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Rico-Porras JM, Mora P, Palomeque T, Montiel EE, Cabral-de-Mello DC, Lorite P. Heterochromatin Is Not the Only Place for satDNAs: The High Diversity of satDNAs in the Euchromatin of the Beetle Chrysolina americana (Coleoptera, Chrysomelidae). Genes (Basel) 2024; 15:395. [PMID: 38674330 PMCID: PMC11049206 DOI: 10.3390/genes15040395] [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: 02/20/2024] [Revised: 03/16/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
The satellitome of the beetle Chrysolina americana Linneo, 1758 has been characterized through chromosomal analysis, genomic sequencing, and bioinformatics tools. C-banding reveals the presence of constitutive heterochromatin blocks enriched in A+T content, primarily located in pericentromeric regions. Furthermore, a comprehensive satellitome analysis unveils the extensive diversity of satellite DNA families within the genome of C. americana. Using fluorescence in situ hybridization techniques and the innovative CHRISMAPP approach, we precisely map the localization of satDNA families on assembled chromosomes, providing insights into their organization and distribution patterns. Among the 165 identified satDNA families, only three of them exhibit a remarkable amplification and accumulation, forming large blocks predominantly in pericentromeric regions. In contrast, the remaining, less abundant satDNA families are dispersed throughout euchromatic regions, challenging the traditional association of satDNA with heterochromatin. Overall, our findings underscore the complexity of repetitive DNA elements in the genome of C. americana and emphasize the need for further exploration to elucidate their functional significance and evolutionary implications.
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Affiliation(s)
- José M. Rico-Porras
- Department of Experimental Biology, Genetics Area, University of Jaén, Paraje las Lagunillas s/n, 23071 Jaén, Spain; (J.M.R.-P.); (P.M.); (T.P.)
| | - Pablo Mora
- Department of Experimental Biology, Genetics Area, University of Jaén, Paraje las Lagunillas s/n, 23071 Jaén, Spain; (J.M.R.-P.); (P.M.); (T.P.)
| | - Teresa Palomeque
- Department of Experimental Biology, Genetics Area, University of Jaén, Paraje las Lagunillas s/n, 23071 Jaén, Spain; (J.M.R.-P.); (P.M.); (T.P.)
| | - Eugenia E. Montiel
- Department of Biology, Genetics, Faculty of Sciences, Autonomous University of Madrid, 28049 Madrid, Spain;
- Center for Research in Biodiversity and Global Change, Autonomous University of Madrid, 28049 Madrid, Spain
| | - Diogo C. Cabral-de-Mello
- Department of General and Applied Biology, Institute of Biosciences/IB, UNESP—São Paulo State University, Rio Claro 13506-900, SP, Brazil;
| | - Pedro Lorite
- Department of Experimental Biology, Genetics Area, University of Jaén, Paraje las Lagunillas s/n, 23071 Jaén, Spain; (J.M.R.-P.); (P.M.); (T.P.)
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Gálvez-Galván A, Garrido-Ramos MA, Prieto P. Bread wheat satellitome: a complex scenario in a huge genome. PLANT MOLECULAR BIOLOGY 2024; 114:8. [PMID: 38291213 PMCID: PMC10827815 DOI: 10.1007/s11103-023-01404-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/01/2023] [Indexed: 02/01/2024]
Abstract
In bread wheat (Triticum aestivum L.), chromosome associations during meiosis are extremely regulated and initiate at the telomeres and subtelomeres, which are enriched in satellite DNA (satDNA). We present the study and characterization of the bread wheat satellitome to shed light on the molecular organization of wheat subtelomeres. Our results revealed that the 2.53% of bread wheat genome is composed by satDNA and subtelomeres are particularly enriched in such DNA sequences. Thirty-four satellite DNA (21 for the first time in this work) have been identified, analyzed and cytogenetically validated. Many of the satDNAs were specifically found at particular subtelomeric chromosome regions revealing the asymmetry in subtelomere organisation among the wheat subgenomes, which might play a role in proper homologous recognition and pairing during meiosis. An integrated physical map of the wheat satellitome was also constructed. To the best of our knowledge, our results show that the combination of both cytogenetics and genome research allowed the first comprehensive analysis of the wheat satellitome, shedding light on the complex wheat genome organization, especially on the polymorphic nature of subtelomeres and their putative implication in chromosome recognition and pairing during meiosis.
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Affiliation(s)
- Ana Gálvez-Galván
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Avda. Menéndez Pidal, Campus Alameda del Obispo S/N, 14004, Córdoba, Spain
| | - Manuel A Garrido-Ramos
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva S/N, 18071, Granada, Spain.
| | - Pilar Prieto
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Avda. Menéndez Pidal, Campus Alameda del Obispo S/N, 14004, Córdoba, Spain.
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de Moraes RLR, de Menezes Cavalcante Sassi F, Vidal JAD, Goes CAG, dos Santos RZ, Stornioli JHF, Porto-Foresti F, Liehr T, Utsunomia R, de Bello Cioffi M. Chromosomal Rearrangements and Satellite DNAs: Extensive Chromosome Reshuffling and the Evolution of Neo-Sex Chromosomes in the Genus Pyrrhulina (Teleostei; Characiformes). Int J Mol Sci 2023; 24:13654. [PMID: 37686460 PMCID: PMC10563077 DOI: 10.3390/ijms241713654] [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: 08/23/2023] [Revised: 08/31/2023] [Accepted: 09/02/2023] [Indexed: 09/10/2023] Open
Abstract
Chromosomal rearrangements play a significant role in the evolution of fish genomes, being important forces in the rise of multiple sex chromosomes and in speciation events. Repetitive DNAs constitute a major component of the genome and are frequently found in heterochromatic regions, where satellite DNA sequences (satDNAs) usually represent their main components. In this work, we investigated the association of satDNAs with chromosome-shuffling events, as well as their potential relevance in both sex and karyotype evolution, using the well-known Pyrrhulina fish model. Pyrrhulina species have a conserved karyotype dominated by acrocentric chromosomes present in all examined species up to date. However, two species, namely P. marilynae and P. semifasciata, stand out for exhibiting unique traits that distinguish them from others in this group. The first shows a reduced diploid number (with 2n = 32), while the latter has a well-differentiated multiple X1X2Y sex chromosome system. In addition to isolating and characterizing the full collection of satDNAs (satellitomes) of both species, we also in situ mapped these sequences in the chromosomes of both species. Moreover, the satDNAs that displayed signals on the sex chromosomes of P. semifasciata were also mapped in some phylogenetically related species to estimate their potential accumulation on proto-sex chromosomes. Thus, a large collection of satDNAs for both species, with several classes being shared between them, was characterized for the first time. In addition, the possible involvement of these satellites in the karyotype evolution of P. marilynae and P. semifasciata, especially sex-chromosome formation and karyotype reduction in P. marilynae, could be shown.
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Affiliation(s)
- Renata Luiza Rosa de Moraes
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, SP, Brazil; (R.L.R.d.M.); (F.d.M.C.S.); (J.A.D.V.)
- Institute of Human Genetics, University Hospital Jena, 07747 Jena, Germany
| | - Francisco de Menezes Cavalcante Sassi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, SP, Brazil; (R.L.R.d.M.); (F.d.M.C.S.); (J.A.D.V.)
- Institute of Human Genetics, University Hospital Jena, 07747 Jena, Germany
| | - Jhon Alex Dziechciarz Vidal
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, SP, Brazil; (R.L.R.d.M.); (F.d.M.C.S.); (J.A.D.V.)
| | - Caio Augusto Gomes Goes
- Faculdade de Ciências, UNESP, Bauru 17033-36, SP, Brazil; (C.A.G.G.); (R.Z.d.S.); (F.P.-F.); (R.U.)
| | - Rodrigo Zeni dos Santos
- Faculdade de Ciências, UNESP, Bauru 17033-36, SP, Brazil; (C.A.G.G.); (R.Z.d.S.); (F.P.-F.); (R.U.)
| | - José Henrique Forte Stornioli
- Institute of Biological Sciences and Health, Universidade Federal Rural do Rio de Janeiro, Seropédica 23890-000, RJ, Brazil;
| | - Fábio Porto-Foresti
- Faculdade de Ciências, UNESP, Bauru 17033-36, SP, Brazil; (C.A.G.G.); (R.Z.d.S.); (F.P.-F.); (R.U.)
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, 07747 Jena, Germany
| | - Ricardo Utsunomia
- Faculdade de Ciências, UNESP, Bauru 17033-36, SP, Brazil; (C.A.G.G.); (R.Z.d.S.); (F.P.-F.); (R.U.)
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, SP, Brazil; (R.L.R.d.M.); (F.d.M.C.S.); (J.A.D.V.)
- Institute of Human Genetics, University Hospital Jena, 07747 Jena, Germany
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