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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.
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Affiliation(s)
| | - Valentina G Kuznetsova
- Department of Karyosystematics, Zoological Institute, Russian Academy of Sciences, St. Petersburg 199034, Russia
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2
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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.
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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
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3
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Pezenti LF, Dionisio JF, Sosa-Gómez DR, de Souza RF, da Rosa R. Transposable elements in the transcriptome of the velvetbean caterpillar Anticarsia gemmatalis Hübner, 1818 (Lepidoptera: Erebidae). Genome 2023. [DOI: 10.1139/gen-2022-0066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Transposable elements (TEs) are DNA sequences that possess the ability to move from one genomic location to another. These sequences contribute to a significant fraction of the genomes of most eukaryotes and can impact their architecture and regulation. In this paper, we present the first data related to the identification and characterization of TEs present in the transcriptome of Anticarsia gemmatalis. Approximately, 835 transcripts showed significant similarity to TEs and (or) characteristic domains. Retrotransposons accounted for 71.2% (595 sequences) of the identified elements, while DNA transposons were less abundant, with 240 annotations (28.8%). TEs were classified into 30 superfamilies, with SINE3/5S and Gypsy being the most abundant. Based on the sequences of TEs found in the transcriptome, we were able to locate conserved regions in the chromosomes of this species. The analysis of differential expression of TEs in susceptible and resistant strains, challenged and not challenged with Bacillus thuringiensis ( Bt) from in silico analysis, indicated that exposure to Bt can regulate the transcription of mobile genetic elements in the velvetbean caterpillar. Thus, these data contribute significantly to the knowledge of the structure and composition of these elements in the genome of this species, and suggest the role of stress on their expression.
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4
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Expanding the Chromosomal Evolution Understanding of Lygaeioid True Bugs (Lygaeoidea, Pentatomomorpha, Heteroptera) by Classical and Molecular Cytogenetic Analysis. Genes (Basel) 2023; 14:genes14030725. [PMID: 36980997 PMCID: PMC10048555 DOI: 10.3390/genes14030725] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
The Lygaeoidea comprise about 4660 in 790 genera and 16 families. Using standard chromosome staining and FISH with 18S rDNA and telomeric (TTAGG)n probes, we studied male karyotypes and meiosis in 10 species of Lygaeoidea belonging to eight genera of the families Blissidae, Cymidae, Heterogastridae, Lygaeidae, and Rhyparochromidae. Chromosome numbers were shown to range from 12 to 28, with 2n = 14 being predominant. All species have an XY system and all but one has a pair of m-chromosomes. The exception is Spilostethus saxatilis (Lygaeidae: Lygaeinae); in another species of Lygaeinae, Thunbergia floridulus, m-chromosomes were present, which represent the first finding for this subfamily. All species have an inverted sequence of sex chromosome divisions (“post-reduction”). The 18S rDNA loci were observed on one or both sex chromosomes in Kleidocerys resedae and Th. floridulus, respectively (Lygaeidae), while on an autosomal bivalent in all other species. The rDNA loci tended to be close to the end of the chromosome. Using (TTAGG)n—FISH, we were able to show for the first time that the Lygaeoidea lack the canonical “insect” telomere motif (TTAGG)n. We speculate that this ancestral motif is absent from the entire infraorder Pentatomomorpha being replaced by some other telomere repeat motif sequences.
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Comparative molecular cytogenetics in five species of stingless bees (Hymenoptera, Apidae). ZOOL ANZ 2022. [DOI: 10.1016/j.jcz.2022.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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6
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Gasparotto AE, Milani D, Martí E, Ferretti ABSM, Bardella VB, Hickmann F, Zrzavá M, Marec F, Cabral-de-Mello DC. A step forward in the genome characterization of the sugarcane borer, Diatraea saccharalis: karyotype analysis, sex chromosome system and repetitive DNAs through a cytogenomic approach. Chromosoma 2022; 131:253-267. [PMID: 36219241 DOI: 10.1007/s00412-022-00781-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/10/2022] [Accepted: 09/16/2022] [Indexed: 11/26/2022]
Abstract
Moths of the family Crambidae include a number of pests that cause economic losses to agricultural crops. Despite their economic importance, little is known about their genome architecture and chromosome evolution. Here, we characterized the chromosomes and repetitive DNA of the sugarcane borer Diatraea saccharalis using a combination of low-pass genome sequencing, bioinformatics, and cytogenetic methods, focusing on the sex chromosomes. Diploid chromosome numbers differed between the sexes, i.e., 2n = 33 in females and 2n = 34 in males. This difference was caused by the occurrence of a WZ1Z2 trivalent in female meiosis, indicating a multiple sex-chromosome system WZ1Z2/Z1Z1Z2Z2. A strong interstitial telomeric signal was observed on the W chromosome, indicating a fusion of the ancestral W chromosome with an autosome. Among repetitive DNAs, transposable elements (TEs) accounted for 39.18% (males) to 41.35% (females), while satDNAs accounted for only 0.214% (males) and 0.215% (females) of the genome. FISH mapping revealed different chromosomal organization of satDNAs, such as single localized clusters, spread repeats, and non-clustered repeats. Two TEs mapped by FISH were scattered. Although we found a slight enrichment of some satDNAs in the female genome, they were not differentially enriched on the W chromosome. However, we found enriched FISH signals for TEs on the W chromosome, suggesting their involvement in W chromosome degeneration and differentiation. These data shed light on karyotype and repetitive DNA dynamics due to multiple chromosome fusions in D. saccharalis, contribute to the understanding of genome structure in Lepidoptera and are important for future genomic studies.
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Affiliation(s)
- Ana E Gasparotto
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Universidade Estadual Paulista, Rio Claro, SP, 13506-900, Brazil
| | - Diogo Milani
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Universidade Estadual Paulista, Rio Claro, SP, 13506-900, Brazil
| | - Emiliano Martí
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Universidade Estadual Paulista, Rio Claro, SP, 13506-900, Brazil
| | - Ana Beatriz S M Ferretti
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Universidade Estadual Paulista, Rio Claro, SP, 13506-900, Brazil
| | - Vanessa B Bardella
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Universidade Estadual Paulista, Rio Claro, SP, 13506-900, Brazil
| | - Frederico Hickmann
- Department of Entomology and Acarology, Luiz de Queiroz College of Agriculture, (USP/ESALQ), University of São Paulo, Piracicaba, SP, Brazil
| | - Magda Zrzavá
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
| | - Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Universidade Estadual Paulista, Rio Claro, SP, 13506-900, Brazil.
- Department of Experimental Biology, Genetics Area, University of Jaen, Paraje las Lagunillas s/n, 23071, Jaen, Spain.
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Pellicer J, Balant M, Fernández P, Rodríguez González R, Hidalgo O. Morphological and Genome-Wide Evidence of Homoploid Hybridisation in Urospermum (Asteraceae). PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11020182. [PMID: 35050070 PMCID: PMC8779322 DOI: 10.3390/plants11020182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 05/11/2023]
Abstract
The genus Urospermum is distributed in the Mediterranean region and Macaronesia, and has been introduced to other extra-Mediterranean regions. Although the two species constituting the genus, U. dalechampii and U. picroides, are frequently found together, hybrids have so far only been reported once, from Morocco. However, we found certain individuals in Catalonia, whose intermediate morphology suggested a potential hybrid origin. In this study, we applied morphological and molecular methods to investigate the origin of those individuals. Intermediate features at phenotype, karyological, cytogenetic, and genomic levels were identified in morphologically intermediate individuals, supporting their homoploid hybrid origin. Chloroplast sequence data suggest that U. dalechampii is the maternal progenitor of the hybrid. Together with the intermediate traits displayed, the lack of fertile seeds suggests that hybrids are probably F1. Future monitoring studies will be, nonetheless, needed to evaluate the extent of hybridisation and its potential impact on the biology of the genus.
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Affiliation(s)
- Jaume Pellicer
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., Parc de Montjuïc, 08038 Barcelona, Spain; (M.B.); (P.F.); (R.R.G.)
- Royal Botanic Gardens, Kew, Kew Green, Richmond TW9 3AE, UK
- Correspondence: (J.P.); (O.H.); Tel.: +34-932890611 (J.P. & O.H.)
| | - Manica Balant
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., Parc de Montjuïc, 08038 Barcelona, Spain; (M.B.); (P.F.); (R.R.G.)
| | - Pol Fernández
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., Parc de Montjuïc, 08038 Barcelona, Spain; (M.B.); (P.F.); (R.R.G.)
| | - Roi Rodríguez González
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., Parc de Montjuïc, 08038 Barcelona, Spain; (M.B.); (P.F.); (R.R.G.)
| | - Oriane Hidalgo
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., Parc de Montjuïc, 08038 Barcelona, Spain; (M.B.); (P.F.); (R.R.G.)
- Royal Botanic Gardens, Kew, Kew Green, Richmond TW9 3AE, UK
- Correspondence: (J.P.); (O.H.); Tel.: +34-932890611 (J.P. & O.H.)
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Nhim S, Gimenez S, Nait-Saidi R, Severac D, Nam K, d'Alençon E, Nègre N. H3K9me2 genome-wide distribution in the holocentric insect Spodoptera frugiperda (Lepidoptera: Noctuidae). Genomics 2021; 114:384-397. [PMID: 34971718 DOI: 10.1016/j.ygeno.2021.12.014] [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: 07/09/2021] [Revised: 11/02/2021] [Accepted: 12/15/2021] [Indexed: 11/04/2022]
Abstract
BACKGROUND Eukaryotic genomes are packaged by Histone proteins in a structure called chromatin. There are different chromatin types. Euchromatin is typically associated with decondensed, transcriptionally active regions and heterochromatin to more condensed regions of the chromosomes. Methylation of Lysine 9 of Histone H3 (H3K9me) is a conserved biochemical marker of heterochromatin. In many organisms, heterochromatin is usually localized at telomeric as well as pericentromeric regions but can also be found at interstitial chromosomal loci. This distribution may vary in different species depending on their general chromosomal organization. Holocentric species such as Spodoptera frugiperda (Lepidoptera: Noctuidae) possess dispersed centromeres instead of a monocentric one and thus no observable pericentromeric compartment. To identify the localization of heterochromatin in such species we performed ChIP-Seq experiments and analyzed the distribution of the heterochromatin marker H3K9me2 in the Sf9 cell line and whole 4th instar larvae (L4) in relation to RNA-Seq data. RESULTS In both samples we measured an enrichment of H3K9me2 at the (sub) telomeres, rDNA loci, and satellite DNA sequences, which could represent dispersed centromeric regions. We also observed that density of H3K9me2 is positively correlated with transposable elements and protein-coding genes. But contrary to most model organisms, H3K9me2 density is not correlated with transcriptional repression. CONCLUSION This is the first genome-wide ChIP-Seq analysis conducted in S. frugiperda for H3K9me2. Compared to model organisms, this mark is found in expected chromosomal compartments such as rDNA and telomeres. However, it is also localized at numerous dispersed regions, instead of the well described large pericentromeric domains, indicating that H3K9me2 might not represent a classical heterochromatin marker in Lepidoptera. (242 words).
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Affiliation(s)
- Sandra Nhim
- DGIMI, Univ Montpellier, INRAE, Montpellier, France
| | | | | | - Dany Severac
- MGX, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Kiwoong Nam
- DGIMI, Univ Montpellier, INRAE, Montpellier, France
| | | | - Nicolas Nègre
- DGIMI, Univ Montpellier, INRAE, Montpellier, France.
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Poignet M, Johnson Pokorná M, Altmanová M, Majtánová Z, Dedukh D, Albrecht T, Reif J, Osiejuk TS, Reifová R. Comparison of Karyotypes in Two Hybridizing Passerine Species: Conserved Chromosomal Structure but Divergence in Centromeric Repeats. Front Genet 2021; 12:768987. [PMID: 34938317 PMCID: PMC8687609 DOI: 10.3389/fgene.2021.768987] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/10/2021] [Indexed: 11/23/2022] Open
Abstract
Changes in chromosomal structure involving chromosomal rearrangements or copy number variation of specific sequences can play an important role in speciation. Here, we explored the chromosomal structure of two hybridizing passerine species; the common nightingale (Luscinia megarhynchos) and the thrush nightingale (Luscinia luscinia), using conventional cytogenetic approaches, immunostaining of meiotic chromosomes, fluorescence in situ hybridization as well as comparative genomic hybridization (CGH). We found that the two nightingale species show conserved karyotypes with the same diploid chromosome number of 2n = 84. In addition to standard chromosomes, both species possessed a small germline restricted chromosome of similar size as a microchromosome. Just a few subtle changes in chromosome morphology were observed between the species, suggesting that only a limited number of chromosomal rearrangements occurred after the species divergence. The interspecific CGH experiment suggested that the two nightingale species might have diverged in centromeric repetitive sequences in most macro- and microchromosomes. In addition, some chromosomes showed changes in copy number of centromeric repeats between the species. The observation of very similar karyotypes in the two nightingale species is consistent with a generally slow rate of karyotype evolution in birds. The divergence of centromeric sequences between the two species could theoretically cause meiotic drive or reduced fertility in interspecific hybrids. Nevertheless, further studies are needed to evaluate the potential role of chromosomal structural variations in nightingale speciation.
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Affiliation(s)
- Manon Poignet
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martina Johnson Pokorná
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Marie Altmanová
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Zuzana Majtánová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Dmitry Dedukh
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Tomáš Albrecht
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jiří Reif
- Institute for Environmental Studies, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Zoology and Laboratory of Ornithology, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Tomasz S. Osiejuk
- Department of Behavioural Ecology, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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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.
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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
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11
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Sochorová J, Gálvez F, Matyášek R, Garcia S, Kovařík A. Analyses of the Updated "Animal rDNA Loci Database" with an Emphasis on Its New Features. Int J Mol Sci 2021; 22:11403. [PMID: 34768834 PMCID: PMC8584138 DOI: 10.3390/ijms222111403] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/17/2021] [Accepted: 10/20/2021] [Indexed: 11/17/2022] Open
Abstract
We report on a major update to the animal rDNA loci database, which now contains cytogenetic information for 45S and 5S rDNA loci in more than 2600 and 1000 species, respectively.The data analyses show the following: (i) A high variability in 5S and 45S loci numbers, with both showing 50-fold or higher variability. However, karyotypes with an extremely high number of loci were rare, and medians generally converged to two 5S sites and two 45S rDNA sites per diploid genome. No relationship was observed between the number of 5S and 45S loci. (ii) The position of 45S rDNA on sex chromosomes was relatively frequent in some groups, particularly in arthropods (14% of karyotypes). Furthermore, 45S rDNA was almost exclusively located in microchromosomes when these were present (in birds and reptiles). (iii) The proportion of active NORs (positively stained with silver staining methods) progressively decreased with an increasing number of 45S rDNA loci, and karyotypes with more than 12 loci showed, on average, less than 40% of active loci. In conclusion, the updated version of the database provides some new insights into the organization of rRNA genes in chromosomes. We expect that its updated content will be useful for taxonomists, comparative cytogeneticists, and evolutionary biologists. .
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Affiliation(s)
- Jana Sochorová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265 Brno, Czech Republic; (J.S.); (R.M.)
| | - Francisco Gálvez
- Bioscripts—Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Spain;
| | - Roman Matyášek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265 Brno, Czech Republic; (J.S.); (R.M.)
| | - Sònia Garcia
- Institut Botànic de Barcelona (IBB-CSIC), Passeig del Migdia s/n, 08038 Barcelona, Spain;
| | - Aleš Kovařík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265 Brno, Czech Republic; (J.S.); (R.M.)
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Menezes RST, Cabral-de-Mello DC, Milani D, Bardella VB, Almeida EAB. The relevance of chromosome fissions for major ribosomal DNA dispersion in hymenopteran insects. J Evol Biol 2021; 34:1466-1476. [PMID: 34331340 DOI: 10.1111/jeb.13909] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 07/04/2021] [Accepted: 07/28/2021] [Indexed: 01/20/2023]
Abstract
Ribosomal DNA (rDNA) loci are essential for cellular metabolism due to their participation in ribosome biogenesis. Although these genes have been widely cytogenetically mapped, the evolutionary mechanisms behind their variability in number and chromosomal location remain elusive, even in well-known biological groups, such as ants, bees and wasps (Insecta: Hymenoptera). To address this question in Hymenoptera and therefore advance the understanding of rDNA evolution in insects in general, we integrated molecular cytogenetic data, a phylogenomic framework, model-based predictions and genome sequencing. Hence, we assessed the main evolutionary trends shaping the chromosomal distribution of rDNA loci in Hymenoptera. We noticed the conservation of one site of rDNA per haploid genome, suggesting that a single 45S rDNA locus is the putative ancestral pattern for aculeate Hymenoptera. Moreover, our results highlighted a nonrandom distribution of rDNA in Hymenoptera karyotypes, as well as a lineage-specific preferential location. The proximal location of rDNA is favoured in species with multiple loci and in the two families of Hymenoptera that show the highest range of chromosome numbers: Formicidae and Vespidae. We propose that chromosome fissions have played a crucial role in the distribution pattern of rDNA loci through the evolutionary diversification of Hymenoptera. Moreover, our genomic analysis of two species, one with a single locus of rDNA and one with multiple loci, supported that loci multiplication is followed by sequence divergence. Our results provide detailed information about the number and chromosomal position of rDNA in Hymenoptera and, therefore, broaden our knowledge regarding rDNA evolutionary dynamics in insects.
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Affiliation(s)
- Rodolpho S T Menezes
- Laboratório de Biologia Comparada e Abelhas, Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras (FFCLRP), Universidade de São Paulo (USP), Ribeirão Preto, Brazil
| | - Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Diogo Milani
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Vanessa B Bardella
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Eduardo A B Almeida
- Laboratório de Biologia Comparada e Abelhas, Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras (FFCLRP), Universidade de São Paulo (USP), Ribeirão Preto, Brazil
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13
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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: 5] [Impact Index Per Article: 1.7] [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.
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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
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14
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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: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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.
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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.
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15
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Teixeira GA, de Aguiar HJAC, Petitclerc F, Orivel J, Lopes DM, Barros LAC. Evolutionary insights into the genomic organization of major ribosomal DNA in ant chromosomes. INSECT MOLECULAR BIOLOGY 2021; 30:340-354. [PMID: 33586259 DOI: 10.1111/imb.12699] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/28/2021] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
The major rDNA genes are composed of tandem repeats and are part of the nucleolus organizing regions (NORs). They are highly conserved and therefore useful in understanding the evolutionary patterns of chromosomal locations. The evolutionary dynamics of the karyotype may affect the organization of rDNA genes within chromosomes. In this study, we physically mapped 18S rDNA genes in 13 Neotropical ant species from four subfamilies using fluorescence in situ hybridization. Furthermore, a survey of published rDNA cytogenetic data for 50 additional species was performed, which allowed us to detect the evolutionary patterns of these genes in ant chromosomes. Species from the Neotropical, Palearctic, and Australian regions, comprising a total of 63 species from 19 genera within six subfamilies, were analysed. Most of the species (48 out of 63) had rDNA genes restricted to a single chromosome pair in their intrachromosomal regions. The position of rDNA genes within the chromosomes appears to hinder their dispersal throughout the genome, as translocations and ectopic recombination are uncommon in intrachromosomal regions because they can generate meiotic abnormalities. Therefore, rDNA genes restricted to a single chromosome pair seem to be a plesiomorphic feature in ants, while multiple rDNA sites, observed in distinct subfamilies, may have independent origins in different genera.
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Affiliation(s)
- G A Teixeira
- Programa de Pós-graduação em Biologia Celular e Estrutural, Universidade Federal de Viçosa, Viçosa, Brazil
- Laboratório de Citogenética de Insetos, Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Brazil
| | - H J A C de Aguiar
- Universidade Federal do Amapá, Campus Binacional, BR 156, n° 3051, Bairro Universidade, Oiapoque, 68980-000, Brazil
| | - F Petitclerc
- CNRS, UMR EcoFoG, AgroParisTech, CIRAD, INRA, Université de Guyane, Université des Antilles, Campus Agronomique, Kourou, France
| | - J Orivel
- CNRS, UMR EcoFoG, AgroParisTech, CIRAD, INRA, Université de Guyane, Université des Antilles, Campus Agronomique, Kourou, France
| | - D M Lopes
- Laboratório de Citogenética de Insetos, Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Brazil
| | - L A C Barros
- Universidade Federal do Amapá, Campus Binacional, BR 156, n° 3051, Bairro Universidade, Oiapoque, 68980-000, Brazil
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16
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Cabral-de-Mello DC, Zrzavá M, Kubíčková S, Rendón P, Marec F. The Role of Satellite DNAs in Genome Architecture and Sex Chromosome Evolution in Crambidae Moths. Front Genet 2021; 12:661417. [PMID: 33859676 PMCID: PMC8042265 DOI: 10.3389/fgene.2021.661417] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/04/2021] [Indexed: 12/21/2022] Open
Abstract
Tandem repeats are important parts of eukaryotic genomes being crucial e.g., for centromere and telomere function and chromatin modulation. In Lepidoptera, knowledge of tandem repeats is very limited despite the growing number of sequenced genomes. Here we introduce seven new satellite DNAs (satDNAs), which more than doubles the number of currently known lepidopteran satDNAs. The satDNAs were identified in genomes of three species of Crambidae moths, namely Ostrinia nubilalis, Cydalima perspectalis, and Diatraea postlineella, using graph-based computational pipeline RepeatExplorer. These repeats varied in their abundance and showed high variability within and between species, although some degree of conservation was noted. The satDNAs showed a scattered distribution, often on both autosomes and sex chromosomes, with the exception of both satellites in D. postlineella, in which the satDNAs were located at a single autosomal locus. Three satDNAs were abundant on the W chromosomes of O. nubilalis and C. perspectalis, thus contributing to their differentiation from the Z chromosomes. To provide background for the in situ localization of the satDNAs, we performed a detailed cytogenetic analysis of the karyotypes of all three species. This comparative analysis revealed differences in chromosome number, number and location of rDNA clusters, and molecular differentiation of sex chromosomes.
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Affiliation(s)
- Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP-Univ Estadual Paulista, Rio Claro, Brazil.,Biology Centre, Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia
| | - Magda Zrzavá
- Biology Centre, Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia.,Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | | | - Pedro Rendón
- IAEA-TCLA-Consultant-USDA-APHIS-Moscamed Program Guatemala, Guatemala City, Guatemala
| | - František Marec
- Biology Centre, Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia
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17
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Boštjančić LL, Bonassin L, Anušić L, Lovrenčić L, Besendorfer V, Maguire I, Grandjean F, Austin CM, Greve C, Hamadou AB, Mlinarec J. The Pontastacus leptodactylus (Astacidae) Repeatome Provides Insight Into Genome Evolution and Reveals Remarkable Diversity of Satellite DNA. Front Genet 2021; 11:611745. [PMID: 33552130 PMCID: PMC7859515 DOI: 10.3389/fgene.2020.611745] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/21/2020] [Indexed: 12/14/2022] Open
Abstract
Pontastacus leptodactylus is a native European crayfish species found in both freshwater and brackish environments. It has commercial importance for fisheries and aquaculture industries. Up till now, most studies concerning P. leptodactylus have focused onto gaining knowledge about its phylogeny and population genetics. However, little is known about the chromosomal evolution and genome organization of this species. Therefore, we performed clustering analysis of a low coverage genomic dataset to identify and characterize repetitive DNA in the P. leptodactylus genome. In addition, the karyogram of P. leptodactylus (2n = 180) is presented here for the first time consisting of 75 metacentric, 14 submetacentric, and a submetacentric/metacentric heteromorphic chromosome pair. We determined the genome size to be at ~18.7 gigabase pairs. Repetitive DNA represents about 54.85% of the genome. Satellite DNA repeats are the most abundant type of repetitive DNA, making up to ~28% of the total amount of repetitive elements, followed by the Ty3/Gypsy retroelements (~15%). Our study established a surprisingly high diversity of satellite repeats in P. leptodactylus. The genome of P. leptodactylus is by far the most satellite-rich genome discovered to date with 258 satellite families described. Of the five mapped satellite DNA families on chromosomes, PlSAT3-411 co-localizes with the AT-rich DAPI positive probable (peri)centromeric heterochromatin on all chromosomes, while PlSAT14-79 co-localizes with the AT-rich DAPI positive (peri)centromeric heterochromatin on one chromosome and is also located subterminally and intercalary on some chromosomes. PlSAT1-21 is located intercalary in the vicinity of the (peri)centromeric heterochromatin on some chromosomes, while PlSAT6-70 and PlSAT7-134 are located intercalary on some P. leptodactylus chromosomes. The FISH results reveal amplification of interstitial telomeric repeats (ITRs) in P. leptodactylus. The prevalence of repetitive elements, especially the satellite DNA repeats, may have provided a driving force for the evolution of the P. leptodactylus genome.
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Affiliation(s)
| | - Lena Bonassin
- Division of Molecular Biology, Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Lucija Anušić
- Division of Molecular Biology, Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Leona Lovrenčić
- Division of Zoology, Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Višnja Besendorfer
- Division of Molecular Biology, Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Ivana Maguire
- Division of Zoology, Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Frederic Grandjean
- Laboratoire Ecologie Biologie des Interactions-UMR CNRS 7267, University of Poitiers, Poitiers, France
| | - Christopher M. Austin
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, VIC, Australia
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
| | - Alexander Ben Hamadou
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
| | - Jelena Mlinarec
- Division of Molecular Biology, Department of Biology, University of Zagreb, Zagreb, Croatia
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18
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Sproul JS, Barton LM, Maddison DR. Repetitive DNA Profiles Reveal Evidence of Rapid Genome Evolution and Reflect Species Boundaries in Ground Beetles. Syst Biol 2021; 69:1137-1148. [PMID: 32267949 DOI: 10.1093/sysbio/syaa030] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 03/16/2020] [Accepted: 03/30/2020] [Indexed: 12/11/2022] Open
Abstract
Genome architecture is a complex, multidimensional property of an organism defined by the content and spatial organization of the genome's component parts. Comparative study of entire genome architecture in model organisms is shedding light on mechanisms underlying genome regulation, evolution, and diversification, but such studies require costly analytical approaches which make extensive comparative study impractical for most groups. However, lower-cost methods that measure a single architectural component (e.g., distribution of one class of repeats) have potential as a new data source for evolutionary studies insofar as that measure correlates with more complex biological phenomena, and for which it could serve as part of an explanatory framework. We investigated copy number variation (CNV) profiles in ribosomal DNA (rDNA) as a simple measure reflecting the distribution of rDNA subcomponents across the genome. We find that signatures present in rDNA CNV profiles strongly correlate with species boundaries in the breve species group of Bembidion, and vary across broader taxonomic sampling in Bembidion subgenus Plataphus. Profiles of several species show evidence of re-patterning of rDNA-like sequences throughout the genome, revealing evidence of rapid genome evolution (including among sister pairs) not evident from analysis of traditional data sources such as multigene data sets. Major re-patterning of rDNA-like sequences has occurred frequently within the evolutionary history of Plataphus. We confirm that CNV profiles represent an aspect of genomic architecture (i.e., the linear distribution of rDNA components across the genome) via fluorescence in-situ hybridization. In at least one species, novel rDNA-like elements are spread throughout all chromosomes. We discuss the potential of copy number profiles of rDNA, or other repeats, as a low-cost tool for incorporating signal of genomic architecture variation in studies of species delimitation and genome evolution. [Bembidion; Carabidae; copy number variation profiles; rapid genome evolution; ribosomal DNA; species delimitation.].
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Affiliation(s)
- John S Sproul
- Department of Integrative Biology, Oregon State University, 3029 Cordley Hall, Corvallis, OR 97331, USA.,Department of Biology, University of Rochester, 402 Hutchison Hall, PO Box 270211, Rochester, NY 14627, USA
| | - Lindsey M Barton
- Department of Integrative Biology, Oregon State University, 3029 Cordley Hall, Corvallis, OR 97331, USA
| | - David R Maddison
- Department of Integrative Biology, Oregon State University, 3029 Cordley Hall, Corvallis, OR 97331, USA
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19
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Karyotype evolution and preliminary molecular assessment of genera in the family Scorpiopidae (Arachnida: Scorpiones). ZOOLOGY 2020; 144:125882. [PMID: 33278760 DOI: 10.1016/j.zool.2020.125882] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 11/13/2020] [Accepted: 11/14/2020] [Indexed: 11/20/2022]
Abstract
The scorpions represent an ancient and morphologically conserved order of arachnids. Despite that, their karyotypes may differ considerably even among closely related species. In this study, we identify the trends of the karyotype evolution in the family Scorpiopidae based on integrating cytogenetic data and multi-locus molecular phylogenetic approaches. We detected considerable variability in diploid numbers of chromosomes (from 48 to 147), 18S rRNA gene cluster positions (from terminal to pericentromeric) at the interspecific level. Moreover, we identified independent fusions, fissions and inversions in the evolution of the family Scorpiopidae, leading to a remarkable diversification of the karyotypes. The dynamic system of the karyotype changes in this group is further documented by the presence of interstitial telomeric sequences (ITS) in two species. The cytogenetic differences observed among the analyzed species highlight the potential of this type of data for species-level taxonomy in scorpion lineages with monocentric chromosomes. Additionally, the results of our phylogenetic analyses support the monophyly of the family Scorpiopidae, but rendered several genera para- or polyphyletic.
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20
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Baez M, Kuo YT, Dias Y, Souza T, Boudichevskaia A, Fuchs J, Schubert V, Vanzela ALL, Pedrosa-Harand A, Houben A. Analysis of the small chromosomal Prionium serratum (Cyperid) demonstrates the importance of reliable methods to differentiate between mono- and holocentricity. Chromosoma 2020; 129:285-297. [PMID: 33165742 PMCID: PMC7665975 DOI: 10.1007/s00412-020-00745-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/27/2020] [Accepted: 10/28/2020] [Indexed: 12/21/2022]
Abstract
For a long time, the Cyperid clade (Thurniceae-Juncaceae-Cyperaceae) was considered a group of species possessing holocentromeres exclusively. The basal phylogenetic position of Prionium serratum (Thunb.) Drège (Thurniceae) within Cyperids makes this species an important specimen to understand the centromere evolution within this clade. In contrast to the expectation, the chromosomal distribution of the centromere-specific histone H3 (CENH3), alpha-tubulin and different centromere-associated post-translational histone modifications (H3S10ph, H3S28ph and H2AT120ph) demonstrate a monocentromeric organisation of P. serratum chromosomes. Analysis of the high-copy repeat composition resulted in the identification of two centromere-localised satellite repeats. Hence, monocentricity was the ancestral condition for the Juncaceae-Cyperaceae-Thurniaceae Cyperid clade, and holocentricity in this clade has independently arisen at least twice after differentiation of the three families, once in Juncaceae and the other one in Cyperaceae. In this context, methods suitable for the identification of holocentromeres are discussed.
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Affiliation(s)
- M Baez
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany.,Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - Y T Kuo
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - Y Dias
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany.,Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - T Souza
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany.,Laboratory of Cytogenetics and Plant Diversity, Department of General Biology, Center for Biological Sciences, State University of Londrina, Londrina, Paraná, 86057-970, Brazil
| | - A Boudichevskaia
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany.,KWS SAAT SE & Co. KGaA, 37574, Einbeck, Germany
| | - J Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - V Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany
| | - A L L Vanzela
- Laboratory of Cytogenetics and Plant Diversity, Department of General Biology, Center for Biological Sciences, State University of Londrina, Londrina, Paraná, 86057-970, Brazil
| | - A Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - A Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Stadt Seeland, Germany.
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21
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Kuznetsova V, Maryańska‐Nadachowska A, Anokhin B, Shapoval N, Shapoval A. Chromosomal analysis of eight species of dragonflies (Anisoptera) and damselflies (Zygoptera) using conventional cytogenetics and fluorescence in situ hybridization: Insights into the karyotype evolution of the ancient insect order Odonata. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12429] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Valentina Kuznetsova
- Department of Karyosystematics Zoological Institute Russian Academy of Sciences St. Petersburg Russia
| | | | - Boris Anokhin
- Department of Karyosystematics Zoological Institute Russian Academy of Sciences St. Petersburg Russia
| | - Nazar Shapoval
- Department of Karyosystematics Zoological Institute Russian Academy of Sciences St. Petersburg Russia
| | - Anatoly Shapoval
- Biological Station “Rybachy” Zoological Institute Russian Academy of Sciences Rybachy, Kaliningrad District Russia
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22
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Šťáhlavský F, Nguyen P, Sadílek D, Štundlová J, Just P, Haddad CR, Koç H, Ranawana KB, Stockmann M, Yağmur EA, Kovařík F. Evolutionary dynamics of rDNA clusters on chromosomes of buthid scorpions (Chelicerata: Arachnida). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
We examined the distribution of genes for major ribosomal RNAs (rDNA) on holokinetic chromosomes of 74 species belonging to 19 genera of scorpions from the family Buthidae using fluorescence in situ hybridization (FISH). Our analysis revealed differences between the two main evolutionary lineages within the family. The genera belonging to the ‘Buthus group’, with a proposed Laurasian origin, possess one pair of rDNA mainly in an interstitial position, with the only exceptions being the terminal location found in some Hottentotta and Buthacus species, possibly as a result of chromosome fissions. All the remaining buthid ‘groups’ possess rDNA found strictly in a terminal position. However, the number of signals may increase from an ancestral state of one pair of rDNA loci to up to seven signals in Reddyanus ceylonensis Kovařík et al., 2016. Despite the differences in evolutionary dynamics of the rDNA clusters between the ‘Buthus group’ and other lineages investigated, we found a high incidence of reciprocal translocations and presence of multivalent associations during meiosis in the majority of the genera studied. These phenomena seem to be typical for the whole family Buthidae.
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Affiliation(s)
- František Šťáhlavský
- Department of Zoology, Faculty of Science, Charles University, Viničná, Prague, Czech Republic
| | - Petr Nguyen
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská, České Budějovice, Czech Republic
| | - David Sadílek
- Department of Zoology, Faculty of Science, Charles University, Viničná, Prague, Czech Republic
| | - Jana Štundlová
- Department of Zoology, Faculty of Science, Charles University, Viničná, Prague, Czech Republic
| | - Pavel Just
- Department of Zoology, Faculty of Science, Charles University, Viničná, Prague, Czech Republic
| | - Charles R Haddad
- Department of Zoology and Entomology, University of the Free State, Bloemfontein, South Africa
| | - Halil Koç
- Department of Biology, Faculty of Arts and Science, Sinop University, Sinop, Turkey
| | - Kithsiri B Ranawana
- Department of Zoology, Faculty of Science, University of Peradeniya, Sri Lanka
| | | | - Ersen Aydin Yağmur
- Alaşehir Vocational School, Celal Bayar University, Alaşehir, Manisa, Turkey
| | - František Kovařík
- Department of Zoology, Faculty of Science, Charles University, Viničná, Prague, Czech Republic
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Costa L, Jimenez H, Carvalho R, Carvalho-Sobrinho J, Escobar I, Souza G. Divide to Conquer: Evolutionary History of Allioideae Tribes (Amaryllidaceae) Is Linked to Distinct Trends of Karyotype Evolution. FRONTIERS IN PLANT SCIENCE 2020; 11:320. [PMID: 32318079 PMCID: PMC7155398 DOI: 10.3389/fpls.2020.00320] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 03/04/2020] [Indexed: 06/11/2023]
Abstract
Allioideae (e.g., chives, garlics, onions) comprises three mainly temperate tribes: Allieae (800 species from the northern hemisphere), Gilliesieae (80 South American species), and Tulbaghieae (26 Southern African species). We reconstructed the phylogeny of Allioideae (190 species plus 257 species from Agapanthoideae and Amaryllidoideae) based on ITS, matK, ndhF, and rbcL to investigate its historical biogeography and karyotype evolution using newly generated cytomolecular data for Chilean Gilliesieae genera Gethyum, Miersia, Solaria, and Speea. The crown group of Allioideae diversified ∼62 Mya supporting a Gondwanic origin for the subfamily and vicariance as the cause of the intercontinental disjunction of the tribes. Our results support the hypothesis of the Indian tectonic plate carrying Allieae to northern hemisphere ('out-of-India' hypothesis). The colonization of the northern hemisphere (∼30 Mya) is correlated with a higher diversification rate in Allium associated to stable x = 8, increase of polyploidy and the geographic expansion in Europe and North America. Tulbaghieae presented x = 6, but with numerical stability (2n = 12). In contrast, the tribe Gilliesieae (x = 6) varied considerably in genome size (associated with Robertsonian translocations), rDNA sites distribution and chromosome number. Our data indicate that evolutionary history of Allioideae tribes is linked to distinct trends of karyotype evolution.
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Affiliation(s)
- Lucas Costa
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Horace Jimenez
- Laboratory of Plant Cytogenetics, Department of Biology, Federal Rural University of Pernambuco, Recife, Brazil
| | - Reginaldo Carvalho
- Laboratory of Plant Cytogenetics, Department of Biology, Federal Rural University of Pernambuco, Recife, Brazil
| | - Jefferson Carvalho-Sobrinho
- Laboratory of Plant Cytogenetics, Department of Biology, Federal Rural University of Pernambuco, Recife, Brazil
| | - Inelia Escobar
- Department of Botany, University of Concepción, Concepción, Chile
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
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Magalhães BRDS, Sosa-Goméz DR, Dionísio JF, Dias FC, Baldissera JNDC, Rincão MP, Da Rosa R. Cytogenetic markers applied to cytotaxonomy in two soybean pests: Anticarsia gemmatalis (Hübner, 1818) and Chrysodeixis includens (Walker, 1858). PLoS One 2020; 15:e0230244. [PMID: 32160240 PMCID: PMC7065768 DOI: 10.1371/journal.pone.0230244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 02/26/2020] [Indexed: 11/27/2022] Open
Abstract
Anticarsia gemmatalis (Hübner, 1818) and Chrysodeixis includens (Walker, 1858) are species of Lepidoptera that cause great damages in the soybean plantations of Brazil. Despite the importance they have in this regard, there are no studies on the chromosomal organization of these species and recently, A. gemmatalis, which belonged to the Noctuidae family, was allocated to the Erebidae family. Therefore, the objective of this paper was to analyze, through conventional and molecular cytogenetic markers, both species of Lepidoptera. A 2n = 62 was observed, with ZZ/ZW sex chromosome system and holokinetic chromosomes for both species. There was homogeneity in the number of 18S rDNA sites for both species. However, variations in heterochromatin distribution were observed between both species. The cytogenetic analyses enabled separation of the species, corroborating the transference of A. gemmatalis, from the family Noctuidae to the family Erebidae, suggesting new cytotaxonomic characteristics.
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Affiliation(s)
| | | | - Jaqueline Fernanda Dionísio
- Laboratório de Citogenética Animal, Departamento de Biologia Geral, Universidade Estadual de Londrina, Brasil
| | - Felipe Cordeiro Dias
- Laboratório de Citogenética Animal, Departamento de Biologia Geral, Universidade Estadual de Londrina, Brasil
| | | | - Matheus Pires Rincão
- Laboratório de Citogenética Animal, Departamento de Biologia Geral, Universidade Estadual de Londrina, Brasil
| | - Renata Da Rosa
- Laboratório de Citogenética Animal, Departamento de Biologia Geral, Universidade Estadual de Londrina, Brasil
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Micolino R, Cristiano MP, Travenzoli NM, Lopes DM, Cardoso DC. Chromosomal dynamics in space and time: evolutionary history of Mycetophylax ants across past climatic changes in the Brazilian Atlantic coast. Sci Rep 2019; 9:18800. [PMID: 31827151 PMCID: PMC6906305 DOI: 10.1038/s41598-019-55135-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/01/2019] [Indexed: 12/14/2022] Open
Abstract
Fungus-farming ants of the genus Mycetophylax exhibit intra and interspecific chromosome variability, which makes them suitable for testing hypotheses about possible chromosomal rearrangements that endure lineage diversification. We combined cytogenetic and molecular data from Mycetophylax populations from coastal environments to trace the evolutionary history of the clade in light of chromosomal changes under a historical and geographic context. Our cytogenetic analyses revealed chromosomal differences within and among species. M. morschi exhibited three distinct karyotypes and considerable variability in the localization of 45S rDNA clusters. The molecular phylogeny was congruent with our cytogenetic findings. Biogeographical and divergence time dating analyses estimated that the most recent common ancestor of Mycetophylax would have originated at about 30 Ma in an area including the Amazon and Southern Grasslands, and several dispersion and vicariance events may have occurred before the colonization of the Brazilian Atlantic coast. Diversification of the psammophilous Mycetophylax first took place in the Middle Miocene (ca. 18-10 Ma) in the South Atlantic coast, while "M. morschi" lineages diversified during the Pliocene-Pleistocene transition (ca. 3-2 Ma) through founder-event dispersal for the Northern coastal regions. Psammophilous Mycetophylax diversification fits into the major global climatic events that have had a direct impact on the changes in sea level as well as deep ecological impact throughout South America. We assume therefore that putative chromosomal rearrangements correlated with increased ecological stress during the past climatic transitions could have intensified and/or accompanied the divergence of the psammophilous Mycetophylax. We further reiterate that "M. morschi" comprises a complex of at least three well-defined lineages, and we emphasize the role of this integrative approach for the identification and delimitation of evolutionary lineages.
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Affiliation(s)
- Ricardo Micolino
- Departamento de Genética, Universidade Federal do Paraná (UFPR), Curitiba, PR, Brazil
- Departamento de Biodiversidade, Evolução e Meio Ambiente, Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil
| | - Maykon Passos Cristiano
- Departamento de Biodiversidade, Evolução e Meio Ambiente, Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil
| | | | - Denilce Meneses Lopes
- Departamento de Biologial Geral, Universidade Federal de Viçosa (UFV), Viçosa, MG, Brazil
| | - Danon Clemes Cardoso
- Departamento de Genética, Universidade Federal do Paraná (UFPR), Curitiba, PR, Brazil.
- Departamento de Biodiversidade, Evolução e Meio Ambiente, Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil.
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Chromosomal study of Khawia abbottinae (Cestoda: Caryophyllidea): karyotype and localization of telomeric and ribosomal sequences after fluorescence in situ hybridization (FISH). Parasitol Res 2019; 118:2789-2800. [DOI: 10.1007/s00436-019-06450-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 08/28/2019] [Indexed: 01/27/2023]
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Hora KH, Marec F, Roessingh P, Menken SBJ. Limited intrinsic postzygotic reproductive isolation despite chromosomal rearrangements between closely related sympatric species of small ermine moths (Lepidoptera: Yponomeutidae). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz090] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Abstract
In evolutionarily young species and sympatric host races of phytophagous insects, postzygotic incompatibility is often not yet fully developed, but reduced fitness of hybrids is thought to facilitate further divergence. However, empirical evidence supporting this hypothesis is limited. To assess the role of reduced hybrid fitness, we studied meiosis and fertility in hybrids of two closely related small ermine moths, Yponomeuta padella and Yponomeuta cagnagella, and determined the extent of intrinsic postzygotic reproductive isolation. We found extensive rearrangements between the karyotypes of the two species and irregularities in meiotic chromosome pairing in their hybrids. The fertility of reciprocal F1 and, surprisingly, also of backcrosses with both parental species was not significantly decreased compared with intraspecific offspring. The results indicate that intrinsic postzygotic reproductive isolation between these closely related species is limited. We conclude that the observed chromosomal rearrangements are probably not the result of an accumulation of postzygotic incompatibilities preventing hybridization. Alternative explanations, such as adaptation to new host plants, are discussed.
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Affiliation(s)
- Katerina H Hora
- Institute for Biodiversity and Ecosystem Dynamics, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
| | - Peter Roessingh
- Institute for Biodiversity and Ecosystem Dynamics, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Steph B J Menken
- Institute for Biodiversity and Ecosystem Dynamics, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
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How dynamic could be the 45S rDNA cistron? An intriguing variability in a grasshopper species revealed by integration of chromosomal and genomic data. Chromosoma 2019; 128:165-175. [DOI: 10.1007/s00412-019-00706-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/25/2019] [Accepted: 04/29/2019] [Indexed: 10/26/2022]
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Cuadrado Á, De Bustos A, Figueroa RI. Chromosomal markers in the genus Karenia: Towards an understanding of the evolution of the chromosomes, life cycle patterns and phylogenetic relationships in dinoflagellates. Sci Rep 2019; 9:3072. [PMID: 30816125 PMCID: PMC6395649 DOI: 10.1038/s41598-018-35785-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 11/07/2018] [Indexed: 12/12/2022] Open
Abstract
Dinoflagellates are a group of protists whose genome is unique among eukaryotes in terms of base composition, chromosomal structure and gene expression. Even after decades of research, the structure and behavior of their amazing chromosomes-which without nucleosomes exist in a liquid crystalline state-are still poorly understood. We used flow cytometry and fluorescence in situ hybridization (FISH) to analyze the genome size of three species of the toxic dinoflagellate genus Karenia as well the organization and behavior of the chromosomes in different cell-cycle stages. FISH was also used to study the distribution patterns of ribosomal DNA (45S rDNA), telomeric and microsatellites repeats in order to develop chromosomal markers. The results revealed several novel and important features regarding dinoflagellate chromosomes during mitosis, including their telocentric behavior and radial arrangement along the nuclear envelope. Additionally, using the (AG)10 probe we identified an unusual chromosome in K. selliformis and especially in K. mikimotoi that is characterized by AG repeats along its entire length. This feature was employed to easily differentiate morphologically indistinguishable life-cycle stages. The evolutionary relationship between Karenia species is discussed with respect to differences in both DNA content and the chromosomal distribution patterns of the DNA sequences analyzed.
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Affiliation(s)
- Ángeles Cuadrado
- Universidad de Alcala (UAH), Dpto Biomedicina y Biotecnología, 28805 Alcalá de Henares, Madrid, Spain.
| | - Alfredo De Bustos
- Universidad de Alcala (UAH), Dpto Biomedicina y Biotecnología, 28805 Alcalá de Henares, Madrid, Spain
| | - Rosa I Figueroa
- Instituto Español de Oceanografia (IEO), Subida a Radio Faro 50, 36390, Vigo, Spain.
- Aquatic Ecology, Biology Building, Lund University, 22362, Lund, Sweden.
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30
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Štundlová J, Šmíd J, Nguyen P, Šťáhlavský F. Cryptic diversity and dynamic chromosome evolution in Alpine scorpions (Euscorpiidae: Euscorpius). Mol Phylogenet Evol 2019; 134:152-163. [PMID: 30743063 DOI: 10.1016/j.ympev.2019.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 01/09/2019] [Accepted: 02/03/2019] [Indexed: 12/28/2022]
Abstract
Over time, mountain biota has undergone complex evolutionary histories that have left imprints on its genomic arrangement, geographical distribution and diversity of contemporary lineages. Knowledge on these biogeographical aspects still lags behind for invertebrates inhabiting the Alpine region. In the present study, we examined three scorpion species of the subgenus Euscorpius (Alpiscorpius) from the European Alps using cytogenetic and molecular phylogenetic approaches to determine the variation and population structure of extant lineages at both chromosome and genetic level, and to provide an insight into the species diversification histories. We detected considerable intraspecific variability in chromosome complements and localization of the 18S rDNA loci in all studied species. Such chromosome differences were noticeable as the existence of three [in E. (A.) alpha and E. (A.) germanus] or four [in E. (A.) gamma] range-restricted karyotypic races. These races differed from one another either by 2n [in E. (A.) alpha 2n = 54, 60, 90; in E. (A.) gamma 2n = 58, 60, 88, 86-92], or by the karyotypic formula [in E. (A.) germanus 2n = 34m + 12sm; 36m + 10sm; 42m + 4sm]. Using mitochondrial (16S rRNA, COI) and nuclear (28S rDNA) genetic markers, we examined genetic variation and reconstructed phylogenetic relationships among the karyotypic races. Both approaches provided evidence for the existence of ten deeply divergent lineages exhibiting the features of local endemics and indicating the presence of cryptic species. Molecular dating analyses suggest that these lineages diversified during the Plio-Pleistocene and this process was presumably accompanied by dynamic structural changes in the genome organization.
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Affiliation(s)
- Jana Štundlová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 12844 Prague, Czech Republic.
| | - Jiří Šmíd
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 12844 Prague, Czech Republic; Department of Zoology, National Museum, Cirkusová 1740, Prague, Czech Republic
| | - Petr Nguyen
- Institute of Entomology, Biology Centre CAS, Branišovská 31, 37005 České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1760, 37005 České Budějovice, Czech Republic
| | - František Šťáhlavský
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 12844 Prague, Czech Republic
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31
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Menezes RST, Gazoni T, Costa MA. Cytogenetics of warrior wasps (Vespidae:Synoeca) reveals intense evolutionary dynamics of ribosomal DNA clusters and an unprecedented number of microchromosomes in Hymenoptera. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/bly210] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Rodolpho S T Menezes
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras – Universidade de São Paulo (FFCLRP/USP), Ribeirão Preto, SP, Brazil
| | - Thiago Gazoni
- Departamento de Biologia – Universidade Estadual Paulista (UNESP), Instituto de Biociências, Rio Claro, SP, Brazil
| | - Marco A Costa
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
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32
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Anjos A, Paladini A, Evangelista O, Cabral‐de‐Mello DC. Insights into chromosomal evolution of Cicadomorpha using fluorochrome staining and mapping 18S rRNA and H3 histone genes. J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12254] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Allison Anjos
- Departamento de BiologiaInstituto de BiociênciasUNESP Rio Claro SP Brazil
| | - Andressa Paladini
- Departamento de Ecologia e EvoluçãoUniversidade Federal de Santa Maria Santa Maria RS Brazil
| | - Olivia Evangelista
- Australian National Insect CollectionCSIRO National Research Collections Australia Canberra Australia
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Ubinski CV, Carvalho LS, Schneider MC. Mechanisms of karyotype evolution in the Brazilian scorpions of the subfamily Centruroidinae (Buthidae). Genetica 2018; 146:475-486. [PMID: 30206751 DOI: 10.1007/s10709-018-0038-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 09/05/2018] [Indexed: 01/09/2023]
Abstract
The recently-revised subfamily Centruroidinae is part of the New World clade of buthid scorpions. In this study, we analyzed the cytogenetic characteristics of nine of the 10 Brazilian centruroidines, and one undescribed species of the genus Ischnotelson, using a phylogenetic approach to determine the chromosomal rearrangements responsible for the differentiation of karyotypes among the species. The cytogenetic data recorded in the present study supported the new taxonomic arrangement of the Centruroidinae, with all the species of the same genus sharing the same or similar diploid numbers, i.e., 2n = 20 or 22 in Troglorhopalurus lacrau and T. translucidus, 2n = 25 or 26 in Ischnotelson sp., I. guanambiensis and I. peruassu, and 2n = 28 in Jaguajir agamemnon, J. pintoi and J. rochae. The karyotype modelling in the ChromEvol software indicated 2n = 18 as the ancestral diploid number of the Centruroidinae. The differentiation of karyotypes among the centruroidine genera was based on increasing chromosome numbers resulting from progressive fission events. These changes probably occurred prior to the diversification of the genera Ischnotelson, Jaguajir, Physoctonus and Rhopalurus, and appear to have played a more important role in karyotype evolution at the intergeneric level than the interspecific one. However, the observed increase in diploid numbers was not accompanied by changes in the number or location of ribosomal genes or telomeric sequences. The identification of meiotic cells in female specimens also allowed us to discuss the mechanisms of achiasmatic meiosis in scorpions.
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Affiliation(s)
- Crislaine Vanessa Ubinski
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, UNIFESP, Av. Prof. Artur Riedel, 275, Diadema, São Paulo, 09972-270, Brazil
| | - Leonardo Sousa Carvalho
- Universidade Federal do Piauí, UFPI, Campus Amílcar Ferreira Sobral, BR 343, Km 3.5, Floriano, Piauí, 64800-000, Brazil
| | - Marielle Cristina Schneider
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, UNIFESP, Av. Prof. Artur Riedel, 275, Diadema, São Paulo, 09972-270, Brazil.
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34
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Sex Chromosomes of the Iconic Moth Abraxas grossulariata (Lepidoptera, Geometridae) and Its Congener A. sylvata. Genes (Basel) 2018; 9:genes9060279. [PMID: 29857494 PMCID: PMC6027526 DOI: 10.3390/genes9060279] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/25/2018] [Accepted: 05/28/2018] [Indexed: 01/28/2023] Open
Abstract
The magpie moth, Abraxas grossulariata, is an iconic species in which female heterogamety was discovered at the beginning of the 20th century. However, the sex chromosomes of this species have not yet been cytologically identified. We describe the sex chromosomes of A. grossulariata and its congener, A. sylvata. Although these species split only around 9.5 million years ago, and both species have the expected WZ/ZZ chromosomal system of sex determination and their sex chromosomes share the major ribosomal DNA (rDNA) representing the nucleolar organizer region (NOR), we found major differences between their karyotypes, including between their sex chromosomes. The species differ in chromosome number, which is 2n = 56 in A. grossularita and 2n = 58 in A. sylvata. In addition, A. grossularita autosomes exhibit massive autosomal blocks of heterochromatin, which is a very rare phenomenon in Lepidoptera, whereas the autosomes of A. sylvata are completely devoid of distinct heterochromatin. Their W chromosomes differ greatly. Although they are largely composed of female-specific DNA sequences, as shown by comparative genomic hybridization, cross-species W-chromosome painting revealed considerable sequence differences between them. The results suggest a relatively rapid molecular divergence of Abraxas W chromosomes by the independent spreading of female-specific repetitive sequences.
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Sember A, Bohlen J, Šlechtová V, Altmanová M, Pelikánová Š, Ráb P. Dynamics of tandemly repeated DNA sequences during evolution of diploid and tetraploid botiid loaches (Teleostei: Cobitoidea: Botiidae). PLoS One 2018; 13:e0195054. [PMID: 29590207 PMCID: PMC5874072 DOI: 10.1371/journal.pone.0195054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/15/2018] [Indexed: 12/16/2022] Open
Abstract
Polyploidization has played an important role in the evolution of vertebrates, particularly at the base of Teleostei-an enormously successful ray-finned fish group with additional genome doublings on lower taxonomic levels. The investigation of post-polyploid genome dynamics might provide important clues about the evolution and ecology of respective species and can help to decipher the role of polyploidy per se on speciation. Few studies have attempted to investigate the dynamics of repetitive DNA sequences in the post-polyploid genome using molecular cytogenetic tools in fishes, though recent efforts demonstrated their usefulness. The demonstrably monophyletic freshwater loach family Botiidae, branching to evolutionary diploid and tetraploid lineages separated >25 Mya, offers a suited model group for comparing the long-term repetitive DNA evolution. For this, we integrated phylogenetic analyses with cytogenetical survey involving Giemsa- and Chromomycin A3 (CMA3)/DAPI stainings and fluorescence in situ hybridization with 5S/45S rDNA, U2 snDNA and telomeric probes in representative sample of 12 botiid species. The karyotypes of all diploids were composed of 2n = 50 chromosomes, while majority of tetraploids had 2n = 4x = 100, with only subtle interspecific karyotype differences. The exceptional karyotype of Botia dario (2n = 4x = 96) suggested centric fusions behind the 2n reduction. Variable patterns of FISH signals revealed cases of intraspecific polymorphisms, rDNA amplification, variable degree of correspondence with CMA3+ sites and almost no phylogenetic signal. In tetraploids, either additivity or loci gain/loss was recorded. Despite absence of classical interstitial telomeric sites, large blocks of interspersed rDNA/telomeric regions were found in diploids only. We uncovered different molecular drives of studied repetitive DNA classes within botiid genomes as well as the advanced stage of the re-diploidization process in tetraploids. Our results may contribute to link genomic approach with molecular cytogenetic analyses in addressing the origin and mechanism of this polyploidization event.
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Affiliation(s)
- Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
| | - Jörg Bohlen
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
| | - Vendula Šlechtová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
| | - Marie Altmanová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2, Czech Republic
| | - Šárka Pelikánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
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Insights into the karyotype evolution and speciation of the beetle Euchroma gigantea (Coleoptera: Buprestidae). Chromosome Res 2018. [PMID: 29524007 DOI: 10.1007/s10577-018-9576-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Euchroma Dejean, 1833 (Buprestidae: Coleoptera) is a monotypic genus comprising the species Euchroma gigantea, with populations presenting a degree of karyotypic variation/polymorphism rarely found within a single taxonomic (specific) unit, as well as drastically incompatible meiotic configurations in populations from extremes of the species range. To better understand the complex karyotypic evolution of E. gigantea, the karyotypes of specimens from five populations in Brazil were investigated using molecular cytogenetics and phylogenetic approaches. Herein, we used FISH with histone genes as well as sequencing of the COI to determine differential distribution of markers and relationships among populations. The analyses revealed new karyotypes, with variability for chromosome number and morphology of multiple sex chromosome mechanisms, occurrence of B chromosome variants (punctiform and large ones), and high dispersion of histone genes in different karyotypes. These data indicate that chromosomal polymorphism in E. gigantea is greater than previously reported, and that the species can be a valuable model for cytogenetic studies. The COI phylogenetic and haplotype analyses highlighted the formation of three groups with chromosomally polymorphic individuals. Finally, we compared the different karyotypes and proposed a model for the chromosomal evolution of this species. The species E. gigantea includes at least three cytogenetically polymorphic lineages. Moreover, in each of these lineages, different chromosomal rearrangements have been fixed. Dispersion of repetitive sequences may have favored the high frequency of these rearrangements, which could be related to both adaptation of the species to different habitats and the speciation process.
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Šťáhlavský F, Štundlová J, Lowe G, Stockmann M, Kovařík F. Application of cytogenetic markers in the taxonomy of flat rock scorpions (Scorpiones: Hormuridae), with the description of Hadogenes weygoldti sp. n. ZOOL ANZ 2018. [DOI: 10.1016/j.jcz.2018.01.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Orosova M, Spakulova M. Tapeworm chromosomes: their value in systematics with instructions for cytogenetic study. Folia Parasitol (Praha) 2018. [PMID: 29528298 DOI: 10.14411/fp.2018.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The history and value of cytogenetic features for addressing questions of the evolution and systematics of tapeworms (Cestoda) are briefly reviewed along with instructions for collecting karyological data. As a supplement to worm morphology, chromosome number and morphology have been helpful in determining the systematic status of some genera in the Diphyllobothriidae and species in the Bothriocephallidea. In addition, many new techniques for chromosome analysis have been recently applied in morphological and molecular studies of invertebrates, including tapeworms. Methods of molecular karyology, fluorescence in situ hybridisation, and chromosomal location of satellite DNA, microsatellites or histone genes may also provide useful data to inference of taxonomic relationships and for revealing trends or general lines of chromosome evolution. However, as karyological data are available only for few tapeworms, they are seldom an integral part of evolutionary and taxonomic studies of cestodes. A primary reason for this lack of karyological data may lie in general difficulties in working with tapeworm chromosomes. To address these problems, herein we present a well-tested, step-by-step illustrated guide on the fixation of tapeworm material and preparation of their chromosomes for cytogenetic studies. The technique requires standard glassware, few reagents and simple equipment such as needles; it can also be used on other neodermatan flatworms.
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Affiliation(s)
- Martina Orosova
- Institute of Parasitology, Slovak Academy of Sciences, Kosice, Slovakia
| | - Marta Spakulova
- Institute of Parasitology, Slovak Academy of Sciences, Kosice, Slovakia
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Šťáhlavský F, Opatova V, Just P, Lotz LN, Haddad CR. Molecular technique reveals high variability of 18S rDNA distribution in harvestmen (Opiliones, Phalangiidae) from South Africa. COMPARATIVE CYTOGENETICS 2018; 12:41-59. [PMID: 29675136 PMCID: PMC5904373 DOI: 10.3897/compcytogen.v12i1.21744] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 12/27/2017] [Indexed: 06/08/2023]
Abstract
The knowledge of cytogenetics in the harvestmen family Phalangiidae has been based on taxa from the Northern Hemisphere. We performed cytogenetic analysis on Guruia africana (Karsch, 1878) (2n=24) and four species of the genus Rhampsinitus Simon, 1879 (2n=24, 26, 34) from South Africa. Fluorescence in situ hybridization with an 18S rDNA probe was used to analyze the number and the distribution of this cluster in the family Phalangiidae for the first time. The results support the cytogenetic characteristics typical for the majority of harvestmen taxa, i.e. the predominance of small biarmed chromosomes and the absence of morphologically well-differentiated sex chromosomes as an ancestral state. We identified the number of 18S rDNA sites ranging from two in R. qachasneki Kauri, 1962 to seven in one population of R. leighi Pocock, 1903. Moreover, we found differences in the number and localization of 18S rDNA sites in R. leighi between populations from two localities and between sexes of R. capensis (Loman, 1898). The heterozygous states of the 18S rDNA sites in these species may indicate the presence of XX/XY and ZZ/ZW sex chromosomes, and the possible existence of these systems in harvestmen is discussed. The variability of the 18S rDNA sites indicates intensive chromosomal changes during the differentiation of the karyotypes, which is in contrast to the usual uniformity in chromosomal morphology known from harvestmen so far.
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Affiliation(s)
- František Šťáhlavský
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, CZ-12844 Praha, Czech Republic
| | - Vera Opatova
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, AL 36849, USA
| | - Pavel Just
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, CZ-12844 Praha, Czech Republic
| | - Leon N. Lotz
- Department of Arachnology, National Museum, P.O. Box 266, Bloemfontein 9300, South Africa
| | - Charles R. Haddad
- Department of Zoology and Entomology, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
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Evolution of Karyotypes in Chameleons. Genes (Basel) 2017; 8:genes8120382. [PMID: 29231849 PMCID: PMC5748700 DOI: 10.3390/genes8120382] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 11/29/2017] [Accepted: 11/30/2017] [Indexed: 01/04/2023] Open
Abstract
The reconstruction of the evolutionary dynamics of karyotypes and sex determining systems in squamate reptiles is precluded by the lack of data in many groups including most chameleons (Squamata: Acrodonta: Chamaeleonidae). We performed cytogenetic analysis in 16 species of chameleons from 8 genera covering the phylogenetic diversity of the family and also phylogenetic reconstruction of karyotype evolution in this group. In comparison to other squamates, chameleons demonstrate rather variable karyotypes, differing in chromosome number, morphology and presence of interstitial telomeric signal (ITS). On the other hand, the location of rDNA is quite conserved among chameleon species. Phylogenetic analysis combining our new results and previously published data tentatively suggests that the ancestral chromosome number for chameleons is 2n = 36, which is the same as assumed for other lineages of the clade Iguania, i.e., agamids and iguanas. In general, we observed a tendency for the reduction of chromosome number during the evolution of chameleons, however, in Rieppeleon brevicaudatus, we uncovered a chromosome number of 2n = 62, very unusual among squamates, originating from a number of chromosome splits. Despite the presence of the highly differentiated ZZ/ZW sex chromosomes in the genus Furcifer, we did not detect any unequivocal sexual differences in the karyotypes of any other studied species of chameleons tested using differential staining and comparative genomic hybridization, suggesting that sex chromosomes in most chameleons are only poorly differentiated.
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Vershinina AO, Lukhtanov VA. Evolutionary mechanisms of runaway chromosome number change in Agrodiaetus butterflies. Sci Rep 2017; 7:8199. [PMID: 28811556 PMCID: PMC5557896 DOI: 10.1038/s41598-017-08525-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/10/2017] [Indexed: 11/17/2022] Open
Abstract
Despite predictions of the classic, hybrid-sterility model of chromosomal speciation, some organisms demonstrate high rate of karyotype evolution. This rate is especially impressive in Agrodiaetus butterflies that rapidly evolved the greatest chromosome number diversity known in animal kingdom within a single subgenus. Here we analyzed karyotype evolution in Agrodiaetus using phylogenetic comparative methods. We found that chromosome numbers possess a strong phylogenetic signal. This disproves the chromosome megaevolution model that proposes multiple chromosome rearrangements to accumulate independently in each of closely related species. We found that Brownian motion gives a more adequate description of observed trait changes than Ornstein-Uhlenbeck model. This indicates that chromosome numbers evolve via random walk along branches of the phylogeny. We discovered a correlation between karyotype changes and phylogeny branch lengths. This gradual pattern is inconsistent with the hybrid-sterility model which, due to association of major chromosome changes with cladogenetic events, predicts a high degree of punctualism in karyotype evolution. Thus, low underdominace of chromosomal rearrangements and/or prevalence of the recombination-suppression model over the hybrid-sterility model of chromosome speciation are the most common engines of the runaway chromosome number change observed.
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Affiliation(s)
- Alisa O Vershinina
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, Universitetskaya nab. 1, 199034, St. Petersburg, Russia.
- Department of Ecology & Evolutionary Biology, University of California Santa Cruz, 95064, Santa Cruz, CA, USA.
| | - Vladimir A Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, Universitetskaya nab. 1, 199034, St. Petersburg, Russia.
- Department of Entomology, St Petersburg State University, Universitetskaya nab. 7/9, 199034, St. Petersburg, Russia.
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Warchałowska-Śliwa E, Grzywacz B, Heller KG, Chobanov DP. Comparative analysis of chromosomes in the Palaearctic bush-crickets of tribe Pholidopterini (Orthoptera, Tettigoniinae). COMPARATIVE CYTOGENETICS 2017; 11:309-324. [PMID: 28919967 PMCID: PMC5596980 DOI: 10.3897/compcytogen.v11i2.12070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/28/2017] [Indexed: 06/07/2023]
Abstract
The present study focused on the evolution of the karyotype in four genera of the tribe Pholidopterini: Eupholidoptera Mařan, 1953, Parapholidoptera Mařan, 1953, Pholidoptera Wesmaël, 1838, Uvarovistia Mařan, 1953. Chromosomes were analyzed using fluorescence in situ hybridization (FISH) with 18S rDNA and (TTAGG) n telomeric probes, and classical techniques, such as C-banding, silver impregnation and fluorochrome DAPI/CMA3 staining. Most species retained the ancestral diploid chromosome number 2n = 31 (male) or 32 (female), while some of the taxa, especially a group of species within genus Pholidoptera, evolved a reduced chromosome number 2n = 29. All species show the same sex determination system X0/XX. In some taxa, a pericentric inversion has changed the morphology of the ancestral acrocentric X chromosome to the biarmed X. The rDNA loci coincided with active NORs and C-band/CG-rich segments. A comparison of the location of the single rDNA/NOR in the genus Pholidoptera suggests that reduced chromosome number results from Robertsonian translocation between two pairs of autosomes, one carrying the rDNA/NOR. The results constitute a step towards better understanding of the chromosomal reorganization and evolution within the tribe Phaneropterini and the whole subfamily Tettigoniinae.
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Affiliation(s)
- Elżbieta Warchałowska-Śliwa
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Krakow, Poland
| | - Beata Grzywacz
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Krakow, Poland
| | | | - Dragan P. Chobanov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Boul., 1000 Sofia, Bulgaria
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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.
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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
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Mattos VF, Carvalho LS, Cella DM, Schneider MC. Location of 45S Ribosomal Genes in Mitotic and Meiotic Chromosomes of Buthid Scorpions. Zoolog Sci 2016; 31:603-7. [PMID: 25186932 DOI: 10.2108/zs140005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Buthid scorpions exhibit a high variability in diploid number within genera and even within species. Cytogenetically, Buthidae differs from other families of Scorpiones based on its low diploid numbers, holocentric chromosomes, and complex chromosomal chains, which form during meiosis. In this study, we analyzed the distribution of the 45S ribosomal DNA (rDNA) genes in the mitotic and meiotic chromosomes of seven buthid species belonging to the genera Rhopalurus and Tityus with the ultimate goal of elucidating the chromosome organization in these scorpions. The chromosome number ranged from 2n=6 to 2n=28. Despite the high variance in diploid number, all species examined carried their 45S rDNA sites in the terminal region of exactly two chromosomes. Analyses of meiotic cells revealed 45S rDNA clusters in the chromosomal chains of Rhopalurus agamemnon, Tityus bahiensis, Tityus confluens, and Tityus martinpaechi, or in bivalent-like configuration in Rhopalurus rochai, Tityus bahiensis, Tityus confluens, Tityus fasciolatus, and Tityus paraguayensis. In the species examined, the 45S rDNA sites colocalized with constitutive heterochromatin regions. In light of the high chromosome variability and maintenance of number and terminal position of 45S rDNA sites in buthids, the heterochromatin may act to conserve the integrity of the ribosomal genes.
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Affiliation(s)
- Viviane Fagundes Mattos
- 1 Universidade Estadual Paulista, UNESP, Instituto de Biociências, Departamento de Biologia, Avenida 24-A, 1515, Caixa Postal 199, 13506-900, Rio Claro, Sao Paulo, Brazil
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Kuznetsova VG, Khabiev GN, Anokhin BA. Cytogenetic study on antlions (Neuroptera, Myrmeleontidae): first data on telomere structure and rDNA location. COMPARATIVE CYTOGENETICS 2016; 10:647-656. [PMID: 28123685 PMCID: PMC5240515 DOI: 10.3897/compcytogen.v10i4.10775] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/08/2016] [Indexed: 06/06/2023]
Abstract
Myrmeleontidae, commonly known as "antlions", are the most diverse family of the insect order Neuroptera, with over 1700 described species (in 191 genera) of which 37 species (in 21 genera) have so far been studied in respect to standard karyotypes. In the present paper we provide first data on the occurrence of the "insect-type" telomeric repeat (TTAGG) n and location of 18S rDNA clusters in the antlion karyotypes studied using fluorescence in situ hybridization (FISH). We show that males of Palpares libelluloides (Linnaeus, 1764) (Palparinae), Acanthaclisis occitanica (Villers, 1789) (Acanthaclisinae) and Distoleon tetragrammicus (Fabricius, 1798) (Nemoleontinae) have rDNA clusters on a large bivalent, two last species having an additional rDNA cluster on one of the sex chromosomes, most probably the X. (TTAGG) n - containing telomeres are clearly characteristic of Palpares libelluloides and Acanthaclisis occitanica; the presence of this telomeric motif in Distoleon tetragrammicus is questionable. In addition, we detected the presence of the (TTAGG) n telomeric repeat in Libelloides macaronius (Scopoli, 1763) from the family Ascalaphidae (owlflies), a sister group to the Myrmeleontidae. We presume that the "insect" motif (TTAGG) n was present in a common ancestor of the families Ascalaphidae and Myrmeleontidae within the neuropteran suborder Myrmeleontiformia.
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Affiliation(s)
- Valentina G. Kuznetsova
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, 199034, St. Petersburg, Russia
| | - Gadzhimurad N. Khabiev
- Prikaspiyskiy Institute of Biological Resources, Dagestan Scientific Centre, Russian Academy of Sciences, ul. M. Gadzhieva 45, 367025 Makhachkala, Russia
| | - Boris A. Anokhin
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, 199034, St. Petersburg, Russia
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Anjos A, Rocha GC, Paladini A, Mariguela TC, Cabral-de-Mello DC. Karyotypes and Repetitive DNA Evolution in Six Species of the Genus Mahanarva (Auchenorrhyncha: Cercopidae). Cytogenet Genome Res 2016; 149:321-327. [PMID: 27811473 DOI: 10.1159/000450730] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2016] [Indexed: 11/19/2022] Open
Abstract
Insects of the Cercopidae family are widely distributed and comprise 59 genera and 431 species in the New World. They are xylemophagous, causing losses in agricultural and pasture grasses, and are considered as emerging pests. Chromosomally, these insects have been studied by standard techniques, revealing variable diploid numbers and primarily X0 sex chromosome systems (males). We performed chromosome studies in 6 Mahanarva (Cercopidae) species using standard and differential chromosome staining as well as mapping of repetitive DNAs. Moreover, the relationship between the repetitive DNAs was analyzed at the interspecific level. A diploid chromosome number of 2n = 19,X0 was documented, with chromosomes gradually decreasing in size. Neutral or GC-rich regions were detected which varied depending on the species. Fluorescence in situ hybridization with a (TTAGG)n telomeric motif probe revealed terminal signals, matching those of the Cot DNAs obtained from each species, that were also restricted to the terminal regions of all chromosomes. Dot blot analysis with the Cot fraction from M. quadripunctata showed that at least part of the repetitive genome is shared among the 6 species. Our data highlight the conservation of chromosomal features and organization of repetitive DNAs in the genus Mahanarva, suggesting a low differentiation for chromosomes and repetitive DNAs in most of the 6 species studied.
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Affiliation(s)
- Allison Anjos
- Departamento de Biologia, Instituto de Biociências, UNESP, Rio Claro, Brazil
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Hernández-Roldán JL, Dapporto L, Dincă V, Vicente JC, Hornett EA, Šíchová J, Lukhtanov VA, Talavera G, Vila R. Integrative analyses unveil speciation linked to host plant shift inSpialiabutterflies. Mol Ecol 2016; 25:4267-84. [DOI: 10.1111/mec.13756] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 06/25/2016] [Accepted: 07/05/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Juan L. Hernández-Roldán
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra); Passeig Marítim de la Barceloneta 37 E-08003 Barcelona Spain
- Departamento de Biología (Zoología); Facultad de Ciencias de la Universidad Autónoma de Madrid; C/ Darwin 2 E-28049 Madrid Spain
| | - Leonardo Dapporto
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra); Passeig Marítim de la Barceloneta 37 E-08003 Barcelona Spain
- Department of Biology; University of Florence; Via Madonna del Piano 6 50019 Sesto Fiorentino FI Italy
| | - Vlad Dincă
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra); Passeig Marítim de la Barceloneta 37 E-08003 Barcelona Spain
- Biodiversity Institute of Ontario; University of Guelph; Guelph Ontario Canada N1G 2W1
| | | | - Emily A. Hornett
- Department of Zoology; University of Cambridge; Cambridge CB2 3EJ UK
| | - Jindra Šíchová
- Institute of Entomology; Biology Centre ASCR; 370 05 České Budějovice Czech Republic
| | - Vladimir A. Lukhtanov
- Department of Karyosystematics; Zoological Institute of Russian Academy of Sciences; Universitetskaya nab. 1 199034 St. Petersburg Russia
- Department of Entomology; St. Petersburg State University; Universitetskaya nab. 7/9 199034 St. Petersburg Russia
| | - Gerard Talavera
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra); Passeig Marítim de la Barceloneta 37 E-08003 Barcelona Spain
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology; Harvard University; Cambridge MA 02138 USA
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra); Passeig Marítim de la Barceloneta 37 E-08003 Barcelona Spain
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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]
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49
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Svojanovská H, Nguyen P, Hiřman M, Tuf IH, Wahab RA, Haddad CR, Šťáhlavský F. Karyotype Evolution in Harvestmen of the Suborder Cyphophthalmi (Opiliones). Cytogenet Genome Res 2016; 148:227-36. [PMID: 27245985 DOI: 10.1159/000445863] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2016] [Indexed: 11/19/2022] Open
Abstract
The morphologically uniform suborder Cyphophthalmi represents a basal group of harvestmen (Opiliones). As such, it plays an important role in the reconstruction of the karyotype evolution within this arachnid order. The cytogenetic analysis of 6 representatives of the suborder Cyphophthalmi, namely Miopsalis sp. (2n = 30; Stylocellidae), Austropurcellia arcticosa (Cantrell, 1980) (2n = 30; Pettalidae), Parapurcellia amatola de Bivort & Giribet, 2010 (2n = 32; Pettalidae), Paramiopsalis aff. ramulosus Juberthie, 1962 (2n = 28; Sironidae), Cyphophthalmus duricorius Joseph, 1868 (2n = 24; Sironidae), and Siro carpaticus Rafalski, 1956 (2n = 52; Sironidae) was performed. Fluorescence in situ hybridization with 18S rDNA probe was used to analyze the distribution of major ribosomal RNA genes in harvestmen. We confront the obtained cytogenetic data with current hypotheses on cyphophthalmid phylogeny to reconstruct their karyotype evolution. We conclude that the ancestral karyotype of harvestmen consisted of 2n = 30 elements with 1 chromosome pair bearing terminal rDNA clusters. The rDNA locus was multiplicated in the evolution of Cyphophthalmi. However, decreases as well as increases in the number of chromosomes have been detected in the karyotype evolution of Cyphophthalmi. Our data thus reveal unexpected diversity in cyphophthalmid karyotypes.
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Affiliation(s)
- Hana Svojanovská
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
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Pita S, Lorite P, Nattero J, Galvão C, Alevi KCC, Teves SC, Azeredo-Oliveira MTV, Panzera F. New arrangements on several species subcomplexes of Triatoma genus based on the chromosomal position of ribosomal genes (Hemiptera - Triatominae). INFECTION GENETICS AND EVOLUTION 2016; 43:225-31. [PMID: 27245153 DOI: 10.1016/j.meegid.2016.05.028] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 05/18/2016] [Accepted: 05/19/2016] [Indexed: 11/28/2022]
Abstract
The hemipteran subfamily Triatominae includes 150 blood-sucking species, vectors of Chagas disease. By far the most specious genus is Triatoma, assembled in groups, complexes and subcomplexes based on morphological similarities, geographic distribution and genetic data. However, many molecular studies questioned the species integration of several subcomplexes as monophyletic units. In triatomines, chromosomal position of major ribosomal DNA (rDNA) loci is extremely variable but seems to be species-specific and an evolutionary conserved genetic trait, so that closely related species tend to have ribosomal clusters in the same chromosomal location. Considering that the autosomal position as the ancestral character for all heteropteran species, including triatomines, we suggest that the movement of rDNA loci from autosomes to sex chromosomes rapidly established reproductive barriers between divergent lineages. We proposed that the rDNA translocation from the autosomes to the sex chromosomes restrict reproductive compatibility and eventually promote speciation processes. We analyzed the chromosomal position of 45S rDNA clusters in almost all species of the matogrossensis, rubrovaria, maculata and sordida subcomplexes. The fluorescent in situ hybridization results are discussed considering the available genetic data and we proposed new arrangements in the species that constitute each one of these subcomplexes.
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Affiliation(s)
- Sebastián Pita
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Pedro Lorite
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Jaén, Spain
| | - Julieta Nattero
- Cátedra de Introducción a la Biología, Facultad de Ciencias Exactas Físicas y Naturales, Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), Universidad Nacional de Córdoba (UNC-CONICET), Córdoba, Argentina
| | - Cleber Galvão
- Laboratório Nacional e Internacional de Referência em Taxonomia de Triatomíneos, Instituto Oswaldo Cruz - FIOCRUZ, Rio de Janeiro, Brazil
| | - Kaio C C Alevi
- Laboratorio de Biologia Celular, Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista "Júlio de Mesquita Filho" (IBILCE-UNESP), São José do Rio Preto, São Paulo, Brazil
| | - Simone C Teves
- Laboratório Interdisciplinar de Vigilância Entomológica em Diptera e Hemiptera (LIVEDIH), Instituto Oswaldo Cruz/Fundação Oswaldo Cruz, Rio de Janeiro, Brazil; Programa de Pós-Graduação em Biologia Animal, Universidade Federal Rural do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maria T V Azeredo-Oliveira
- Laboratorio de Biologia Celular, Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista "Júlio de Mesquita Filho" (IBILCE-UNESP), São José do Rio Preto, São Paulo, Brazil
| | - Francisco Panzera
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.
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