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João Da Silva M, Gazoni T, Haddad CFB, Parise-Maltempi PP. Analysis in Proceratophrys boiei genome illuminates the satellite DNA content in a frog from the Brazilian Atlantic forest. Front Genet 2023; 14:1101397. [PMID: 37065500 PMCID: PMC10095563 DOI: 10.3389/fgene.2023.1101397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/13/2023] [Indexed: 03/31/2023] Open
Abstract
Satellite DNAs (satDNAs) are one of the most abundant elements in genomes. Characterized as tandemly organized sequences that can be amplified into multiple copies, mainly in heterochromatic regions. The frog P. boiei (2n = 22, ZZ♂/ZW♀) is found in the Brazilian Atlantic forest and has an atypical pattern of heterochromatin distribution when compared to other anuran amphibians, with large pericentromeric blocks on all chromosomes. In addition, females of Proceratophrys boiei have a metacentric sex chromosome W showing heterochromatin in all chromosomal extension. In this work, we performed high-throughput genomic, bioinformatic, and cytogenetic analyses to characterize the satellite DNA content (satellitome) in P. boiei, mainly due to high amount of C-positive heterochromatin and the highly heterochromatic W sex chromosome. After all the analyses, it is remarkable that the satellitome of P. boiei is composed of a high number of satDNA families (226), making P. boiei the frog species with the highest number of satellites described so far. Consistent with the observation of large centromeric C-positive heterochromatin blocks, the genome of P. boiei is enriched with high copy number of repetitive DNAs, with total satDNA abundance comprising 16.87% of the genome. We successfully mapped via Fluorescence in situ hybridization the two most abundant repeats in the genome, PboSat01-176 and PboSat02-192, highlighting the presence of certain satDNAs sequences in strategic chromosomal regions (e.g., centromere and pericentromeric region), which leads to their participation in crucial processes for genomic organization and maintenance. Our study reveals a great diversity of satellite repeats that are driving genomic organization in this frog species. The characterization and approaches regarding satDNAs in this species of frog allowed the confirmation of some insights from satellite biology and a possible relationship with the evolution of sex chromosomes, especially in anuran amphibians, including P. boiei, for which data were not available.
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Affiliation(s)
- Marcelo João Da Silva
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências (IB), Universidade Estadual Paulista (UNESP), São Paulo, Brazil
| | - Thiago Gazoni
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências (IB), Universidade Estadual Paulista (UNESP), São Paulo, Brazil
| | - Célio Fernando Baptista Haddad
- Departamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências (IB), Universidade Estadual Paulista (UNESP), São Paulo, Brazil
| | - Patricia Pasquali Parise-Maltempi
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências (IB), Universidade Estadual Paulista (UNESP), São Paulo, Brazil
- *Correspondence: Patricia Pasquali Parise-Maltempi,
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FERRO JUANM, TAFFAREL ALBERTO, TOMATIS CRISTIAN, BORTEIRO CLAUDIO, KOLENC FRANCISCO, GATTO KALEBP, LOURENÇO LUCIANAB, BALDO DIEGO. Cytogenetics of four foam-nesting frog species of the Physalaemus gracilis group (Anura, Leptodactylidae). AN ACAD BRAS CIENC 2022; 94:e20200092. [DOI: 10.1590/0001-3765202220200092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/24/2020] [Indexed: 11/21/2022] Open
Affiliation(s)
| | | | | | | | | | - KALEB P. GATTO
- Universidade Estadual de Campinas, Brazil; Universidade Estadual Paulista, Brazil
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Silva MJDA, Santos MD, Gazoni T, Cholak LR, Haddad CFB, Parise-Maltempi PP. Cytogenetic approaches provide evidence of a conserved diploid number and cytological differences between Proceratophrys species (Anura: Odontophrynidae). AN ACAD BRAS CIENC 2021; 93:e20201650. [PMID: 34586322 DOI: 10.1590/0001-3765202120201650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/17/2021] [Indexed: 05/31/2023] Open
Abstract
Taxonomic and cytogenetic aspects of Proceratophrys have not been thoroughly clarified in the literature; thus, the objective of the present study was to provide unprecedent karyotype data regarding P. schirchi, P. laticeps and P. melanopogon. Additionally, the karyotype of P. boiei (2n = 22) and its ZZ / ZW sex chromosome system was analyzed for different populations of southeastern and southern Brazil. All Proceratophrys species have a diploid number of 2n = 22 chromosomes. In P. schirchi, a strong C-band was found in the long arm in one of the homologues of the pair 8 in female metaphasic cells, denoting that this chromosome pair could represent the heteromorphic sex chromosome in a ZZ / ZW sex system. Despite the conserved number of chromosomes, there are considerable chromosomal differences in P. melanopogon and P. boiei (southern Brazil), strongly differentiating them cytogenetically from other species of the genus. Moreover, with the confirmation of chromosomal heteromorphism related to sexual differentiation in P. boiei and the possible description of this system in P. schirchi, the Proceratophrys genus can be regarded as an interesting group for evolutionary studies and sex chromosome differentiation in anurans.
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Affiliation(s)
- Marcelo João DA Silva
- Universidade Estadual Paulista, Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Avenida 24A, 1515, Bela Vista, 13506-900 Rio Claro, SP, Brazil
| | - Murilo D Santos
- Universidade Estadual Paulista, Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Avenida 24A, 1515, Bela Vista, 13506-900 Rio Claro, SP, Brazil
| | - Thiago Gazoni
- Universidade Estadual Paulista, Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Avenida 24A, 1515, Bela Vista, 13506-900 Rio Claro, SP, Brazil
| | - Luiza R Cholak
- Universidade Estadual Paulista, Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Avenida 24A, 1515, Bela Vista, 13506-900 Rio Claro, SP, Brazil
| | - Célio Fernando B Haddad
- Universidade Estadual Paulista, Departamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências, Avenida 24A, 1515, Bela Vista, 13506-906 Rio Claro, SP, Brazil
| | - Patricia P Parise-Maltempi
- Universidade Estadual Paulista, Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Avenida 24A, 1515, Bela Vista, 13506-900 Rio Claro, SP, Brazil
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da Silva MJ, Fogarin Destro R, Gazoni T, Narimatsu H, Pereira Dos Santos PS, Haddad CFB, Parise-Maltempi PP. Great Abundance of Satellite DNA in Proceratophrys (Anura, Odontophrynidae) Revealed by Genome Sequencing. Cytogenet Genome Res 2020; 160:141-147. [PMID: 32146462 DOI: 10.1159/000506531] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2020] [Indexed: 01/04/2023] Open
Abstract
Most eukaryotic genomes contain substantial portions of repetitive DNA sequences. These are located primarily in highly compacted heterochromatin and, in many cases, are one of the most abundant components of the sex chromosomes. In this sense, the anuran Proceratophrys boiei represents an interesting model for analyses on repetitive sequences by means of cytogenetic techniques, since it has a karyotype with large blocks of heterochromatin and a ZZ/ZW sex chromosome system. The present study describes, for the first time, families of satellite DNA (satDNA) in the frog P. boiei. Its genome size was estimated at 1.6 Gb, of which 41% correspond to repetitive sequences, including satDNAs, rDNAs, transposable elements, and other elements characterized as non-repetitive. The satDNAs were mapped by FISH in the centromeric and pericentromeric regions of all chromosomes, suggesting a possible involvement of these sequences in centromere function. SatDNAs are also present in the W sex chromosome, occupying the entire heterochromatic area, indicating a probable contribution of this class of repetitive DNA to the differentiation of the sex chromosomes in this species. This study is a valuable contribution to the existing knowledge on repetitive sequences in amphibians. We show the presence of repetitive DNAs, especially satDNAs, in the genome of P. boiei that might be of relevance in genome organization and regulation, setting the stage for a deeper functional genome analysis of Proceratophrys.
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Unraveling the Sex Chromosome Heteromorphism of the Paradoxical Frog Pseudis tocantins. PLoS One 2016; 11:e0156176. [PMID: 27214234 PMCID: PMC4877019 DOI: 10.1371/journal.pone.0156176] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/10/2016] [Indexed: 11/25/2022] Open
Abstract
The paradoxical frog Pseudis tocantins is the only species in the Hylidae family with known heteromorphic Z and W sex chromosomes. The Z chromosome is metacentric and presents an interstitial nucleolar organizer region (NOR) on the long arm that is adjacent to a pericentromeric heterochromatic band. In contrast, the submetacentric W chromosome carries a pericentromeric NOR on the long arm, which is adjacent to a clearly evident heterochromatic band that is larger than the band found on the Z chromosome and justify the size difference observed between these chromosomes. Here, we provide evidence that the non-centromeric heterochromatic bands in Zq and Wq differ not only in size and location but also in composition, based on comparative genomic hybridization (CGH) and an analysis of the anuran PcP190 satellite DNA. The finding of PcP190 sequences in P. tocantins extends the presence of this satellite DNA, which was previously detected among Leptodactylidae and Hylodidae, suggesting that this family of repetitive DNA is even older than it was formerly considered. Seven groups of PcP190 sequences were recognized in the genome of P. tocantins. PcP190 probes mapped to the heterochromatic band in Wq, and a Southern blot analysis indicated the accumulation of PcP190 in the female genome of P. tocantins, which suggests the involvement of this satellite DNA in the evolution of the sex chromosomes of this species.
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Dynamics of vertebrate sex chromosome evolution: from equal size to giants and dwarfs. Chromosoma 2015; 125:553-71. [DOI: 10.1007/s00412-015-0569-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 12/09/2015] [Accepted: 12/10/2015] [Indexed: 11/26/2022]
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Demographic processes in the montane Atlantic rainforest: Molecular and cytogenetic evidence from the endemic frog Proceratophrys boiei. Mol Phylogenet Evol 2012; 62:880-8. [DOI: 10.1016/j.ympev.2011.11.004] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Revised: 11/04/2011] [Accepted: 11/07/2011] [Indexed: 01/27/2023]
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Do Nascimento FAC, Lisboa BS, Skuk GO, Sá ROD. Description of the Tadpole ofProceratophrys renalis(Miranda-Ribeiro, 1920) (Anura: Cycloramphidae). J HERPETOL 2010. [DOI: 10.2994/057.005.0309] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Nascimento J, Quinderé YRSD, Recco-Pimentel SM, Lima JRF, Lourenço LB. Heteromorphic Z and W sex chromosomes in Physalaemus ephippifer (Steindachner, 1864) (Anura, Leiuperidae). Genetica 2010; 138:1127-32. [DOI: 10.1007/s10709-010-9501-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Accepted: 09/13/2010] [Indexed: 11/30/2022]
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Duarte TC, Veiga-Menoncello ACP, Lima JFR, Strüssmann C, Del-Grande ML, Giaretta AA, Pereira EG, Rossa-Feres DC, Recco-Pimentel SM. Chromosome analysis in Pseudopaludicola (Anura, Leiuperidae), with description of sex chromosomes XX/XY in P. saltica. Hereditas 2010; 147:43-52. [DOI: 10.1111/j.1601-5223.2009.02153.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Targueta C, Rivera M, Souza M, Recco-Pimentel S, Lourenço L. Cytogenetic contributions for the study of the Amazonian Engystomops (Anura; Leiuperidae) assessed in the light of phylogenetic relationships. Mol Phylogenet Evol 2010; 54:709-25. [DOI: 10.1016/j.ympev.2009.10.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Revised: 08/21/2009] [Accepted: 10/09/2009] [Indexed: 10/20/2022]
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Siqueira S, Aguiar O, Souza MB, Lima AP, Recco-Pimentel SM. Unusual intra-individual karyotypical variation and evidence of cryptic species in Amazonian populations ofPristimantis(Anura, Terrarana). Hereditas 2009; 146:141-51. [DOI: 10.1111/j.1601-5223.2009.02104.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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