1
|
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.
Collapse
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.)
| |
Collapse
|
2
|
Fonseca-Carvalho M, Veríssimo G, Lopes M, Ferreira D, Louzada S, Chaves R. Answering the Cell Stress Call: Satellite Non-Coding Transcription as a Response Mechanism. Biomolecules 2024; 14:124. [PMID: 38254724 PMCID: PMC10813801 DOI: 10.3390/biom14010124] [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: 12/21/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
Organisms are often subjected to conditions that promote cellular stress. Cell responses to stress include the activation of pathways to defend against and recover from the stress, or the initiation of programmed cell death to eliminate the damaged cells. One of the processes that can be triggered under stress is the transcription and variation in the number of copies of satellite DNA sequences (satDNA), which are involved in response mechanisms. Satellite DNAs are highly repetitive tandem sequences, mainly located in the centromeric and pericentromeric regions of eukaryotic chromosomes, where they form the constitutive heterochromatin. Satellite non-coding RNAs (satncRNAs) are important regulators of cell processes, and their deregulation has been associated with disease. Also, these transcripts have been associated with stress-response mechanisms in varied eukaryotic species. This review intends to explore the role of satncRNAs when cells are subjected to adverse conditions. Studying satDNA transcription under various stress conditions and deepening our understanding of where and how these sequences are involved could be a key factor in uncovering important facts about the functions of these sequences.
Collapse
Affiliation(s)
- Marisa Fonseca-Carvalho
- CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.F.-C.); (G.V.); (M.L.); (D.F.); (S.L.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Gabriela Veríssimo
- CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.F.-C.); (G.V.); (M.L.); (D.F.); (S.L.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Mariana Lopes
- CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.F.-C.); (G.V.); (M.L.); (D.F.); (S.L.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Daniela Ferreira
- CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.F.-C.); (G.V.); (M.L.); (D.F.); (S.L.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Sandra Louzada
- CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.F.-C.); (G.V.); (M.L.); (D.F.); (S.L.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Raquel Chaves
- CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.F.-C.); (G.V.); (M.L.); (D.F.); (S.L.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| |
Collapse
|
3
|
Lima JF, Carvalho LS, Carvalho MA, Schneider MC. Chromosome diversity in Buthidae and Chactidae scorpions from Brazilian fauna: Diploid number and distribution of repetitive DNA sequences. Genet Mol Biol 2023; 46:e20220083. [PMID: 37216321 DOI: 10.1590/1678-4685-gmb-2022-0083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/23/2023] [Indexed: 05/24/2023] Open
Abstract
In this work, we analyzed cytogenetically eight Chactidae and Buthidae, including the localization of repetitive DNA sequences. The chactids possess monocentric chromosomes and the highest diploid numbers (2n=50 in Brotheas amazonicus, 2n=36 in Chactopsis amazonica, 2n=30 in Neochactas sp.) when compared with buthids (2n=10 in Tityus bahiensis, 2n=14 in Tityus apiacas and Tityus metuendus, 2n=18 in Tityus aba, 2n=26 in Ischnotelson peruassu). The localization of rDNA genes and (TTAGG)n sequences exhibited a conserved pattern of two terminal/subterminal ribosomal cistrons and terminal telomere signals. However, the comparison between the data of C-banding, DAPI after FISH and Cot-DNA fraction indicated a variable quantity and distribution of these regions, as follow: (i) positive heterochromatin and Cot-DNA signals (B. amazonicus and I. peruassu), (ii) small blocks of heterochromatin with large Cot-DNA signals (T. metuendus), (iii) positive heterochromatic regions and absence of Cot-DNA signals (T. aba and T. apiacas), and (iv) negative heterochromatin and Cot-DNA signals (T. bahiensis). Therefore, our results revealed that there still is not a clear relation between quantity of heterochromatin and presence of monocentric or holocentric chromosomes and occurrence of chromosomal rearrangements, indicating that repetitive regions in scorpions must be analyzed using different cytogenetic approaches.
Collapse
Affiliation(s)
- Juliana Figueiredo Lima
- Universidade de São Paulo (USP), Instituto de Biociências, Departamento de Zoologia, Programa de Pós-Graduação em Zoologia, São Paulo, SP, Brazil
| | | | - Marcos André Carvalho
- Universidade Federal de Mato Grosso (UFMT), Departamento de Biologia e Zoologia, Cuiabá, MT, Brazil
| | | |
Collapse
|
4
|
Pereira JA, Cabral-de-Mello DC, Lopes DM. The Satellite DNAs Populating the Genome of Trigona hyalinata and the Sharing of a Highly Abundant satDNA in Trigona Genus. Genes (Basel) 2023; 14:418. [PMID: 36833345 PMCID: PMC9957317 DOI: 10.3390/genes14020418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/08/2023] Open
Abstract
Among Meliponini species, c-heterochromatin can occupy large portions of chromosomes. This characteristic could be useful for understanding evolutionary patterns of satellite DNAs (satDNAs), although few sequences have been characterized in these bees. In Trigona, phylogenetically represented by clades A and B, the c-heterochromatin is mostly located in one chromosome arm. Here we used different techniques, including restriction endonucleases and genome sequencing followed by chromosomal analysis, to identify satDNAs that may be contributing to the evolution of c-heterochromatin in Trigona. Our results revealed a highly abundant ThyaSat01-301 satDNA, corresponding to about 13.77% of the Trigona hyalinata genome. Another seven satDNAs were identified, one corresponding to 2.24%, and the other six corresponding to 0.545% of the genome. The satDNA ThyaSat01-301 was shown to be one of the main constituents of the c-heterochromatin of this species, as well as of other species belonging to clade B of Trigona. However, this satDNA was not observed on the chromosomes of species from clade A, demonstrating that the c-heterochromatin is evolving divergently between species of clade A and B, as a consequence of the evolution of repetitive DNA sequences. Finally, our data suggest the molecular diversification of the karyotypes, despite a conservated macrochromosomal structure on the genus.
Collapse
Affiliation(s)
- Jaqueline A. Pereira
- Laboratório de Citogenética de Insetos, Departamento de Biologia Geral, Universidade Federal de Viçosa, P.H. Rolfs Avenue, Viçosa 36570-900, Minas Gerais, Brazil
| | - Diogo C. Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociêcias/IB, UNESP–Universidade Estadual Paulista, 24 A Avenue, Rio Claro 13506-900, São Paulo, Brazil
- Department of Experimental Biology, Genetics Area, University of Jaén, Paraje las Lagunillas s/n, 23071 Jaén, Spain
| | - Denilce M. Lopes
- Laboratório de Citogenética de Insetos, Departamento de Biologia Geral, Universidade Federal de Viçosa, P.H. Rolfs Avenue, Viçosa 36570-900, Minas Gerais, Brazil
| |
Collapse
|
5
|
Mora P, Pita S, Montiel EE, Rico-Porras JM, Palomeque T, Panzera F, Lorite P. Making the Genome Huge: The Case of Triatoma delpontei, a Triatominae Species with More than 50% of Its Genome Full of Satellite DNA. Genes (Basel) 2023; 14:genes14020371. [PMID: 36833298 PMCID: PMC9957312 DOI: 10.3390/genes14020371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/17/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
The genome of Triatoma delpontei Romaña & Abalos 1947 is the largest within Heteroptera, approximately two to three times greater than other evaluated Heteroptera genomes. Here, the repetitive fraction of the genome was determined and compared with its sister species Triatoma infestans Klug 1834, in order to shed light on the karyotypic and genomic evolution of these species. The T. delpontei repeatome analysis showed that the most abundant component in its genome is satellite DNA, which makes up more than half of the genome. The T. delpontei satellitome includes 160 satellite DNA families, most of them also present in T. infestans. In both species, only a few satellite DNA families are overrepresented on the genome. These families are the building blocks of the C-heterochromatic regions. Two of these satellite DNA families that form the heterochromatin are the same in both species. However, there are satellite DNA families highly amplified in the heterochromatin of one species that in the other species are in low abundance and located in the euchromatin. Therefore, the present results depicted the great impact of the satellite DNA sequences in the evolution of Triatominae genomes. Within this scenario, satellitome determination and analysis led to a hypothesis that explains how satDNA sequences have grown on T. delpontei to reach its huge genome size within true bugs.
Collapse
Affiliation(s)
- Pablo Mora
- Department of Experimental Biology, Genetics Area, University of Jaén, Paraje las Lagunillas s/n, 23071 Jaén, Spain
| | - Sebastián Pita
- Evolutionary Genetic Section, Faculty of Science, University of the Republic, Iguá 4225, Montevideo 11400, Uruguay
- Correspondence: (S.P.); (P.L.)
| | - Eugenia E. Montiel
- Department of Experimental Biology, Genetics Area, University of Jaén, Paraje las Lagunillas s/n, 23071 Jaén, Spain
| | - José M. Rico-Porras
- Department of Experimental Biology, Genetics Area, University of Jaén, Paraje las Lagunillas s/n, 23071 Jaén, Spain
| | - Teresa Palomeque
- Department of Experimental Biology, Genetics Area, University of Jaén, Paraje las Lagunillas s/n, 23071 Jaén, Spain
| | - Francisco Panzera
- Evolutionary Genetic Section, Faculty of Science, University of the Republic, Iguá 4225, Montevideo 11400, Uruguay
| | - Pedro Lorite
- Department of Experimental Biology, Genetics Area, University of Jaén, Paraje las Lagunillas s/n, 23071 Jaén, Spain
- Correspondence: (S.P.); (P.L.)
| |
Collapse
|
6
|
Anjos A, Milani D, Bardella VB, Paladini A, Cabral-de-Mello DC. Evolution of satDNAs on holocentric chromosomes: insights from hemipteran insects of the genus Mahanarva. CHROMOSOME RESEARCH : AN INTERNATIONAL JOURNAL ON THE MOLECULAR, SUPRAMOLECULAR AND EVOLUTIONARY ASPECTS OF CHROMOSOME BIOLOGY 2023; 31:5. [PMID: 36705735 DOI: 10.1007/s10577-023-09710-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/09/2022] [Accepted: 12/05/2022] [Indexed: 01/28/2023]
Abstract
Satellite DNAs (satDNAs) constitute one of the main components of eukaryote genomes and are involved in chromosomal organization and diversification. Although largely studied, little information was gathered about their evolution on holocentric species, i.e., diffuse centromeres, which, due to differences in repeat organization, could result in different evolutionary patterns. Here, we combined bioinformatics and cytogenetic approaches to evaluate the evolution of the satellitomes in Mahanarva holocentric insects. In two species, de novo identification revealed a high number of satDNAs, 110 and 113, with an extreme monomer length range of 18-4228 bp. The overall abundance of satDNAs was observed to be 6.67% in M. quadripunctata and 1.98% in M. spectabilis, with different abundances for the shared satDNAs. Chromosomal mapping of the most abundant repeats of M. quadripunctata and M. spectabilis on other Mahanarva reinforced the dynamic nature of satDNAs. Variable patterns of chromosomal distribution for the satDNAs were noticed, with the occurrence of clusters on distinct numbers of chromosomes and at different positions and the occurrence of scattered signals or nonclustered satDNAs. Altogether, our data demonstrated the high dynamism of satDNAs in Mahanarva with the involvement of this genomic fraction in chromosome diversification of the genus. The general characteristics and patterns of evolution of satDNAs are similar to those observed on monocentric chromosomes, suggesting that the differential organization of genome compartments observed on holocentric chromosomes compared with monocentric chromosomes does not have a large impact on the evolution of satDNAs. Analysis of the satellitomes of other holocentric species in a comparative manner will shed light on this issue.
Collapse
Affiliation(s)
- Allison Anjos
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, UNESP, Rio Claro, SP, 13506-900, Brazil
| | - Diogo Milani
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, UNESP, Rio Claro, SP, 13506-900, Brazil
| | - Vanessa B Bardella
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, UNESP, Rio Claro, SP, 13506-900, Brazil
| | - Andressa Paladini
- Departamento de Ecologia e Evolução, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, UNESP, Rio Claro, SP, 13506-900, Brazil.
- Department of Experimental Biology, Genetics Area, University of Jaén, Paraje las Lagunillas s/n, 23071, Jaen, Spain.
| |
Collapse
|
7
|
Silva BSML, Picorelli ACR, Kuhn GCS. In Silico Identification and Characterization of Satellite DNAs in 23 Drosophila Species from the Montium Group. Genes (Basel) 2023; 14:genes14020300. [PMID: 36833227 PMCID: PMC9957191 DOI: 10.3390/genes14020300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/24/2023] Open
Abstract
Satellite DNA (satDNA) is a class of tandemly repeated non-protein coding DNA sequences which can be found in abundance in eukaryotic genomes. They can be functional, impact the genomic architecture in many ways, and their rapid evolution has consequences for species diversification. We took advantage of the recent availability of sequenced genomes from 23 Drosophila species from the montium group to study their satDNA landscape. For this purpose, we used publicly available whole-genome sequencing Illumina reads and the TAREAN (tandem repeat analyzer) pipeline. We provide the characterization of 101 non-homologous satDNA families in this group, 93 of which are described here for the first time. Their repeat units vary in size from 4 bp to 1897 bp, but most satDNAs show repeat units < 100 bp long and, among them, repeats ≤ 10 bp are the most frequent ones. The genomic contribution of the satDNAs ranges from ~1.4% to 21.6%. There is no significant correlation between satDNA content and genome sizes in the 23 species. We also found that at least one satDNA originated from an expansion of the central tandem repeats (CTRs) present inside a Helitron transposon. Finally, some satDNAs may be useful as taxonomic markers for the identification of species or subgroups within the group.
Collapse
|
8
|
Gutiérrez J, Aleix-Mata G, Montiel EE, Cabral-de-Mello DC, Marchal JA, Sánchez A. Satellitome Analysis on Talpa aquitania Genome and Inferences about the satDNAs Evolution on Some Talpidae. Genes (Basel) 2022; 14:117. [PMID: 36672858 PMCID: PMC9859602 DOI: 10.3390/genes14010117] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023] Open
Abstract
In the genus Talpa a new species, named Talpa aquitania, has been recently described. Only cytogenetic data are available for the nuclear genome of this species. In this work, we characterize the satellitome of the T. aquitania genome that presents 16 different families, including telomeric sequences, and they represent 1.24% of the genome. The first satellite DNA family (TaquSat1-183) represents 0.558%, and six more abundant families, including TaquSat1-183, comprise 1.13%, while the remaining 11 sat-DNAs represent only 0.11%. The average A + T content of the SatDNA families was 50.43% and the median monomer length was 289.24 bp. The analysis of these SatDNAs indicated that they have different grades of clusterization, homogenization, and degeneration. Most of the satDNA families are present in the genomes of the other Talpa species analyzed, while in the genomes of other more distant species of Talpidae, only some of them are present, in accordance with the library hypothesis. Moreover, chromosomal localization by FISH revealed that some satDNAs are localized preferentially on centromeric and non-centromeric heterochromatin in T. aquitania and also in the sister species T. occidentalis karyotype. The differences observed between T. aquitania and the close relative T. occidentalis and T. europaea suggested that the satellitome is a very dynamic component of the genomes and that the satDNAs could be responsible for chromosomal differences between the species. Finally, in a broad context, these data contribute to the understanding of the evolution of satellitomes on mammals.
Collapse
Affiliation(s)
- Juana Gutiérrez
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain
| | - Gaël Aleix-Mata
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain
| | - Eugenia E. Montiel
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain
| | - Diogo C. Cabral-de-Mello
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP—Universidade Estadual Paulista, Rio Claro, São Paulo 13506-900, Brazil
| | - Juan Alberto Marchal
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain
| | - Antonio Sánchez
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain
| |
Collapse
|
9
|
Telomeres and Their Neighbors. Genes (Basel) 2022; 13:genes13091663. [PMID: 36140830 PMCID: PMC9498494 DOI: 10.3390/genes13091663] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/21/2022] Open
Abstract
Telomeres are essential structures formed from satellite DNA repeats at the ends of chromosomes in most eukaryotes. Satellite DNA repeat sequences are useful markers for karyotyping, but have a more enigmatic role in the eukaryotic cell. Much work has been done to investigate the structure and arrangement of repetitive DNA elements in classical models with implications for species evolution. Still more is needed until there is a complete picture of the biological function of DNA satellite sequences, particularly when considering non-model organisms. Celebrating Gregor Mendel’s anniversary by going to the roots, this review is designed to inspire and aid new research into telomeres and satellites with a particular focus on non-model organisms and accessible experimental and in silico methods that do not require specialized equipment or expensive materials. We describe how to identify telomere (and satellite) repeats giving many examples of published (and some unpublished) data from these techniques to illustrate the principles behind the experiments. We also present advice on how to perform and analyse such experiments, including details of common pitfalls. Our examples are a selection of recent developments and underexplored areas of research from the past. As a nod to Mendel’s early work, we use many examples from plants and insects, especially as much recent work has expanded beyond the human and yeast models traditional in telomere research. We give a general introduction to the accepted knowledge of telomere and satellite systems and include references to specialized reviews for the interested reader.
Collapse
|
10
|
Montiel EE, Mora P, Rico-Porras JM, Palomeque T, Lorite P. Satellitome of the Red Palm Weevil, Rhynchophorus ferrugineus (Coleoptera: Curculionidae), the Most Diverse Among Insects. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.826808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The red palm weevil, Rhynchophorus ferrugineus, is the most harmful species among those pests affecting palm trees. Its impact causes important economic losses around the World. Nevertheless, the genetic information of Rh. ferrugineus is very scarce. Last year, the first genome assembly was published including a rough description of its repeatome. However, no information has been added about one of the main components of repeated DNA, the satellite DNA. Herein, we presented the characterization of the satellitome of this important species that includes 112 satellite DNA families, the largest number in an insect genome. These satellite DNA families made up around 25% of the genome while the most abundant family, RferSat01-169, alone represented 20.4%. Chromosomal location of most abundant satellite DNA families performed by fluorescence in situ hybridization showed that all of them are dispersed in the euchromatin on all chromosomes but some of them are also specifically accumulated either on the pericentromeric heterochromatic regions of all chromosomes or on specific chromosomes. Finally, the transcription of satellitome families was analyzed through Rh. ferrugineus development. It was found that 55 out of 112 satellite DNA families showed transcription, some families seemed to be transcribed across all stages while a few appeared to be stage-specific, indicating a possible role of those satellite DNA sequences in the development of this species.
Collapse
|
11
|
Satellitome Analysis and Transposable Elements Comparison in Geographically Distant Populations of Spodoptera frugiperda. Life (Basel) 2022; 12:life12040521. [PMID: 35455012 PMCID: PMC9026859 DOI: 10.3390/life12040521] [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: 02/28/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 11/29/2022] Open
Abstract
Spodoptera frugiperda (fall armyworm) is a member of the superfamily Noctuoidea that accounts for more than a third of all Lepidoptera and includes a considerable number of agricultural and forest pest species. Spodoptera frugiperda is a polyphagous species that is a significant agricultural pest worldwide, emphasizing its economic importance. Spodoptera frugiperda’s genome size, assembly, phylogenetic classification, and transcriptome analysis have all been previously described. However, the different studies reported different compositions of repeated DNA sequences that occupied the whole assembled genome, and the Spodoptera frugiperda genome also lacks the comprehensive study of dynamic satellite DNA. We conducted a comparative analysis of repetitive DNA across geographically distant populations of Spodoptera frugiperda, particularly satellite DNA, using publicly accessible raw genome data from eight different geographical regions. Our results showed that most transposable elements (TEs) were commonly shared across all geographically distant samples, except for the Maverick and PIF/Harbinger elements, which have divergent repeat copies. The TEs age analysis revealed that most TEs families consist of young copies 1–15 million years old; however, PIF/Harbinger has some older/degenerated copies of 30–35 million years old. A total of seven satellite DNA families were discovered, accounting for approximately 0.65% of the entire genome of the Spodoptera frugiperda fall armyworm. The repeat profiling analysis of satellite DNA families revealed differential read depth coverage or copy numbers. The satellite DNA families range in size from the lowest 108 bp SfrSat06-108 families to the largest (1824 bp) SfrSat07-1824 family. We did not observe a statistically significant correlation between monomer length and K2P divergence, copy number, or abundance of each satellite family. Our findings suggest that the satellite DNA families identified in Spodoptera frugiperda account for a considerable proportion of the genome’s repetitive fraction. The satellite DNA families’ repeat profiling revealed a point mutation along the reference sequences. Limited TEs differentiation exists among geographically distant populations of Spodoptera frugiperda.
Collapse
|
12
|
Ibiapino A, Báez M, García MA, Costea M, Stefanović S, Pedrosa-Harand A. Karyotype asymmetry in Cuscuta L. subgenus Pachystigma reflects its repeat DNA composition. Chromosome Res 2022; 30:91-107. [PMID: 35089455 DOI: 10.1007/s10577-021-09683-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 12/25/2022]
Abstract
Cuscuta is a cytogenetically diverse genus, with karyotypes varying 18-fold in chromosome number and 127-fold in genome size. Each of its four subgenera also presents particular chromosomal features, such as bimodal karyotypes in Pachystigma. We used low coverage sequencing of the Cuscuta nitida genome (subgenus Pachystigma), as well as chromosome banding and molecular cytogenetics of three subgenus representatives, to understand the origin of bimodal karyotypes. All three species, C. nitida, C. africana (2n = 28) and C. angulata (2n = 30), showed heterochromatic bands mainly in the largest chromosome pairs. Eighteen satellite DNAs were identified in C. nitida genome, two showing similarity to mobile elements. The most abundant were present at the largest pairs, as well as the highly abundant ribosomal DNAs. The most abundant Ty1/Copia and Ty3/Gypsy elements were also highly enriched in the largest pairs, except for the Ty3/Gypsy CRM, which also labelled the pericentromeric regions of the smallest chromosomes. This accumulation of repetitive DNA in the larger pairs indicates that these sequences are largely responsible for the formation of bimodal karyotypes in the subgenus Pachystigma. The repetitive DNA fraction is directly linked to karyotype evolution in Cuscuta.
Collapse
Affiliation(s)
- Amalia Ibiapino
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Mariana Báez
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil.,Plant Breeding Department, University of Bonn, Bonn, Germany
| | | | - Mihai Costea
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, Canada
| | - Saša Stefanović
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil.
| |
Collapse
|
13
|
Affiliation(s)
| | - Francisco J. Ruiz-Ruano
- Department of Organismal Biology – Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- School of Biological Sciences, Norwich Research Park University of East Anglia, Norwich, UK
| |
Collapse
|
14
|
Santander MD, Cabral-de-Mello DC, Taffarel A, Martí E, Martí DA, Palacios-Gimenez OM, Castillo ERD. New insights into the six decades of Mesa’s hypothesis of chromosomal evolution in Ommexechinae grasshoppers (Orthoptera: Acridoidea). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlaa188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
In Acridoidea grasshoppers, chromosomal rearrangements are frequently found as deviations from the standard acrocentric karyotype (2n = 23♂/24♀, FN = 23♂/24♀) in either phylogenetically unrelated species or shared by closely related ones, i.e. genus. In the South American subfamily Ommexechinae, most of the species show a unique karyotype (2n = 23♂/24♀, FN = 25♂/26♀) owing to the occurrence of a large autosomal pair (L1) with submetacentric morphology. In the early 1960s, Alejo Mesa proposed the hypothesis of an ancestral pericentric inversion to explain this karyotype variation. Furthermore, in Ommexechinae, extra chromosomal rearrangements (e.g. centric fusions) are recorded between the ancestral X chromosome and autosomes that originated the so-called neo-sex chromosomes. However, the evolutionary significance of the pericentric inversions and centric fusions in Ommexechinae remains poorly explored. Aiming for a better understanding of chromosomal evolution in Ommexechinae, we performed a detailed cytogenetic analysis in five species. Our findings support the hypothesis about the occurrence of an early pericentric inversion in the ancestor of Ommexechinae. Moreover, our results show a complex karyotype diversification pattern due to several chromosome rearrangements, variations in heterochromatin and repetitive DNA dynamics. Finally, the chromosomal mapping of U2 snDNA in L1 provided new insights about the morphological evolution of this autosomal pair and revealed unnoticed chromosome reorganizations.
Collapse
Affiliation(s)
- Mylena D Santander
- Laboratorio de Genética Evolutiva Dr. Claudio J. Bidau. Instituto de Biología Subtropical (IBS) CONICET-UNaM. FCEQyN. Posadas, Misiones, Argentina
- Departamento de Genética e Biologia Evolutiva. Instituto de Biociências, Universidade de São Paulo (USP). São Paulo, São Paulo, Brazil
| | - Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Universidade Estadual Paulista (UNESP), Instituto de Biociências/IB. Rio Claro, São Paulo, Brazil
| | - Alberto Taffarel
- Laboratorio de Genética Evolutiva Dr. Claudio J. Bidau. Instituto de Biología Subtropical (IBS) CONICET-UNaM. FCEQyN. Posadas, Misiones, Argentina
| | - Emiliano Martí
- Departamento de Biologia Geral e Aplicada, Universidade Estadual Paulista (UNESP), Instituto de Biociências/IB. Rio Claro, São Paulo, Brazil
| | - Dardo A Martí
- Laboratorio de Genética Evolutiva Dr. Claudio J. Bidau. Instituto de Biología Subtropical (IBS) CONICET-UNaM. FCEQyN. Posadas, Misiones, Argentina
| | - Octavio M Palacios-Gimenez
- Department of Organismal Biology – Systematic Biology Program, Evolutionary Biology Centre, Uppsala University
| | - Elio Rodrigo D Castillo
- Laboratorio de Genética Evolutiva Dr. Claudio J. Bidau. Instituto de Biología Subtropical (IBS) CONICET-UNaM. FCEQyN. Posadas, Misiones, Argentina
| |
Collapse
|
15
|
Comparative Analysis of Transposable Elements in Genus Calliptamus Grasshoppers Revealed That Satellite DNA Contributes to Genome Size Variation. INSECTS 2021; 12:insects12090837. [PMID: 34564277 PMCID: PMC8466570 DOI: 10.3390/insects12090837] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/01/2021] [Accepted: 09/14/2021] [Indexed: 12/15/2022]
Abstract
Simple Summary Calliptamus is a genus of grasshoppers belonging to the family Acrididae. The genus Calliptamus includes approximately 17 recognized species. Calliptamus abbreviatus, Calliptamus italicus, and Calliptamus barbarus are three species that are widely found in northern China. These species are polyphagous, feeding on a variety of wild plants as well as crops, particularly legumes. The genome sizes, phylogenetic position, and transcriptome analysis of the genus Calliptamus were already known previous to this research. The repeatome analysis of these species was missing, which is directly linked to the larger genome sizes of the grasshoppers. Here, we classified repetitive DNA sequences at the level of superfamilies and sub-families, and found that LINE, TcMar-Tc1 and Ty3-gypsy LTR retrotransposons dominated the repeatomes of all genomes, accounting for 16–34% of the total genomes of these species. Satellite DNA dynamic evolutionary changes in all three genomes played a role in genome size evolution. This study would be a valuable source for future genome assemblies. Abstract Transposable elements (TEs) play a significant role in both eukaryotes and prokaryotes genome size evolution, structural changes, duplication, and functional variabilities. However, the large number of different repetitive DNA has hindered the process of assembling reference genomes, and the genus level TEs diversification of the grasshopper massive genomes is still under investigation. The genus Calliptamus diverged from Peripolus around 17 mya and its species divergence dated back about 8.5 mya, but their genome size shows rather large differences. Here, we used low-coverage Illumina unassembled short reads to investigate the effects of evolutionary dynamics of satDNAs and TEs on genome size variations. The Repeatexplorer2 analysis with 0.5X data resulted in 52%, 56%, and 55% as repetitive elements in the genomes of Calliptamus barbarus, Calliptamus italicus, and Calliptamus abbreviatus, respectively. The LINE and Ty3-gypsy LTR retrotransposons and TcMar-Tc1 dominated the repeatomes of all genomes, accounting for 16–35% of the total genomes of these species. Comparative analysis unveiled that most of the transposable elements (TEs) except satDNAs were highly conserved across three genomes in the genus Calliptamus grasshoppers. Out of a total of 20 satDNA families, 17 satDNA families were commonly shared with minor variations in abundance and divergence between three genomes, and 3 were Calliptamus barbarus specific. Our findings suggest that there is a significant amplification or contraction of satDNAs at genus phylogeny which is the main cause that made genome size different.
Collapse
|
16
|
Kuhn GCS, Heringer P, Dias GB. Structure, Organization, and Evolution of Satellite DNAs: Insights from the Drosophila repleta and D. virilis Species Groups. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2021; 60:27-56. [PMID: 34386871 DOI: 10.1007/978-3-030-74889-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The fact that satellite DNAs (satDNAs) in eukaryotes are abundant genomic components, can perform functional roles, but can also change rapidly across species while being homogenous within a species, makes them an intriguing and fascinating genomic component to study. It is also becoming clear that satDNAs represent an important piece in genome architecture and that changes in their structure, organization, and abundance can affect the evolution of genomes and species in many ways. Since the discovery of satDNAs more than 50 years ago, species from the Drosophila genus have continuously been used as models to study several aspects of satDNA biology. These studies have been largely concentrated in D. melanogaster and closely related species from the Sophophora subgenus, even though the vast majority of all Drosophila species belong to the Drosophila subgenus. This chapter highlights some studies on the satDNA structure, organization, and evolution in two species groups from the Drosophila subgenus: the repleta and virilis groups. We also discuss and review the classification of other abundant tandem repeats found in these species in the light of the current information available.
Collapse
Affiliation(s)
- Gustavo C S Kuhn
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil.
| | - Pedro Heringer
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Guilherme Borges Dias
- Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| |
Collapse
|
17
|
Montiel EE, Panzera F, Palomeque T, Lorite P, Pita S. Satellitome Analysis of Rhodnius prolixus, One of the Main Chagas Disease Vector Species. Int J Mol Sci 2021; 22:6052. [PMID: 34205189 PMCID: PMC8199985 DOI: 10.3390/ijms22116052] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 12/13/2022] Open
Abstract
The triatomine Rhodnius prolixus is the main vector of Chagas disease in countries such as Colombia and Venezuela, and the first kissing bug whose genome has been sequenced and assembled. In the repetitive genome fraction (repeatome) of this species, the transposable elements represented 19% of R. prolixus genome, being mostly DNA transposon (Class II elements). However, scarce information has been published regarding another important repeated DNA fraction, the satellite DNA (satDNA), or satellitome. Here, we offer, for the first time, extended data about satellite DNA families in the R. prolixus genome using bioinformatics pipeline based on low-coverage sequencing data. The satellitome of R. prolixus represents 8% of the total genome and it is composed by 39 satDNA families, including four satDNA families that are shared with Triatoma infestans, as well as telomeric (TTAGG)n and (GATA)n repeats, also present in the T. infestans genome. Only three of them exceed 1% of the genome. Chromosomal hybridization with these satDNA probes showed dispersed signals over the euchromatin of all chromosomes, both in autosomes and sex chromosomes. Moreover, clustering analysis revealed that most abundant satDNA families configured several superclusters, indicating that R. prolixus satellitome is complex and that the four most abundant satDNA families are composed by different subfamilies. Additionally, transcription of satDNA families was analyzed in different tissues, showing that 33 out of 39 satDNA families are transcribed in four different patterns of expression across samples.
Collapse
Affiliation(s)
- Eugenia E. Montiel
- Department of Experimental Biology, Genetics, University of Jaén. Paraje las Lagunillas sn., 23071 Jaén, Spain; (E.E.M.); (T.P.)
| | - Francisco Panzera
- Evolutionary Genetic Section, Faculty of Science, University of the Republic, Iguá 4225, Montevideo 11400, Uruguay;
| | - Teresa Palomeque
- Department of Experimental Biology, Genetics, University of Jaén. Paraje las Lagunillas sn., 23071 Jaén, Spain; (E.E.M.); (T.P.)
| | - Pedro Lorite
- Department of Experimental Biology, Genetics, University of Jaén. Paraje las Lagunillas sn., 23071 Jaén, Spain; (E.E.M.); (T.P.)
| | - Sebastián Pita
- Evolutionary Genetic Section, Faculty of Science, University of the Republic, Iguá 4225, Montevideo 11400, Uruguay;
| |
Collapse
|
18
|
Cytogenetic Analysis, Heterochromatin Characterization and Location of the rDNA Genes of Hycleus scutellatus (Coleoptera, Meloidae); A Species with an Unexpected High Number of rDNA Clusters. INSECTS 2021; 12:insects12050385. [PMID: 33925926 PMCID: PMC8146434 DOI: 10.3390/insects12050385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/17/2021] [Accepted: 04/23/2021] [Indexed: 01/12/2023]
Abstract
Simple Summary The family Meloidae contains approximately 3000 species, commonly known as blister beetles for their ability to secrete a substance called cantharidin, which causes irritation and blistering in contact with animal or human skin. In recent years there have been numerous studies focused on the anticancer action of cantharidin and its derivatives. Despite the recent interest in blister beetles, cytogenetic and molecular studies in this group are scarce and most of them use only classical chromosome staining techniques. The main aim of our study was to provide new information in Meloidae. In this study, cytogenetic and molecular analyses were applied for the first time in the family Meloidae. We applied fluorescence staining with DAPI and the position of ribosomal DNA in Hycleus scutellatus was mapped by FISH. Hycleus is one of the most species-rich genera of Meloidae but no cytogenetic data have yet been published for this particular genus. Additionally, we isolated a satellite DNA family located within the pericentromeric regions of all chromosomes. The results obtained in this study may be a suitable starting point to initiate more extensive cytogenetic analyses in this important species-rich genus, and in the family Meloidae in general. Abstract Meloidae are commonly known as blister beetles, so called for the secretion of cantharidin, a toxic substance that causes irritation and blistering. There has been a recent increase in the interest of the cantharidin anticancer potential of this insect group. Cytogenetic and molecular data in this group are scarce. In this study, we performed a karyotype analysis of Hycleus scutellatus, an endemic species of the Iberian Peninsula. We determined its chromosome number, 2n = 20, as well as the presence of the X and Y sex chromosomes. In addition to a karyotype analysis, we carried out DAPI staining. By fluorescence in situ hybridization we mapped the rDNA clusters on 12 different chromosomes. Compared to others, this species shows an unusually high number of chromosomes carrying rDNA. This is one of the highest numbers of rDNA sites found in the Polyphaga suborder (Coleoptera). Additionally, we isolated a satellite DNA family (Hyscu-H), which was located within the pericentromeric regions of all chromosomes, including the sex chromosomes. The results suggest that Hyscu-H is likely to be one of the most abundant satellite DNA repeats in H. scutellatus.
Collapse
|
19
|
Thakur J, Packiaraj J, Henikoff S. Sequence, Chromatin and Evolution of Satellite DNA. Int J Mol Sci 2021; 22:ijms22094309. [PMID: 33919233 PMCID: PMC8122249 DOI: 10.3390/ijms22094309] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 12/15/2022] Open
Abstract
Satellite DNA consists of abundant tandem repeats that play important roles in cellular processes, including chromosome segregation, genome organization and chromosome end protection. Most satellite DNA repeat units are either of nucleosomal length or 5–10 bp long and occupy centromeric, pericentromeric or telomeric regions. Due to high repetitiveness, satellite DNA sequences have largely been absent from genome assemblies. Although few conserved satellite-specific sequence motifs have been identified, DNA curvature, dyad symmetries and inverted repeats are features of various satellite DNAs in several organisms. Satellite DNA sequences are either embedded in highly compact gene-poor heterochromatin or specialized chromatin that is distinct from euchromatin. Nevertheless, some satellite DNAs are transcribed into non-coding RNAs that may play important roles in satellite DNA function. Intriguingly, satellite DNAs are among the most rapidly evolving genomic elements, such that a large fraction is species-specific in most organisms. Here we describe the different classes of satellite DNA sequences, their satellite-specific chromatin features, and how these features may contribute to satellite DNA biology and evolution. We also discuss how the evolution of functional satellite DNA classes may contribute to speciation in plants and animals.
Collapse
Affiliation(s)
- Jitendra Thakur
- Department of Biology, Emory University, Atlanta, GA 30322, USA;
- Correspondence:
| | - Jenika Packiaraj
- Department of Biology, Emory University, Atlanta, GA 30322, USA;
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
- Fred Hutchinson Cancer Research Center, Howard Hughes Medical Institute, Seattle, WA 98109, USA
| |
Collapse
|
20
|
Cabral-de-Mello DC, Zrzavá M, Kubíčková S, Rendón P, Marec F. The Role of Satellite DNAs in Genome Architecture and Sex Chromosome Evolution in Crambidae Moths. Front Genet 2021; 12:661417. [PMID: 33859676 PMCID: PMC8042265 DOI: 10.3389/fgene.2021.661417] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/04/2021] [Indexed: 12/21/2022] Open
Abstract
Tandem repeats are important parts of eukaryotic genomes being crucial e.g., for centromere and telomere function and chromatin modulation. In Lepidoptera, knowledge of tandem repeats is very limited despite the growing number of sequenced genomes. Here we introduce seven new satellite DNAs (satDNAs), which more than doubles the number of currently known lepidopteran satDNAs. The satDNAs were identified in genomes of three species of Crambidae moths, namely Ostrinia nubilalis, Cydalima perspectalis, and Diatraea postlineella, using graph-based computational pipeline RepeatExplorer. These repeats varied in their abundance and showed high variability within and between species, although some degree of conservation was noted. The satDNAs showed a scattered distribution, often on both autosomes and sex chromosomes, with the exception of both satellites in D. postlineella, in which the satDNAs were located at a single autosomal locus. Three satDNAs were abundant on the W chromosomes of O. nubilalis and C. perspectalis, thus contributing to their differentiation from the Z chromosomes. To provide background for the in situ localization of the satDNAs, we performed a detailed cytogenetic analysis of the karyotypes of all three species. This comparative analysis revealed differences in chromosome number, number and location of rDNA clusters, and molecular differentiation of sex chromosomes.
Collapse
Affiliation(s)
- Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP-Univ Estadual Paulista, Rio Claro, Brazil.,Biology Centre, Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia
| | - Magda Zrzavá
- Biology Centre, Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia.,Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | | | - Pedro Rendón
- IAEA-TCLA-Consultant-USDA-APHIS-Moscamed Program Guatemala, Guatemala City, Guatemala
| | - František Marec
- Biology Centre, Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia
| |
Collapse
|
21
|
Boštjančić LL, Bonassin L, Anušić L, Lovrenčić L, Besendorfer V, Maguire I, Grandjean F, Austin CM, Greve C, Hamadou AB, Mlinarec J. The Pontastacus leptodactylus (Astacidae) Repeatome Provides Insight Into Genome Evolution and Reveals Remarkable Diversity of Satellite DNA. Front Genet 2021; 11:611745. [PMID: 33552130 PMCID: PMC7859515 DOI: 10.3389/fgene.2020.611745] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/21/2020] [Indexed: 12/14/2022] Open
Abstract
Pontastacus leptodactylus is a native European crayfish species found in both freshwater and brackish environments. It has commercial importance for fisheries and aquaculture industries. Up till now, most studies concerning P. leptodactylus have focused onto gaining knowledge about its phylogeny and population genetics. However, little is known about the chromosomal evolution and genome organization of this species. Therefore, we performed clustering analysis of a low coverage genomic dataset to identify and characterize repetitive DNA in the P. leptodactylus genome. In addition, the karyogram of P. leptodactylus (2n = 180) is presented here for the first time consisting of 75 metacentric, 14 submetacentric, and a submetacentric/metacentric heteromorphic chromosome pair. We determined the genome size to be at ~18.7 gigabase pairs. Repetitive DNA represents about 54.85% of the genome. Satellite DNA repeats are the most abundant type of repetitive DNA, making up to ~28% of the total amount of repetitive elements, followed by the Ty3/Gypsy retroelements (~15%). Our study established a surprisingly high diversity of satellite repeats in P. leptodactylus. The genome of P. leptodactylus is by far the most satellite-rich genome discovered to date with 258 satellite families described. Of the five mapped satellite DNA families on chromosomes, PlSAT3-411 co-localizes with the AT-rich DAPI positive probable (peri)centromeric heterochromatin on all chromosomes, while PlSAT14-79 co-localizes with the AT-rich DAPI positive (peri)centromeric heterochromatin on one chromosome and is also located subterminally and intercalary on some chromosomes. PlSAT1-21 is located intercalary in the vicinity of the (peri)centromeric heterochromatin on some chromosomes, while PlSAT6-70 and PlSAT7-134 are located intercalary on some P. leptodactylus chromosomes. The FISH results reveal amplification of interstitial telomeric repeats (ITRs) in P. leptodactylus. The prevalence of repetitive elements, especially the satellite DNA repeats, may have provided a driving force for the evolution of the P. leptodactylus genome.
Collapse
Affiliation(s)
| | - Lena Bonassin
- Division of Molecular Biology, Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Lucija Anušić
- Division of Molecular Biology, Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Leona Lovrenčić
- Division of Zoology, Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Višnja Besendorfer
- Division of Molecular Biology, Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Ivana Maguire
- Division of Zoology, Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Frederic Grandjean
- Laboratoire Ecologie Biologie des Interactions-UMR CNRS 7267, University of Poitiers, Poitiers, France
| | - Christopher M. Austin
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, VIC, Australia
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
| | - Alexander Ben Hamadou
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
| | - Jelena Mlinarec
- Division of Molecular Biology, Department of Biology, University of Zagreb, Zagreb, Croatia
| |
Collapse
|
22
|
Molecular cytogenetics in the study of repetitive sequences helping to understand the evolution of heterochromatin in Melipona (Hymenoptera, Meliponini). Genetica 2021; 149:55-62. [PMID: 33449238 DOI: 10.1007/s10709-020-00111-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 11/27/2020] [Indexed: 10/22/2022]
Abstract
The eukaryote genome is enriched by different types of repetitive DNA sequences and is most abundant in heterochromatin regions. Historically, no function has been assigned to these sequences, which makes them the target of studies that have demonstrated their structural and functional importance in the genome. Despite having a constant chromosome number, the genus Melipona has species with wide variation in heterochromatin content, from 8 to 73%, which is an important feature to be investigated regarding its origin and evolution. In the present study, a repetitive DNA sequence of Melipona mondury was isolated by restriction enzyme digestion. This sequence was used to hybridize chromosomes of eight Melipona species that include representatives of the four subgenera and present divergent characteristics in relation to the heterochromatin content. Considering that rDNA localization has shown differences in Melipona, 16 species of this genus were analyzed with 18S rDNA probe. Our data suggest that heterochromatin growth occurred independently in the Michmelia and Melikerria subgenera, considering that the isolated repetitive DNA sequence was shared only by the Michmelia species. Amplification possibly occurred from the centromeric region, causing the displacement of the rDNA sites to the ends of the chromosomes. The repetitive DNA sequence used is a constituent of Michmelia heterochromatin, which that arose from the common ancestor of the species of this subgenus.
Collapse
|
23
|
Lauria Sneideman MP, Meller VH. Drosophila Satellite Repeats at the Intersection of Chromatin, Gene Regulation and Evolution. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2021; 60:1-26. [PMID: 34386870 DOI: 10.1007/978-3-030-74889-0_1] [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] [Indexed: 01/24/2023]
Abstract
Satellite repeats make up a large fraction of the genomes of many higher eukaryotes. Until recently these sequences were viewed as molecular parasites with few functions. Drosophila melanogaster and related species have a wealth of diverse satellite repeats. Comparative studies of Drosophilids have been instrumental in understanding how these rapidly evolving sequences change and move. Remarkably, satellite repeats have been found to modulate gene expression and mediate genetic conflicts between chromosomes and between closely related fly species. This suggests that satellites play a key role in speciation. We have taken advantage of the depth of research on satellite repeats in flies to review the known functions of these sequences and consider their central role in evolution and gene expression.
Collapse
Affiliation(s)
| | - Victoria H Meller
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA.
| |
Collapse
|
24
|
de Lima LG, Hanlon SL, Gerton JL. Origins and Evolutionary Patterns of the 1.688 Satellite DNA Family in Drosophila Phylogeny. G3 (BETHESDA, MD.) 2020; 10:4129-4146. [PMID: 32934018 PMCID: PMC7642928 DOI: 10.1534/g3.120.401727] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 09/09/2020] [Indexed: 12/11/2022]
Abstract
Satellite DNAs (satDNAs) are a ubiquitous feature of eukaryotic genomes and are usually the major components of constitutive heterochromatin. The 1.688 satDNA, also known as the 359 bp satellite, is one of the most abundant repetitive sequences in Drosophila melanogaster and has been linked to several different biological functions. We investigated the presence and evolution of the 1.688 satDNA in 16 Drosophila genomes. We find that the 1.688 satDNA family is much more ancient than previously appreciated, being shared among part of the melanogaster group that diverged from a common ancestor ∼27 Mya. We found that the 1.688 satDNA family has two major subfamilies spread throughout Drosophila phylogeny (∼360 bp and ∼190 bp). Phylogenetic analysis of ∼10,000 repeats extracted from 14 of the species revealed that the 1.688 satDNA family is present within heterochromatin and euchromatin. A high number of euchromatic repeats are gene proximal, suggesting the potential for local gene regulation. Notably, heterochromatic copies display concerted evolution and a species-specific pattern, whereas euchromatic repeats display a more typical evolutionary pattern, suggesting that chromatin domains may influence the evolution of these sequences. Overall, our data indicate the 1.688 satDNA as the most perduring satDNA family described in Drosophila phylogeny to date. Our study provides a strong foundation for future work on the functional roles of 1.688 satDNA across many Drosophila species.
Collapse
Affiliation(s)
| | - Stacey L Hanlon
- Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | | |
Collapse
|
25
|
Bardella VB, Milani D, Cabral-de-Mello DC. Analysis of Holhymenia histrio genome provides insight into the satDNA evolution in an insect with holocentric chromosomes. Chromosome Res 2020; 28:369-380. [PMID: 32951078 DOI: 10.1007/s10577-020-09642-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/04/2020] [Accepted: 09/10/2020] [Indexed: 12/20/2022]
Abstract
Satellite DNAs (satDNA) are fast-evolving repetitive sequences organized in large tandem arrays, with characteristic enrichment in heterochromatin. Knowledge about evolutionary dynamics of this genome fraction is mostly restricted to its characterization in species with monocentric chromosomes, i.e., localized centromeres. In holocentric species, with non-localized centromeres, satDNAs have been largely ignored. Here we advance the understanding of satDNA evolution among holocentric species by characterization of the most abundant satDNAs in the hemipteran Holhymenia histrio, integrating genomic and chromosomal analyses. High plasticity at chromosomal and molecular levels was noticed for 34 satDNAs populating H. histrio genome. One satDNA family in particular (HhiSat01-184) was highly amplified on multiple chromosomes and also highly polymorphic. Our data support the emergence of a new satDNA family from this abundant satDNA, confined to a single chromosome. Moreover, we present new information about composition of a peculiar chromosome in Coreidae, the m-chromosome, and of the X chromosome. Overall, the molecular and chromosomal patterns for satDNAs in the holocentric species H. histrio seem to be similar to those observed in monocentric species.
Collapse
Affiliation(s)
- Vanessa Bellini Bardella
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Universidade Estadual Paulista, Rio Claro, São Paulo, 13506-900, Brazil
| | - Diogo Milani
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Universidade Estadual Paulista, Rio Claro, São Paulo, 13506-900, Brazil
| | - Diogo Cavalcanti Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Universidade Estadual Paulista, Rio Claro, São Paulo, 13506-900, Brazil.
| |
Collapse
|
26
|
Satellitome Analysis in the Ladybird Beetle Hippodamia variegata (Coleoptera, Coccinellidae). Genes (Basel) 2020; 11:genes11070783. [PMID: 32668664 PMCID: PMC7397073 DOI: 10.3390/genes11070783] [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: 06/18/2020] [Revised: 07/09/2020] [Accepted: 07/09/2020] [Indexed: 12/29/2022] Open
Abstract
Hippodamia variegata is one of the most commercialized ladybirds used for the biological control of aphid pest species in many economically important crops. This species is the first Coccinellidae whose satellitome has been studied by applying new sequencing technologies and bioinformatics tools. We found that 47% of the H. variegata genome is composed of repeated sequences. We identified 30 satellite DNA (satDNA) families with a median intragenomic divergence of 5.75% and A+T content between 45.6% and 74.7%. This species shows satDNA families with highly variable sizes although the most common size is 100–200 bp. However, we highlight the existence of a satDNA family with a repeat unit of 2 kb, the largest repeat unit described in Coleoptera. PCR amplifications for fluorescence in situ hybridization (FISH) probe generation were performed for the four most abundant satDNA families. FISH with the most abundant satDNA family as a probe shows its pericentromeric location on all chromosomes. This location is coincident with the heterochromatin revealed by C-banding and DAPI staining, also analyzed in this work. Hybridization signals for other satDNA families were located only on certain bivalents and the X chromosome. These satDNAs could be very useful as chromosomal markers due to their reduced location.
Collapse
|
27
|
Shah A, Hoffman JI, Schielzeth H. Comparative Analysis of Genomic Repeat Content in Gomphocerine Grasshoppers Reveals Expansion of Satellite DNA and Helitrons in Species with Unusually Large Genomes. Genome Biol Evol 2020; 12:1180-1193. [PMID: 32539114 PMCID: PMC7486953 DOI: 10.1093/gbe/evaa119] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2020] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic organisms vary widely in genome size and much of this variation can be explained by differences in the abundance of repetitive elements. However, the phylogenetic distributions and turnover rates of repetitive elements are largely unknown, particularly for species with large genomes. We therefore used de novo repeat identification based on low coverage whole-genome sequencing to characterize the repeatomes of six species of gomphocerine grasshoppers, an insect clade characterized by unusually large and variable genome sizes. Genome sizes of the six species ranged from 8.4 to 14.0 pg DNA per haploid genome and thus include the second largest insect genome documented so far (with the largest being another acridid grasshopper). Estimated repeat content ranged from 79% to 96% and was strongly correlated with genome size. Averaged over species, these grasshopper repeatomes comprised significant amounts of DNA transposons (24%), LINE elements (21%), helitrons (13%), LTR retrotransposons (12%), and satellite DNA (8.5%). The contribution of satellite DNA was particularly variable (ranging from <1% to 33%) as was the contribution of helitrons (ranging from 7% to 20%). The age distribution of divergence within clusters was unimodal with peaks ∼4-6%. The phylogenetic distribution of repetitive elements was suggestive of an expansion of satellite DNA in the lineages leading to the two species with the largest genomes. Although speculative at this stage, we suggest that the expansion of satellite DNA could be secondary and might possibly have been favored by selection as a means of stabilizing greatly expanded genomes.
Collapse
Affiliation(s)
- Abhijeet Shah
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
- Institute of Ecology and Evolution, Friedrich Schiller University Jena, Jena, Germany
| | - Joseph I Hoffman
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
| | - Holger Schielzeth
- Institute of Ecology and Evolution, Friedrich Schiller University Jena, Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Germany
| |
Collapse
|
28
|
Suntronpong A, Singchat W, Kruasuwan W, Prakhongcheep O, Sillapaprayoon S, Muangmai N, Somyong S, Indananda C, Kraichak E, Peyachoknagul S, Srikulnath K. Characterization of centromeric satellite DNAs (MALREP) in the Asian swamp eel (Monopterus albus) suggests the possible origin of repeats from transposable elements. Genomics 2020; 112:3097-3107. [PMID: 32470643 DOI: 10.1016/j.ygeno.2020.05.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 04/21/2020] [Accepted: 05/24/2020] [Indexed: 01/04/2023]
Abstract
Centromeric satellite DNA (cen-satDNA) sequences of the Asian swamp eel (Monopterus albus) were characterized. Three GC-rich cen-satDNA sequences were detected as a 233 bp MALREP-A and a 293 bp MALREP-B localized to all chromosomes, and a 293 bp MALREP-C distributed on eight chromosome pairs. Sequence lengths of MALREP-B and MALREP-C were 60 bp larger than that of MALREP-A, showing partial homology with core sequences (233 bp). Size differences between MALREP-A and MALREP-B/C suggest the possible occurrence of two satDNA families. The presence of an additional 60 bp in MALREP-B/C resulted from an ancient dimer of 233 bp monomers and subsequent mutation and homogenization between the two monomers. All MALREPs showed partial homology with transposable elements (TEs), suggesting that the MALREPs originated from the TEs. The MALREPs might have been acquired in the Asian swamp eel, thereby promoting fixation in the species.
Collapse
Affiliation(s)
- Aorarat Suntronpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand.
| | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand.
| | - Worarat Kruasuwan
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
| | - Ornjira Prakhongcheep
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
| | - Siwapech Sillapaprayoon
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand.
| | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand.
| | - Suthasinee Somyong
- National Omics Center, National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani 12120, Thailand.
| | - Chantra Indananda
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
| | - Ekaphan Kraichak
- Department of Botany, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
| | - Surin Peyachoknagul
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand; Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok 10900, Thailand; Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand; Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand; Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan.
| |
Collapse
|
29
|
Shatskikh AS, Kotov AA, Adashev VE, Bazylev SS, Olenina LV. Functional Significance of Satellite DNAs: Insights From Drosophila. Front Cell Dev Biol 2020; 8:312. [PMID: 32432114 PMCID: PMC7214746 DOI: 10.3389/fcell.2020.00312] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 04/08/2020] [Indexed: 12/12/2022] Open
Abstract
Since their discovery more than 60 years ago, satellite repeats are still one of the most enigmatic parts of eukaryotic genomes. Being non-coding DNA, satellites were earlier considered to be non-functional “junk,” but recently this concept has been extensively revised. Satellite DNA contributes to the essential processes of formation of crucial chromosome structures, heterochromatin establishment, dosage compensation, reproductive isolation, genome stability and development. Genomic abundance of satellites is under stabilizing selection owing of their role in the maintenance of vital regions of the genome – centromeres, pericentromeric regions, and telomeres. Many satellites are transcribed with the generation of long or small non-coding RNAs. Misregulation of their expression is found to lead to various defects in the maintenance of genomic architecture, chromosome segregation and gametogenesis. This review summarizes our current knowledge concerning satellite functions, the mechanisms of regulation and evolution of satellites, focusing on recent findings in Drosophila. We discuss here experimental and bioinformatics data obtained in Drosophila in recent years, suggesting relevance of our analysis to a wide range of eukaryotic organisms.
Collapse
Affiliation(s)
- Aleksei S Shatskikh
- Laboratory of Analysis of Clinical and Model Tumor Pathologies on the Organismal Level, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Alexei A Kotov
- Laboratory of Biochemical Genetics of Animals, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir E Adashev
- Laboratory of Biochemical Genetics of Animals, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Sergei S Bazylev
- Laboratory of Biochemical Genetics of Animals, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Ludmila V Olenina
- Laboratory of Biochemical Genetics of Animals, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
30
|
Giovannotti M, S'Khifa A, Nisi Cerioni P, Splendiani A, Slimani T, Fioravanti T, Olmo E, Caputo Barucchi V. Isolation and characterization of two satellite DNAs in Atlantolacerta andreanskyi (Werner, 1929) (Reptilia, Lacertidae). JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 334:178-191. [PMID: 32061054 DOI: 10.1002/jez.b.22937] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 11/29/2019] [Accepted: 01/30/2020] [Indexed: 11/07/2022]
Abstract
Two satellite DNAs (satDNAs) have been isolated and characterized from three populations of Atlantolacerta andreanskyi. One satDNA (AAN-TaqI) has been isolated here from the first time. It is characterized by a tendency to AT enrichment (AT = 54.2%) and monomer length ranging from 187 to 199 bp. FISH experiments showed that this element occurs in subterminal position on the short arms of all chromosomes of the complement. The analyses of genetic variability of AAN-TaqI showed that the concerted evolution is acting effectively on these repeats that form separate clusters consistent with the geographic origin in the phylogenetic tree, thus supporting the hypothesis that A. andreanskyi would be a species complex. In addition, in the population from Jbel Aoulime this satDNA is already differentiated into two subfamilies. The other satDNA belongs to the family of IMO-TaqI already isolated in other lacertids. Differently from AAN-TaqI, concerted evolution does not seem to act effectively on this element that is not differentiated between populations. These results confirm that IMO-TaqI (AT = 53.4%) is conserved in both chromosomal position and most of its sequence in the lacertids from which it has been characterized so far. Its remarkable evolutionary conservation for about 45 million years could indicate that this satDNA may have a functional role that future investigations could unveil. Once again, this study shows how satDNAs coexisting in the same genome may differ in their evolutionary pattern, even though the reasons underlying this phenomenon in the species here studied have still to be fully understood.
Collapse
Affiliation(s)
- Massimo Giovannotti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Abderrahim S'Khifa
- Laboratory Biodiversity and Ecosystem Dynamics, Faculty of Sciences Semlalia, Cadi Ayyad University, Boulevard Prince Moulay Abdellah, Marrakech, Morocco
| | - Paola Nisi Cerioni
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Andrea Splendiani
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Tahar Slimani
- Laboratory Biodiversity and Ecosystem Dynamics, Faculty of Sciences Semlalia, Cadi Ayyad University, Boulevard Prince Moulay Abdellah, Marrakech, Morocco
| | - Tatiana Fioravanti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Ettore Olmo
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Vincenzo Caputo Barucchi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| |
Collapse
|
31
|
Ekhteraei-Tousi S, Lewerentz J, Larsson J. Painting of Fourth and the X-Linked 1.688 Satellite in D. melanogaster is Involved in Chromosome-Wide Gene Regulation. Cells 2020; 9:cells9020323. [PMID: 32019091 PMCID: PMC7072490 DOI: 10.3390/cells9020323] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/23/2020] [Accepted: 01/28/2020] [Indexed: 01/01/2023] Open
Abstract
Chromosome-specific regulatory mechanisms provide a model to understand the coordinated regulation of genes on entire chromosomes or on larger genomic regions. In fruit flies, two chromosome-wide systems have been characterized: The male-specific lethal (MSL) complex, which mediates dosage compensation and primarily acts on the male X-chromosome, and Painting of fourth (POF), which governs chromosome-specific regulation of genes located on the 4th chromosome. How targeting of one specific chromosome evolves is still not understood; but repeated sequences, in forms of satellites and transposable elements, are thought to facilitate the evolution of chromosome-specific targeting. The highly repetitive 1.688 satellite has been functionally connected to both these systems. Considering the rapid evolution and the necessarily constant adaptation of regulatory mechanisms, such as dosage compensation, we hypothesised that POF and/or 1.688 may still show traces of dosage-compensation functions. Here, we test this hypothesis by transcriptome analysis. We show that loss of Pof decreases not only chromosome 4 expression but also reduces the X-chromosome expression in males. The 1.688 repeat deletion, Zhr1 (Zygotic hybrid rescue), does not affect male dosage compensation detectably; however, Zhr1 in females causes a stimulatory effect on X-linked genes with a strong binding affinity to the MSL complex (genes close to high-affinity sites). Lack of pericentromeric 1.688 also affected 1.688 expression in trans and was linked to the differential expression of genes involved in eggshell formation. We discuss our results with reference to the connections between POF, the 1.688 satellite and dosage compensation, and the role of the 1.688 satellite in hybrid lethality.
Collapse
|
32
|
Paço A, Freitas R, Vieira-da-Silva A. Conversion of DNA Sequences: From a Transposable Element to a Tandem Repeat or to a Gene. Genes (Basel) 2019; 10:E1014. [PMID: 31817529 PMCID: PMC6947457 DOI: 10.3390/genes10121014] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 11/18/2019] [Accepted: 11/29/2019] [Indexed: 01/24/2023] Open
Abstract
Eukaryotic genomes are rich in repetitive DNA sequences grouped in two classes regarding their genomic organization: tandem repeats and dispersed repeats. In tandem repeats, copies of a short DNA sequence are positioned one after another within the genome, while in dispersed repeats, these copies are randomly distributed. In this review we provide evidence that both tandem and dispersed repeats can have a similar organization, which leads us to suggest an update to their classification based on the sequence features, concretely regarding the presence or absence of retrotransposons/transposon specific domains. In addition, we analyze several studies that show that a repetitive element can be remodeled into repetitive non-coding or coding sequences, suggesting (1) an evolutionary relationship among DNA sequences, and (2) that the evolution of the genomes involved frequent repetitive sequence reshuffling, a process that we have designated as a "DNA remodeling mechanism". The alternative classification of the repetitive DNA sequences here proposed will provide a novel theoretical framework that recognizes the importance of DNA remodeling for the evolution and plasticity of eukaryotic genomes.
Collapse
Affiliation(s)
- Ana Paço
- MED-Mediterranean Institute for Agriculture, Environment and Development, University of Évora, 7002–554 Évora, Portugal;
| | - Renata Freitas
- IBMC-Institute for Molecular and Cell Biology, University of Porto, R. Campo Alegre 823, 4150–180 Porto, Portugal;
- I3S-Institute for Innovation and Health Research, University of Porto, Rua Alfredo Allen, 208, 4200–135 Porto, Portugal
- ICBAS-Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
| | - Ana Vieira-da-Silva
- MED-Mediterranean Institute for Agriculture, Environment and Development, University of Évora, 7002–554 Évora, Portugal;
| |
Collapse
|
33
|
Corbett-Detig RB, Said I, Calzetta M, Genetti M, McBroome J, Maurer NW, Petrarca V, Della Torre A, Besansky NJ. Fine-Mapping Complex Inversion Breakpoints and Investigating Somatic Pairing in the Anopheles gambiae Species Complex Using Proximity-Ligation Sequencing. Genetics 2019; 213:1495-1511. [PMID: 31666292 PMCID: PMC6893396 DOI: 10.1534/genetics.119.302385] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/21/2019] [Indexed: 11/18/2022] Open
Abstract
Chromosomal inversions are fundamental drivers of genome evolution. In the main Afrotropical malaria vector species, belonging to the Anopheles gambiae species complex, inversions play an important role in local adaptation and have a rich history of cytological study. Despite the importance and ubiquity of some chromosomal inversions across the species complex, inversion breakpoints are often challenging to map molecularly due to the presence of large repetitive regions. Here, we develop an approach that uses Hi-C sequencing data to molecularly fine-map the breakpoints of inversions. We demonstrate that this approach is robust and likely to be widely applicable for both identification and fine-mapping inversion breakpoints in species whose inversions have heretofore been challenging to characterize. We apply our method to interrogate the previously unknown inversion breakpoints of 2Rbc and 2Rd in An. coluzzii We found that inversion breakpoints occur in large repetitive regions, and, strikingly, among three inversions analyzed, two breakpoints appear to be reused in two separate inversions. These breakpoint-adjacent regions are strongly enriched for the presence of a 30 bp satellite repeat sequence. Because low frequency inversion breakpoints are not correlated with genomic regions containing this satellite, we suggest that interrupting this particular repeat may result in arrangements with higher relative fitness. Additionally, we use heterozygous individuals to quantitatively investigate the impacts of somatic pairing in the regions immediately surrounding inversion breakpoints. Finally, we discuss important considerations for possible applications of this approach for inversion breakpoint identification in a range of organisms.
Collapse
Affiliation(s)
- Russell B Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, California 95064
- Genomics Institute, University of California Santa Cruz, California 95064
| | - Iskander Said
- Department of Biomolecular Engineering, University of California Santa Cruz, California 95064
| | - Maria Calzetta
- Dipartimento di Sanità Pubblica e Malattie Infettive and Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "La Sapienza", 00185 Rome, Italy
| | - Max Genetti
- Department of Biomolecular Engineering, University of California Santa Cruz, California 95064
| | - Jakob McBroome
- Department of Biomolecular Engineering, University of California Santa Cruz, California 95064
| | - Nicholas W Maurer
- Department of Biomolecular Engineering, University of California Santa Cruz, California 95064
| | - Vincenzo Petrarca
- Dipartimento di Sanità Pubblica e Malattie Infettive and Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "La Sapienza", 00185 Rome, Italy
| | - Alessandra Della Torre
- Dipartimento di Sanità Pubblica e Malattie Infettive and Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "La Sapienza", 00185 Rome, Italy
| | - Nora J Besansky
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, Indiana 46556
| |
Collapse
|
34
|
Mora P, Vela J, Ruiz-Mena A, Palomeque T, Lorite P. Isolation of a Pericentromeric Satellite DNA Family in Chnootriba argus ( Henosepilachna argus) with an Unusual Short Repeat Unit (TTAAAA) for Beetles. INSECTS 2019; 10:insects10090306. [PMID: 31546864 PMCID: PMC6780895 DOI: 10.3390/insects10090306] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/11/2019] [Accepted: 09/17/2019] [Indexed: 12/30/2022]
Abstract
Ladybird beetles (Coccinellidae) are one of the largest groups of beetles. Among them, some species are of economic interest since they can act as a biological control for some agricultural pests whereas other species are phytophagous and can damage crops. Chnootriba argus (Coccinellidae, Epilachnini) has large heterochromatic pericentromeric blocks on all chromosomes, including both sexual chromosomes. Classical digestion of total genomic DNA using restriction endonucleases failed to find the satellite DNA located on these heterochromatic regions. Cloning of C0t-1 DNA resulted in the isolation of a repetitive DNA with a repeat unit of six base pairs, TTAAAA. The amount of TTAAAA repeat in the C. argus genome was about 20%. Fluorescence in situ hybridization (FISH) analysis and digestion of chromosomes with the endonuclease Tru9I revealed that this repetitive DNA could be considered as the putative pericentromeric satellite DNA (satDNA) in this species. The presence of this satellite DNA was tested in other species of the tribe Epilachnini and it is also present in Epilachna paenulata. In both species, the TTAAAA repeat seems to be the main satellite DNA and it is located on the pericentromeric region on all chromosomes. The size of this satDNA, which has only six base pairs is unusual in Coleoptera satellite DNAs, where satDNAs usually have repeat units of a much larger size. Southern hybridization and FISH proved that this satDNA is conserved in some Epilachnini species but not in others. This result is in concordance with the controversial phylogenetic relationships among the genera of the tribe Epilachnini, where the limits between genera are unclear.
Collapse
Affiliation(s)
- Pablo Mora
- Department of Experimental Biology, Genetic Area, University of Jaén, 23071 Jaén, Spain.
| | - Jesús Vela
- Department of Experimental Biology, Genetic Area, University of Jaén, 23071 Jaén, Spain.
| | - Areli Ruiz-Mena
- Department of Experimental Biology, Genetic Area, University of Jaén, 23071 Jaén, Spain.
| | - Teresa Palomeque
- Department of Experimental Biology, Genetic Area, University of Jaén, 23071 Jaén, Spain.
| | - Pedro Lorite
- Department of Experimental Biology, Genetic Area, University of Jaén, 23071 Jaén, Spain.
| |
Collapse
|
35
|
Dutrillaux AM, Dutrillaux B. Different behaviour of C-banded peri-centromeric heterochromatin between sex chromosomes and autosomes in Polyphagan beetles. COMPARATIVE CYTOGENETICS 2019; 13:179-192. [PMID: 31327988 PMCID: PMC6620206 DOI: 10.3897/compcytogen.v13i2.34746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/21/2019] [Indexed: 06/10/2023]
Abstract
Heterochromatin variation was studied after C-banding of male karyotypes with a XY sex formula from 224 species belonging to most of the main families of Coleoptera. The karyotypes were classified in relation with the ratio heterochromatin/euchromatin total amounts and the amounts of heterochromatin on autosomes and gonosomes were compared. The C-banded karyotypes of 19 species, representing characteristic profiles are presented. This analysis shows that there is a strong tendency for the homogenization of the size of the peri-centromeric C-banded heterochromatin on autosomes. The amount of heterochromatin on the X roughly follows the variations of autosomes. At contrast, the C-banded heterochromatin of the Y, most frequently absent or very small and rarely amplified, looks quite independent from that of other chromosomes. We conclude that the Xs and autosomes, but not the Y, possibly share some, but not all mechanisms of heterochromatin amplification/reduction. The theoretical models of heterochromatin expansion are discussed in the light of these data.
Collapse
Affiliation(s)
- Anne-Marie Dutrillaux
- UMR7205 MNHN CNRS UMPC EPHE Institut de Systématique, Evolution, Biodiversité. Muséum National d’histoire Naturelle, Sorbonne Universités, 57, rue Cuvier, CP39, UMR7205 Paris, FranceSorbonne UniversitésParisFrance
| | - Bernard Dutrillaux
- UMR7205 MNHN CNRS UMPC EPHE Institut de Systématique, Evolution, Biodiversité. Muséum National d’histoire Naturelle, Sorbonne Universités, 57, rue Cuvier, CP39, UMR7205 Paris, FranceSorbonne UniversitésParisFrance
| |
Collapse
|
36
|
Palacios-Gimenez OM, Bardella VB, Lemos B, Cabral-de-Mello DC. Satellite DNAs are conserved and differentially transcribed among Gryllus cricket species. DNA Res 2018; 25:137-147. [PMID: 29096008 PMCID: PMC5909420 DOI: 10.1093/dnares/dsx044] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/19/2017] [Indexed: 11/21/2022] Open
Abstract
Satellite DNA (satDNA) is an abundant class of non-coding repetitive DNA that is preferentially found as tandemly repeated arrays in gene-poor heterochromatin but is also present in gene-rich euchromatin. Here, we used DNA- and RNA-seq from Gryllus assimilis to address the content and transcriptional patterns of satDNAs. We also mapped RNA-seq libraries for other Gryllus species against the satDNAs found in G. assimilis and G. bimaculatus genomes to investigate their evolutionary conservation and transcriptional profiles in Gryllus. Through DNA-seq read clustering analysis using RepeatExplorer, dotplots analysis and fluorescence in situ hybridization mapping, we found that ∼4% of the G. assimilis genome is represented by 11 well-defined A + T-rich satDNA families. These are mainly located in heterochromatic areas, with some repeats able to form high-order repeat structures. By in silico transcriptional analysis we identified satDNAs that are conserved in Gryllus but differentially transcribed. The data regarding satDNA presence in G. assimilis genome were discussed in an evolutionary context, with transcriptional data enabling comparisons between sexes and across tissues when possible. We discuss hypotheses for the conservation and transcription of satDNAs in Gryllus, which might result from their role in sexual differentiation at the chromatin level, heterochromatin formation and centromeric function.
Collapse
Affiliation(s)
- Octavio Manuel Palacios-Gimenez
- Departamento de Biologia, Instituto de Biociências/IB, UNESP-Univ Estadual Paulista, Rio Claro, São Paulo, Brazil.,Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard University T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Vanessa Bellini Bardella
- Departamento de Biologia, Instituto de Biociências/IB, UNESP-Univ Estadual Paulista, Rio Claro, São Paulo, Brazil
| | - Bernardo Lemos
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard University T. H. Chan School of Public Health, Boston, MA 02115, USA
| | | |
Collapse
|
37
|
Cacheux L, Ponger L, Gerbault-Seureau M, Loll F, Gey D, Richard FA, Escudé C. The Targeted Sequencing of Alpha Satellite DNA in Cercopithecus pogonias Provides New Insight Into the Diversity and Dynamics of Centromeric Repeats in Old World Monkeys. Genome Biol Evol 2018; 10:1837-1851. [PMID: 29860303 PMCID: PMC6061836 DOI: 10.1093/gbe/evy109] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2018] [Indexed: 02/06/2023] Open
Abstract
Alpha satellite is the major repeated DNA element of primate centromeres. Specific evolutionary mechanisms have led to a great diversity of sequence families with peculiar genomic organization and distribution, which have till now been studied mostly in great apes. Using high throughput sequencing of alpha satellite monomers obtained by enzymatic digestion followed by computational and cytogenetic analysis, we compare here the diversity and genomic distribution of alpha satellite DNA in two related Old World monkey species, Cercopithecus pogonias and Cercopithecus solatus, which are known to have diverged about 7 Ma. Two main families of monomers, called C1 and C2, are found in both species. A detailed analysis of our data sets revealed the existence of numerous subfamilies within the centromeric C1 family. Although the most abundant subfamily is conserved between both species, our fluorescence in situ hybridization (FISH) experiments clearly show that some subfamilies are specific for each species and that their distribution is restricted to a subset of chromosomes, thereby pointing to the existence of recurrent amplification/homogenization events. The pericentromeric C2 family is very abundant on the short arm of all acrocentric chromosomes in both species, pointing to specific mechanisms that lead to this distribution. Results obtained using two different restriction enzymes are fully consistent with a predominant monomeric organization of alpha satellite DNA that coexists with higher order organization patterns in the C. pogonias genome. Our study suggests a high dynamics of alpha satellite DNA in Cercopithecini, with recurrent apparition of new sequence variants and interchromosomal sequence transfer.
Collapse
Affiliation(s)
- Lauriane Cacheux
- Département Adaptations du Vivant, Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
- Département Origines et Evolution, Institut de Systématique, Evolution, Biodiversité, UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
| | - Loïc Ponger
- Département Adaptations du Vivant, Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
| | - Michèle Gerbault-Seureau
- Département Origines et Evolution, Institut de Systématique, Evolution, Biodiversité, UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
| | - François Loll
- Département Adaptations du Vivant, Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
| | - Delphine Gey
- Service de Systématique Moléculaire, UMS 2700 CNRS, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
| | - Florence Anne Richard
- Département Origines et Evolution, Institut de Systématique, Evolution, Biodiversité, UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
- Université Versailles St-Quentin, Montigny-le-Bretonneux, France
| | - Christophe Escudé
- Département Adaptations du Vivant, Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
| |
Collapse
|
38
|
Vlahovic I, Gluncic M, Rosandic M, Ugarkovic Ð, Paar V. Regular Higher Order Repeat Structures in Beetle Tribolium castaneum Genome. Genome Biol Evol 2018; 9:2668-2680. [PMID: 27492235 PMCID: PMC5737470 DOI: 10.1093/gbe/evw174] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2016] [Indexed: 02/07/2023] Open
Abstract
Higher order repeats (HORs) containing tandems of primary and secondary repeat units (head-to-tail “tandem within tandem pattern”), referred to as regular HORs, are typical for primate alpha satellite DNAs and most pronounced in human genome. Regular HORs are known to be a result of recent evolutionary processes. In non-primate genomes mostly so called complex HORs have been found, without head to tail tandem of primary repeat units. In beetle Tribolium castaneum, considered as a model case for genome studies, large tandem repeats have been identified, but no HORs have been reported. Here, using our novel robust repeat finding algorithm Global Repeat Map, we discover two regular and six complex HORs in T. castaneum. In organizational pattern, the integrity and homogeneity of regular HORs in T. castaneum resemble human regular HORs (with T. castaneum monomers different from human alpha satellite monomers), involving a wider range of monomer lengths than in human HORs. Similar regular higher order repeat structures have previously not been found in insects. Some of these novel HORs in T. castaneum appear as most regular among known HORs in non-primate genomes, although with substantial riddling. This is intriguing, in particular from the point of view of role of non-coding repeats in modulation of gene expression.
Collapse
Affiliation(s)
- Ines Vlahovic
- Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Matko Gluncic
- Faculty of Science, University of Zagreb, Zagreb, Croatia
| | | | | | - Vladimir Paar
- Faculty of Science, University of Zagreb, Zagreb, Croatia.,Croatian Academy of Sciences and Arts, Zagreb, Croatia
| |
Collapse
|
39
|
Pita S, Mora P, Vela J, Palomeque T, Sánchez A, Panzera F, Lorite P. Comparative Analysis of Repetitive DNA between the Main Vectors of Chagas Disease: Triatoma infestans and Rhodnius prolixus. Int J Mol Sci 2018; 19:ijms19051277. [PMID: 29695139 PMCID: PMC5983683 DOI: 10.3390/ijms19051277] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 04/13/2018] [Accepted: 04/19/2018] [Indexed: 01/26/2023] Open
Abstract
Chagas disease or American trypanosomiasis affects six to seven million people worldwide, mostly in Latin America. This disease is transmitted by hematophagous insects known as “kissing bugs” (Hemiptera, Triatominae), with Triatoma infestans and Rhodnius prolixus being the two most important vector species. Despite the fact that both species present the same diploid chromosome number (2n = 22), they have remarkable differences in their total DNA content, chromosome structure and genome organization. Variations in the DNA genome size are expected to be due to differences in the amount of repetitive DNA sequences. The T. infestans genome-wide analysis revealed the existence of 42 satellite DNA families. BLAST searches of these sequences against the R. prolixus genome assembly revealed that only four of these satellite DNA families are shared between both species, suggesting a great differentiation between the Triatoma and Rhodnius genomes. Fluorescence in situ hybridization (FISH) location of these repetitive DNAs in both species showed that they are dispersed on the euchromatic regions of all autosomes and the X chromosome. Regarding the Y chromosome, these common satellite DNAs are absent in T. infestans but they are present in the R. prolixus Y chromosome. These results support a different origin and/or evolution in the Y chromosome of both species.
Collapse
Affiliation(s)
- Sebastián Pita
- Evolutionary Genetic Section, Faculty of Science, University of the Republic, Iguá 4225, Montevideo 11400, Uruguay.
| | - Pablo Mora
- Department of Experimental Biology, Genetics , University of Jaén, Paraje Las Lagunillas s/n., 23071 Jaén, Spain.
| | - Jesús Vela
- Department of Experimental Biology, Genetics , University of Jaén, Paraje Las Lagunillas s/n., 23071 Jaén, Spain.
| | - Teresa Palomeque
- Department of Experimental Biology, Genetics , University of Jaén, Paraje Las Lagunillas s/n., 23071 Jaén, Spain.
| | - Antonio Sánchez
- Department of Experimental Biology, Genetics , University of Jaén, Paraje Las Lagunillas s/n., 23071 Jaén, Spain.
| | - Francisco Panzera
- Evolutionary Genetic Section, Faculty of Science, University of the Republic, Iguá 4225, Montevideo 11400, Uruguay.
| | - Pedro Lorite
- Department of Experimental Biology, Genetics , University of Jaén, Paraje Las Lagunillas s/n., 23071 Jaén, Spain.
| |
Collapse
|
40
|
Ruiz-Ruano FJ, Castillo-Martínez J, Cabrero J, Gómez R, Camacho JPM, López-León MD. High-throughput analysis of satellite DNA in the grasshopper Pyrgomorpha conica reveals abundance of homologous and heterologous higher-order repeats. Chromosoma 2018; 127:323-340. [PMID: 29549528 DOI: 10.1007/s00412-018-0666-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 02/13/2018] [Accepted: 03/06/2018] [Indexed: 12/25/2022]
Abstract
Satellite DNA (satDNA) constitutes an important fraction of repetitive DNA in eukaryotic genomes, but it is barely known in most species. The high-throughput analysis of satDNA in the grasshopper Pyrgomorpha conica revealed 87 satDNA variants grouped into 76 different families, representing 9.4% of the genome. Fluorescent in situ hybridization (FISH) analysis of the 38 most abundant satDNA families revealed four different patterns of chromosome distribution. Homology search between the 76 satDNA families showed the existence of 15 superfamilies, each including two or more families, with the most abundant superfamily representing more than 80% of all satDNA found in this species. This also revealed the presence of two types of higher-order repeats (HORs), one showing internal homologous subrepeats, as conventional HORs, and an additional type showing non-homologous internal subrepeats, the latter arising by the combination of a given satDNA family with a non-annotated sequence, or with telomeric DNA. Interestingly, the heterologous subrepeats included in these HORs showed higher divergence within the HOR than outside it, suggesting that heterologous HORs show poor homogenization, in high contrast with conventional (homologous) HORs. Finally, heterologous HORs can show high differences in divergence between their constituent subrepeats, suggesting the possibility of regional homogenization.
Collapse
Affiliation(s)
- Francisco J Ruiz-Ruano
- Departamento de Genética. Facultad de Ciencias, Universidad de Granada, 18071, Granada, Spain
| | - Jesús Castillo-Martínez
- Departamento de Genética. Facultad de Ciencias, Universidad de Granada, 18071, Granada, Spain.,Facultad de Medicina, Universidad Católica de Valencia, C/Quevedo 2, 46001, Valencia, Spain
| | - Josefa Cabrero
- Departamento de Genética. Facultad de Ciencias, Universidad de Granada, 18071, Granada, Spain
| | - Ricardo Gómez
- Departamento de Ciencia y Tecnología Agroforestal, E.T.S. de Ingenieros Agrónomos, Universidad de Castilla La Mancha, 02071, Albacete, Spain
| | - Juan Pedro M Camacho
- Departamento de Genética. Facultad de Ciencias, Universidad de Granada, 18071, Granada, Spain
| | | |
Collapse
|
41
|
Giovannotti M, Nisi Cerioni P, Rojo V, Olmo E, Slimani T, Splendiani A, Caputo Barucchi V. Characterization of a satellite DNA in the genera Lacerta andTimon(Reptilia, Lacertidae) and its role in the differentiation of the W chromosome. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2018; 330:83-95. [DOI: 10.1002/jez.b.22790] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 12/04/2017] [Accepted: 01/09/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Massimo Giovannotti
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; via Brecce Bianche Ancona Italy
| | - Paola Nisi Cerioni
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; via Brecce Bianche Ancona Italy
| | - Verónica Rojo
- AllGenetics & Biology SL; Edificio CICA; Campus de Elviña s/n, A Coruña Spain
- Department of Molecular and Cell Biology; Evolutionary Biology Group (GIBE); Universidade da Coruña; A Fraga 10, A Coruña Spain
| | - Ettore Olmo
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; via Brecce Bianche Ancona Italy
| | - Tahar Slimani
- Cadi Ayyad University; Faculty of Sciences Semlalia; Laboratory Biodiversity and Ecosystem Dynamics; Marrakech Morocco
| | - Andrea Splendiani
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; via Brecce Bianche Ancona Italy
| | - Vincenzo Caputo Barucchi
- Dipartimento di Scienze della Vita e dell'Ambiente; Università Politecnica delle Marche; via Brecce Bianche Ancona Italy
- Consiglio Nazionale delle Ricerche; Istituto di Scienze Marine Sezione Pesca Marittima; Largo Fiera della Pesca; Ancona Italy
| |
Collapse
|
42
|
Liehr T, Buleu O, Karamysheva T, Bugrov A, Rubtsov N. New Insights into Phasmatodea Chromosomes. Genes (Basel) 2017; 8:genes8110327. [PMID: 29149047 PMCID: PMC5704240 DOI: 10.3390/genes8110327] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/13/2017] [Accepted: 11/13/2017] [Indexed: 12/15/2022] Open
Abstract
Currently, approximately 3000 species of stick insects are known; however, chromosome numbers, which range between 21 and 88, are known for only a few of these insects. Also, centromere banding staining (C-banding) patterns were described for fewer than 10 species, and fluorescence in situ hybridization (FISH) was applied exclusively in two Leptynia species. Interestingly, 10–25% of stick insects (Phasmatodea) are obligatory or facultative parthenogenetic. As clonal and/or bisexual reproduction can affect chromosomal evolution, stick insect karyotypes need to be studied more intensely. Chromosome preparation from embryos of five Phasmatodea species (Medauroidea extradentata, Sungaya inexpectata, Sipyloidea sipylus, Phaenopharos khaoyaiensis, and Peruphasma schultei) from four families were studied here by C-banding and FISH applying ribosomal deoxyribonucleic acid (rDNA) and telomeric repeat probes. For three species, data on chromosome numbers and structure were obtained here for the first time, i.e., S. inexpectata, P. khaoyaiensis, and P. schultei. Large C-positive regions enriched with rDNA were identified in all five studied, distantly related species. Some of these C-positive blocks were enriched for telomeric repeats, as well. Chromosomal evolution of stick insects is characterized by variations in chromosome numbers as well as transposition and amplification of repetitive DNA sequences. Here, the first steps were made towards identification of individual chromosomes in Phasmatodea.
Collapse
Affiliation(s)
- Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Am Klinikum 1, D-07747 Jena, Germany.
| | - Olesya Buleu
- Novosibirsk State University, 630090 Novosibirsk, Russia.
| | - Tatyana Karamysheva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia.
| | - Alexander Bugrov
- Novosibirsk State University, 630090 Novosibirsk, Russia.
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia.
| | - Nikolai Rubtsov
- Novosibirsk State University, 630090 Novosibirsk, Russia.
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia.
| |
Collapse
|
43
|
High-throughput analysis unveils a highly shared satellite DNA library among three species of fish genus Astyanax. Sci Rep 2017; 7:12726. [PMID: 29018237 PMCID: PMC5635008 DOI: 10.1038/s41598-017-12939-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/20/2017] [Indexed: 01/08/2023] Open
Abstract
The high-throughput analysis of satellite DNA (satDNA) content, by means of Illumina sequencing, unveiled 45 satDNA families in the genome of Astyanax paranae, with repeat unit length (RUL) ranging from 6 to 365 bp and marked predominance of short satellites (median length = 59 bp). The analysis of chromosomal location of 35 satDNAs in A. paranae, A. fasciatus and A. bockmanni revealed that most satellites are shared between the three species and show highly similar patterns of chromosome distribution. The high similarity in satellite DNA content between these species is most likely due to their recent common descent. Among the few differences found, the ApaSat44-21 satellite was present only on the B chromosome of A. paranae, but not on the A or B chromosomes of the two other species. Likewise, the ApaSat20-18 satellite was B-specific in A. paranae but was however present on A and B chromosomes of A. fasciatus and A. bockmanni. The isochromosome nature of B chromosomes in these species was evidenced by the symmetric location of many satDNAs on both B chromosome arms, and the lower symmetry observed in the A. fasciatus BfMa chromosome suggests that it is older than those analyzed in A. paranae and A. bockmanni.
Collapse
|
44
|
Garrido-Ramos MA. Satellite DNA: An Evolving Topic. Genes (Basel) 2017; 8:genes8090230. [PMID: 28926993 PMCID: PMC5615363 DOI: 10.3390/genes8090230] [Citation(s) in RCA: 222] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/12/2017] [Accepted: 09/13/2017] [Indexed: 12/22/2022] Open
Abstract
Satellite DNA represents one of the most fascinating parts of the repetitive fraction of the eukaryotic genome. Since the discovery of highly repetitive tandem DNA in the 1960s, a lot of literature has extensively covered various topics related to the structure, organization, function, and evolution of such sequences. Today, with the advent of genomic tools, the study of satellite DNA has regained a great interest. Thus, Next-Generation Sequencing (NGS), together with high-throughput in silico analysis of the information contained in NGS reads, has revolutionized the analysis of the repetitive fraction of the eukaryotic genomes. The whole of the historical and current approaches to the topic gives us a broad view of the function and evolution of satellite DNA and its role in chromosomal evolution. Currently, we have extensive information on the molecular, chromosomal, biological, and population factors that affect the evolutionary fate of satellite DNA, knowledge that gives rise to a series of hypotheses that get on well with each other about the origin, spreading, and evolution of satellite DNA. In this paper, I review these hypotheses from a methodological, conceptual, and historical perspective and frame them in the context of chromosomal organization and evolution.
Collapse
Affiliation(s)
- Manuel A Garrido-Ramos
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
| |
Collapse
|
45
|
Pita S, Lorite P, Vela J, Mora P, Palomeque T, Thi KP, Panzera F. Holocentric chromosome evolution in kissing bugs (Hemiptera: Reduviidae: Triatominae): diversification of repeated sequences. Parasit Vectors 2017; 10:410. [PMID: 28874168 PMCID: PMC5586013 DOI: 10.1186/s13071-017-2349-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 08/28/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The analysis of the chromosomal and genome evolution in organisms with holocentric chromosomes is restricted by the lack of primary constriction or centromere. An interesting group is the hemipteran subfamily Triatominae, vectors of Chagas disease, which affects around 6 to 7 million people worldwide. This group exhibits extensive variability in the number and chromosomal location of repeated sequences such as heterochromatin and ribosomal genes. This paper tries to reveal the significant differences of the repeated sequences among Triatoma species through the use of genomic DNA probes. METHODS We analysed the chromosomal distribution and evolution of repeated sequences in Triatoma species by genomic in situ hybridization (GISH) using genomic DNA probes from two North American Triatoma species. These genomic probes were hybridized both on their own chromosomes and on other Triatoma species from North and South America, with different amounts and chromosome location of C-heterochromatin. The results were compared with those previously described using South American Triatoma genomic probes. RESULTS We observed two chromosomal hybridization patterns: (i) very intense hybridization signals concentrated on specific chromosomal regions or particular chromosomes; and (ii) lower intensity hybridization signals dispersed along all chromosomes. Self-GISH on T. rubrofasciata and T. dimidiata chromosomes presented strong hybridization signals on all C-heterochromatin regions. However, when we perform genomic cross-hybridizations, only strong signals are detected on the Y chromosome, leaving the C-heterochromatic autosomal regions unmarked. CONCLUSIONS We confirm that repeated DNA of the Y chromosome is shared among Triatoma species and probably represents an ancestral character of the Triatomini tribe. On the contrary, autosomal heterochromatic regions are constituted by species-specific DNA repeats, most probably satDNA families, suggesting that Triatoma speciation involved the amplification of diverse types of autosomal repeats. Molecular characterization of principal repetitive DNAs seems to be an appropriate approach to infer evolutionary relationships in triatomines.
Collapse
Affiliation(s)
- Sebastián Pita
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Calle Iguá 4225, 11400 Montevideo, Uruguay
| | - Pedro Lorite
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje Lagunillas s/n, 23071 Jaén, Spain
| | - Jesús Vela
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje Lagunillas s/n, 23071 Jaén, Spain
| | - Pablo Mora
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje Lagunillas s/n, 23071 Jaén, Spain
| | - Teresa Palomeque
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje Lagunillas s/n, 23071 Jaén, Spain
| | - Khoa Pham Thi
- Center for Molecular Biology, IRD, Duytan University, Danang, Vietnam
| | - Francisco Panzera
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Calle Iguá 4225, 11400 Montevideo, Uruguay
| |
Collapse
|
46
|
Milani D, Ramos É, Loreto V, Martí DA, Cardoso AL, de Moraes KCM, Martins C, Cabral-de-Mello DC. The satellite DNA AflaSAT-1 in the A and B chromosomes of the grasshopper Abracris flavolineata. BMC Genet 2017; 18:81. [PMID: 28851268 PMCID: PMC5575873 DOI: 10.1186/s12863-017-0548-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/22/2017] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Satellite DNAs (satDNAs) are organized in repetitions directly contiguous to one another, forming long arrays and composing a large portion of eukaryote genomes. These sequences evolve according to the concerted evolution model, and homogenization of repeats is observed at the intragenomic level. Satellite DNAs are the primary component of heterochromatin, located primarily in centromeres and telomeres. Moreover, satDNA enrichment in specific chromosomes has been observed, such as in B chromosomes, that can provide clues about composition, origin and evolution of this chromosome. In this study, we isolated and characterized a satDNA in A and B chromosomes of Abracris flavolineata by integrating cytogenetic, molecular and genomics approaches at intra- and inter-population levels, with the aim to understand the evolution of satDNA and composition of B chromosomes. RESULTS AflaSAT-1 satDNA was shared with other species and in A. flavolineata, was associated with another satDNA, AflaSAT-2. Chromosomal mapping revealed centromeric blocks variable in size in almost all chromosomes (except pair 11) of A complement for both satDNAs, whereas for B chromosome, only a small centromeric signal occurred. In distinct populations, variable number of AflaSAT-1 chromosomal sites correlated with variability in copy number. Instead of such variability, low sequence diversity was observed in A complement, but monomers from B chromosome were more variable, presenting also exclusive mutations. AflaSAT-1 was transcribed in five tissues of adults in distinct life cycle phases. CONCLUSIONS The sharing of AflaSAT-1 with other species is consistent with the library hypothesis and indicates common origin in a common ancestor; however, AflaSAT-1 was highly amplified in the genome of A. flavolineata. At the population level, homogenization of repeats in distinct populations was documented, but dynamic expansion or elimination of repeats was also observed. Concerning the B chromosome, our data provided new information on the composition in A. flavolineata. Together with previous results, the sequences of heterochromatic nature were not likely highly amplified in the entire B chromosome. Finally, the constitutive transcriptional activity suggests a possible unknown functional role, which should be further investigated.
Collapse
Affiliation(s)
- Diogo Milani
- Departamento de Biologia, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, São Paulo CEP 13506-900 Brazil
| | - Érica Ramos
- Departamento de Morfologia, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Botucatu, São Paulo Brazil
| | - Vilma Loreto
- Departamento de Genética, UFPE - Univ Federal de Pernambuco, Centro de Biociências/CB, Recife, Pernambuco Brazil
| | | | - Adauto Lima Cardoso
- Departamento de Morfologia, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Botucatu, São Paulo Brazil
| | | | - Cesar Martins
- Departamento de Morfologia, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Botucatu, São Paulo Brazil
| | - Diogo Cavalcanti Cabral-de-Mello
- Departamento de Biologia, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, São Paulo CEP 13506-900 Brazil
| |
Collapse
|
47
|
Selection Constrains High Rates of Tandem Repetitive DNA Mutation in Daphnia pulex. Genetics 2017; 207:697-710. [PMID: 28811387 DOI: 10.1534/genetics.117.300146] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/11/2017] [Indexed: 12/26/2022] Open
Abstract
A long-standing evolutionary puzzle is that all eukaryotic genomes contain large amounts of tandemly-repeated DNA whose sequence motifs and abundance vary greatly among even closely related species. To elucidate the evolutionary forces governing tandem repeat dynamics, quantification of the rates and patterns of mutations in repeat copy number and tests of its selective neutrality are necessary. Here, we used whole-genome sequences of 28 mutation accumulation (MA) lines of Daphnia pulex, in addition to six isolates from a non-MA population originating from the same progenitor, to both estimate mutation rates of abundances of repeat sequences and evaluate the selective regime acting upon them. We found that mutation rates of individual repeats were both high and highly variable, ranging from additions/deletions of 0.29-105 copies per generation (reflecting changes of 0.12-0.80% per generation). Our results also provide evidence that new repeat sequences are often formed from existing ones. The non-MA population isolates showed a signal of either purifying or stabilizing selection, with 33% lower variation in repeat copy number on average than the MA lines, although the level of selective constraint was not evenly distributed across all repeats. The changes between many pairs of repeats were correlated, and the pattern of correlations was significantly different between the MA lines and the non-MA population. Our study demonstrates that tandem repeats can experience extremely rapid evolution in copy number, which can lead to high levels of divergence in genome-wide repeat composition between closely related species.
Collapse
|
48
|
Palacios-Gimenez OM, Dias GB, de Lima LG, Kuhn GCES, Ramos É, Martins C, Cabral-de-Mello DC. High-throughput analysis of the satellitome revealed enormous diversity of satellite DNAs in the neo-Y chromosome of the cricket Eneoptera surinamensis. Sci Rep 2017; 7:6422. [PMID: 28743997 PMCID: PMC5527012 DOI: 10.1038/s41598-017-06822-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/19/2017] [Indexed: 12/31/2022] Open
Abstract
Satellite DNAs (satDNAs) constitute large portion of eukaryote genomes, comprising non-protein-coding sequences tandemly repeated. They are mostly found in heterochromatic regions of chromosomes such as around centromere or near telomeres, in intercalary heterochromatin, and often in non-recombining segments of sex chromosomes. We examined the satellitome in the cricket Eneoptera surinamensis (2n = 9, neo-X1X2Y, males) to characterize the molecular evolution of its neo-sex chromosomes. To achieve this, we analyzed illumina reads using graph-based clustering and complementary analyses. We found an unusually high number of 45 families of satDNAs, ranging from 4 bp to 517 bp, accounting for about 14% of the genome and showing different modular structures and high diversity of arrays. FISH mapping revealed that satDNAs are located mostly in C-positive pericentromeric regions of the chromosomes. SatDNAs enrichment was also observed in the neo-sex chromosomes in comparison to autosomes. Especially astonishing accumulation of satDNAs loci was found in the highly differentiated neo-Y, including 39 satDNAs over-represented in this chromosome, which is the greatest satDNAs diversity yet reported for sex chromosomes. Our results suggest possible involvement of satDNAs in genome increasing and in molecular differentiation of the neo-sex chromosomes in this species, contributing to the understanding of sex chromosome composition and evolution in Orthoptera.
Collapse
Affiliation(s)
| | - Guilherme Borges Dias
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Leonardo Gomes de Lima
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Érica Ramos
- UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Departamento de Morfologia, Botucatu, São Paulo, Brazil
| | - Cesar Martins
- UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Departamento de Morfologia, Botucatu, São Paulo, Brazil
| | | |
Collapse
|
49
|
Lorite P, Muñoz-López M, Carrillo J, Sanllorente O, Vela J, Mora P, Tinaut A, Torres M, Palomeque T. Concerted evolution, a slow process for ant satellite DNA: study of the satellite DNA in the Aphaenogaster genus (Hymenoptera, Formicidae). ORG DIVERS EVOL 2017. [DOI: 10.1007/s13127-017-0333-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
50
|
W-enriched satellite sequence in the Indian meal moth, Plodia interpunctella (Lepidoptera, Pyralidae). Chromosome Res 2017; 25:241-252. [PMID: 28500471 DOI: 10.1007/s10577-017-9558-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 04/24/2017] [Accepted: 04/27/2017] [Indexed: 10/19/2022]
Abstract
The W chromosome of most lepidopteran species represents the largest heterochromatin entity in the female genome. Although satellite DNA is a typical component of constitutive heterochromatin, there are only a few known satellite DNAs (satDNAs) located on the W chromosome in moths and butterflies. In this study, we isolated and characterized new satDNA (PiSAT1) from microdissected W chromosomes of the Indian meal moth, Plodia interpunctella. Even though the PiSAT1 is mainly localized near the female-specific segment of the W chromosome, short arrays of this satDNA also occur on autosomes and/or the Z chromosome. Probably due to the predominant location in the non-recombining part of the genome, PiSAT1 exhibits a relatively large nucleotide variability in its monomers. However, at least a part of all predicted functional motifs is located in conserved regions. Moreover, we detected polyadenylated transcripts of PiSAT1 in all developmental stages and in both sexes (female and male larvae, pupae and adults). Our results suggest a potential structural and functional role of PiSAT1 in the P. interpunctella genome, which is consistent with accumulating evidence for the important role of satDNAs in eukaryotic genomes.
Collapse
|