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Ibiapino A, Báez M, García MA, Costea M, Stefanović S, Pedrosa-Harand A. Karyotype asymmetry in Cuscuta L. subgenus Pachystigma reflects its repeat DNA composition. Chromosome Res 2022; 30:91-107. [PMID: 35089455 DOI: 10.1007/s10577-021-09683-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 12/25/2022]
Abstract
Cuscuta is a cytogenetically diverse genus, with karyotypes varying 18-fold in chromosome number and 127-fold in genome size. Each of its four subgenera also presents particular chromosomal features, such as bimodal karyotypes in Pachystigma. We used low coverage sequencing of the Cuscuta nitida genome (subgenus Pachystigma), as well as chromosome banding and molecular cytogenetics of three subgenus representatives, to understand the origin of bimodal karyotypes. All three species, C. nitida, C. africana (2n = 28) and C. angulata (2n = 30), showed heterochromatic bands mainly in the largest chromosome pairs. Eighteen satellite DNAs were identified in C. nitida genome, two showing similarity to mobile elements. The most abundant were present at the largest pairs, as well as the highly abundant ribosomal DNAs. The most abundant Ty1/Copia and Ty3/Gypsy elements were also highly enriched in the largest pairs, except for the Ty3/Gypsy CRM, which also labelled the pericentromeric regions of the smallest chromosomes. This accumulation of repetitive DNA in the larger pairs indicates that these sequences are largely responsible for the formation of bimodal karyotypes in the subgenus Pachystigma. The repetitive DNA fraction is directly linked to karyotype evolution in Cuscuta.
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Affiliation(s)
- Amalia Ibiapino
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Mariana Báez
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil.,Plant Breeding Department, University of Bonn, Bonn, Germany
| | | | - Mihai Costea
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, Canada
| | - Saša Stefanović
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil.
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Rosas-Ramos N, Mas-Peinado P, Gil-Tapetado D, Recuero E, Ruiz JL, García-París M. Catalogue, distribution, taxonomic notes, and conservation of the Western Palearctic endemic hunchback beetles (Tenebrionidae, Misolampus). Zookeys 2020; 963:81-129. [PMID: 32922132 PMCID: PMC7458947 DOI: 10.3897/zookeys.963.53500] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/10/2020] [Indexed: 11/12/2022] Open
Abstract
Hunchback darkling beetles of the Ibero-Maghrebian genus Misolampus Latreille, 1807 (Tenebrionidae, Stenochiinae) encompass six species: M. gibbulus (Herbst, 1799), M. goudotii Guérin-Méneville, 1834, M. lusitanicus Brême, 1842, M. ramburii Brême, 1842, M. scabricollis Graells, 1849, and M. subglaber Rosenhauer, 1856. Previously known distribution ranges of the species were delineated using many old records, the persistence of such populations being questionable under the current situation of global biodiversity loss. Additionally, the status of geographically isolated populations of the genus have been the subject of taxonomic controversy. An exhaustive bibliographical revision and field search was undertaken, and the Misolampus collection of the Museo Nacional de Ciencias Naturales (MNCN-CSIC) was revised. The aims are to (i) provide an updated geographic distribution range for the species of Misolampus; (ii) to determine the taxonomic status of controversial populations; (iii) to provide a catalogue for Misolampus; and (iv) to discuss the conservation status of these saproxylic beetles. As a result, a catalogue including synonymies and type localities, geographical records, diagnoses, and information on natural history for all species of Misolampus is presented. The results reveal that the distribution ranges of the species of Misolampus have not undergone a reduction in the last century, and indicate the presence of the genus in areas where it had never been recorded before. The morphological variability of M. goudotii drove the proposal of different taxa that are here formally synonymised as follows: M. goudotii Guérin-Méneville, 1834 = M. erichsoni Vauloger de Beaupré, 1900, syn. nov. = M. peyerimhoffi Antoine, 1926, syn. nov.
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Affiliation(s)
- Natalia Rosas-Ramos
- Departamento de Biología Animal (Área de Zoología), Facultad de Biología (Edificio de Farmacia, planta 5), Universidad de Salamanca, Campus Miguel de Unamuno s/n, 37007 Salamanca, SpainMuseo Nacional de Ciencias NaturalesMadridSpain
- Departamento de Biodiversidad y Biología Evolutiva. Museo Nacional de Ciencias Naturales, MNCN-CSIC. c/ José Gutiérrez Abascal, 2. 28006, Madrid, SpainUniversidad de SalamancaSalamancaSpain
| | - Paloma Mas-Peinado
- Departamento de Biodiversidad y Biología Evolutiva. Museo Nacional de Ciencias Naturales, MNCN-CSIC. c/ José Gutiérrez Abascal, 2. 28006, Madrid, SpainUniversidad de SalamancaSalamancaSpain
- Centro de Investigación en Biodiversidad y Cambio Global CIBC-UAM, Facultad de Ciencias, Universidad Autónoma de Madrid, c/Darwin 2, 28049-Madrid, SpainUniversidad Autónoma de MadridMadridSpain
| | - Diego Gil-Tapetado
- Departamento de Biodiversidad y Biología Evolutiva. Museo Nacional de Ciencias Naturales, MNCN-CSIC. c/ José Gutiérrez Abascal, 2. 28006, Madrid, SpainUniversidad de SalamancaSalamancaSpain
- Departamento de Biología, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, c/ José Antonio Novais, 12, 28040-Madrid, SpainUniversidad Complutense de MadridMadridSpain
| | - Ernesto Recuero
- Departamento de Biodiversidad y Biología Evolutiva. Museo Nacional de Ciencias Naturales, MNCN-CSIC. c/ José Gutiérrez Abascal, 2. 28006, Madrid, SpainUniversidad de SalamancaSalamancaSpain
| | - José L. Ruiz
- Instituto de Estudios Ceutíes. Paseo del Revellín, 30. 51001 Ceuta, SpainInstituto de Estudios CeutíesCeutaSpain
| | - Mario García-París
- Departamento de Biodiversidad y Biología Evolutiva. Museo Nacional de Ciencias Naturales, MNCN-CSIC. c/ José Gutiérrez Abascal, 2. 28006, Madrid, SpainUniversidad de SalamancaSalamancaSpain
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Bardella VB, da Rosa JA, Vanzela ALL. Origin and distribution of AT-rich repetitive DNA families in Triatoma infestans (Heteroptera). INFECTION GENETICS AND EVOLUTION 2014; 23:106-14. [PMID: 24524986 DOI: 10.1016/j.meegid.2014.01.035] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 01/26/2014] [Accepted: 01/29/2014] [Indexed: 11/17/2022]
Abstract
Triatoma infestans, one of the most important vectors of Trypanosoma cruzi, is very interesting model, because it shows large interpopulation variation in the amount and distribution of heterochromatin. This polymorphism involved the three large pairs up to almost all autosomal pairs, including the sex chromosomes. To understand the dynamics of heterochromatin variation in T. infestans, we isolated the AT-rich satDNA portion of this insect using reassociation kinetics (C0t), followed by cloning, sequencing and FISH. After chromosome localization, immunolabeling with anti-5-methylcytosine, anti-H4K5ac and anti-H3K9me2 antibodies was performed to determine the functional characteristics of heterochromatin. The results allowed us to reorganize the karyotype of T. infestans in accordance with the distribution of the families of repetitive DNA using seven different markers. We found that two arrays with lengths of 79 and 33bp have a strong relationship with transposable element sequences, suggesting that these two families of satDNA probably originated from Polintons. The results also allowed us to identify at least four chromosome rearrangements involved in the amplification/dispersion of AT-rich satDNA of T. infestans. These data should be very useful in new studies including those examining the cytogenomic and population aspects of this very important species of insect.
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Affiliation(s)
- Vanessa Bellini Bardella
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, IBILCE/UNESP, 15054-000 São José do Rio Preto, São Paulo, Brazil.
| | - João Aristeu da Rosa
- Departamento de Ciências Biológicas, Faculdade de Ciências Famacêuticas de Araraquara, FCFAR/UNESP, 14801-902 Araraquara, São Paulo, Brazil.
| | - André Luís Laforga Vanzela
- Departamento de Biologia Geral, CCB, Universidade Estadual de Londrina, 86051-990 Londrina, Paraná, Brazil.
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Satellite DNA-like elements associated with genes within euchromatin of the beetle Tribolium castaneum. G3-GENES GENOMES GENETICS 2012; 2:931-41. [PMID: 22908042 PMCID: PMC3411249 DOI: 10.1534/g3.112.003467] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 06/18/2012] [Indexed: 01/30/2023]
Abstract
In the red flour beetle Tribolium castaneum the major TCAST satellite DNA accounts for 35% of the genome and encompasses the pericentromeric regions of all chromosomes. Because of the presence of transcriptional regulatory elements and transcriptional activity in these sequences, TCAST satellite DNAs also have been proposed to be modulators of gene expression within euchromatin. Here, we analyze the distribution of TCAST homologous repeats in T. castaneum euchromatin and study their association with genes as well as their potential gene regulatory role. We identified 68 arrays composed of TCAST-like elements distributed on all chromosomes. Based on sequence characteristics the arrays were composed of two types of TCAST-like elements. The first type consists of TCAST satellite-like elements in the form of partial monomers or tandemly arranged monomers, up to tetramers, whereas the second type consists of TCAST-like elements embedded with a complex unit that resembles a DNA transposon. TCAST-like elements were also found in the 5′ untranslated region (UTR) of the CR1-3_TCa retrotransposon, and therefore retrotransposition may have contributed to their dispersion throughout the genome. No significant difference in the homogenization of dispersed TCAST-like elements was found either at the level of local arrays or chromosomes nor among different chromosomes. Of 68 TCAST-like elements, 29 were located within introns, with the remaining elements flanked by genes within a 262 to 404,270 nt range. TCAST-like elements are statistically overrepresented near genes with immunoglobulin-like domains attesting to their nonrandom distribution and a possible gene regulatory role.
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Mravinac B, Plohl M. Parallelism in evolution of highly repetitive DNAs in sibling species. Mol Biol Evol 2010; 27:1857-67. [PMID: 20203289 DOI: 10.1093/molbev/msq068] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Characterization of heterochromatin in the flour beetle Tribolium audax revealed two highly repetitive DNA families, named TAUD1 and TAUD2, which together constitute almost 60% of the whole genome. Both families originated from a common ancestral approximately 110-bp repeating unit. Tandem arrangement of these elements in TAUD1 is typical for satellite DNAs, whereas TAUD2 represents a dispersed family based on 1412-bp complex higher-order repeats composed of inversely oriented approximately 110 bp units. Comparison with repetitive DNAs in the sibling species Tribolium madens showed similarities in nucleotide sequence and length of basic repeating units and also revealed structural and organizational parallelism in tandem and dispersed families assembled from these elements. In both Tribolium species, one tandem and one dispersed family build equivalent distribution patterns in the pericentromeric heterochromatin of all chromosomes including supernumeraries. Differences in the nucleotide sequence and in the complexity of higher-order structures between families of the same type suggest a scenario according to which rearranged variants of the corresponding ancestral families were formed and distributed in genomes during or after the speciation event, following the same principles independently in each descendant species. We assume that random effects of sequence dynamics should be constrained by organizational and structural features of repeating units and possible requirements for spatial distribution of particular sequence elements. An interspersed pattern of repetitive families also points to the intensive recombination events in heterochromatin. Synergy between the meiotic bouquet stage and satellite DNA sequence dynamics could make a positive feedback loop that promotes the observed genome-wide distribution. At the same time, considering the abundance of these DNAs in heterochromatin spanning the (peri)centromeric chromosomal segments, we speculate that diverged repetitive sequences might represent the DNA basis of reproductive barrier between the two sibling species.
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Affiliation(s)
- Brankica Mravinac
- Division of Molecular Biology, Ruder Bosković Institute, Zagreb, Croatia
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Abstract
The study of insect satellite DNAs (satDNAs) indicates the evolutionary conservation of certain features despite their sequence heterogeneity. Such features can include total length, monomer length, motifs, particular regions and/or secondary and tertiary structures. satDNAs may act as protein-binding sites, structural domains or sites for epigenetic modifications. The selective constraints in the evolution of satDNAs may be due to the satDNA sequence interaction with specific proteins important in heterochromatin formation and possible a role in controlling gene expression. The transcription of satDNA has been described in vertebrates, invertebrates and plants. In insects, differential satDNA expression has been observed in different cells, developmental stages, sex and caste of the individuals. These transcription differences may suggest their involvement in gene-regulation processes. In addition, the satDNA or its transcripts appear to be involved in heterochromatin formation and in chromatin-elimination processes. The importance of transposable elements to insect satDNA is shown by their presence as a constituent of satDNA in several species of insects (including possible active elements). In addition, they may be involved in the formation of centromeres and telomeres and in the homogenization and expansion of satDNA.
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Affiliation(s)
- T Palomeque
- Departamento de Biología Experimental, Area de Genética, Universidad de Jaén, Jaén, Spain.
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Palomeque T, Antonio Carrillo J, Muñoz-López M, Lorite P. Detection of a mariner-like element and a miniature inverted-repeat transposable element (MITE) associated with the heterochromatin from ants of the genus Messor and their possible involvement for satellite DNA evolution. Gene 2006; 371:194-205. [PMID: 16507338 DOI: 10.1016/j.gene.2005.11.032] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Revised: 11/21/2005] [Accepted: 11/28/2005] [Indexed: 11/27/2022]
Abstract
The satellite DNA of ants Messor bouvieri, M. barbarus and M. structor, studied in a previous paper, is organized as tandemly repeated 79-bp monomers in the three species showing high sequence similarity. In the present paper, a mariner-like element (Mboumar) and a new MITE (miniature inverted-repeat transposable element) called IRE-130, inserted into satellite DNA from M. bouvieri, are analyzed. The study of Mboumar element, of its transcription and the putative transposase that it would encode, suggests that it could be an active element. Mboumar elements inserted into IRE-130 elements have also been detected. It is the first time, to our knowledge, that a MITE has been described in Hymenoptera and it is also the first time that a mariner-like element inserted into a MITE has been detected. A mariner-like element, inserted into satellite DNA from M. structor and in M. barbarus, also has been found. The results seem to indicate that transposition events have participated in the satellite DNA mobilization and evolution.
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Affiliation(s)
- Teresa Palomeque
- Departamento de Biología Experimental. Area de Genética. Universidad de Jaén. 23071, Jaén, Spain.
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Mravinac B, Ugarković E, Franjević D, Plohl M. Long inversely oriented subunits form a complex monomer of Tribolium brevicornis satellite DNA. J Mol Evol 2005; 60:513-25. [PMID: 15883886 DOI: 10.1007/s00239-004-0236-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2004] [Accepted: 11/07/2004] [Indexed: 10/25/2022]
Abstract
Highly abundant satellite DNA named TBREV is detected and characterized in the beetle Tribolium brevicornis (Insecta: Coleoptera). An outstanding peculiarity of the TBREV satellite monomer is its complex structure based on the two approximately 470-bp-long subunits, inversely oriented within a 1061-bp-long monomer sequence. The proposed evolutionary history demonstrates a clear trend toward increased complexity and length of the TBREV satellite monomer. This tendency has been observed on three levels: first as direct and inverted duplications of short sequence motifs, then by inverse duplication of the approximately 470-bp sequence segment, and, finally, by spread of inversely duplicated elements in a higher-order register and formation of extant monomers. Inversely oriented subunits share a similarity of 82% and have a high capacity to form a thermodynamically stable dyad structure that is, to our knowledge, the longest ever described in any satellite monomer. Analysis of divergences between inversely oriented subunits shows a tendency to a further reduction in similarity between them. Except in its centromeric localization, the TBREV satellite does not show similarity to other known Tribolium satellites, either in nucleotide sequence or in monomer length and complexity. However, TBREV shares common features of other Tribolium satellites that might be under functional constraints: nonconstant rate of evolution along the monomer sequence, short inverted repeats in the vicinity of an A+T tract, nonrandom distribution of A or T >/=3 tracts, and CENP-B box-like motifs. Although long inverted subunits might reinforce structural characteristics of the satellite monomer, their nucleotide sequence does not seem to be under constraints in order to preserve the dyad structure.
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Affiliation(s)
- Brankica Mravinac
- Department of Molecular Biology, Ruder Bosković Institute, Bijenicka cesta 54,, HR-10002, Zagreb, Croatia
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