1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Silva DMZDA, Ruiz-Ruano FJ, Utsunomia R, Martín-Peciña M, Castro JP, Freire PP, Carvalho RF, Hashimoto DT, Suh A, Oliveira C, Porto-Foresti F, Artoni RF, Foresti F, Camacho JPM. Long-term persistence of supernumerary B chromosomes in multiple species of Astyanax fish. BMC Biol 2021; 19:52. [PMID: 33740955 PMCID: PMC7976721 DOI: 10.1186/s12915-021-00991-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/24/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Eukaryote genomes frequently harbor supernumerary B chromosomes in addition to the "standard" A chromosome set. B chromosomes are thought to arise as byproducts of genome rearrangements and have mostly been considered intraspecific oddities. However, their evolutionary transcendence beyond species level has remained untested. RESULTS Here we reveal that the large metacentric B chromosomes reported in several fish species of the genus Astyanax arose in a common ancestor at least 4 million years ago. We generated transcriptomes of A. scabripinnis and A. paranae 0B and 1B individuals and used these assemblies as a reference for mapping all gDNA and RNA libraries to quantify coverage differences between B-lacking and B-carrying genomes. We show that the B chromosomes of A. scabripinnis and A. paranae share 19 protein-coding genes, of which 14 and 11 were also present in the B chromosomes of A. bockmanni and A. fasciatus, respectively. Our search for B-specific single-nucleotide polymorphisms (SNPs) identified the presence of B-derived transcripts in B-carrying ovaries, 80% of which belonged to nobox, a gene involved in oogenesis regulation. Importantly, the B chromosome nobox paralog is expressed > 30× more than the A chromosome paralog. This indicates that the normal regulation of this gene is altered in B-carrying females, which could potentially facilitate B inheritance at higher rates than Mendelian law prediction. CONCLUSIONS Taken together, our results demonstrate the long-term survival of B chromosomes despite their lack of regular pairing and segregation during meiosis and that they can endure episodes of population divergence leading to species formation.
Collapse
Affiliation(s)
- Duílio Mazzoni Zerbinato de Andrade Silva
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
| | - Francisco J Ruiz-Ruano
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden.
- Departamento de Genética, Universidad de Granada, 18071, Granada, Spain.
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK.
| | - Ricardo Utsunomia
- Departamento de Genética, Instituto de Ciências Biológicas e da Saúde, ICBS, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, 23897-000, Brazil
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista, UNESP, Campus de Bauru, Bauru, SP, 17033-360, Brazil
| | | | - Jonathan Pena Castro
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, UFSCAR, São Carlos, SP, 13565-905, Brazil
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, UEPG, Ponta Grossa, PR, 84030-900, Brazil
| | - Paula Paccielli Freire
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
- Departamento de Imunologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, USP, São Paulo, SP, 05508-900, Brazil
| | - Robson Francisco Carvalho
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
| | - Diogo T Hashimoto
- Centro de Aquicultura, Universidade Estadual Paulista, UNESP, Campus Jaboticabal, Jaboticabal, SP, 14884-900, Brazil
| | - Alexander Suh
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK
| | - Claudio Oliveira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
| | - Fábio Porto-Foresti
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista, UNESP, Campus de Bauru, Bauru, SP, 17033-360, Brazil
| | - Roberto Ferreira Artoni
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, UFSCAR, São Carlos, SP, 13565-905, Brazil
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, UEPG, Ponta Grossa, PR, 84030-900, Brazil
| | - Fausto Foresti
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
| | | |
Collapse
|
3
|
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.
Collapse
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.)
| |
Collapse
|
4
|
Favarato RM, Braga Ribeiro L, Ota RP, Nakayama CM, Feldberg E. Cytogenetic Characterization of Two Metynnis Species (Characiformes, Serrasalmidae) Reveals B Chromosomes Restricted to the Females. Cytogenet Genome Res 2019; 158:38-45. [DOI: 10.1159/000499954] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2018] [Indexed: 11/19/2022] Open
Abstract
Karyotypes and chromosomal characteristics with focus on B chromosomes of 2 species of the serrasalmid genus Metynnis, namely M. lippincottianus and M. maculatus, were examined using conventional (C-banding) and molecular (FISH mapping of minor and major rDNAs and Rex1, Rex3, and Rex6 retrotransposable elements) protocols. Both species possessed a diploid chromosome number of 2n = 62 and karyotypes composed of 32 metacentric + 28 submetacentric + 2 subtelocentric and 32 metacentric + 26 submetacentric + 4 subtelocentric, respectively; one small B element was found in the female genome of M. lippincottianus. C-banding revealed heterochromatin in the pericentromeric and terminal portions of all chromosomes of both species; the B chromosome was entirely heterochromatic. FISH showed 18S rDNA sites in 2 chromosome pairs in both species (pairs 19 and 22), and a large block in the B chromosome, while 5S rDNA signals were detected in the first pair of subtelocentric chromosomes in both species, moreover in M. maculatus an additional labeled pair 4 was observed. Mapping of the Rex1, Rex3, and Rex6 retrotransposable elements in the genomes of M. lippincottianus and M. maculatus indicated that they were dispersed throughout nearly all the chromosomes of the complement, except for the B chromosome of M. lippincottianus.
Collapse
|
5
|
Borges AT, Cioffi MB, Bertollo LAC, Soares RX, Costa GWWF, Molina WF. Paracentric Inversions Differentiate the Conservative Karyotypes in Two Centropomus Species (Teleostei: Centropomidae). Cytogenet Genome Res 2019; 157:239-248. [PMID: 30991393 DOI: 10.1159/000499748] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2018] [Indexed: 11/19/2022] Open
Abstract
Centropomus is the sole genus of the Centropomidae family (Teleostei), comprising 12 species widely distributed throughout the Western Atlantic and Eastern Pacific, with 6 of them occurring in the Western Atlantic in extensive sympatry. Their life history and phylogenetic relationships are well characterized; however, aspects of chromosomal evolution are still unknown. Here, cytogenetic analyses of 2 Centropomus species of great economic value (C. undecimalis and C. mexicanus) were performed using conventional (Giemsa, Ag-NOR, and fluorochrome staining, C- and replication banding) and molecular (chromosomal mapping of 18S and 5S rDNA, H2A-H2B and H3 hisDNA, and (TTAGGG)n repeats) approaches. The karyotypes of both species were composed of 48 solely acrocentric chromosomes (2n = 48; FN = 48), but the single ribosomal site was located in varying positions in the long arms of the second largest chromosome pair. Replication bands were generally similar, although conspicuous differences were observed in some chromosome regions. In both species, the histone H3 genes were located on 3 apparently homeologous chromosome pairs, but the exact position of these clusters differed slightly. Interspecific hisDNA and rDNA site displacements can indicate the occurrence of multiple paracentric inversions during the evolutionary diversification of the Centropomus genomes. Although the karyotypes remained similar in both species, our data demonstrate an unsuspected microstructural reorganization between them, driven most likely by a series of paracentric inversions.
Collapse
|
6
|
Carducci F, Barucca M, Canapa A, Biscotti MA. Rex Retroelements and Teleost Genomes: An Overview. Int J Mol Sci 2018; 19:ijms19113653. [PMID: 30463278 PMCID: PMC6274825 DOI: 10.3390/ijms19113653] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/31/2018] [Accepted: 11/16/2018] [Indexed: 01/29/2023] Open
Abstract
Repetitive DNA is an intriguing portion of the genome still not completely discovered and shows a high variability in terms of sequence, genomic organization, and evolutionary mode. On the basis of the genomic organization, it includes satellite DNAs, which are organized as long arrays of head-to-tail linked repeats, and transposable elements, which are dispersed throughout the genome. These repeated elements represent a considerable fraction of vertebrate genomes contributing significantly in species evolution. In this review, we focus our attention on Rex1, Rex3 and Rex6, three elements specific of teleost genomes. We report an overview of data available on these retroelements highlighting their significative impact in chromatin and heterochromatin organization, in the differentiation of sex chromosomes, in the formation of supernumerary chromosomes, and in karyotype evolution in teleosts.
Collapse
Affiliation(s)
- Federica Carducci
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy.
| | - Marco Barucca
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy.
| | - Adriana Canapa
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy.
| | - Maria Assunta Biscotti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy.
| |
Collapse
|
7
|
Taboada X, Rey M, Bouza C, Viñas A. Cytogenomic analysis of several repetitive DNA elements in turbot (Scophthalmus maximus). Gene 2018; 644:4-12. [PMID: 29246535 DOI: 10.1016/j.gene.2017.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 11/23/2017] [Accepted: 12/11/2017] [Indexed: 11/29/2022]
Abstract
Repetitive DNA plays a fundamental role in the organization, size and evolution of eukaryotic genomes. The sequencing of the turbot revealed a small and compact genome, as in all flatfish studied to date. The assembly of repetitive regions is still incomplete because it is difficult to correctly identify their position, number and array. The combination of classical cytogenetic techniques along with high quality sequencing is essential to increase the knowledge of the structure and composition of these sequences and, thus, of the structure and function of the whole genome. In this work, the in silico analysis of H1 histone, 5S rDNA, telomeric and Rex repetitive sequences, was compared to their chromosomal mapping by fluorescent in situ hybridization (FISH), providing a more comprehensive picture of these elements in the turbot genome. FISH assays confirmed the location of H1 in LG8; 5S rDNA in LG4 and LG6; telomeric sequences at the end of all chromosomes whereas Rex elements were dispersed along most chromosomes. The discrepancies found between both approaches could be related to the sequencing methodology applied in this species and also to the resolution limitations of the FISH technique. Turbot cytogenomic analyses have proven to add new chromosomal landmarks in the karyotype of this species, representing a powerful tool to investigate targeted genomic sequences or regions in the genetic and physical maps of this species.
Collapse
Affiliation(s)
- Xoana Taboada
- Departamento de Zoología, Genética y Antropología Física, Facultad de Biología, CIBUS, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Magalí Rey
- Departamento de Zoología, Genética y Antropología Física, Facultad de Biología, CIBUS, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Carmen Bouza
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Ana Viñas
- Departamento de Zoología, Genética y Antropología Física, Facultad de Biología, CIBUS, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| |
Collapse
|
8
|
Merlo MA, Iziga R, Portela-Bens S, Cross I, Kosyakova N, Liehr T, Manchado M, Rebordinos L. Analysis of the histone cluster in Senegalese sole (Solea senegalensis): evidence for a divergent evolution of two canonical histone clusters. Genome 2016; 60:441-453. [PMID: 28177835 DOI: 10.1139/gen-2016-0143] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The Senegalese sole (Solea senegalensis) is commercially very important and a priority species for aquaculture product diversification. The main histone cluster was identified within two BAC clones. However, two replacement histones (H1.0 and H3.3) were found in another BAC clone. Different types of canonical histones H2A and H2B were found within the same species for the first time. Phylogenetic analysis demonstrated that the different types of H1, H2A, and H2B histones were all more similar to each other than to canonical histones from other species. The canonical histone H3 of S. senegalensis differs from subtypes H3.1 and H3.2 in humans at the site of residue 96, where a serine is found instead of an alanine. This same polymorphism has been found only in Danio rerio. The karyotype of S. senegalensis comprises 21 pairs of chromosomes, distributed in 3 metacentric pairs, 2 submetacentric pairs, 4 subtelocentric pairs, and 12 acrocentric pairs. The two BAC clones that contain the clusters of canonical histones were both mapped on the largest metacentric pair, and mFISH analysis confirmed the co-location with the dmrt1 gene in that pair. Three chromosome markers have been identified which, in addition to those previously described, account for 18 chromosome pairs in S. senegalensis.
Collapse
Affiliation(s)
- Manuel Alejandro Merlo
- a Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Cádiz, Spain
| | - Roger Iziga
- a Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Cádiz, Spain
| | - Silvia Portela-Bens
- a Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Cádiz, Spain
| | - Ismael Cross
- a Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Cádiz, Spain
| | - Nadezda Kosyakova
- b Institut für Humangenetik, Universitätsklinikum Jena, 07743 Jena, Germany
| | - Thomas Liehr
- b Institut für Humangenetik, Universitätsklinikum Jena, 07743 Jena, Germany
| | - Manuel Manchado
- c Centro IFAPA "El Toruño", 11500 Puerto de Santa María, Cádiz, Spain
| | - Laureana Rebordinos
- a Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Cádiz, Spain
| |
Collapse
|