1
|
Gokhman VE, Kuznetsova VG. Structure and Evolution of Ribosomal Genes of Insect Chromosomes. INSECTS 2024; 15:593. [PMID: 39194798 DOI: 10.3390/insects15080593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 07/25/2024] [Accepted: 08/02/2024] [Indexed: 08/29/2024]
Abstract
Currently, clusters of 45S and 5S ribosomal DNA (rDNA) have been studied in about 1000 and 100 species of the class Insecta, respectively. Although the number of insect species with known 45S rDNA clusters (also referred to as nucleolus-organizing regions, or NORs) constitutes less than 0.1 percent of the described members of this enormous group, certain conclusions can already be drawn. Since haploid karyotypes with single 45S and 5S rDNA clusters predominate in both basal and derived insect groups, this character state is apparently ancestral for the class Insecta in general. Nevertheless, the number, chromosomal location, and other characteristics of both 45S and 5S rDNA sites substantially vary across different species, and sometimes even within the same species. There are several main factors and molecular mechanisms that either maintain these parameters or alter them on the short-term and/or long-term scale. Chromosome structure (i.e., monocentric vs. holokinetic chromosomes), excessive numbers of rRNA gene copies per cluster, interactions with transposable elements, pseudogenization, and meiotic recombination are perhaps the most important among them.
Collapse
Affiliation(s)
| | - Valentina G Kuznetsova
- Department of Karyosystematics, Zoological Institute, Russian Academy of Sciences, St. Petersburg 199034, Russia
| |
Collapse
|
2
|
Cabral-de-Mello DC, Mora P, Rico-Porras JM, Ferretti ABSM, Palomeque T, Lorite P. The spread of satellite DNAs in euchromatin and insights into the multiple sex chromosome evolution in Hemiptera revealed by repeatome analysis of the bug Oxycarenus hyalinipennis. INSECT MOLECULAR BIOLOGY 2023; 32:725-737. [PMID: 37615351 DOI: 10.1111/imb.12868] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/07/2023] [Indexed: 08/25/2023]
Abstract
Satellite DNAs (satDNAs) are highly repeated tandem sequences primarily located in heterochromatin, although their occurrence in euchromatin has been reported. Here, our aim was to advance the understanding of satDNA and multiple sex chromosome evolution in heteropterans. We combined cytogenetic and genomic approaches to study, for the first time, the satDNA composition of the genome in an Oxycarenidae bug, Oxycarenus hyalinipennis. The species exhibits a male karyotype of 2n = 19 (14A + 2 m + X1 X2 Y), with a highly differentiated Y chromosome, as demonstrated by C-banding and comparative genomic hybridization, revealing an enrichment of repeats from the male genome. Additionally, comparative analysis between males and females revealed that the 26 identified satDNA families are significantly biased towards male genome, accumulating in discrete regions in the Y chromosome. Exceptionally, the OhyaSat04-125 family was found to be distributed virtually throughout the entire extension of the Y chromosome. This suggests an important role of satDNA in Y chromosome differentiation, in comparison of other repeats, which collectively shows similar abundance between sexes, about 50%. Furthermore, chromosomal mapping of all satDNA families revealed an unexpected high spread in euchromatic regions, covering the entire extension, irrespective of their abundance. Only discrete regions of heterochromatin on the Y chromosome and of the m-chromosomes (peculiar chromosomes commonly observed in heteropterans) were enriched with satDNAs. The putative causes of the intense enrichment of satDNAs in euchromatin are discussed, including the possible existence of burst cycles similar to transposable elements and as a result of holocentricity. These data challenge the classical notion that euchromatin is not enriched with satDNAs.
Collapse
Affiliation(s)
- Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP-Universidade Estadual Paulista, Rio Claro, Brazil
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Jaén, Spain
| | - Pablo Mora
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Jaén, Spain
| | - José M Rico-Porras
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Jaén, Spain
| | - Ana B S M Ferretti
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP-Universidade Estadual Paulista, Rio Claro, Brazil
| | - Teresa Palomeque
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Jaén, Spain
| | - Pedro Lorite
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Jaén, Spain
| |
Collapse
|
3
|
Dalíková M, Provazníková I, Provazník J, Grof-Tisza P, Pepi A, Nguyen P. The Role of Repetitive Sequences in Repatterning of Major Ribosomal DNA Clusters in Lepidoptera. Genome Biol Evol 2023; 15:evad090. [PMID: 37226278 PMCID: PMC10257491 DOI: 10.1093/gbe/evad090] [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: 05/31/2022] [Revised: 04/27/2023] [Accepted: 05/09/2023] [Indexed: 05/26/2023] Open
Abstract
Genes for major ribosomal RNAs (rDNA) are present in multiple copies mainly organized in tandem arrays. The number and position of rDNA loci can change dynamically and their repatterning is presumably driven by other repetitive sequences. We explored a peculiar rDNA organization in several representatives of Lepidoptera with either extremely large or numerous rDNA clusters. We combined molecular cytogenetics with analyses of second- and third-generation sequencing data to show that rDNA spreads as a transcription unit and reveal association between rDNA and various repeats. Furthermore, we performed comparative long read analyses among the species with derived rDNA distribution and moths with a single rDNA locus, which is considered ancestral. Our results suggest that satellite arrays, rather than mobile elements, facilitate homology-mediated spread of rDNA via either integration of extrachromosomal rDNA circles or ectopic recombination. The latter arguably better explains preferential spread of rDNA into terminal regions of lepidopteran chromosomes as efficiency of ectopic recombination depends on the proximity of homologous sequences to telomeres.
Collapse
Affiliation(s)
- Martina Dalíková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Irena Provazníková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jan Provazník
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Patrick Grof-Tisza
- Institute of Biology, Laboratory of Evolutionary Entomology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Adam Pepi
- Department of Biology, Tufts University
| | - Petr Nguyen
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| |
Collapse
|
4
|
Raban R, Gendron WAC, Akbari OS. A perspective on the expansion of the genetic technologies to support the control of neglected vector-borne diseases and conservation. FRONTIERS IN TROPICAL DISEASES 2022. [DOI: 10.3389/fitd.2022.999273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
Genetic-based technologies are emerging as promising tools to support vector population control. Vectors of human malaria and dengue have been the main focus of these development efforts, but in recent years these technologies have become more flexible and adaptable and may therefore have more wide-ranging applications. Culex quinquefasciatus, for example, is the primary vector of avian malaria in Hawaii and other tropical islands. Avian malaria has led to the extinction of numerous native bird species and many native bird species continue to be threatened as climate change is expanding the range of this mosquito. Genetic-based technologies would be ideal to support avian malaria control as they would offer alternatives to interventions that are difficult to implement in natural areas, such as larval source reduction, and limit the need for chemical insecticides, which can harm beneficial species in these natural areas. This mosquito is also an important vector of human diseases, such as West Nile and Saint Louis encephalitis viruses, so genetic-based control efforts for this species could also have a direct impact on human health. This commentary will discuss the current state of development and future needs for genetic-based technologies in lesser studied, but important disease vectors, such as C. quinquefasciatus, and make comparisons to technologies available in more studied vectors. While most current genetic control focuses on human disease, we will address the impact that these technologies could have on both disease and conservation focused vector control efforts and what is needed to prepare these technologies for evaluation in the field. The versatility of genetic-based technologies may result in the development of many important tools to control a variety of vectors that impact human, animal, and ecosystem health.
Collapse
|
5
|
Contributions to Trachelyopterus (Siluriformes: Auchenipteridae) species diagnosis by cytotaxonomic autapomorphies: from U2 snRNA chromosome polymorphism to rDNA and histone gene synteny. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00560-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
6
|
Husemann M, Dey LS, Sadílek D, Ueshima N, Hawlitschek O, Song H, Weissman DB. Evolution of chromosome number in grasshoppers (Orthoptera: Caelifera: Acrididae). ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00543-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractOrthoptera have some of the largest genomes of all insects. At the same time, the architecture of their genomes remains poorly understood. Comparative cytological data across a wide range of taxa, even for basic parameters such as chromosome number, may provide important insights into the evolution of these genomes and help answer the question of why some species attained such large sizes. We collected and compiled more than 1,000 records of chromosome numbers of 339 genera (13.8% of 2,452 known genera) and 769 species (6.2% of 12,250 known species) of Caelifera, the suborder of Orthoptera that includes those taxa with short antennae. Within the family Acrididae, most of the records come from the subfamilies Oedipodinae (N = 325), Melanoplinae (N = 192) and Gomphocerinae (N = 254). Out of the 621 investigated species of Acrididae, 459 (73.9%) shared a chromosome number of 2n♂ = 23. Chromosome numbers of 2n♂ = 17 (12.2%) and 2n♂ = 21 (9.9%) were less common. The remaining 4.0% of species exhibited different chromosome numbers between 2n♂ = 8 (6 + XY) and 2n♂ = 27. Plotted on a phylogenetic tree, our results confirm that chromosome numbers, especially in the largest grasshopper family Acrididae, are highly conserved with a basic count of 2n♂ = 23 (22 + X0), sometimes reduced to, e.g., 2n♂ = 17 (16 + X0) in some genera of the slant-faced grasshopper subfamily Gomphocerinae. Species with divergent chromosome numbers occur in many of the groups we studied, but are not a systematic trait and have evolved multiple times independently. Our study supports the view that chromosome numbers are much more stable across the investigated Caelifera compared to Ensifera, the second suborder of Orthoptera that includes the long antennae bush crickets and crickets. Our results significantly extend our knowledge on the diversity of this character in Caelifera.
Collapse
|
7
|
Vicari MR, Bruschi DP, Cabral-de-Mello DC, Nogaroto V. Telomere organization and the interstitial telomeric sites involvement in insects and vertebrates chromosome evolution. Genet Mol Biol 2022; 45:e20220071. [DOI: 10.1590/1678-4685-gmb-2022-0071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 09/24/2022] [Indexed: 11/16/2022] Open
|
8
|
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
|
9
|
Martí E, Milani D, Bardella VB, Albuquerque L, Song H, Palacios-Gimenez OM, Cabral-de-Mello DC. Cytogenomic analysis unveils mixed molecular evolution and recurrent chromosomal rearrangements shaping the multigene families on Schistocerca grasshopper genomes. Evolution 2021; 75:2027-2041. [PMID: 34155627 DOI: 10.1111/evo.14287] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/11/2021] [Accepted: 05/26/2021] [Indexed: 11/26/2022]
Abstract
Multigene families are essential components of eukaryotic genomes and play key roles either structurally and functionally. Their modes of evolution remain elusive even in the era of genomics, because multiple multigene family sequences coexist in genomes, particularly in large repetitive genomes. Here, we investigate how the multigene families 18S rDNA, U2 snDNA, and H3 histone evolved in 10 species of Schistocerca grasshoppers with very large and repeat-enriched genomes. Using sequenced genomes and fluorescence in situ hybridization mapping, we find substantial differences between species, including the number of chromosomal clusters, changes in sequence abundance and nucleotide composition, pseudogenization, and association with transposable elements (TEs). The intragenomic analysis of Schistocerca gregaria using long-read sequencing and genome assembly unveils conservation for H3 histone and recurrent pseudogenization for 18S rDNA and U2 snDNA, likely promoted by association with TEs and sequence truncation. Remarkably, TEs were frequently associated with truncated copies, were also among the most abundant in the genome, and revealed signatures of recent activity. Our findings suggest a combined effect of concerted and birth-and-death models driving the evolution of multigene families in Schistocerca over the last 8 million years, and the occurrence of intra- and interchromosomal rearrangements shaping their chromosomal distribution. Despite the conserved karyotype in Schistocerca, our analysis highlights the extensive reorganization of repetitive DNAs in Schistocerca, contributing to the advance of comparative genomics for this important grasshopper genus.
Collapse
Affiliation(s)
- Emiliano Martí
- Departamento de Biologia Geral e Aplicada, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, 13506-900, Brazil
| | - Diogo Milani
- Departamento de Biologia Geral e Aplicada, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, 13506-900, Brazil
| | - Vanessa B Bardella
- Departamento de Biologia Geral e Aplicada, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, 13506-900, Brazil
| | - Lucas Albuquerque
- Departamento de Biologia Geral e Aplicada, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, 13506-900, Brazil
| | - Hojun Song
- Department of Entomology, Texas A&M University, College Station, Texas, 77843
| | - Octavio M Palacios-Gimenez
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, SE-75236, Sweden.,Population Ecology Group, Institute of Ecology and Evolution, Friedrich Schiller University Jena, Jena, DE-07743, Germany
| | - Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, 13506-900, Brazil
| |
Collapse
|
10
|
Provazníková I, Hejníčková M, Visser S, Dalíková M, Carabajal Paladino LZ, Zrzavá M, Voleníková A, Marec F, Nguyen P. Large-scale comparative analysis of cytogenetic markers across Lepidoptera. Sci Rep 2021; 11:12214. [PMID: 34108567 PMCID: PMC8190105 DOI: 10.1038/s41598-021-91665-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/24/2021] [Indexed: 11/25/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) allows identification of particular chromosomes and their rearrangements. Using FISH with signal enhancement via antibody amplification and enzymatically catalysed reporter deposition, we evaluated applicability of universal cytogenetic markers, namely 18S and 5S rDNA genes, U1 and U2 snRNA genes, and histone H3 genes, in the study of the karyotype evolution in moths and butterflies. Major rDNA underwent rather erratic evolution, which does not always reflect chromosomal changes. In contrast, the hybridization pattern of histone H3 genes was well conserved, reflecting the stable organisation of lepidopteran genomes. Unlike 5S rDNA and U1 and U2 snRNA genes which we failed to detect, except for 5S rDNA in a few representatives of early diverging lepidopteran lineages. To explain the negative FISH results, we used quantitative PCR and Southern hybridization to estimate the copy number and organization of the studied genes in selected species. The results suggested that their detection was hampered by long spacers between the genes and/or their scattered distribution. Our results question homology of 5S rDNA and U1 and U2 snRNA loci in comparative studies. We recommend the use of histone H3 in studies of karyotype evolution.
Collapse
Affiliation(s)
- Irena Provazníková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Martina Hejníčková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Sander Visser
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Martina Dalíková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | | | - Magda Zrzavá
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Anna Voleníková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - František Marec
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Petr Nguyen
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic.
| |
Collapse
|
11
|
Gazoni T, Dorigon NS, da Silva MJ, Cholak LR, Haddad CFB, Parise-Maltempi PP. Chromosome Mapping of U2 snDNA in Species of Leptodactylus (Anura, Leptodactylidae). Cytogenet Genome Res 2021; 161:63-69. [PMID: 33823507 DOI: 10.1159/000515047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 02/05/2021] [Indexed: 11/19/2022] Open
Abstract
Small nuclear RNA (snRNA) is a class of molecules involved in the processing of pre-mRNA and in regulatory cell processes. snRNAs are always associated with a set of specific proteins. The complexes are referred to as small nuclear ribonucleoproteins, and spliceosome U RNAs are their most common snRNA components. The repetitive sequences of U snDNAs have been cytogenetically mapped in several species of Arthropoda, fishes, and mammals; however, their distribution remains unknown in amphibians. Here, we show results of FISH mapping of U2 snDNA repetitive sequences in species of the amphibian genus Leptodactylus to reveal the distribution patterns of this sequence in their karyotypes. The probe hybridized in the metacentric chromosome pair 6 in Leptodactylus fuscus, L. gracilis, L. latrans, L. chaquensis, L. petersii, L. podicipinus, and L. brevipes. A different pattern was observed in L. labyrinthicus with hybridization signals in 4 chromosome pairs. The same localization of U2 gene sequences in most of the species analyzed suggests a relatively conserved pattern and a similarity of the chromosome 6 among these species of Leptodactylus.
Collapse
Affiliation(s)
- Thiago Gazoni
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Rio Claro, Brazil
| | - Nathália S Dorigon
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Rio Claro, Brazil
| | - Marcelo J da Silva
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Rio Claro, Brazil
| | - Luiza R Cholak
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Rio Claro, Brazil
| | - Célio F B Haddad
- Departamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Rio Claro, Brazil
| | - Patricia P Parise-Maltempi
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Rio Claro, Brazil
| |
Collapse
|
12
|
Buleu O, Jetybayev I, Mofidi-Neyestanak M, Bugrov A. Karyotypes diversity in some Iranian Pamphagidae grasshoppers (Orthoptera, Acridoidea, Pamphagidae): new insights on the evolution of the neo-XY sex chromosomes. COMPARATIVE CYTOGENETICS 2020; 14:549-566. [PMID: 33224444 PMCID: PMC7674378 DOI: 10.3897/compcytogen.v14.i4.53688] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 10/04/2020] [Indexed: 05/17/2023]
Abstract
For the first time, cytogenetic features of grasshoppers from Iran have been studied. In this paper we conducted a comparative cytogenetic analysis of six species from the family Pamphagidae. The species studied belong to subfamilies Thrinchinae Stål, 1876 (Eremopeza bicoloripes (Moritz, 1928), E. saussurei (Uvarov, 1918)) and Pamphaginae (Saxetania paramonovi (Dirsh, 1927), Tropidauchen escalerai Bolívar, 1912, Tropidauchen sp., and Paranothrotes citimus Mistshenko, 1951). We report information about the chromosome number and morphology, C-banding patterns, and localization of ribosomal DNA clusters and telomeric (TTAGG)n repeats. Among these species, only S. paramonovi had an ancestral Pamphagidae karyotype (2n=18+X0♂; FN=19♂). The karyotypes of the remaining species differed from the ancestral karyotypes. The karyotypes of E. bicoloripes and E. saussurei, despite having the same chromosome number (2n=18+X0♂) had certain biarmed chromosomes (FN=20♂ and FN=34♂ respectively). The karyotypes of T. escalerai and Tropidauchen sp. consisted of eight pairs of acrocentric autosomes, one submetacentric neo-X chromosome and one acrocentric neo-Y chromosome in males (2n=16+neo-X neo-Y♂). The karyotype of P. citimus consisted of seven pairs of acrocentric autosomes, submetacentric the neo-X1 and neo-Y and acrocentric the neo-X2 chromosomes (2n=14+neo-X1 neo-X2 neo-Y♂). Comparative analysis of the localization and size of C-positive regions, the position of ribosomal clusters and the telomeric DNA motif in the chromosomes of the species studied, revealed early unknown features of their karyotype evolution. The data obtained has allowed us to hypothesize that the origin and early phase of evolution of the neo-Xneo-Y♂ sex chromosome in the subfamily Pamphaginae, are linked to the Iranian highlands.
Collapse
Affiliation(s)
- Olesya Buleu
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091, Novosibirsk, Russia
| | - Ilyas Jetybayev
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Pr. Lavrentjeva 10, 630090, Novosibirsk, Russia
| | - Mohsen Mofidi-Neyestanak
- Iranian Research Institute of Plant Protection, Hayk Mirzayans Insect Museum, Agricultural Research, Education and Extension Organization, Tehran, Iran
| | - Alexander Bugrov
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091, Novosibirsk, Russia
| |
Collapse
|
13
|
Cavalcante MG, Nagamachi CY, Pieczarka JC, Noronha RCR. Evolutionary insights in Amazonian turtles (Testudines, Podocnemididae): co-location of 5S rDNA and U2 snRNA and wide distribution of Tc1/Mariner. Biol Open 2020; 9:bio049817. [PMID: 32229487 PMCID: PMC7197720 DOI: 10.1242/bio.049817] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/18/2020] [Indexed: 12/29/2022] Open
Abstract
Eukaryotic genomes exhibit substantial accumulation of repetitive DNA sequences. These sequences can participate in chromosomal reorganization events and undergo molecular cooption to interfere with the function and evolution of genomes. In turtles, repetitive DNA sequences appear to be accumulated at probable break points and may participate in events such as non-homologous recombination and chromosomal rearrangements. In this study, repeated sequences of 5S rDNA, U2 snRNA and Tc1/Mariner transposons were amplified from the genomes of the turtles, Podocnemis expansa and Podocnemis unifilis, and mapped by fluorescence in situ hybridization. Our data confirm the 2n=28 chromosomes for these species (the second lowest 2n in the order Testudines). We observe high conservation of the co-located 5S rDNA and U2 snRNA genes on a small chromosome pair (pair 13), and surmise that this represents the ancestral condition. Our analysis reveals a wide distribution of the Tc1/Mariner transposons and we discuss how the mobility of these transposons can act on karyotypic reorganization events (contributing to the 2n decrease of those species). Our data add new information for the order Testudines and provide important insights into the dynamics and organization of these sequences in the chelonian genomes.
Collapse
Affiliation(s)
- Manoella Gemaque Cavalcante
- Centro de Estudos Avançados da Biodiversidade, Cytogenetics Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Cleusa Yoshiko Nagamachi
- Centro de Estudos Avançados da Biodiversidade, Cytogenetics Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Julio Cesar Pieczarka
- Centro de Estudos Avançados da Biodiversidade, Cytogenetics Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Renata Coelho Rodrigues Noronha
- Centro de Estudos Avançados da Biodiversidade, Cytogenetics Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| |
Collapse
|
14
|
Xu D, Sember A, Zhu Q, Oliveira EAD, Liehr T, Al-Rikabi ABH, Xiao Z, Song H, Cioffi MDB. Deciphering the Origin and Evolution of the X 1X 2Y System in Two Closely-Related Oplegnathus Species (Oplegnathidae and Centrarchiformes). Int J Mol Sci 2019; 20:E3571. [PMID: 31336568 PMCID: PMC6678977 DOI: 10.3390/ijms20143571] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/05/2019] [Accepted: 07/13/2019] [Indexed: 01/18/2023] Open
Abstract
Oplegnathus fasciatus and O. punctatus (Teleostei: Centrarchiformes: Oplegnathidae), are commercially important rocky reef fishes, endemic to East Asia. Both species present an X1X2Y sex chromosome system. Here, we investigated the evolutionary forces behind the origin and differentiation of these sex chromosomes, with the aim to elucidate whether they had a single or convergent origin. To achieve this, conventional and molecular cytogenetic protocols, involving the mapping of repetitive DNA markers, comparative genomic hybridization (CGH), and whole chromosome painting (WCP) were applied. Both species presented similar 2n, karyotype structure and hybridization patterns of repetitive DNA classes. 5S rDNA loci, besides being placed on the autosomal pair 22, resided in the terminal region of the long arms of both X1 chromosomes in females, and on the X1 and Y chromosomes in males. Furthermore, WCP experiments with a probe derived from the Y chromosome of O. fasciatus (OFAS-Y) entirely painted the X1 and X2 chromosomes in females and the X1, X2, and Y chromosomes in males of both species. CGH failed to reveal any sign of sequence differentiation on the Y chromosome in both species, thereby suggesting the shared early stage of neo-Y chromosome differentiation. Altogether, the present findings confirmed the origin of the X1X2Y sex chromosomes via Y-autosome centric fusion and strongly suggested their common origin.
Collapse
Affiliation(s)
- Dongdong Xu
- Key Lab of Mariculture and Enhancement of Zhejiang Province, Marine Fishery Institute of Zhejiang Province, Zhoushan 316100, China
- College of Fisheries, Zhejiang Ocean University, Zhoushan 316100, China
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Qihui Zhu
- Key Lab of Mariculture and Enhancement of Zhejiang Province, Marine Fishery Institute of Zhejiang Province, Zhoushan 316100, China
| | - Ezequiel Aguiar de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos SP 13565-905, Brazil
- Secretaria de Estado de Educação de Mato Grosso-SEDUC-MT, Cuiabá MT 78049-909, Brazil
| | - Thomas Liehr
- University Clinic Jena, Institute of Human Genetics, 07747 Jena, Germany
| | | | - Zhizhong Xiao
- Laboratory for Marine Biology and Biotechnology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
| | - Hongbin Song
- Key Lab of Mariculture and Enhancement of Zhejiang Province, Marine Fishery Institute of Zhejiang Province, Zhoushan 316100, China
- College of Fisheries, Zhejiang Ocean University, Zhoushan 316100, China
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos SP 13565-905, Brazil.
- University Clinic Jena, Institute of Human Genetics, 07747 Jena, Germany.
| |
Collapse
|
15
|
Buleu OG, Jetybayev IY, Chobanov DP, Bugrov AG. Comparative analysis of C-heterochromatin, ribosomal and telomeric DNA markers in chromosomes of Pamphagidae grasshoppers from Morocco. COMPARATIVE CYTOGENETICS 2019; 13:61-74. [PMID: 30854170 PMCID: PMC6403196 DOI: 10.3897/compcytogen.v13i1.32039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/30/2019] [Indexed: 05/19/2023]
Abstract
The karyotypes and the localization of C-bands, clusters of ribosomal DNA and telomeric repeats of 10 species of the family Pamphagidae from Morocco are described for the first time. The species studied belong to the subfamilies Pamphaginae and Thrinchinae. All species have karyotypes consisting of 19 and 20 acrocentric chromosomes and X0/XX sex chromosome system in males and females, respectively (2n♂=19, NF=19; 2n♀=20, NF=20). Despite the karyotype conservatism, we revealed differences in the location and size of C-heterochromatin blocks and ribosomal DNA clusters. A comparative analysis of these differences shows that karyotype divergences in this group is connected not to structural chromosome rearrangements, but to the evolution of repetitive DNA.
Collapse
Affiliation(s)
- Olesya G. Buleu
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, RussiaInstitute of Systematics and Ecology of Animals, Russian Academy of SciencesNovosibirskRussia
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091 Novosibirsk, RussiaNovosibirsk State UniversityNovosibirskRussia
| | - Ilyas Y. Jetybayev
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091 Novosibirsk, RussiaNovosibirsk State UniversityNovosibirskRussia
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Pr. Lavrentjeva 10, 630090 Novosibirsk, RussiaInstitute of Cytology and Genetics, Russian Academy of SciencesNovosibirskRussia
| | - Dragan P. Chobanov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Tsar Osvobodotel Boul. 1, Sofia 1000, BulgariaInstitute of Biodiversity and Ecosystem Research, Bulgarian Academy of SciencesSofiaBulgaria
| | - Alexander G. Bugrov
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, RussiaInstitute of Systematics and Ecology of Animals, Russian Academy of SciencesNovosibirskRussia
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091 Novosibirsk, RussiaNovosibirsk State UniversityNovosibirskRussia
| |
Collapse
|
16
|
Palacios-Gimenez OM, Milani D, Lemos B, Castillo ER, Martí DA, Ramos E, Martins C, Cabral-de-Mello DC. Uncovering the evolutionary history of neo-XY sex chromosomes in the grasshopper Ronderosia bergii (Orthoptera, Melanoplinae) through satellite DNA analysis. BMC Evol Biol 2018; 18:2. [PMID: 29329524 PMCID: PMC5767042 DOI: 10.1186/s12862-017-1113-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 12/08/2017] [Indexed: 03/26/2023] Open
Abstract
BACKGROUND Neo-sex chromosome systems arose independently multiple times in evolution, presenting the remarkable characteristic of repetitive DNAs accumulation. Among grasshoppers, occurrence of neo-XY was repeatedly noticed in Melanoplinae. Here we analyzed the most abundant tandem repeats of R. bergii (2n = 22, neo-XY♂) using deep Illumina sequencing and graph-based clustering in order to address the neo-sex chromosomes evolution. RESULTS The analyses revealed ten families of satDNAs comprising about ~1% of the male genome, which occupied mainly C-positive regions of autosomes. Regarding the sex chromosomes, satDNAs were recorded within centromeric or interstitial regions of the neo-X chromosome and four satDNAs occurred in the neo-Y, two of them being exclusive (Rber248 and Rber299). Using a combination of probes we uncovered five well-defined cytological variants for neo-Y, originated by multiple paracentric inversions and satDNA amplification, besides fragmented neo-Y. These neo-Y variants were distinct in frequency between embryos and adult males. CONCLUSIONS The genomic data together with cytogenetic mapping enabled us to better understand the neo-sex chromosome dynamics in grasshoppers, reinforcing differentiation of neo-X and neo-Y and revealing the occurrence of multiple additional rearrangements involved in the neo-Y evolution of R. bergii. We discussed the possible causes that led to differences in frequency for the neo-Y variants between embryos and adults. Finally we hypothesize about the role of DNA satellites in R. bergii as well as putative historical events involved in the evolution of the R. bergii neo-XY.
Collapse
Affiliation(s)
- Octavio M. Palacios-Gimenez
- Departamento de Biologia, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, São Paulo 13506-900 Brazil
| | - Diogo Milani
- Departamento de Biologia, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, São Paulo 13506-900 Brazil
| | - Bernardo Lemos
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard University T. H. Chan School of Public Health, Boston, Massachusetts 02115 USA
| | | | | | - Erica Ramos
- 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 C. Cabral-de-Mello
- Departamento de Biologia, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, São Paulo 13506-900 Brazil
| |
Collapse
|
17
|
Anjos A, Paladini A, Mariguela TC, Cabral-de-Mello DC. U1 snDNA chromosomal mapping in ten spittlebug species (Cercopidade, Auchenorrhyncha, Hemiptera). Genome 2018; 61:59-62. [DOI: 10.1139/gen-2017-0151] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Spittlebugs, which belong to the family Cercopidae (Auchenorrhyncha, Hemiptera), form a large group of xylem-feeding insects that are best known for causing damage to plantations and pasture grasses. The holocentric chromosomes of these insects remain poorly studied in regards to the organization of different classes of repetitive DNA. To improve chromosomal maps based on repetitive DNAs and to better understand the chromosomal organization and evolutionary dynamics of multigene families in spittlebugs, we physically mapped the U1 snRNA gene with fluorescence in situ hybridization (FISH) in 10 species of Cercopidae belonging to three different genera. All the U1 snDNA clusters were autosomal and located in interstitial position. In seven species, they were restricted to one autosome per haploid genome, while three species of the genus Mahanarva showed two clusters in two different autosomes. Although it was not possible to precisely define the ancestral location of this gene, it was possible to observe the presence of at least one cluster located in a small bivalent in all karyotypes. The karyotype stability observed in Cercopidae is also observed in respect to the distribution of U1 snDNA. Our data are discussed in light of possible mechanisms for U1 snDNA conservation and compared with the available data from other species.
Collapse
Affiliation(s)
- Allison Anjos
- Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, SP, Brazil
| | - Andressa Paladini
- Departamento de Ecologia e Evolução, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Tatiane C. Mariguela
- Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, SP, Brazil
| | - Diogo C. Cabral-de-Mello
- Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, SP, Brazil
| |
Collapse
|
18
|
Jetybayev IY, Bugrov AG, Buleu OG, Bogomolov AG, Rubtsov NB. Origin and Evolution of the Neo-Sex Chromosomes in Pamphagidae Grasshoppers through Chromosome Fusion and Following Heteromorphization. Genes (Basel) 2017; 8:genes8110323. [PMID: 29137168 PMCID: PMC5704236 DOI: 10.3390/genes8110323] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 11/16/2022] Open
Abstract
In most phylogenetic lineages, the evolution of sex chromosomes is accompanied by their heteromorphization and degradation of one of them. The neo-sex chromosomes are useful model for studying early stages of these processes. Recently two lineages of the neo-sex chromosomes on different stages of heteromorphization was discovered in Pamphagidae family. The neo-sex chromosome heteromorphization was analyzed by generation of DNA probes derived from the neo-Xs and neo-Ys followed with chromosome painting in nineteen species of Pamphagidae family. The homologous regions of the neo-sex chromosomes were determined in closely related species with the painting procedure and image analysis with application of the Visualization of the Specific Signal in Silico software package. Results of these analyses and distribution of C-positive regions in the neo-sex chromosomes revealed details of the heteromorphization of the neo-sex chromosomes in species from both phylogenetic lineages of Pamphagidae grasshoppers. The hypothetical mechanism of the neo-Y degradation was suggested. It includes expansion of different repeats from the proximal neo-Y chromosome region by inversions, spreading them towards distal region. Amplification of these repeats leads to formation of C-positive regions and elimination of the C-negative regions located between them.
Collapse
Affiliation(s)
- Ilyas Yerkinovich Jetybayev
- The Federal Research Center, Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Lavrentjev Ave., 10, 630090 Novosibirsk, Russia.
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091 Novosibirsk, Russia.
| | - Alexander Gennadievich Bugrov
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091 Novosibirsk, Russia.
- Novosibirsk State University, Department of Natural Sciences, Pirogov str., 2, 630090 Novosibirsk, Russia.
| | - Olesya Georgievna Buleu
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091 Novosibirsk, Russia.
- Novosibirsk State University, Department of Natural Sciences, Pirogov str., 2, 630090 Novosibirsk, Russia.
| | - Anton Gennadievich Bogomolov
- The Federal Research Center, Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Lavrentjev Ave., 10, 630090 Novosibirsk, Russia.
- Novosibirsk State University, Department of Natural Sciences, Pirogov str., 2, 630090 Novosibirsk, Russia.
| | - Nikolay Borisovich Rubtsov
- The Federal Research Center, Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Lavrentjev Ave., 10, 630090 Novosibirsk, Russia.
- Novosibirsk State University, Department of Natural Sciences, Pirogov str., 2, 630090 Novosibirsk, Russia.
| |
Collapse
|
19
|
Tracking the evolutionary pathway of sex chromosomes among fishes: characterizing the unique XX/XY1Y2 system in Hoplias malabaricus (Teleostei, Characiformes). Chromosoma 2017; 127:115-128. [DOI: 10.1007/s00412-017-0648-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/16/2017] [Accepted: 10/17/2017] [Indexed: 10/18/2022]
|
20
|
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: 48] [Impact Index Per Article: 6.9] [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
|
21
|
Chromosomal localization of Wolbachia inserts in the genomes of two subspecies of Chorthippus parallelus forming a Pyrenean hybrid zone. Chromosome Res 2017; 25:215-225. [PMID: 28477267 DOI: 10.1007/s10577-017-9557-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/22/2017] [Accepted: 04/24/2017] [Indexed: 01/08/2023]
Abstract
Wolbachia are endosymbiotic bacteria of arthropods and nematodes that can manipulate the reproduction of various host organisms to facilitate their own maternal transmission. Moreover, Wolbachia's presence in host germ cells may contribute to the many cases of lateral gene transfer from Wolbachia to host genomes that have been described. A previous study in Chorthippus parallelus, a well-known orthopteroid forming a hybrid zone in the Pyrenees, identified Wolbachia sequences from two major supergroups in the genomes of infected and uninfected Chorthippus parallelus parallelus (Cpp) and Chorthippus parallelus erythropus (Cpe) subspecies. In this study, we map the Wolbachia genomic inserts to specific regions on the chromosomes of Cpp and Cpe by fluorescent in situ hybridization (FISH) using tyramides to increase the accuracy and detection of these insertions. Additionally, we consider some of the possible roles that these bacterial inserts play in the organization and function of the grasshopper genome, as well as how they can serve as markers for phylogenetic relationships of these organisms.
Collapse
|
22
|
Castillo ERD, Taffarel A, Maronna MM, Cigliano MM, Palacios-Gimenez OM, Cabral-de-Mello DC, Martí DA. Phylogeny and chromosomal diversification in the Dichroplus elongatus species group (Orthoptera, Melanoplinae). PLoS One 2017; 12:e0172352. [PMID: 28245223 PMCID: PMC5330476 DOI: 10.1371/journal.pone.0172352] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 02/04/2017] [Indexed: 11/19/2022] Open
Abstract
In an attempt to track the chromosomal differentiation in the Dichroplus elongatus species group, we analyzed the karyotypes of four species with classical cytogenetic and mapping several multigene families through fluorescent in situ hybridization (FISH). We improved the taxon sampling of the D. elongatus species group adding new molecular data to infer the phylogeny of the genus and reconstruct the karyotype evolution. Our molecular analyses recovered a fully resolved tree with no evidence for the monophyly of Dichroplus. However, we recovered several stable clades within the genus, including the D. elongatus species group, under the different strategies of tree analyses (Maximum Parsimony and Maximum Likelihood). The chromosomal data revealed minor variation in the D. elongatus species group's karyotypes caused by chromosome rearrangements compared to the phylogenetically related D. maculipennis species group. The karyotypes of D. intermedius and D. exilis described herein showed the standard characteristics found in most Dichroplini, 2n = 23/24, X0♂ XX♀, Fundamental number (FN) = 23/24. However, we noticed two established pericentric inversions in D. intermedius karyotype, raising the FN to 27♂/28♀. A strong variation in the heterochromatic blocks distribution was evidenced at interespecific level. The multigene families' mapping revealed significant variation, mainly in rDNA clusters. These variations are probably caused by micro chromosomal changes, such as movement of transposable elements (TEs) and ectopic recombination. These observations suggest a high genomic dynamism for these repetitive DNA sequences in related species. The reconstruction of the chromosome character "variation in the FN" posits the FN = 23/24 as the ancestral state, and it is hypothesized that variations due to pericentric inversions has arisen independently three times in the evolutionary history of Dichroplus. One of these independent events occurred in the D. elongatus species group, where D. intermedius is the unique case with the highest FN described in the tribe Dichroplini.
Collapse
Affiliation(s)
- Elio R. D. Castillo
- Laboratorio de Genética Evolutiva. Instituto de Biología Subtropical (IBS) CONICET-UNaM. FCEQyN, Félix de Azara 1552, Piso 6°. Posadas, Misiones, Argentina
| | - Alberto Taffarel
- Laboratorio de Genética Evolutiva. Instituto de Biología Subtropical (IBS) CONICET-UNaM. FCEQyN, Félix de Azara 1552, Piso 6°. Posadas, Misiones, Argentina
- Comité Ejecutivo de Desarrollo e Innovación Tecnológica (CEDIT). Posadas, Misiones, Argentina
| | - Maximiliano M. Maronna
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, Travessa 14, São Paulo, Brazil
| | - María Marta Cigliano
- Museo de La Plata, CEPAVE, CCT La Plata, CONICET-UNLP. La Plata, Buenos Aires, Argentina
| | - Octavio M. Palacios-Gimenez
- UNESP—Universidade Estadual Paulista, Instituto de Biociências/IB, Departamento de Biologia, Rio Claro/SP, Brazil
| | - Diogo C. Cabral-de-Mello
- UNESP—Universidade Estadual Paulista, Instituto de Biociências/IB, Departamento de Biologia, Rio Claro/SP, Brazil
| | - Dardo A. Martí
- Laboratorio de Genética Evolutiva. Instituto de Biología Subtropical (IBS) CONICET-UNaM. FCEQyN, Félix de Azara 1552, Piso 6°. Posadas, Misiones, Argentina
| |
Collapse
|
23
|
Jetybayev IY, Bugrov AG, Ünal M, Buleu OG, Rubtsov NB. Molecular cytogenetic analysis reveals the existence of two independent neo-XY sex chromosome systems in Anatolian Pamphagidae grasshoppers. BMC Evol Biol 2017; 17:20. [PMID: 28251879 PMCID: PMC5333169 DOI: 10.1186/s12862-016-0868-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Neo-XY sex chromosome determination is a rare event in short horned grasshoppers, but it appears with unusual frequency in the Pamphagidae family. The neo-Y chromosomes found in several species appear to have undergone heterochromatinization and degradation, but this subject needs to be analyzed in other Pamphagidae species. We perform here karyotyping and molecular cytogenetic analyses in 12 Pamphagidae species from the center of biodiversity of this group in the previously-unstudied Anatolian plateau. RESULTS The basal karyotype for the Pamphagidae family, consisting of 18 acrocentric autosomes and an acrocentric X chromosome (2n♂ = 19, X0; 2n♀ = 20, XX), was found only in G. adaliae. The karyotype of all other studied species consisted of 16 acrocentric autosomes and a neo-XY sex chromosome system (2n♂♀ = 18, neo-XX♀/neo-XY♂). Two different types of neo-Y chromosomes were found. One of them was typical for three species of the Glyphotmethis genus, and showed a neo-Y chromosome being similar in size to the XR arm of the neo-X, with the addition of two small subproximal interstitial C-blocks. The second type of the neo-Y chromosome was smaller and more heterochromatinized than the XR arm, and was typical for all Nocarodeini species studied. The chromosome distribution of C-positive regions and clusters of ribosomal DNA (rDNA) and telomeric repeats yielded additional information on evolution of these neo-XY systems. CONCLUSION Most Pamphagidae species in the Anatolian region were found to have neo-XY sex chromosome systems, belonging to two different evolutionary lineages, marked by independent X-autosome fusion events occurred within the Trinchinae and Pamphaginae subfamilies. The high density of species carrying neo-XY systems in the Anatolian region, and the different evolutionary stage for the two lineages found, one being older than the other, indicates that this region has a long history of neo-XY sex chromosome formation.
Collapse
Affiliation(s)
- Ilyas Yerkinovich Jetybayev
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Pr. Lavrentjeva 10, 630090, Novosibirsk, Russia. .,Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091, Novosibirsk, Russia.
| | - Alexander Gennadievich Bugrov
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091, Novosibirsk, Russia.,Novosibirsk State University, Pirogov str., 2, 630090, Novosibirsk, Russia
| | - Mustafa Ünal
- Fen-Edebiyat Fakültesi, Biyoloji Bölümü, Abant İzzet Baysal Üniversitesi, TR-14030, Bolu, Türkiye
| | - Olesya Georgievna Buleu
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091, Novosibirsk, Russia.,Novosibirsk State University, Pirogov str., 2, 630090, Novosibirsk, Russia
| | - Nikolay Borisovich Rubtsov
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Pr. Lavrentjeva 10, 630090, Novosibirsk, Russia.,Novosibirsk State University, Pirogov str., 2, 630090, Novosibirsk, Russia
| |
Collapse
|
24
|
Pucci MB, Barbosa P, Nogaroto V, Almeida MC, Artoni RF, Scacchetti PC, Pansonato-Alves JC, Foresti F, Moreira-Filho O, Vicari MR. Chromosomal Spreading of Microsatellites and (TTAGGG)n Sequences in the Characidium zebra and C. gomesi Genomes (Characiformes: Crenuchidae). Cytogenet Genome Res 2016; 149:182-190. [DOI: 10.1159/000447959] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2016] [Indexed: 11/19/2022] Open
Abstract
Sex chromosome evolution involves the accumulation of repeat sequences such as multigenic families, noncoding repetitive DNA (satellite, minisatellite, and microsatellite), and mobile elements such as transposons and retrotransposons. Most species of Characidium exhibit heteromorphic ZZ/ZW sex chromosomes; the W is characterized by an intense accumulation of repetitive DNA including dispersed satellite DNA sequences and transposable elements. The aim of this study was to analyze the distribution pattern of 18 different tandem repeats, including (GATA)n and (TTAGGG)n, in the genomes of C. zebra and C. gomesi, especially in the C. gomesi W chromosome. In the C. gomesi W chromosome, weak signals were seen for (CAA)10, (CAC)10, (CAT)10, (CGG)10, (GAC)10, and (CA)15 probes. (GA)15 and (TA)15 hybridized to the autosomes but not to the W chromosome. The (GATA)n probe hybridized to the short arms of the W chromosome as well as the (CG)15 probe. The (GATA)n repeat is known to be a protein-binding motif. GATA-binding proteins are necessary for the decondensation of heterochromatic regions that hold coding genes, especially in some heteromorphic sex chromosomes that may keep genes related to oocyte development. The (TAA)10 repeat is accumulated in the entire W chromosome, and this microsatellite accumulation is probably involved in the sex chromosome differentiation process and crossover suppression in C. gomesi. These additional data on the W chromosome DNA composition help to explain the evolution of sex chromosomes in Characidium.
Collapse
|
25
|
Chromosomal evolutionary dynamics of four multigene families in Coreidae and Pentatomidae (Heteroptera) true bugs. Mol Genet Genomics 2016; 291:1919-25. [DOI: 10.1007/s00438-016-1229-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 06/22/2016] [Indexed: 12/31/2022]
|
26
|
Castillo ERD, Taffarel A, Mariottini Y, Fernández-Arhex V, Martí DA, Bidau CJ. Neo-sex Chromosomes in the Maculipennis Species Group (Dichroplus: Acrididae, Melanoplinae): The Cases of D. maculipennis and D. vittigerum. Zoolog Sci 2016; 33:303-10. [PMID: 27268985 DOI: 10.2108/zs150165] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
South American melanopline grasshoppers display a disproportionate number of derived karyotypes, including many cases of neo-sex chromosome systems. This is especially true of the genus Dichroplus and its Maculipennis species group. We analyzed the karyotype and neo-sex chromosomes in mitosis and meiosis of Dichroplus maculipennis and D. vittigerum from Argentina using conventional and fluorescent cytogenetic protocols in order to elucidate the behavior and origin of these neo-XY systems in relation to the current phylogeny of this group. Our results showed that D. maculipennis (2n = 22♂/22♀; neoXY/neoXX) and D. vittigerum, whose karyotype is described here for the first time (2n = 18♂/18♀; neoXY/neoXX), show highly evolved neo-XY systems, although with significant differences between them. Furthermore, both species differ for two autosomal fixed Robertsonian fusions present in D. vittigerum. Analysis of karyotypic character state optimization strongly suggests the independent origin and evolution of neo-sex systems within this species group.
Collapse
Affiliation(s)
- Elio R D Castillo
- 1 Laboratorio de Genética Evolutiva. Instituto de Biología Subtropical (IBS) CONICET- Universidad Nacional de Misiones. Félix de Azara 1552, Piso 6°. CP3300. Posadas, Misiones Argentina.,2 Comité Ejecutivo de Desarrollo e Innovación Tecnológica (CEDIT) Félix de Azara 1890, Piso 5°, Posadas, Misiones 3300, Argentina
| | - Alberto Taffarel
- 1 Laboratorio de Genética Evolutiva. Instituto de Biología Subtropical (IBS) CONICET- Universidad Nacional de Misiones. Félix de Azara 1552, Piso 6°. CP3300. Posadas, Misiones Argentina.,2 Comité Ejecutivo de Desarrollo e Innovación Tecnológica (CEDIT) Félix de Azara 1890, Piso 5°, Posadas, Misiones 3300, Argentina
| | - Yanina Mariottini
- 3 Centro de Estudios Parasitológicos y de Vectores (CEPAVE), CCT La Plata CONICET, Bulevar 120 e/60 y 64 S/N. 1900, La Plata, Argentina
| | - Valeria Fernández-Arhex
- 4 CONICET- INTA EEA Bariloche, Bote Modesta Victoria, 4450 (8400),Bariloche, Río Negro, Argentina
| | - Dardo A Martí
- 1 Laboratorio de Genética Evolutiva. Instituto de Biología Subtropical (IBS) CONICET- Universidad Nacional de Misiones. Félix de Azara 1552, Piso 6°. CP3300. Posadas, Misiones Argentina
| | | |
Collapse
|
27
|
The 5S rDNA in two Abracris grasshoppers (Ommatolampidinae: Acrididae): molecular and chromosomal organization. Mol Genet Genomics 2016; 291:1607-13. [PMID: 27106499 DOI: 10.1007/s00438-016-1204-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/30/2016] [Indexed: 10/21/2022]
Abstract
The 5S ribosomal DNA (rDNA) sequences are subject of dynamic evolution at chromosomal and molecular levels, evolving through concerted and/or birth-and-death fashion. Among grasshoppers, the chromosomal location for this sequence was established for some species, but little molecular information was obtained to infer evolutionary patterns. Here, we integrated data from chromosomal and nucleotide sequence analysis for 5S rDNA in two Abracris species aiming to identify evolutionary dynamics. For both species, two arrays were identified, a larger sequence (named type-I) that consisted of the entire 5S rDNA gene plus NTS (non-transcribed spacer) and a smaller (named type-II) with truncated 5S rDNA gene plus short NTS that was considered a pseudogene. For type-I sequences, the gene corresponding region contained the internal control region and poly-T motif and the NTS presented partial transposable elements. Between the species, nucleotide differences for type-I were noticed, while type-II was identical, suggesting pseudogenization in a common ancestor. At chromosomal point to view, the type-II was placed in one bivalent, while type-I occurred in multiple copies in distinct chromosomes. In Abracris, the evolution of 5S rDNA was apparently influenced by the chromosomal distribution of clusters (single or multiple location), resulting in a mixed mechanism integrating concerted and birth-and-death evolution depending on the unit.
Collapse
|
28
|
Šíchová J, Ohno M, Dincă V, Watanabe M, Sahara K, Marec F. Fissions, fusions, and translocations shaped the karyotype and multiple sex chromosome constitution of the northeast-Asian wood white butterfly,Leptidea amurensis. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12756] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Jindra Šíchová
- Institute of Entomology; Biology Centre CAS; 370 05 České Budějovice Czech Republic
- Faculty of Science; University of South Bohemia; 370 05 České Budějovice Czech Republic
| | - Mizuki Ohno
- Laboratory of Applied Entomology; Faculty of Agriculture; Iwate University; Morioka 020-8550 Japan
| | - Vlad Dincă
- Biodiversity Institute of Ontario; University of Guelph; Guelph Ontario N1G 2W1 Canada
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu-Fabra); 08003 Barcelona Spain
| | - Michihito Watanabe
- NPO Mt. Fuji Nature Conservation Center; 6603 Funatsu, Fujikawaguchiko-machi Yamanashi 401-0301 Japan
| | - Ken Sahara
- Laboratory of Applied Entomology; Faculty of Agriculture; Iwate University; Morioka 020-8550 Japan
| | - František Marec
- Institute of Entomology; Biology Centre CAS; 370 05 České Budějovice Czech Republic
- Faculty of Science; University of South Bohemia; 370 05 České Budějovice Czech Republic
| |
Collapse
|
29
|
Bugrov AG, Jetybayev IE, Karagyan GH, Rubtsov NB. Sex chromosome diversity in Armenian toad grasshoppers (Orthoptera, Acridoidea, Pamphagidae). COMPARATIVE CYTOGENETICS 2016; 10:45-59. [PMID: 27186337 PMCID: PMC4856925 DOI: 10.3897/compcytogen.v10i1.6407] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 10/09/2015] [Indexed: 05/19/2023]
Abstract
Although previous cytogenetic analysis of Pamphagidae grasshoppers pointed to considerable karyotype uniformity among most of the species in the family, our study of species from Armenia has discovered other, previously unknown karyotypes, differing from the standard for Pamphagidae mainly in having unusual sets of sex chromosomes. Asiotmethis turritus (Fischer von Waldheim, 1833), Paranocaracris rubripes (Fischer von Waldheim, 1846), and Nocaracris cyanipes (Fischer von Waldheim, 1846) were found to have the karyotype 2n♂=16+neo-XY and 2n♀=16+neo-XX, the neo-X chromosome being the result of centromeric fusion of an ancient acrocentric X chromosome and a large acrocentric autosome. The karyotype of Paranothrotes opacus (Brunner von Wattenwyl, 1882) was found to be 2n♂=14+X1X2Y and 2n♀=14+X1X1X2X2., the result of an additional chromosome rearrangement involving translocation of the neo-Y and another large autosome. Furthermore, evolution of the sex chromosomes in these species has involved different variants of heterochromatinization and miniaturization of the neo-Y. The karyotype of Eremopeza festiva (Saussure, 1884), in turn, appeared to have the standard sex determination system described earlier for Pamphagidae grasshoppers, 2n♂=18+X0 and 2n♀=18+XX, but all the chromosomes of this species were found to have small second C-positive arms. Using fluorescent in situ hybridization (FISH) with 18S rDNA and telomeric (TTAGG)n DNA repeats to yield new data on the structural organization of chromosomes in the species studied, we found that for most of them, clusters of repeats homologous to 18S rDNA localize on two, three or four pairs of autosomes and on the X. In Eremopeza festiva, however, FISH with labelled 18S rDNA painted C-positive regions of all autosomes and the X chromosome; clusters of telomeric repeats localized primarily on the ends of the chromosome arms. Overall, we conclude that the different stages of neo-Y degradation revealed in the Pamphagidae species studied make the family a very promising and useful model for studying sex chromosome evolution.
Collapse
Affiliation(s)
- Alexander G. Bugrov
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze St. 11, 630091 Novosibirsk, Russia
| | - Ilyas E. Jetybayev
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze St. 11, 630091 Novosibirsk, Russia
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Pr. Lavrentjeva, 630090 Novosibirsk, Russia
| | - Gayane H. Karagyan
- Scientific Center of Zoology and Hydroecology NAS RA, P. Sevak 7, 0014 Yerevan, Armenia
| | - Nicolay B. Rubtsov
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Pr. Lavrentjeva, 630090 Novosibirsk, Russia
| |
Collapse
|
30
|
Palacios-Gimenez OM, Carvalho CR, Ferrari Soares FA, Cabral-de-Mello DC. Contrasting the Chromosomal Organization of Repetitive DNAs in Two Gryllidae Crickets with Highly Divergent Karyotypes. PLoS One 2015; 10:e0143540. [PMID: 26630487 PMCID: PMC4667936 DOI: 10.1371/journal.pone.0143540] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 11/05/2015] [Indexed: 11/19/2022] Open
Abstract
A large percentage of eukaryotic genomes consist of repetitive DNA that plays an important role in the organization, size and evolution. In the case of crickets, chromosomal variability has been found using classical cytogenetics, but almost no information concerning the organization of their repetitive DNAs is available. To better understand the chromosomal organization and diversification of repetitive DNAs in crickets, we studied the chromosomes of two Gryllidae species with highly divergent karyotypes, i.e., 2n(♂) = 29,X0 (Gryllus assimilis) and 2n = 9, neo-X1X2Y (Eneoptera surinamensis). The analyses were performed using classical cytogenetic techniques, repetitive DNA mapping and genome-size estimation. Conserved characteristics were observed, such as the occurrence of a small number of clusters of rDNAs and U snDNAs, in contrast to the multiple clusters/dispersal of the H3 histone genes. The positions of U2 snDNA and 18S rDNA are also conserved, being intermingled within the largest autosome. The distribution and base-pair composition of the heterochromatin and repetitive DNA pools of these organisms differed, suggesting reorganization. Although the microsatellite arrays had a similar distribution pattern, being dispersed along entire chromosomes, as has been observed in some grasshopper species, a band-like pattern was also observed in the E. surinamensis chromosomes, putatively due to their amplification and clustering. In addition to these differences, the genome of E. surinamensis is approximately 2.5 times larger than that of G. assimilis, which we hypothesize is due to the amplification of repetitive DNAs. Finally, we discuss the possible involvement of repetitive DNAs in the differentiation of the neo-sex chromosomes of E. surinamensis, as has been reported in other eukaryotic groups. This study provided an opportunity to explore the evolutionary dynamics of repetitive DNAs in two non-model species and will contribute to the understanding of chromosomal evolution in a group about which little chromosomal and genomic information is known.
Collapse
Affiliation(s)
| | - Carlos Roberto Carvalho
- UFV–Univ. Federal de Viçosa, Centro de Ciências Biológicas, Departamento de Biologia Geral, Viçosa, MG, Brazil
| | | | - Diogo C. Cabral-de-Mello
- UNESP—Univ. Estadual Paulista, Instituto de Biociências/IB, Departamento de Biologia, Rio Claro, SP, Brazil
| |
Collapse
|
31
|
Giardini MC, Milla FH, Lanzavecchia S, Nieves M, Cladera JL. Sex chromosomes in mitotic and polytene tissues of Anastrepha fraterculus (Diptera, Tephritidae) from Argentina: a review. Zookeys 2015:83-94. [PMID: 26798255 PMCID: PMC4714065 DOI: 10.3897/zookeys.540.6058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 09/02/2015] [Indexed: 11/12/2022] Open
Abstract
Cytogenetics, which is considered a fundamental tool to understand basic genetic and genomic issues of species, has greatly contributed to the description of polymorphisms both at inter- and intra-specific level. In fact, cytogenetics was one of the first approaches used to propose Anastrephafraterculus (Diptera: Tephritidae) as a complex of cryptic species. Different morphological variants of sex chromosomes have been reported among Argentinean populations of Anastrephafraterculus. However, since this high structural variability in sex chromosomes does not pose a reproductive barrier, their role in speciation is yet to be unveiled. This review provides an update on general aspects of cytogenetics in Argentinean Anastrephafraterculus populations, focused on the prevalence of X-Y arrangements.
Collapse
Affiliation(s)
- María Cecilia Giardini
- Laboratorio de Genética de Insectos de Importancia Económica, Instituto de Genética 'Ewald A. Favret', CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina
| | - Fabián H Milla
- Laboratorio de Genética de Insectos de Importancia Económica, Instituto de Genética 'Ewald A. Favret', CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina
| | - Silvia Lanzavecchia
- Laboratorio de Genética de Insectos de Importancia Económica, Instituto de Genética 'Ewald A. Favret', CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina
| | - Mariela Nieves
- Grupo de Investigación en Biología Evolutiva, Departamento de Ecología, Genética y Evolución, IEGEBA-Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Jorge L Cladera
- Laboratorio de Genética de Insectos de Importancia Económica, Instituto de Genética 'Ewald A. Favret', CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina
| |
Collapse
|
32
|
Scacchetti PC, Utsunomia R, Pansonato-Alves JC, da Costa Silva GJ, Vicari MR, Artoni RF, Oliveira C, Foresti F. Repetitive DNA Sequences and Evolution of ZZ/ZW Sex Chromosomes in Characidium (Teleostei: Characiformes). PLoS One 2015; 10:e0137231. [PMID: 26372604 PMCID: PMC4570811 DOI: 10.1371/journal.pone.0137231] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 08/14/2015] [Indexed: 11/18/2022] Open
Abstract
Characidium constitutes an interesting model for cytogenetic studies, since a large degree of karyotype variation has been detected in this group, like the presence/absence of sex and supernumerary chromosomes and variable distribution of repetitive sequences in different species/populations. In this study, we performed a comparative cytogenetic analysis in 13 Characidium species collected at different South American river basins in order to investigate the karyotype diversification in this group. Chromosome analyses involved the karyotype characterization, cytogenetic mapping of repetitive DNA sequences and cross-species chromosome painting using a W-specific probe obtained in a previous study from Characidium gomesi. Our results evidenced a conserved diploid chromosome number of 2n = 50, and almost all the species exhibited homeologous ZZ/ZW sex chromosomes in different stages of differentiation, except C. cf. zebra, C. tenue, C. xavante and C. stigmosum. Notably, some ZZ/ZW sex chromosomes showed 5S and/or 18S rDNA clusters, while no U2 snDNA sites could be detected in the sex chromosomes, being restricted to a single chromosome pair in almost all the analyzed species. In addition, the species Characidium sp. aff. C. vidali showed B chromosomes with an inter-individual variation of 1 to 4 supernumerary chromosomes per cell. Notably, these B chromosomes share sequences with the W-specific probe, providing insights about their origin. Results presented here further confirm the extensive karyotype diversity within Characidium in contrast with a conserved diploid chromosome number. Such chromosome differences seem to constitute a significant reproductive barrier, since several sympatric Characidium species had been described during the last few years and no interespecific hybrids were found.
Collapse
Affiliation(s)
- Priscilla Cardim Scacchetti
- Universidade Estadual Paulista (UNESP), Instituto de Biociências de Botucatu/IBB, Departamento de Morfologia, Botucatu, SP, Brazil
- * E-mail:
| | - Ricardo Utsunomia
- Universidade Estadual Paulista (UNESP), Instituto de Biociências de Botucatu/IBB, Departamento de Morfologia, Botucatu, SP, Brazil
| | - José Carlos Pansonato-Alves
- Universidade Estadual Paulista (UNESP), Instituto de Biociências de Botucatu/IBB, Departamento de Morfologia, Botucatu, SP, Brazil
| | - Guilherme José da Costa Silva
- Universidade Estadual Paulista (UNESP), Instituto de Biociências de Botucatu/IBB, Departamento de Morfologia, Botucatu, SP, Brazil
| | - Marcelo Ricardo Vicari
- Universidade Estadual de Ponta Grossa (UEPG), Departamento de Biologia Estrutural, Molecular e Genética, Ponta Grossa, PR, Brazil
| | - Roberto Ferreira Artoni
- Universidade Estadual de Ponta Grossa (UEPG), Departamento de Biologia Estrutural, Molecular e Genética, Ponta Grossa, PR, Brazil
| | - Claudio Oliveira
- Universidade Estadual Paulista (UNESP), Instituto de Biociências de Botucatu/IBB, Departamento de Morfologia, Botucatu, SP, Brazil
| | - Fausto Foresti
- Universidade Estadual Paulista (UNESP), Instituto de Biociências de Botucatu/IBB, Departamento de Morfologia, Botucatu, SP, Brazil
| |
Collapse
|
33
|
Silva DMZA, Utsunomia R, Pansonato-Alves JC, Oliveira C, Foresti F. Chromosomal Mapping of Repetitive DNA Sequences in Five Species of Astyanax (Characiformes, Characidae) Reveals Independent Location of U1 and U2 snRNA Sites and Association of U1 snRNA and 5S rDNA. Cytogenet Genome Res 2015; 146:144-152. [PMID: 26329975 DOI: 10.1159/000438813] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2015] [Indexed: 11/19/2022] Open
Abstract
Astyanax is a genus of Characidae fishes currently composed of 155 valid species. Previous cytogenetic studies revealed high chromosomal diversification among them, and several studies have been performed using traditional cytogenetic techniques to investigate karyotypes and chromosomal locations of 18S and 5S rDNA genes. However, only a few studies are currently available about other repetitive sequences. Here, the chromosomal location of small nuclear RNA genes, identified as U1 and U2 snRNA clusters, was established and compared to the distribution of 5S rDNA and histone clusters in 5 Astyanax species (A. paranae, A. fasciatus, A. bockmanni, A. altiparanae, and A. jordani) using FISH. The cytogenetic mapping of U1 and U2 snRNA demonstrated a conserved pattern in the number of sites per genome independent of the location in Astyanax species. The location of the U1 snRNA gene was frequently associated with 5S rDNA sequences, indicating a possible interaction between the distinct repetitive DNA families. Finally, comparisons involving the location of U1 and U2 snRNA clusters in the chromosomes of Astyanax species revealed a very diverse pattern, suggesting that many rearrangements have occurred during the diversification process of this group.
Collapse
Affiliation(s)
- Duilio M Z A Silva
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | | | | | | | | |
Collapse
|
34
|
Schemberger MO, Oliveira JIN, Nogaroto V, Almeida MC, Artoni RF, Cestari MM, Moreira-Filho O, Vicari MR. Construction and characterization of a repetitive DNA library in Parodontidae (Atinopterygii:Characiformes): a genomic and evolutionary approach to the degeneration of the w sex cromosome. Zebrafish 2015; 11:518-27. [PMID: 25122415 DOI: 10.1089/zeb.2014.1013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Repetitive DNA sequences, including tandem and dispersed repeats, comprise a large portion of eukaryotic genomes and are important for gene regulation, sex chromosome differentiation, and karyotype evolution. In Parodontidae, only the repetitive DNAs WAp and pPh2004 and rDNAs were previously studied using fluorescence in situ hybridization. This study aimed to build a library of repetitive DNA in Parodontidae. We isolated 40 clones using Cot-1; 17 of these clones exhibited similarity to repetitive DNA sequences, including satellites, minisatellites, microsatellites, and class I and class II transposable elements (TEs), from Danio rerio and other organisms. The physical mapping of the clones to chromosomes revealed the presence of a satellite DNA, a Helitron element, and degenerate short interspersed element (SINE), long interspersed element (LINE), and tc1-mariner elements on the sex chromosomes. Some clones exhibited dispersed signals; other sequences were not detected. The 5S rDNA was detected on an autosomal pair. These elements likely function in the molecular degeneration of the W chromosome in Parodontidae. Thus, the location of these elements on the chromosomes is important for understanding the function of these repetitive DNAs and for integrative studies with genome sequencing. The presented data demonstrate that an intensive invasion of TEs occurred during W sex chromosome differentiation in the Parodontidae.
Collapse
Affiliation(s)
- Michelle Orane Schemberger
- 1 Programa de Pós-Graduação em Genética, Departamento de Genética, Centro Politécnico, Universidade Federal do Paraná , Curitiba, Paraná State, Brazil
| | | | | | | | | | | | | | | |
Collapse
|
35
|
Cytogenetics of Aspidogaster limacoides (Trematoda, Aspidogastrea): karyotype, spermatocyte division, and genome size. Parasitol Res 2015; 114:1473-83. [DOI: 10.1007/s00436-015-4330-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 01/19/2015] [Indexed: 10/24/2022]
|
36
|
Palacios-Gimenez OM, Marti DA, Cabral-de-Mello DC. Neo-sex chromosomes of Ronderosia bergi: insight into the evolution of sex chromosomes in grasshoppers. Chromosoma 2015; 124:353-65. [DOI: 10.1007/s00412-015-0505-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 12/27/2014] [Accepted: 01/05/2015] [Indexed: 10/24/2022]
|
37
|
Pita S, Panzera F, Sánchez A, Panzera Y, Palomeque T, Lorite P. Distribution and evolution of repeated sequences in genomes of Triatominae (Hemiptera-Reduviidae) inferred from genomic in situ hybridization. PLoS One 2014; 9:e114298. [PMID: 25478792 PMCID: PMC4257613 DOI: 10.1371/journal.pone.0114298] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 11/07/2014] [Indexed: 11/18/2022] Open
Abstract
The subfamily Triatominae, vectors of Chagas disease, comprises 140 species characterized by a highly homogeneous chromosome number. We analyzed the chromosomal distribution and evolution of repeated sequences in Triatominae genomes by Genomic in situ Hybridization using Triatoma delpontei and Triatoma infestans genomic DNAs as probes. Hybridizations were performed on their own chromosomes and on nine species included in six genera from the two main tribes: Triatomini and Rhodniini. Genomic probes clearly generate two different hybridization patterns, dispersed or accumulated in specific regions or chromosomes. The three used probes generate the same hybridization pattern in each species. However, these patterns are species-specific. In closely related species, the probes strongly hybridized in the autosomal heterochromatic regions, resembling C-banding and DAPI patterns. However, in more distant species these co-localizations are not observed. The heterochromatic Y chromosome is constituted by highly repeated sequences, which is conserved among 10 species of Triatomini tribe suggesting be an ancestral character for this group. However, the Y chromosome in Rhodniini tribe is markedly different, supporting the early evolutionary dichotomy between both tribes. In some species, sex chromosomes and autosomes shared repeated sequences, suggesting meiotic chromatin exchanges among these heterologous chromosomes. Our GISH analyses enabled us to acquire not only reliable information about autosomal repeated sequences distribution but also an insight into sex chromosome evolution in Triatominae. Furthermore, the differentiation obtained by GISH might be a valuable marker to establish phylogenetic relationships and to test the controversial origin of the Triatominae subfamily.
Collapse
Affiliation(s)
- Sebastian Pita
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Francisco Panzera
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- * E-mail: (PL); (FP)
| | - Antonio Sánchez
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Jaén, Spain
| | - Yanina Panzera
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Teresa Palomeque
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Jaén, Spain
| | - Pedro Lorite
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Jaén, Spain
- * E-mail: (PL); (FP)
| |
Collapse
|
38
|
Palacios-Gimenez OM, Cabral-de-Mello DC. Repetitive DNA chromosomal organization in the cricket Cycloptiloides americanus: a case of the unusual X1X 20 sex chromosome system in Orthoptera. Mol Genet Genomics 2014; 290:623-31. [PMID: 25373534 DOI: 10.1007/s00438-014-0947-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 10/23/2014] [Indexed: 01/25/2023]
Abstract
A common placement for most sex chromosomes that is involved in their evolutionary histories is the accumulation of distinct classes of repetitive DNAs. Here, with the aim of understanding the poorly studied repetitive DNA organization in crickets and its possible role in sex chromosome differentiation, we characterized the chromosomes of the cricket species Cycloptiloides americanus, a species with the remarkable presence of the unusual sex chromosome system X1X20♂/X1X1X2X2♀. For these proposes, we used C-banding and mapping through the fluorescence in situ hybridization of some repetitive DNAs. The C-banding and distribution of highly and moderately repetitive DNAs (C 0t-1 DNA) varied depending of the chromosome. The greater accumulation of repetitive DNAs in the X2 chromosome was evidenced. The microsatellites were spread along entire chromosomes, but (AG)10 and (TAA)10 were less enriched, mainly in the centromeric areas. Among the multigene families, the 18S rDNA was spread throughout almost all of the chromosomes, except for pair 5 and X2, while the U2 snDNA was placed exclusively in the largest chromosome. Finally, the 5S rDNA was exclusively located in the short arms of the sex chromosomes. The obtained data reinforce the importance of chromosomal dissociation and inversion as a primary evolutionary mechanism to generate neo-sex chromosomes in the species studied, followed by the repetitive DNAs accumulation. Moreover the exclusive placement of 5S rDNA in the sex chromosomes suggests the involvement of this sequence in sex chromosome recognition throughout meiosis and, consequently, their maintenance, in addition to their avoiding degeneration.
Collapse
Affiliation(s)
- Octavio M Palacios-Gimenez
- Departamento de Biologia, Instituto de Biociências/IB, UNESP-Univ Estadual Paulista, Rio Claro, São Paulo, CEP 13506-900, Brazil
| | | |
Collapse
|
39
|
U1 snDNA clusters in grasshoppers: chromosomal dynamics and genomic organization. Heredity (Edinb) 2014; 114:207-19. [PMID: 25248465 DOI: 10.1038/hdy.2014.87] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 08/14/2014] [Accepted: 08/18/2014] [Indexed: 11/08/2022] Open
Abstract
The spliceosome, constituted by a protein set associated with small nuclear RNA (snRNA), is responsible for mRNA maturation through intron removal. Among snRNA genes, U1 is generally a conserved repetitive sequence. To unveil the chromosomal/genomic dynamics of this multigene family in grasshoppers, we mapped U1 genes by fluorescence in situ hybridization in 70 species belonging to the families Proscopiidae, Pyrgomorphidae, Ommexechidae, Romaleidae and Acrididae. Evident clusters were observed in all species, indicating that, at least, some U1 repeats are tandemly arrayed. High conservation was observed in the first four families, with most species carrying a single U1 cluster, frequently located in the third or fourth longest autosome. By contrast, extensive variation was observed among Acrididae, from a single chromosome pair carrying U1 to all chromosome pairs carrying it, with occasional occurrence of two or more clusters in the same chromosome. DNA sequence analysis in Eyprepocnemis plorans (species carrying U1 clusters on seven different chromosome pairs) and Locusta migratoria (carrying U1 in a single chromosome pair) supported the coexistence of functional and pseudogenic lineages. One of these pseudogenic lineages was truncated in the same nucleotide position in both species, suggesting that it was present in a common ancestor to both species. At least in E. plorans, this U1 snDNA pseudogenic lineage was associated with 5S rDNA and short interspersed elements (SINE)-like mobile elements. Given that we conclude in grasshoppers that the U1 snDNA had evolved under the birth-and-death model and that its intragenomic spread might be related with mobile elements.
Collapse
|
40
|
Utsunomia R, Scacchetti PC, Pansonato-Alves JC, Oliveira C, Foresti F. Comparative Chromosome Mapping of U2 snRNA and 5S rRNA Genes in Gymnotus Species (Gymnotiformes, Gymnotidae): Evolutionary Dynamics and Sex Chromosome Linkage in G. pantanal. Cytogenet Genome Res 2014; 142:286-92. [DOI: 10.1159/000362258] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2014] [Indexed: 11/19/2022] Open
|