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de Sousa E Souza JF, Guimarães EMC, Figliuolo VSP, Soares SC, de Bello Cioffi M, de Menezes Cavalcante Sassi F, Feldberg E. Chromosomal mapping of repetitive DNA and retroelement sequences and its implications for the chromosomal evolution process in Ctenoluciidae (Characiformes). BMC Ecol Evol 2024; 24:72. [PMID: 38816840 PMCID: PMC11138015 DOI: 10.1186/s12862-024-02262-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 05/22/2024] [Indexed: 06/01/2024] Open
Abstract
Ctenoluciidae is a Neotropical freshwater fish family composed of two genera, Ctenolucius (C. beani and C. hujeta) and Boulengerella (B. cuvieri, B. lateristriga, B. lucius, B. maculata, and B. xyrekes), which present diploid number conservation of 36 chromosomes and a strong association of telomeric sequences with ribosomal DNAs. In the present study, we performed chromosomal mapping of microsatellites and transposable elements (TEs) in Boulengerella species and Ctenolucius hujeta. We aim to understand how those sequences are distributed in these organisms' genomes and their influence on the chromosomal evolution of the group. Our results indicate that repetitive sequences may had an active role in the karyotypic diversification of this family, especially in the formation of chromosomal hotspots that are traceable in the diversification processes of Ctenoluciidae karyotypes. We demonstrate that (GATA)n sequences also accumulate in the secondary constriction formed by the 18 S rDNA site, which shows consistent size heteromorphism between males and females in all Boulengerella species, suggesting an initial process of sex chromosome differentiation.
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Grants
- 573976/2008-2 Center for Studies of Adaptation to Environmental Changes in the Amazon (INCT ADAPTA II, FAPEAM/CNPq
- 573976/2008-2 Center for Studies of Adaptation to Environmental Changes in the Amazon (INCT ADAPTA II, FAPEAM/CNPq
- 573976/2008-2 Center for Studies of Adaptation to Environmental Changes in the Amazon (INCT ADAPTA II, FAPEAM/CNPq
- 573976/2008-2 Center for Studies of Adaptation to Environmental Changes in the Amazon (INCT ADAPTA II, FAPEAM/CNPq
- 301886/2019-9 Conselho Nacional de Desenvolvimento Científico e Tecnológico , Brasil
- 301886/2019-9 Conselho Nacional de Desenvolvimento Científico e Tecnológico , Brasil
- 301886/2019-9 Conselho Nacional de Desenvolvimento Científico e Tecnológico , Brasil
- 301886/2019-9 Conselho Nacional de Desenvolvimento Científico e Tecnológico , Brasil
- 301886/2019-9 Conselho Nacional de Desenvolvimento Científico e Tecnológico , Brasil
- 301886/2019-9 Conselho Nacional de Desenvolvimento Científico e Tecnológico , Brasil
- National Institute of Amazonian Research, Brazil/PPG Genetics, Conservation and Evolutionary Biology (INPA/GCBEv)
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
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Affiliation(s)
- José Francisco de Sousa E Souza
- Conservation and Evolutionary Biology, INPA, National Amazon Research Institute, Av. André Araújo, 2936, Petrópolis, CEP: 69067-375, Caixa Postal 2223, Manaus, 69060-001, Amazonas, Brazil.
| | - Erika Milena Corrêa Guimarães
- Conservation and Evolutionary Biology, INPA, National Amazon Research Institute, Av. André Araújo, 2936, Petrópolis, CEP: 69067-375, Caixa Postal 2223, Manaus, 69060-001, Amazonas, Brazil
| | - Vanessa Susan Pinheiro Figliuolo
- Conservation and Evolutionary Biology, INPA, National Amazon Research Institute, Av. André Araújo, 2936, Petrópolis, CEP: 69067-375, Caixa Postal 2223, Manaus, 69060-001, Amazonas, Brazil
| | - Simone Cardoso Soares
- Conservation and Evolutionary Biology, INPA, National Amazon Research Institute, Av. André Araújo, 2936, Petrópolis, CEP: 69067-375, Caixa Postal 2223, Manaus, 69060-001, Amazonas, Brazil
| | - Marcelo de Bello Cioffi
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil
| | | | - Eliana Feldberg
- Conservation and Evolutionary Biology, INPA, National Amazon Research Institute, Av. André Araújo, 2936, Petrópolis, CEP: 69067-375, Caixa Postal 2223, Manaus, 69060-001, Amazonas, Brazil
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Dulz TA, Azambuja M, Lorscheider CA, Noleto RB, Moreira-Filho O, Nogaroto V, Nascimento VD, Diniz D, de Mello Affonso PRA, Vicari MR. Repetitive DNAs and chromosome evolution in Megaleporinus obtusidens and M. reinhardti (Characiformes: Anostomidae). Genetica 2024:10.1007/s10709-024-00206-3. [PMID: 38587599 DOI: 10.1007/s10709-024-00206-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
The high dynamism of repetitive DNAs is a major driver of chromosome evolution. In particular, the accumulation of repetitive DNA sequences has been reported as part of the differentiation of sex-specific chromosomes. In turn, the fish species of the genus Megaleporinus are a monophyletic clade in which the presence of differentiated ZZ/ZW sex chromosomes represents a synapomorphic condition, thus serving as a suitable model to evaluate the dynamic evolution of repetitive DNA classes. Therefore, transposable elements (TEs) and in tandem repeats were isolated and located on chromosomes of Megaleporinus obtusidens and M. reinhardti to infer their role in chromosome differentiation with emphasis on sex chromosome systems. Despite the conserved karyotype features of both species, the location of repetitive sequences - Rex 1, Rex 3, (TTAGGG)n, (GATA)n, (GA)n, (CA)n, and (A)n - varied both intra and interspecifically, being mainly accumulated in Z and W chromosomes. The physical mapping of repetitive sequences confirmed the remarkable dynamics of repetitive DNA classes on sex chromosomes that might have promoted chromosome diversification and reproductive isolation in Megaleporinus species.
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Affiliation(s)
- Thais Aparecida Dulz
- Graduate Program in Genetics, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Matheus Azambuja
- Graduate Program in Animal Science, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
| | - Carla Andrea Lorscheider
- Department of Biological Sciences, Universidade Estadual do Paraná, União da Vitória, PR, Brazil
| | - Rafael Bueno Noleto
- Department of Biological Sciences, Universidade Estadual do Paraná, União da Vitória, PR, Brazil
| | - Orlando Moreira-Filho
- Department of Genetics and Evolution, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Viviane Nogaroto
- Graduate Program in Animal Science, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
| | | | - Débora Diniz
- Graduate Program in Genetics, Biodiversity and Conservation, Universidade Estadual do Sudoeste da Bahia, Jequié, BA, Brazil
| | | | - Marcelo Ricardo Vicari
- Graduate Program in Genetics, Universidade Federal do Paraná, Curitiba, PR, Brazil
- Graduate Program in Animal Science, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
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Jaito W, Panthum T, Ahmad SF, Singchat W, Muangmai N, Han K, Koga A, Duengkae P, Srikulnath K. Genetic insights: mapping sex-specific loci in Siamese cobra (Naja kaouthia) sheds light on the putative sex determining region. Genes Genomics 2024; 46:113-119. [PMID: 37985546 DOI: 10.1007/s13258-023-01459-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 10/01/2023] [Indexed: 11/22/2023]
Abstract
The location of female-specific/linked loci identified in Siamese cobra (Naja kaouthia) previously has been determined through in silico chromosome mapping of the Indian cobra genome (N. naja) as a reference genome. In the present study, we used in silico chromosome mapping to identify sex-specific and linked loci in Siamese cobra. Many sex-specific and sex-linked loci were successfully mapped on the Z sex chromosome, with 227 of the 475 specific loci frequently mapped in a region covering 57 Mb and positioned at 38,992,675-95,561,177 bp of the Indian cobra genome (N. naja). This suggested the existence of a putative sex-determining region (SDR), with one specific locus (PA100000600) homologous to the TOPBP1 gene. The involvement of TOPBP1 gene may lead to abnormal synaptonemal complexes and meiotic chromosomal defects, resulting in male infertility. These findings offer valuable insights into the genetic basis and functional aspects of sex-specific traits in the Siamese cobra, which will contribute to our understanding of snake genetics and evolutionary biology.
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Affiliation(s)
- Wattanawan Jaito
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- The International Undergraduate Program in Bioscience and Technology, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Department of Microbiology, Dankook University, Cheonan, 31116, Korea
- Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan, 31116, Korea
| | - Akihiko Koga
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- The International Undergraduate Program in Bioscience and Technology, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
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A Perspective of Molecular Cytogenomics, Toxicology, and Epigenetics for the Increase of Heterochromatic Regions and Retrotransposable Elements in Tambaqui (Colossoma macropomum) Exposed to the Parasiticide Trichlorfon. Animals (Basel) 2022; 12:ani12151945. [PMID: 35953934 PMCID: PMC9367383 DOI: 10.3390/ani12151945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary The aim of the present study was to evaluate the Trichlorfon effects on the retrotransposable elements in tambaqui (Colossoma macropomum) genome, which is a highly popular and well-known fish in the Amazon with a large reproduction number mediated by pisciculture. Thereby, tambaqui specimens were submitted to two different Trichlorfon concentrations (30% and 50% of LC50–96 h) under experimental conditions. The retrotransposons were analyzed using the FISH technique and the heterochromatin standard with the C-band technique. The retrotransposons studied presented a dispersed distribution profile in the tambaqui karyotype with Rex3 being more prominent than the others, showing the greatest increase in markings. Furthermore, the heterochromatin profile showed that these retrotransposons can be found in the heterochromatic portions of the chromosomes. Thus, it was observed that Trichlorfon has an activation mechanism for these retroelements, especially Rex3. Abstract Rex retroelements are the best-known transposable elements class and are broadly distributed through fish and also individual genomes, playing an important role in their evolutionary dynamics. Several agents can stress these elements; among them, there are some parasitic compounds such as the organochlorophosphate Trichlorfon. Consequently, knowing that the organochlorophosphate Trichlorfon is indiscriminately used as an antiparasitic in aquaculture, the current study aimed to analyze the effects of this compound on the activation of the Transposable Elements (TEs) Rex1, Rex3, and Rex6 and the structure of heterochromatin in the mitotic chromosomes of the tambaqui (Colossoma macropomum). For this, two concentrations of the pesticide were used: 30% (0.261 mg/L) and 50% (0.435 mg/L) of the recommended LC50–96 h concentration (0.87 mg/L) for this fish species. The results revealed a dispersed distribution for Rex1 and Rex6 retroelements. Rex3 showed an increase in both marking intensity and distribution, as well as enhanced chromosomal heterochromatinization. This probably happened by the mediation of epigenetic adaptive mechanisms, causing the retroelement mobilization to be repressed. However, this behavior was most evident when Trichlorfon concentrations and exposure times were the greatest, reflecting the genetic flexibility necessary for this species to successfully adapt to environmental changes.
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Moura Gama J, Ludwig A, Gazolla CB, Guizelini D, Recco-Pimentel SM, Bruschi DP. A genomic survey of LINE elements in Pipidae aquatic frogs shed light on Rex-elements evolution in these genomes. Mol Phylogenet Evol 2022; 168:107393. [PMID: 35051593 DOI: 10.1016/j.ympev.2022.107393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/09/2021] [Accepted: 12/25/2021] [Indexed: 11/19/2022]
Abstract
The transposable elements (TE) represent a large portion of anuran genomes that act as components of genetic diversification. The LINE order of retrotransposons is among the most representative and diverse TEs and is poorly investigated in anurans. Here we explored the LINE diversity with an emphasis on the elements generically called Rex in Pipidae species, more specifically, in the genomes ofXenopus tropicalis, used as a model genome in the study of anurans,the allotetraploid sister species Xenopus laevis and theAmerican species Pipa carvalhoi. We were able to identify a great diversity of LINEs from five clades, Rex1, L2, CR1, L1 and Tx1, in these three species, and the RTE clade was lost in X. tropicalis. It is clear that elements classified as Rex are distributed in distinct clades. The evolutionary pattern of Rex1 elements denote a complex evolution with independent losses of families and some horizontal transfer events between fishes and amphibians which were supported not only by the phylogenetic inconsistencies but also by the very low Ks values found for the TE sequences. The data obtained here update the knowledge of the LINEs diversity in X. laevis and represent the first study of TEs in P. carvalhoi.
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Affiliation(s)
- Joana Moura Gama
- Programa de Pós-Graduação em Genética (PPG-GEN), Universidade Federal do Paraná (UFPR), Curitiba, Brazil; Laboratório de Citogenética evolutiva e Conservação Animal (LabCeca), Departamento de Genética, Universidade Federal do Paraná (UFPR), Brazil
| | - Adriana Ludwig
- Laboratório de Ciências e Tecnologias Aplicadas em Saúde (LaCTAS), Instituto Carlos Chagas, Fiocruz-PR, Brazil.
| | - Camilla Borges Gazolla
- Programa de Pós-Graduação em Genética (PPG-GEN), Universidade Federal do Paraná (UFPR), Curitiba, Brazil; Laboratório de Citogenética evolutiva e Conservação Animal (LabCeca), Departamento de Genética, Universidade Federal do Paraná (UFPR), Brazil
| | - Dieval Guizelini
- Programa de Pós-Graduação em Bioinformática, Universidade Federal do Paraná, Curitiba, Brazil
| | | | - Daniel Pacheco Bruschi
- Programa de Pós-Graduação em Genética (PPG-GEN), Universidade Federal do Paraná (UFPR), Curitiba, Brazil; Laboratório de Citogenética evolutiva e Conservação Animal (LabCeca), Departamento de Genética, Universidade Federal do Paraná (UFPR), Brazil.
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Solovyeva A, Levakin I, Zorin E, Adonin L, Khotimchenko Y, Podgornaya O. Transposons-Based Clonal Diversity in Trematode Involves Parts of CR1 (LINE) in Eu- and Heterochromatin. Genes (Basel) 2021; 12:genes12081129. [PMID: 34440303 PMCID: PMC8392823 DOI: 10.3390/genes12081129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 01/21/2023] Open
Abstract
Trematode parthenitae have long been believed to form clonal populations, but clonal diversity has been discovered in this asexual stage of the lifecycle. Clonal polymorphism in the model species Himasthla elongata has been previously described, but the source of this phenomenon remains unknown. In this work, we traced cercarial clonal diversity using a simplified amplified fragment length polymorphism (SAFLP) method and characterised the nature of fragments in diverse electrophoretic bands. The repetitive elements were identified in both the primary sequence of the H. elongata genome and in the transcriptome data. Long-interspersed nuclear elements (LINEs) and long terminal repeat retrotransposons (LTRs) were found to represent an overwhelming majority of the genome and the transposon transcripts. Most sequenced fragments from SAFLP pattern contained the reverse transcriptase (RT, ORF2) domains of LINEs, and only a few sequences belonged to ORFs of LTRs and ORF1 of LINEs. A fragment corresponding to a CR1-like (LINE) spacer region was discovered and named CR1-renegade (CR1-rng). In addition to RT-containing CR1 transcripts, we found short CR1-rng transcripts in the redia transcriptome and short contigs in the mobilome. Probes against CR1-RT and CR1-rng presented strikingly different pictures in FISH mapping, despite both being fragments of CR1. In silico data and Southern blotting indicated that CR1-rng is not tandemly organised. CR1 involvement in clonal diversity is discussed.
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Affiliation(s)
- Anna Solovyeva
- Institute of Cytology of the Russian Academy of Science, Tikhoretsky Ave 4, 194064 Saint Petersburg, Russia;
- Zoological Institute of the Russian Academy of Sciences, Universitetskaya Nab 1, 199034 Saint Petersburg, Russia;
- Correspondence:
| | - Ivan Levakin
- Zoological Institute of the Russian Academy of Sciences, Universitetskaya Nab 1, 199034 Saint Petersburg, Russia;
| | - Evgeny Zorin
- All-Russia Research Institute for Agricultural Microbiology, Pushkin 8, 196608 Saint Petersburg, Russia;
| | - Leonid Adonin
- Moscow Institute of Physics and Technology, Institutskiy per 9, 141701 Dolgoprudny, Russia;
| | - Yuri Khotimchenko
- School of Biomedicine, Far Eastern Federal University, Sukhanova St 8, 690091 Vladivostok, Russia;
| | - Olga Podgornaya
- Institute of Cytology of the Russian Academy of Science, Tikhoretsky Ave 4, 194064 Saint Petersburg, Russia;
- Department of Cytology and Histology, Saint Petersburg State University, Universitetskaya Nab 7/9, 199034 Saint Petersburg, Russia
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Souza J, Guimarães E, Pinheiro-Figliuolo V, Cioffi MB, Bertollo LAC, Feldberg E. Chromosomal Analysis of Ctenolucius hujeta Valenciennes, 1850 (Characiformes): A New Piece in the Chromosomal Evolution of the Ctenoluciidae. Cytogenet Genome Res 2021; 161:195-202. [PMID: 34126615 DOI: 10.1159/000515456] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 02/25/2021] [Indexed: 11/19/2022] Open
Abstract
Ctenoluciidae (Characiformes), a family of freshwater fishes, comprises 2 genera, Ctenolucius and Boulengerella, with 7 recognized species. Up to now, only species of the genus Boulengerella have been subjected to cytogenetic studies. Here, we investigated the karyotype and other cytogenetic features of pike characin, Ctenolucius hujeta, using conventional (Giemsa staining, C-banding, Ag-NOR staining) and molecular (rDNA, telomeric sequences, and fiber-FISH mapping) procedures. This species has a diploid chromosome number of 2n = 36, and a karyotype composed of 12m + 20sm + 4a and FN = 68, similar to that found in Boulengerella species. However, differences regarding the number and distribution of several chromosomal markers support a distinct generic status. Colocalization of the 18S and 5S rDNA genes is an exclusive characteristic of the C. hujeta genome, with an interspersed distribution in the chromosomal fiber, an unusual phenomenon among eukaryotes. Additionally, our results support the view that Ctenoluciidae and Lebiasinidae families are closely related.
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Affiliation(s)
- José Souza
- Laboratory of Animal Genetics, National Institute of Amazonian Research (INPA), Manaus, Brazil
| | - Erika Guimarães
- Laboratory of Animal Genetics, National Institute of Amazonian Research (INPA), Manaus, Brazil
| | | | - Marcelo B Cioffi
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Luiz A C Bertollo
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Eliana Feldberg
- Laboratory of Animal Genetics, National Institute of Amazonian Research (INPA), Manaus, Brazil
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Pappalardo AM, Ferrito V, Biscotti MA, Canapa A, Capriglione T. Transposable Elements and Stress in Vertebrates: An Overview. Int J Mol Sci 2021; 22:1970. [PMID: 33671215 PMCID: PMC7922186 DOI: 10.3390/ijms22041970] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/13/2021] [Accepted: 02/14/2021] [Indexed: 12/17/2022] Open
Abstract
Since their identification as genomic regulatory elements, Transposable Elements (TEs) were considered, at first, molecular parasites and later as an important source of genetic diversity and regulatory innovations. In vertebrates in particular, TEs have been recognized as playing an important role in major evolutionary transitions and biodiversity. Moreover, in the last decade, a significant number of papers has been published highlighting a correlation between TE activity and exposition to environmental stresses and dietary factors. In this review we present an overview of the impact of TEs in vertebrate genomes, report the silencing mechanisms adopted by host genomes to regulate TE activity, and finally we explore the effects of environmental and dietary factor exposures on TE activity in mammals, which is the most studied group among vertebrates. The studies here reported evidence that several factors can induce changes in the epigenetic status of TEs and silencing mechanisms leading to their activation with consequent effects on the host genome. The study of TE can represent a future challenge for research for developing effective markers able to detect precocious epigenetic changes and prevent human diseases.
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Affiliation(s)
- Anna Maria Pappalardo
- Department of Biological, Geological and Environmental Sciences-Section of Animal Biology "M. La Greca", University of Catania, Via Androne 81, 95124 Catania, Italy
| | - Venera Ferrito
- Department of Biological, Geological and Environmental Sciences-Section of Animal Biology "M. La Greca", University of Catania, Via Androne 81, 95124 Catania, Italy
| | - Maria Assunta Biscotti
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Adriana Canapa
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Teresa Capriglione
- Department of Biology, University of Naples "Federico II", Via Cinthia 21-Ed7, 80126 Naples, Italy
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Transposable Elements and Teleost Migratory Behaviour. Int J Mol Sci 2021; 22:ijms22020602. [PMID: 33435333 PMCID: PMC7827017 DOI: 10.3390/ijms22020602] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/28/2020] [Accepted: 01/06/2021] [Indexed: 02/07/2023] Open
Abstract
Transposable elements (TEs) represent a considerable fraction of eukaryotic genomes, thereby contributing to genome size, chromosomal rearrangements, and to the generation of new coding genes or regulatory elements. An increasing number of works have reported a link between the genomic abundance of TEs and the adaptation to specific environmental conditions. Diadromy represents a fascinating feature of fish, protagonists of migratory routes between marine and freshwater for reproduction. In this work, we investigated the genomes of 24 fish species, including 15 teleosts with a migratory behaviour. The expected higher relative abundance of DNA transposons in ray-finned fish compared with the other fish groups was not confirmed by the analysis of the dataset considered. The relative contribution of different TE types in migratory ray-finned species did not show clear differences between oceanodromous and potamodromous fish. On the contrary, a remarkable relationship between migratory behaviour and the quantitative difference reported for short interspersed nuclear (retro)elements (SINEs) emerged from the comparison between anadromous and catadromous species, independently from their phylogenetic position. This aspect is likely due to the substantial environmental changes faced by diadromous species during their migratory routes.
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10
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Galbraith JD, Ludington AJ, Suh A, Sanders KL, Adelson DL. New Environment, New Invaders-Repeated Horizontal Transfer of LINEs to Sea Snakes. Genome Biol Evol 2020; 12:2370-2383. [PMID: 33022046 PMCID: PMC7846101 DOI: 10.1093/gbe/evaa208] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2020] [Indexed: 12/12/2022] Open
Abstract
Although numerous studies have found horizontal transposon transfer (HTT) to be widespread across metazoans, few have focused on HTT in marine ecosystems. To investigate potential recent HTTs into marine species, we searched for novel repetitive elements in sea snakes, a group of elapids which transitioned to a marine habitat at most 18 Ma. Our analysis uncovered repeated HTTs into sea snakes following their marine transition. The seven subfamilies of horizontally transferred LINE retrotransposons we identified in the olive sea snake (Aipysurus laevis) are transcribed, and hence are likely still active and expanding across the genome. A search of 600 metazoan genomes found all seven were absent from other amniotes, including terrestrial elapids, with the most similar LINEs present in fish and marine invertebrates. The one exception was a similar LINE found in sea kraits, a lineage of amphibious elapids which independently transitioned to a marine environment 25 Ma. Our finding of repeated horizontal transfer events into marine snakes greatly expands past findings that the marine environment promotes the transfer of transposons. Transposons are drivers of evolution as sources of genomic sequence and hence genomic novelty. We identified 13 candidate genes for HTT-induced adaptive change based on internal or neighboring HTT LINE insertions. One of these, ADCY4, is of particular interest as a part of the KEGG adaptation pathway “Circadian Entrainment.” This provides evidence of the ecological interactions between species influencing evolution of metazoans not only through specific selection pressures, but also by contributing novel genomic material.
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Affiliation(s)
| | | | - Alexander Suh
- Department of Ecology and Genetics-Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Sweden.,Department of Organismal Biology-Systematic Biology, Evolutionary Biology Centre, Uppsala University, Sweden.,School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Kate L Sanders
- School of Biological Sciences, University of Adelaide, Australia
| | - David L Adelson
- School of Biological Sciences, University of Adelaide, Australia
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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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Zhang HH, Peccoud J, Xu MRX, Zhang XG, Gilbert C. Horizontal transfer and evolution of transposable elements in vertebrates. Nat Commun 2020; 11:1362. [PMID: 32170101 PMCID: PMC7070016 DOI: 10.1038/s41467-020-15149-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 02/20/2020] [Indexed: 11/13/2022] Open
Abstract
Horizontal transfer of transposable elements (HTT) is an important process shaping eukaryote genomes, yet very few studies have quantified this phenomenon on a large scale or have evaluated the selective constraints acting on transposable elements (TEs) during vertical and horizontal transmission. Here we screen 307 vertebrate genomes and infer a minimum of 975 independent HTT events between lineages that diverged more than 120 million years ago. HTT distribution greatly differs from null expectations, with 93.7% of these transfers involving ray-finned fishes and less than 3% involving mammals and birds. HTT incurs purifying selection (conserved protein evolution) on all TEs, confirming that producing functional transposition proteins is required for a TE to invade new genomes. In the absence of HTT, DNA transposons appear to evolve neutrally within genomes, unlike most retrotransposons, which evolve under purifying selection. This selection regime indicates that proteins of most retrotransposon families tend to process their own encoding RNA (cis-preference), which helps retrotransposons to persist within host lineages over long time periods. Horizontal transfer (HT) and evolution of transposable elements (TEs) has rarely been quantified on a large scale. Here, the authors screen 307 vertebrate genomes and infer 975 HT events (93% in ray-finned fishes); all TEs involved in HT evolve within genomes under purifying selection, as do most retrotransposons.
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Affiliation(s)
- Hua-Hao Zhang
- College of Pharmacy and Life Science, Jiujiang University, 332000, Jiujiang, China
| | - Jean Peccoud
- UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, 86073, Poitiers, France
| | - Min-Rui-Xuan Xu
- College of Pharmacy and Life Science, Jiujiang University, 332000, Jiujiang, China
| | - Xiao-Gu Zhang
- College of Pharmacy and Life Science, Jiujiang University, 332000, Jiujiang, China.
| | - Clément Gilbert
- Laboratoire Evolution, Génomes, Comportement, Écologie, UMR 9191 CNRS, UMR 247 IRD, Université Paris-Saclay, 91198, Gif-sur-Yvette, France.
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13
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Carducci F, Biscotti MA, Barucca M, Canapa A. Transposable elements in vertebrates: species evolution and environmental adaptation. EUROPEAN ZOOLOGICAL JOURNAL 2019. [DOI: 10.1080/24750263.2019.1695967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- F. Carducci
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - M. A. Biscotti
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - M. Barucca
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - A. Canapa
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona, Italy
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14
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Viana Ferreira AM, Marajó L, Matoso DA, Ribeiro LB, Feldberg E. Chromosomal Mapping of Rex Retrotransposons in Tambaqui (Colossoma macropomum Cuvier, 1818) Exposed to Three Climate Change Scenarios. Cytogenet Genome Res 2019; 159:39-47. [PMID: 31593951 DOI: 10.1159/000502926] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2019] [Indexed: 11/19/2022] Open
Abstract
Greenhouse gas emissions are known to influence the planet's temperature, mainly due to human activities. To allow hypothesis testing, as well as to seek viable alternatives for mitigation, the Intergovernmental Panel on Climate Change (IPCC) suggested 3 main scenarios for changes projected for the year 2100. In this paper, we subjected Colossoma macropomum Cuvier, 1818 (tambaqui) individuals in a microcosm to IPCC scenarios B1 (mild), A1B (intermediate), and A2 (extreme) to test possible impacts on their genome. We found chromosome heterochromatinization in specimens exposed to the A2 scenario, where terminal blocks and interstitial bands were detected on several chromosome pairs. The behavior of Rex1 and Rex3 sequences differed between the test scenarios. Hybridization of Rex1 resulted in diffuse signals which showed a gradual increase in the tested scenarios. For Rex3, an increase was observed in the A2 scenario with blocks on several chromosomes, some of which coincided with heterochromatin. Heterochromatinization is an epigenetic process, which may have occurred as a mechanism for regulating Rex3 activity. The signal pattern of Rex6 did not change, suggesting that other mechanisms are acting to regulate its activity.
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15
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Carducci F, Biscotti MA, Forconi M, Barucca M, Canapa A. An intriguing relationship between teleost Rex3 retroelement and environmental temperature. Biol Lett 2019; 15:20190279. [PMID: 31480936 DOI: 10.1098/rsbl.2019.0279] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The movement and accumulation of transposable elements (TEs) exert a great influence on the host genome, e.g. determining architecture and genome size, providing a substrate for homologous recombination and DNA rearrangements. TEs are also known to be responsive and susceptible to environmental changes. However, the correlation between environmental conditions and the sequence evolution of TEs is still an unexplored field of research. Among vertebrates, teleosts represent a successful group of animals adapted to a wide range of different environments and their genome is constituted by a rich repertoire of TEs. The Rex3 retroelement is a lineage-specific non-LTR retrotransposon and thus represents a valid candidate for performing comparative sequence analyses between species adapted to diverse temperature conditions. Partial reverse transcriptase sequences of the Rex3 retroelement belonging to 39 species of teleosts were investigated through phylogenetic analysis to evaluate whether the species' adaptation to different environments led to the evolution of different Rex3 temperature-related variants. Our findings highlight an intriguing behaviour of the analysed sequences, showing clustering of Rex3 sequences isolated from species living in cold waters (Arctic and Antarctic regions and cold waters of temperate regions) compared with those isolated from species living in warm waters. This is the first evidence to our knowledge of a correlation between environmental temperature and Rex3 retroelement evolution.
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Affiliation(s)
- Federica Carducci
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Maria Assunta Biscotti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Mariko Forconi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Marco Barucca
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Adriana Canapa
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
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16
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Traldi JB, Lui RL, Martinez JDF, Vicari MR, Nogaroto V, Moreira Filho O, Blanco DR. Chromosomal distribution of the retroelements Rex 1, Rex 3 and Rex 6 in species of the genus Harttia and Hypostomus (Siluriformes: Loricariidae). NEOTROPICAL ICHTHYOLOGY 2019. [DOI: 10.1590/1982-0224-20190010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
ABSTRACT The transposable elements (TE) have been widely applied as physical chromosome markers. However, in Loricariidae there are few physical mapping analyses of these elements. Considering the importance of transposable elements for chromosomal evolution and genome organization, this study conducted the physical chromosome mapping of retroelements (RTEs) Rex1, Rex3 and Rex6 in seven species of the genus Harttia and four species of the genus Hypostomus, aiming to better understand the organization and dynamics of genomes of Loricariidae species. The results showed an intense accumulation of RTEs Rex1, Rex3 and Rex6 and dispersed distribution in heterochromatic and euchromatic regions in the genomes of the species studied here. The presence of retroelements in some chromosomal regions suggests their participation in various chromosomal rearrangements. In addition, the intense accumulation of three retroelements in all species of Harttia and Hypostomus, especially in euchromatic regions, can indicate the participation of these elements in the diversification and evolution of these species through the molecular domestication by genomes of hosts, with these sequences being a co-option for new functions.
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