaen University, Faculty of Applied Science and
Engineering, Nong Khai Campus, Muang, Nong Khai, Thailand.
| | - Alongklod Tanomtong
- Khon Kaen UniversityKhon Kaen UniversityDepartment of BiologyMuangKhon KaenThailandKhon Kaen University, Faculty of Science, Department of
Biology, Toxic Substances in Livestock and Aquatic Animals Research Group, Muang, Khon Kaen,
Thailand.
| | - Weerayuth Supiwong
- Khon Kaen UniversityKhon Kaen UniversityFaculty of Applied Science and EngineeringMuangNong KhaiThailandKhon Kaen University, Faculty of Applied Science and
Engineering, Nong Khai Campus, Muang, Nong Khai, Thailand.
| | - Chatmongkon Suwannapoom
- University of PhayaoUniversity of PhayaoDepartment of FisherySchool of Agriculture and Natural ResourcesMuang PhayaoThailandUniversity of Phayao, School of Agriculture and Natural
Resources, Department of Fishery, Muang Phayao, Thailand.
| | - Marcelo de Bello Cioffi
- Universidade Federal de São Carlos
(UFSCar)Universidade Federal de São Carlos (UFSCar)Departamento de Genética e
EvoluçãoSão CarlosSPBrazilUniversidade Federal de São Carlos (UFSCar),
Departamento de Genética e Evolução, São Carlos, SP,
Brazil.
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10
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Saenjundaeng P, Supiwong W, Sassi FMC, Bertollo LAC, Rab P, Kretschmer R, Tanomtong A, Suwannapoom C, Reungsing M, Cioffi MDB. Chromosomes of Asian cyprinid fishes: Variable karyotype patterns and evolutionary trends in the genus Osteochilus (Cyprinidae, Labeoninae, "Osteochilini"). Genet Mol Biol 2020; 43:e20200195. [PMID: 33156892 PMCID: PMC7783954 DOI: 10.1590/1678-4685-gmb-2020-0195] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/29/2020] [Indexed: 11/22/2022] Open
Abstract
The Cyprinidae family is a highly diversified but demonstrably monophyletic lineage of cypriniform fishes. Among them, the genus Osteochilus contains 35 recognized valid species distributed from India, throughout Myanmar, Laos, Thailand, Malaysia, Indonesian archipelago to southern China. In this study, karyotypes and other chromosomal characteristics of five Osteochilus species occurring in Thailand, namely O. lini, O. melanopleura, O. microcephalus, O. vittatus and O. waandersii were examined using conventional and molecular cytogenetic protocols. Our results showed they possessed diploid chromosome number (2n) invariably 2n = 50, but the ratio of uni- and bi-armed chromosomes was highly variable among their karyotypes, indicating extensive chromosomal rearrangements. Only one chromosome pair bearing 5S rDNA sites occurred in most species, except O. melanopleura, where two sites were detected. In contrast, only one chromosomal pair bearing 18S rDNA sites were observed among their karyotypes, but in different positions. These cytogenetic patterns indicated that the cytogenomic divergence patterns of these Osteochilus species were largely corresponding to the inferred phylogenetic tree. Similarly, different patterns of the distributions of rDNAs and microsatellites across genomes of examined species as well as their different karyotype structures indicated significant evolutionary differentiation of Osteochilus genomes.
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Affiliation(s)
- Pasakorn Saenjundaeng
- Faculty of Interdisciplinary Studies, Khon Kaen University, Nong
Khai Campus, Nong Khai 43000, Thailand
| | - Weerayuth Supiwong
- Faculty of Interdisciplinary Studies, Khon Kaen University, Nong
Khai Campus, Nong Khai 43000, Thailand
| | - Francisco M. C. Sassi
- Universidade Federal de São Carlos, Departamento de Genética e
Evolução, São Carlos, SP, Brazil
| | - Luiz A. C. Bertollo
- Universidade Federal de São Carlos, Departamento de Genética e
Evolução, São Carlos, SP, Brazil
| | - Petr Rab
- Czech Academy of Sciences, Institute of Animal Physiology and
Genetics, Laboratory of Fish Genetics, Rumburská 89, Libechov 277 21, Czech
Republic
| | - Rafael Kretschmer
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação
em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Alongklod Tanomtong
- KhonKaen University, Faculty of Science, Department of Biology,
Muang, KhonKaen 40002, Thailand
| | - Chatmongkon Suwannapoom
- University of Phayao, School of Agriculture and Natural Resources,
Department of Fishery, Muang, Phayao 56000, Thailand
| | - Montri Reungsing
- Rajamangala University of Technology Tawan-ok, Faculty of Science
and Technology, Department of Biotechnology, Siracha, Chonburi 20110, Thailand
| | - Marcelo de Bello Cioffi
- Universidade Federal de São Carlos, Departamento de Genética e
Evolução, São Carlos, SP, Brazil
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11
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Carducci F, Barucca M, Canapa A, Carotti E, Biscotti MA. Mobile Elements in Ray-Finned Fish Genomes. Life (Basel) 2020; 10:E221. [PMID: 32992841 PMCID: PMC7599744 DOI: 10.3390/life10100221] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/18/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022] Open
Abstract
Ray-finned fishes (Actinopterygii) are a very diverse group of vertebrates, encompassing species adapted to live in freshwater and marine environments, from the deep sea to high mountain streams. Genome sequencing offers a genetic resource for investigating the molecular bases of this phenotypic diversity and these adaptations to various habitats. The wide range of genome sizes observed in fishes is due to the role of transposable elements (TEs), which are powerful drivers of species diversity. Analyses performed to date provide evidence that class II DNA transposons are the most abundant component in most fish genomes and that compared to other vertebrate genomes, many TE superfamilies are present in actinopterygians. Moreover, specific TEs have been reported in ray-finned fishes as a possible result of an intricate relationship between TE evolution and the environment. The data summarized here underline the biological interest in Actinopterygii as a model group to investigate the mechanisms responsible for the high biodiversity observed in this taxon.
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Affiliation(s)
| | | | | | | | - Maria Assunta Biscotti
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy; (F.C.); (M.B.); (A.C.); (E.C.)
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12
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Grabowska AI, Boroń A, Kirtiklis L, Spóz A, Juchno D, Kotusz J. Chromosomal inheritance of parental rDNAs distribution pattern detected by FISH in diploid F 1 hybrid progeny of Cobitis (Teleostei, Cobitidae) species has non-Mendelian character. JOURNAL OF FISH BIOLOGY 2020; 96:261-273. [PMID: 31755097 DOI: 10.1111/jfb.14216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/21/2019] [Indexed: 06/10/2023]
Abstract
This study was conducted to describe the major and the minor rDNA chromosome distribution in the spined loach Cobitis taenia (2n = 48) and the Danubian loach Cobitis elongatoides (2n = 50), and their laboratory-produced diploid reciprocal F1 hybrid progeny. It was tested by fluorescence in situ hybridisation (FISH) whether the number of 28s and 5s rDNA sites in the karyotypes of diploid hybrids corresponds to the expectations resulting from Mendelian ratio and if nucleolar organiser regions (NOR)were inherited from both parents or nucleolar dominance can be observed in the induced F1 hybrid progeny. Ten (females) or twelve (males) 28s rDNA loci were located in nine uniarm chromosomes of C. taenia. Two of such loci terminally bounded on one acrocentric chromosome were unique and indicated as specific for this species. Large 5s rDNA clusters were located on two acrocentric chromosomes. In C. elongatoides of both sexes, six NOR sites in terminal regions on six meta-submetacentric chromosomes and two 5s rDNA sites on large submetacentrics were detected. The F1 hybrid progeny (2n = 49) was characterised by the intermediate karyotype with the sites of ribosome synthesis on chromosomes inherited from both parents without showing nucleolar dominance. 5s rDNA sites were detected on large submetacentric and two acrocentric chromosomes. The observed number of both 28s and 5s rDNAs signals in F1 diploid Cobitis hybrids was disproportionally inherited from the two parental species, showing inconsistency with the Mendelian ratios. The presented rDNA patterns indicate some marker chromosomes that allow the species of the parental male and female to be recognised in hybrid progeny. The 5s rDNA was found to be a particularly effective diagnostic marker of C. elongatoides to partially discern genomic composition of diploid Cobitis hybrids and presumably allopolyploids resulting from their backcrossing with one of the parental species. Thus, the current study provides insight into the extent of rDNA heredity in Cobitis chromosomes and their cytotaxonomic character.
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Affiliation(s)
- Anna I Grabowska
- Department of Zoology, University of Warmia and Mazury, Olsztyn, Poland
| | - Alicja Boroń
- Department of Zoology, University of Warmia and Mazury, Olsztyn, Poland
| | - Lech Kirtiklis
- Department of Zoology, University of Warmia and Mazury, Olsztyn, Poland
| | - Aneta Spóz
- Department of Zoology, University of Warmia and Mazury, Olsztyn, Poland
| | - Dorota Juchno
- Department of Zoology, University of Warmia and Mazury, Olsztyn, Poland
| | - Jan Kotusz
- Museum of Natural History, University of Wroclaw, Wroclaw, Poland
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13
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Phimphan S, Chaiyasan P, Suwannapoom C, Reungsing M, Juntaree S, Tanomtong A, Supiwong W. Comparative karyotype study of three Cyprinids (Cyprinidae, Cyprininae) in Thailand by classical cytogenetic and FISH techniques. COMPARATIVE CYTOGENETICS 2020; 14:597-612. [PMID: 33384854 PMCID: PMC7772283 DOI: 10.3897/compcytogen.v14i4.54428] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 06/27/2020] [Indexed: 05/13/2023]
Abstract
Three species of ornamental fishes in the subfamily Cyprininae (family Cyprinidae) namely, Epalzeorhynchos frenatum (Fowler, 1934), Puntigrus partipentazona (Fowler, 1934), Scaphognathops bandanensis Boonyaratpalin et Srirungroj, 1971 were studied by classical cytogenetic and fluorescent in situ hybridization (FISH) techniques. Chromosomes were directly prepared from kidney tissues and stained by using conventional and Ag-NOR banding techniques. Microsatellite d(CA)15 and d(CGG)10 probes were hybridized to the chromosomes of three cyprinids. The results show that the three cyprinid species share the same diploid number as 2n=50 but there are differences in the fundamental number (NF) and karyotypes i.e. E. frenatum: NF = 78, 18m+10sm+10st+12a; P. partipentazona: NF = 80, 6m+24sm+14st+6a; S. bandanensis: NF = 66, 4m+12sm+34a. NOR positive masks were observed at the regions adjacent to the telomere of the short arm of the chromosome pairs 10 (submetacentric) and 1 (metacentric) in E. frenatum and P. partipentazona, respectively whereas those were revealed at telomeric regions of the long arm of the chromosome pair 9 (acrocentric) in S. bandanensis. The mapping of d(CA)15 and d(CGG)10 microsatellites shown that hybridization signals are abundantly distributed in telomeric regions of several pairs except d(CA)15 repeats in S. bandanensis, which are distributed throughout all chromosomes and d(CGG)10 repeats in P. partipentazona display the high accumulation only in the first chromosome pair.
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Affiliation(s)
- Sumalee Phimphan
- Biology program, Faculty of Science and Technology, Phetchabun Rajabhat University, Phetchabun 67000, ThailandPhetchabun Rajabhat UniversityPhetchabunThailand
| | - Patcharaporn Chaiyasan
- Toxic Substances in Livestock and Aquatic Animals Research Group, Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen 40002, ThailandKhon Kaen UniversityKhon KaenThailand
| | - Chatmongkon Suwannapoom
- Department of Fishery, School of Agriculture and Natural Resources, University of Phayao, Muang, Phayao 56000, ThailandUniversity of PhayaoPhayaoThailand
| | - Montri Reungsing
- Department of Biotechnology, Faculty of Science and Technology, Rajamangala University of Technology Tawan-ok, Sri Racha, Chon Buri 20110, ThailandRajamangala UniversityChon BuriThailand
| | - Sippakorn Juntaree
- Faculty of Interdisciplinary Studies, Nong Khai Campus, Khon Kaen, University, Muang, Nong Khai 43000, ThailandKhon Kaen UniversityNong KhaiThailand
| | - Alongklod Tanomtong
- Toxic Substances in Livestock and Aquatic Animals Research Group, Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen 40002, ThailandKhon Kaen UniversityKhon KaenThailand
| | - Weerayuth Supiwong
- Faculty of Interdisciplinary Studies, Nong Khai Campus, Khon Kaen, University, Muang, Nong Khai 43000, ThailandKhon Kaen UniversityNong KhaiThailand
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Oliveira EAD, Sassi FDMC, Perez MF, Bertollo LAC, Ráb P, Ezaz T, Hatanaka T, Viana PF, Feldberg E, Oliveira EHCD, Cioffi MDB. Comparative cytogenetic survey of the giant bonytongue Arapaima fish (Osteoglossiformes: Arapaimidae), across different Amazonian and Tocantins/Araguaia River basins. NEOTROPICAL ICHTHYOLOGY 2020. [DOI: 10.1590/1982-0224-2020-0055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract The South American giant fishes of the genus Arapaima, commonly known as pirarucu, are one of the most iconic among Osteoglossiformes. Previously cytogenetic studies have identified their karyotype characteristics; however, characterization of cytotaxonomic differentiation across their distribution range remains unknown. In this study, we compared chromosomal characteristics using conventional and molecular cytogenetic protocols in pirarucu populations from the Amazon and Tocantins-Araguaia river basins to verify if there is differentiation among representatives of this genus. Our data revealed that individuals from all populations present the same diploid chromosome number 2n=56 and karyotype composed of 14 pairs of meta- to submetacentric and 14 pairs of subtelo- to acrocentric chromosomes. The minor and major rDNA sites are in separate chromosomal pairs, in which major rDNA sites corresponds to large heterochromatic blocks. Comparative genomic hybridizations (CGH) showed that the genome of these populations shared a great portion of repetitive elements, due to a lack of substantial specific signals. Our comparative cytogenetic data analysis of pirarucu suggested that, although significant genetic differences occur among populations, their general karyotype patterns remain conserved.
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Affiliation(s)
- Ezequiel A. de Oliveira
- Universidade Federal de São Carlos, Brazil; Secretaria de Estado de Educação de Mato Grosso, Brazil
| | | | | | | | - Petr Ráb
- Czech Academy of Sciences, Czech Republic
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15
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Toma GA, de Moraes RLR, Sassi FDMC, Bertollo LAC, de Oliveira EA, Rab P, Sember A, Liehr T, Hatanaka T, Viana PF, Marinho MMF, Feldberg E, Cioffi MDB. Cytogenetics of the small-sized fish, Copeina guttata (Characiformes, Lebiasinidae): Novel insights into the karyotype differentiation of the family. PLoS One 2019; 14:e0226746. [PMID: 31856256 PMCID: PMC6922430 DOI: 10.1371/journal.pone.0226746] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/04/2019] [Indexed: 11/19/2022] Open
Abstract
Lebiasinidae is a small fish family composed by miniature to small-sized fishes with few cytogenetic data (most of them limited to descriptions of diploid chromosome numbers), thus preventing any evolutionary comparative studies at the chromosomal level. In the present study, we are providing, the first cytogenetic data for the red spotted tetra, Copeina guttata, including the standard karyotype, C-banding, repetitive DNA mapping by fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH), providing chromosomal patterns and novel insights into the karyotype differentiation of the family. Males and females share diploid chromosome number 2n = 42 and karyotype composed of 2 metacentric (m), 4 submetacentric (sm) and 36 subtelocentric to acrocentric (st-a) chromosomes. Blocks of constitutive heterochromatin were observed in the centromeric and interstitial regions of several chromosomes, in addition to a remarkably large distal block, heteromorphic in size, which fully corresponded with the 18S rDNA sites in the fourth chromosomal pair. This overlap was confirmed by 5S/18S rDNA dual-color FISH. On the other hand, 5S rDNA clusters were situated in the long and short arms of the 2nd and 15th pairs, respectively. No sex-linked karyotype differences were revealed by male/female CGH experiments. The genomic probes from other two lebiasinid species, Lebiasina melanoguttata and Pyrrhulina brevis, showed positive hybridization signals only in the NOR region in the genome of C. guttata. We demonstrated that karyotype diversification in lebiasinids was accompanied by a series of structural and numeric chromosome rearrangements of different types, including particularly fusions and fissions.
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Affiliation(s)
- Gustavo Akira Toma
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Renata Luiza Rosa de Moraes
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | | | - Luiz Antonio Carlos Bertollo
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Ezequiel Aguiar de Oliveira
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
- Secretaria de Estado de Educação de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Petr Rab
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | - Terumi Hatanaka
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | | | | | - Eliana Feldberg
- Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Marcelo de Bello Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
- Institute of Human Genetics, University Hospital Jena, Jena, Germany
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16
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Ditcharoen S, Antonio Carlos Bertollo L, Ráb P, Hnátková E, Franco Molina W, Liehr T, Tanomtong A, Triantaphyllidis C, Ozouf-Costaz C, Tongnunui S, Pengseng P, Supiwong W, Aroutiounian R, de Bello Cioffi M. Genomic Organization of Repetitive DNA Elements and Extensive Karyotype Diversity of Silurid Catfishes (Teleostei: Siluriformes): A Comparative Cytogenetic Approach. Int J Mol Sci 2019; 20:E3545. [PMID: 31331072 PMCID: PMC6678683 DOI: 10.3390/ijms20143545] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 07/03/2019] [Accepted: 07/16/2019] [Indexed: 11/30/2022] Open
Abstract
The catfish family Siluridae contains 107 described species distributed in Asia, but with some distributed in Europe. In this study, karyotypes and other chromosomal characteristics of 15 species from eight genera were examined using conventional and molecular cytogenetic protocols. Our results showed the diploid number (2n) to be highly divergent among species, ranging from 2n = 40 to 92, with the modal frequency comprising 56 to 64 chromosomes. Accordingly, the ratio of uni- and bi-armed chromosomes is also highly variable, thus suggesting extensive chromosomal rearrangements. Only one chromosome pair bearing major rDNA sites occurs in most species, except for Wallago micropogon, Ompok siluroides, and Kryptoterus giminus with two; and Silurichthys phaiosoma with five such pairs. In contrast, chromosomes bearing 5S rDNA sites range from one to as high as nine pairs among the species. Comparative genomic hybridization (CGH) experiments evidenced large genomic divergence, even between congeneric species. As a whole, we conclude that karyotype features and chromosomal diversity of the silurid catfishes are unusually extensive, but parallel some other catfish lineages and primary freshwater fish groups, thus making silurids an important model for investigating the evolutionary dynamics of fish chromosomes.
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Affiliation(s)
- Sukhonthip Ditcharoen
- Toxic Substances in Livestock and Aquatic Animals Research Group, Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen 40002, Thailand
| | - Luiz Antonio Carlos Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov 277 21, Czech Republic
| | - Eva Hnátková
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Prague 165 00, Czech Republic
| | - Wagner Franco Molina
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN 59078970, Brazil
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Jena 07747, Germany
| | - Alongklod Tanomtong
- Toxic Substances in Livestock and Aquatic Animals Research Group, Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen 40002, Thailand
| | - Costas Triantaphyllidis
- Department of Genetics, Development and Molecular Biology, Faculty of Sciences, School of Biology, Aristotle University of Thessaloniki, University Campus, Thessaloniki 54124, Greece
| | - Catherine Ozouf-Costaz
- Laboratorie Evolution Paris Seine, Institut de Biologie Paris Seine (IBPS), Sorbonne Universités, Case 5, 7 Quai St Bernard, Paris, 75952 Paris CEDEX 05, France
| | - Sampan Tongnunui
- Department of Conservation Biology, Mahidol University, Kanchanaburi Campus, Sai Yok, Kanchanaburi Province 71150, Thailand
| | - Puan Pengseng
- School of Agricultural of Technology, Walailak University, Thasala, Nakhon Si Thammarat 80160, Thailand
| | - Weerayuth Supiwong
- Faculty of Applied Science and Engineering, Khon Kaen University, Nong Khai Campus, Muang, Nong Khai 43000, Thailand
| | - Rouben Aroutiounian
- Department of Genetics and Cytology, Yerevan State University, Yerevan 0025, Armenia
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil.
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17
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Liu Y, Song M, Luo W, Xia Y, Zeng X. Chromosomal Evolution in the Amolops mantzorum Species Group (Ranidae; Anura) Narrated by Repetitive DNAs. Cytogenet Genome Res 2019; 157:172-178. [PMID: 30955010 DOI: 10.1159/000499416] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2018] [Indexed: 11/19/2022] Open
Abstract
In an attempt to analyze the organization of repetitive DNAs in the amphibian genome, 7 microsatellite motifs and a 5S rDNA sequence were synthesized and mapped in the karyotypes of 5 Amolops species. The results revealed nonrandom distribution of the microsatellite repeats, usually in the heterochromatic regions, as found in other organisms. These microsatellite repeats showed rapid changes among Amolops species, documenting the recent evolutionary history within this lineage. In contrast, 5S rDNA was localized in chromosomes 5 of all species, suggesting that these chromosomes are homologous within the monophyletic clade. Furthermore, the heteromorphic X and Y sex chromosomes (chromosomes 5) of A.mantzorum, had identical patterns of 5S rDNA, indicating that the subtelocentric Y resulted from a pericentric inversion. Several microsatellite repeats were found in the heteromorphic sex chromosomes, verifying the association of repetitive DNAs with sex chromosome differentiation in A. mantzorum.
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18
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Supiwong W, Pinthong K, Seetapan K, Saenjundaeng P, Bertollo LAC, de Oliveira EA, Yano CF, Liehr T, Phimphan S, Tanomtong A, B Cioffi M. Karyotype diversity and evolutionary trends in the Asian swamp eel Monopterus albus (Synbranchiformes, Synbranchidae): a case of chromosomal speciation? BMC Evol Biol 2019; 19:73. [PMID: 30849933 PMCID: PMC6408769 DOI: 10.1186/s12862-019-1393-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 02/15/2019] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Synbranchidae or swamp eels are fishes belonging to the order Synbranchiformes that occur in both freshwater and occasionally in brackish. They are worldwide distributed in tropical and subtropical rivers of four different continents. A large degree of chromosomal variation has been found in this family, mainly through the use of conventional cytogenetic investigations. Inside this group, a still almost unexplored species under the cytogenetic point of view is the Asian swamp eel Monopterus albus, a widely distributed species throughout Asia. Here, we tested the hypothesis of chromosomal speciation, where a case of sympatric speciation may occur as the primary consequence of chromosomal rearrangements. We performed a comparative chromosomal analysis of M. albus from 22 different localities in Thailand, using distinct staining methods (C-banding, Ag-NO3, and Chromomycin A3), and FISH with repetitive DNA probes (5S rDNA, 18S rDNA, Rex1 element and microsatellite repeats). RESULTS This approach evidenced two contrasting karyotypes (named karyomorphs A and B) that varied concerning their 2n and repetitive DNAs distribution, where chromosomal fusions and pericentric inversions were involved in such differentiation. While the karyomorph A has 2n = 24 chromosomes, the karyomorph B has only 2n = 18, both with NF = 24. In addition, karyomorph A contains only acrocentric chromosomes, while karyomorph B contains three unique metacentric pairs. These features highlight that M. albus has already gone through a significant genomic divergence, and may include at least two cryptic species. CONCLUSIONS This marked chromosomal differentiation, likely linked to the lifestyle of these fishes, point to the occurrence of a chromosomal speciation scenario, in which fusions and inversions had a prominent role. This highlights the biodiversity of M. albus and justifies its taxonomic revision, since this nominal species may constitute a species complex.
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Affiliation(s)
- Weerayuth Supiwong
- Faculty of Applied Science and Engineering, Khon Kaen University, Nong Khai Campus, Muang, Nong Khai, 34000 Thailand
| | - Krit Pinthong
- Department of Fundamental Science, Faculty of Science and Technology, Surindra Rajabhat University, Muang, Surin, 32000 Thailand
| | - Kriengkrai Seetapan
- School of Agriculture and Natural Resources, University of Phayao, Tumbol Maeka, Muang, Phayao, 56000 Thailand
| | - Pasakorn Saenjundaeng
- Faculty of Applied Science and Engineering, Khon Kaen University, Nong Khai Campus, Muang, Nong Khai, 34000 Thailand
| | - Luiz A. C. Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo Brazil
| | - Ezequiel A. de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo Brazil
| | - Cassia F. Yano
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo Brazil
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Sumalee Phimphan
- Toxic Substances in Livestock and Aquatic Animals Research Group, Khon Kaen University, Muang, Khon Kaen, 40002 Thailand
| | - Alongklod Tanomtong
- Toxic Substances in Livestock and Aquatic Animals Research Group, Khon Kaen University, Muang, Khon Kaen, 40002 Thailand
| | - Marcelo B Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo Brazil
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
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Nirchio M, Gaviria JI, Siccha-Ramirez ZR, Oliveira C, Foresti F, Milana V, Rossi AR. Chromosomal polymorphism and molecular variability in the pearly razorfish Xyrichtys novacula (Labriformes, Labridae): taxonomic and biogeographic implications. Genetica 2019; 147:47-56. [PMID: 30673915 DOI: 10.1007/s10709-019-00051-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 01/09/2019] [Indexed: 01/28/2023]
Abstract
The pearly razorfish Xyrichtys novacula (Linnaeus, 1758) is a sedentary benthic species distributed in both sides of the Atlantic Ocean and in the Mediterranean Sea. Previous cytogenetic analysis reported different diploid numbers in samples from Italy, Venezuela and Brazil. This research aims to test the hypothesis that samples from American Atlantic coast and Mediterranean Sea belong to the same single evolutionary lineage, characterized by intra-specific chromosome polymorphism. To this purpose a cytogenetic and molecular (mitochondrial COI sequences) survey was undertaken. Results revealed the existence of three different pearly razorfish molecular lineages: one present in Mediterranean Sea and two in the central and south American area, which are characterized by different karyotypes. One of these lineages shows substantial intra-population chromosomal polymorphism (2n = 45-48) determined by Robertsonian fusions that produce large metacentric chromosomes. On the whole data suggest that specimens morphologically identified as X. novacula correspond to three cryptic species.
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Affiliation(s)
- Mauro Nirchio
- Escuela de Ciencias Aplicadas del Mar, Núcleo de Nueva Esparta, Universidad de Oriente, Apartado 174, Porlamar, Isla de Margarita, Venezuela.,Universidad Técnica de Machala, Av. Panamericana km 5½, Via Pasaje, Machala, El Oro, Ecuador
| | - Juan Ignacio Gaviria
- Escuela de Ciencias Aplicadas del Mar, Núcleo de Nueva Esparta, Universidad de Oriente, Apartado 174, Porlamar, Isla de Margarita, Venezuela
| | | | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências Universidade Estadual Paulista-UNESP, Botucatu, São Paulo, 18618-970, Brazil
| | - Fausto Foresti
- Departamento de Morfologia, Instituto de Biociências Universidade Estadual Paulista-UNESP, Botucatu, São Paulo, 18618-970, Brazil
| | - Valentina Milana
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza-Università di Roma, Via Alfonso Borelli 50, 00161, Rome, Italy
| | - Anna Rita Rossi
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza-Università di Roma, Via Alfonso Borelli 50, 00161, Rome, Italy.
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20
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Utsunomia R, Melo S, Scacchetti PC, Oliveira C, Machado MDA, Pieczarka JC, Nagamachi CY, Foresti F. Particular Chromosomal Distribution of Microsatellites in Five Species of the Genus Gymnotus (Teleostei, Gymnotiformes). Zebrafish 2018; 15:398-403. [PMID: 29927722 DOI: 10.1089/zeb.2018.1570] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Microsatellites show great abundance in eukaryotic genomes, although distinct chromosomal distribution patterns might be observed, from small dispersed signals to strong clustered motifs. In Neotropical fishes, the chromosome mapping of distinct microsatellites was employed several times to uncover the origin and evolution of sex and supernumerary chromosomes, whereas a detailed comparative analysis considering different motifs at the chromosomal level is scarce. Here, we report the chromosomal location of several simple sequence repeats (SSRs) in distinct electric knife fishes showing variable diploid chromosome numbers to unveil the structural organization of several microsatellite motifs in distinct Gymnotus species. Our results showed that some SSRs are scattered throughout the genomes, whereas others are particularly clustered displaying intense genomic compartmentalization. Interestingly, the motifs CA, GA, and GAG exhibited a band-like pattern of hybridization, useful for the identification of homologous chromosomes. Finally, the colocalization of SSRs with multigene families is probably related to the association of microsatellites with gene spacers in this case.
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Affiliation(s)
- Ricardo Utsunomia
- 1 Laboratório de Biologia e Genética de Peixes, Department of Morphology, Institute of Biosciences of Botucatu, São Paulo State University , Botucatu, SP, Brazil
| | - Silvana Melo
- 1 Laboratório de Biologia e Genética de Peixes, Department of Morphology, Institute of Biosciences of Botucatu, São Paulo State University , Botucatu, SP, Brazil
| | - Priscilla Cardim Scacchetti
- 1 Laboratório de Biologia e Genética de Peixes, Department of Morphology, Institute of Biosciences of Botucatu, São Paulo State University , Botucatu, SP, Brazil
| | - Claudio Oliveira
- 1 Laboratório de Biologia e Genética de Peixes, Department of Morphology, Institute of Biosciences of Botucatu, São Paulo State University , Botucatu, SP, Brazil
| | - Milla de Andrade Machado
- 2 Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará , Belém, PA, Brazil
| | - Julio Cesar Pieczarka
- 2 Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará , Belém, PA, Brazil
| | - Cleusa Yoshiko Nagamachi
- 2 Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará , Belém, PA, Brazil
| | - Fausto Foresti
- 1 Laboratório de Biologia e Genética de Peixes, Department of Morphology, Institute of Biosciences of Botucatu, São Paulo State University , Botucatu, SP, Brazil
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21
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Campbell CR, Poelstra JW, Yoder AD. What is Speciation Genomics? The roles of ecology, gene flow, and genomic architecture in the formation of species. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly063] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - J W Poelstra
- Department of Biology, Duke University, Durham, NC, USA
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC, USA
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Sarasan T, Jantarat S, Supiwong W, Yeesin P, Srisamoot N, Tanomtong A. Chromosomal Analysis of Two Snakehead Fishes, <i>Channa marulius</i> (Hamilton, 1822) and <i>C. marulioides</i> (Bleeker, 1851) (Perciformes: Channidae) in Thailand. CYTOLOGIA 2018. [DOI: 10.1508/cytologia.83.115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Teamjun Sarasan
- Toxic Substance in Livestock and Aquatic Animals Research Group, Department of Biology, Faculty of Science, Khon Kaen University
| | - Sitthisak Jantarat
- Biology Program, Department of Science, Faculty of Science and Technology, Prince of Songkla University
| | | | - Pun Yeesin
- Department of Technology and Industries, Faculty of Science and Technology, Prince of Songkla University
| | - Nattapong Srisamoot
- Division of Biotechnology, Faculty of Agro-Industrial Technology, Kalasin University
| | - Alongklod Tanomtong
- Toxic Substance in Livestock and Aquatic Animals Research Group, Department of Biology, Faculty of Science, Khon Kaen University
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23
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Yano CF, Bertollo LAC, Rebordinos L, Merlo MA, Liehr T, Portela-Bens S, Cioffi MDB. Evolutionary Dynamics of rDNAs and U2 Small Nuclear DNAs in Triportheus (Characiformes, Triportheidae): High Variability and Particular Syntenic Organization. Zebrafish 2017; 14:146-154. [PMID: 28051362 DOI: 10.1089/zeb.2016.1351] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Multigene families correspond to a group of genes tandemly repeated, showing enormous diversity in both number of units and genomic organization. In fishes, unlike rDNAs that have been well explored in cytogenetic studies, U2 small nuclear RNA (snRNA) genes are poorly investigated concerning their chromosomal localization. All Triportheus species (Characiformes, Triportheidae) studied so far carry a ZZ/ZW sex chromosomes system, where the W chromosome contains a huge 18S rDNA cistron. In some species the syntenic organization of rDNAs on autosomes was also verified. To explore this particular organization, we performed three-color-fluorescence in situ hybridization using 5S, 18S rDNA, and U2 snRNA genes as probes in eight Triportheus species. This work represents the first one analyzing the chromosomal distribution of U2 snRNA genes in genomes of Triportheidae. The variability in number of rDNA clusters, and the divergent syntenies for these three multigene families, put in evidence their evolutionary dynamism, revealing a much more complex organization of these genes than previously supposed for closely related species. Our study also provides additional data on the accumulation of repetitive sequences in the sex-specific chromosome. Besides, the chromosomal organization of U2 snDNAs among fish species is also reviewed.
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Affiliation(s)
- Cassia Fernanda Yano
- 1 Departamento de Genética e Evolução, Universidade Federal de São Carlos , São Carlos, Brazil
| | | | - Laureana Rebordinos
- 2 Laboratorio de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz , Cádiz, Spain
| | - Manuel Alejandro Merlo
- 2 Laboratorio de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz , Cádiz, Spain
| | - Thomas Liehr
- 3 Jena University Hospital, Friedrich Schiller University , Institute of Human Genetics, Jena, Germany
| | - Silvia Portela-Bens
- 2 Laboratorio de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz , Cádiz, Spain
| | - Marcelo de Bello Cioffi
- 1 Departamento de Genética e Evolução, Universidade Federal de São Carlos , São Carlos, Brazil
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Evidence of birth-and-death evolution of 5S rRNA gene in Channa species (Teleostei, Perciformes). Genetica 2016; 144:723-732. [PMID: 27838803 DOI: 10.1007/s10709-016-9938-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 11/07/2016] [Indexed: 10/20/2022]
Abstract
In higher eukaryotes, minor rDNA family codes for 5S rRNA that is arranged in tandem arrays and comprises of a highly conserved 120 bp long coding sequence with a variable non-transcribed spacer (NTS). Initially the 5S rDNA repeats are considered to be evolved by the process of concerted evolution. But some recent reports, including teleost fishes suggested that evolution of 5S rDNA repeat does not fit into the concerted evolution model and evolution of 5S rDNA family may be explained by a birth-and-death evolution model. In order to study the mode of evolution of 5S rDNA repeats in Perciformes fish species, nucleotide sequence and molecular organization of five species of genus Channa were analyzed in the present study. Molecular analyses revealed several variants of 5S rDNA repeats (four types of NTS) and networks created by a neighbor net algorithm for each type of sequences (I, II, III and IV) did not show a clear clustering in species specific manner. The stable secondary structure is predicted and upstream and downstream conserved regulatory elements were characterized. Sequence analyses also shown the presence of two putative pseudogenes in Channa marulius. Present study supported that 5S rDNA repeats in genus Channa were evolved under the process of birth-and-death.
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Li SF, Zhang GJ, Yuan JH, Deng CL, Gao WJ. Repetitive sequences and epigenetic modification: inseparable partners play important roles in the evolution of plant sex chromosomes. PLANTA 2016; 243:1083-95. [PMID: 26919983 DOI: 10.1007/s00425-016-2485-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 02/07/2016] [Indexed: 05/03/2023]
Abstract
The present review discusses the roles of repetitive sequences played in plant sex chromosome evolution, and highlights epigenetic modification as potential mechanism of repetitive sequences involved in sex chromosome evolution. Sex determination in plants is mostly based on sex chromosomes. Classic theory proposes that sex chromosomes evolve from a specific pair of autosomes with emergence of a sex-determining gene(s). Subsequently, the newly formed sex chromosomes stop recombination in a small region around the sex-determining locus, and over time, the non-recombining region expands to almost all parts of the sex chromosomes. Accumulation of repetitive sequences, mostly transposable elements and tandem repeats, is a conspicuous feature of the non-recombining region of the Y chromosome, even in primitive one. Repetitive sequences may play multiple roles in sex chromosome evolution, such as triggering heterochromatization and causing recombination suppression, leading to structural and morphological differentiation of sex chromosomes, and promoting Y chromosome degeneration and X chromosome dosage compensation. In this article, we review the current status of this field, and based on preliminary evidence, we posit that repetitive sequences are involved in sex chromosome evolution probably via epigenetic modification, such as DNA and histone methylation, with small interfering RNAs as the mediator.
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Affiliation(s)
- Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Guo-Jun Zhang
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, 453003, China
| | - Jin-Hong Yuan
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Chuan-Liang Deng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
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Maneechot N, Yano CF, Bertollo LAC, Getlekha N, Molina WF, Ditcharoen S, Tengjaroenkul B, Supiwong W, Tanomtong A, de Bello Cioffi M. Genomic organization of repetitive DNAs highlights chromosomal evolution in the genus Clarias (Clariidae, Siluriformes). Mol Cytogenet 2016; 9:4. [PMID: 26793275 PMCID: PMC4719708 DOI: 10.1186/s13039-016-0215-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 01/07/2016] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND The genus Clarias (Clariidae, Siluriformes) contains at least 61 species naturally spread over vast regions of Asia, India and Africa. However, Clarias species have also been introduced in many different countries and represent the most widespread catfishes in the world. These fishes are also known as "walking catfishes" due to their ability to move over land. A large degree of chromosomal variation has been previously found in this family, mainly using conventional cytogenetic investigations, with diploid chromosome numbers ranging between 48 and 100. In this study, we analyzed the karyotype structure and distribution of four repetitive DNA sequences (5S and 18S rDNAs and (CA)15 and (GA)15 microsatellites) in three Clarias species (C. batrachus, C. gariepinus, C. macrocephalus), as well as in a probable natural hybrid of the two latter species from different Thailand river basins. RESULTS Clarias gariepinus and C. macrocephalus had 2n = 56 and 2n = 54, respectively, as well as karyotypes composed mainly by metacentric and submetacentric chromosomes. Their karyotypes differed in the number and location of 5S and 18S rDNA sites and in the degree of microsatellite accumulation. An intermediate chromosomal pattern incorporating those of the parental species was found in the probable hybrid, confirming its interspecific origin. Clarias batrachus had 2n = 104 chromosomes and its karyotype was dominated by mainly acrocentric elements, indicating that unusual multiple centric fissions were involved in its karyotype differentiation. The karyotype of this species presented an unexpected dispersion of ribosomal DNAs, possessing 54 and 12 sites of 5S and 18S rDNAs, respectively, as well as a high accumulation and differential distribution of both microsatellite repeats, representing 'hot spots' for chromosomal rearrangement. CONCLUSION Both conventional and molecular cytogenetic markers were useful tools for demonstrating remarkable evolutionary dynamism and highlighting multiple chromosomal rearrangements and hybridization events correlated with the notable karyotypic diversity of these walking catfishes.
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Affiliation(s)
- Nuntiya Maneechot
- />Department of Biology, Faculty of Science, Khon Kaen University, Muang District Khon Kaen, Thailand
| | - Cassia Fernanda Yano
- />Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo Brazil
| | | | - Nuntaporn Getlekha
- />Department of Biology, Faculty of Science, Khon Kaen University, Muang District Khon Kaen, Thailand
| | - Wagner Franco Molina
- />Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN Brazil
| | - Sukhonthip Ditcharoen
- />Department of Biology, Faculty of Science, Khon Kaen University, Muang District Khon Kaen, Thailand
| | - Bundit Tengjaroenkul
- />Department of Veterinary Clinical Medicine, Faculty of Veterinary Medicine, Muang, Khon Kaen 40002 Thailand
- />Toxic Substances in Livestock and Aquatic Animals Research Group, Khon Kaen University, Muang, Khon Kaen 40002 Thailand
| | - Weerayuth Supiwong
- />Faculty of Applied Science and Engineering, Khon Kaen University, Nong Khai Campus, Muang, Nong Khai 43000 Thailand
| | - Alongklod Tanomtong
- />Department of Biology, Faculty of Science, Khon Kaen University, Muang District Khon Kaen, Thailand
- />Toxic Substances in Livestock and Aquatic Animals Research Group, Khon Kaen University, Muang, Khon Kaen 40002 Thailand
| | - Marcelo de Bello Cioffi
- />Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo Brazil
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de Oliveira EA, Bertollo LAC, Yano CF, Liehr T, Cioffi MDB. Comparative cytogenetics in the genus Hoplias (Characiformes, Erythrinidae) highlights contrasting karyotype evolution among congeneric species. Mol Cytogenet 2015; 8:56. [PMID: 26225139 PMCID: PMC4518567 DOI: 10.1186/s13039-015-0161-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 07/14/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Erythrinidae fish family contains three genera, Hoplias, Erythrinus and Hoplerythrinus widely distributed in Neotropical region. Remarkably, species from this family are characterized by an extensive karyotype diversity, with 2n ranging from 39 to 54 chromosomes and the occurrence of single and/or multiple sex chromosome systems in some species. However, inside the Hoplias genus, while H. malabaricus was subject of many studies, the cytogenetics of other congeneric species remains poorly explored. In this study, we have investigated chromosomal characteristics of four Hoplias species, namely H. lacerdae, H. brasiliensis, H. intermedius and H. aimara. We used conventional staining techniques (C-banding, Ag-impregnation and CMA3 -fluorescence) as well as fluorescence in situ hybridization (FISH) with minor and major rDNA and microsatellite DNAs as probes in order to analyze the karyotype evolution within the genus. RESULTS All species showed invariably 2n = 50 chromosomes and practically identical karyotypes dominated only by meta- and submetacentric chromosomes, the absence of heteromorphic sex chromosomes, similar pattern of C-positive heterochromatin blocks and homologous Ag-NOR-bearing pairs. The cytogenetic mapping of five repetitive DNA sequences revealed some particular interspecific differences between them. However, the examined chromosomal characteristics indicate that their speciation was not associated with major changes in their karyotypes. CONCLUSION Such conserved karyotypes contrasts with the extensive karyotype diversity that has been observed in other Erythrinidae species, particularly in the congeneric species H. malabaricus. Nevertheless, what forces drive such particularly different modes of karyotype evolution among closely related species? Different life styles, population structure and inner chromosomal characteristics related to similar cases in other vertebrate groups can also account for the contrasting modes of karyotype evolution in Hoplias genus.
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Affiliation(s)
- Ezequiel Aguiar de Oliveira
- />Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP Brazil
- />SEDUC-MT, Cuiabá, MT Brazil
| | | | - Cassia Fernanda Yano
- />Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP Brazil
| | - Thomas Liehr
- />Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Marcelo de Bello Cioffi
- />Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP Brazil
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