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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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Panzera F, Cuadrado Á, Mora P, Palomeque T, Lorite P, Pita S. Differential Spreading of Microsatellites in Holocentric Chromosomes of Chagas Disease Vectors: Genomic and Evolutionary Implications. INSECTS 2023; 14:772. [PMID: 37754740 PMCID: PMC10531928 DOI: 10.3390/insects14090772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/13/2023] [Accepted: 09/17/2023] [Indexed: 09/28/2023]
Abstract
This study focused on analyzing the distribution of microsatellites in holocentric chromosomes of the Triatominae subfamily, insect vectors of Chagas disease. We employed a non-denaturing FISH technique to determine the chromosomal distribution of sixteen microsatellites across twenty-five triatomine species, involving five genera from the two principal tribes: Triatomini and Rhodniini. Three main hybridization patterns were identified: strong signals in specific chromosomal regions, dispersed signals dependent on microsatellite abundance and the absence of signals in certain chromosomal regions or entire chromosomes. Significant variations in hybridization patterns were observed between Rhodniini and Triatomini species. Rhodniini species displayed weak and scattered hybridization signals, indicating a low abundance of microsatellites in their genomes. In contrast, Triatomini species exhibited diverse and abundant hybridization patterns, suggesting that microsatellites are a significant repetitive component in their genomes. One particularly interesting finding was the high abundance of GATA repeats, and to a lesser extent AG repeats, in the Y chromosome of all analyzed Triatomini species. In contrast, the Y chromosome of Rhodniini species did not show enrichment in GATA and AG repeats. This suggests that the richness of GATA repeats on the Y chromosome likely represents an ancestral trait specific to the Triatomini tribe. Furthermore, this information can be used to elucidate the evolutionary relationships between Triatomini and other groups of reduviids, contributing to the understanding of the subfamily's origin. Overall, this study provides a comprehensive understanding of the composition and distribution of microsatellites within Triatominae genomes, shedding light on their significance in the evolutionary processes of these species.
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Affiliation(s)
- Francisco Panzera
- Evolutionary Genetic Section, Faculty of Science, University of the Republic, Iguá 4225, Montevideo 11400, Uruguay;
| | - Ángeles Cuadrado
- Department of Biomedicine and Biotechnology, University of Alcalá (UAH), Alcalá de Henares, 28805 Madrid, Spain;
| | - Pablo Mora
- Department of Experimental Biology, Genetics, University of Jaén, 23071 Jaén, Spain; (P.M.); (T.P.)
| | - Teresa Palomeque
- Department of Experimental Biology, Genetics, University of Jaén, 23071 Jaén, Spain; (P.M.); (T.P.)
| | - Pedro Lorite
- Department of Experimental Biology, Genetics, University of Jaén, 23071 Jaén, Spain; (P.M.); (T.P.)
| | - Sebastián Pita
- Evolutionary Genetic Section, Faculty of Science, University of the Republic, Iguá 4225, Montevideo 11400, Uruguay;
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3
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Boonekamp J, Rodríguez-Muñoz R, Hopwood P, Zuidersma E, Mulder E, Wilson A, Verhulst S, Tregenza T. Telomere length is highly heritable and independent of growth rate manipulated by temperature in field crickets. Mol Ecol 2022; 31:6128-6140. [PMID: 33728719 DOI: 10.1111/mec.15888] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 03/09/2021] [Accepted: 03/12/2021] [Indexed: 01/31/2023]
Abstract
Many organisms are capable of growing faster than they do. Restrained growth rate has functionally been explained by negative effects on lifespan of accelerated growth. However, the underlying mechanisms remain elusive. Telomere attrition has been proposed as a causal agent and has been mostly studied in endothermic vertebrates. We established that telomeres exist as chromosomal-ends in a model insect, the field cricket Gryllus campestris, using terminal restriction fragment and Bal 31 methods. Telomeres comprised TTAGGn repeats of 38 kb on average, more than four times longer than the telomeres of human infants. Bal 31 assays confirmed that telomeric repeats were located at the chromosome-ends. We tested whether rapid growth between day 1, day 65, day 85, and day 125 is achieved at the expense of telomere length by comparing nymphs reared at 23°C with their siblings reared at 28°C, which grew three times faster in the initial 65 days. Surprisingly, neither temperature treatment nor age affected average telomere length. Concomitantly, the broad sense heritability of telomere length was remarkably high at ~100%. Despite high heritability, the evolvability (a mean-standardized measure of genetic variance) was low relative to that of body mass. We discuss our findings in the context of telomere evolution. Some important features of vertebrate telomere biology are evident in an insect species dating back to the Triassic. The apparent lack of an effect of growth rate on telomere length is puzzling, suggesting strong telomere length maintenance during the growth phase. Whether such maintenance of telomere length is adaptive remains elusive and requires further study investigating the links with fitness in the wild.
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Affiliation(s)
- Jelle Boonekamp
- Centre for Ecology & Conservation, School of Biosciences, University of Exeter, Exeter, UK.,Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | | | - Paul Hopwood
- Centre for Ecology & Conservation, School of Biosciences, University of Exeter, Exeter, UK
| | - Erica Zuidersma
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Ellis Mulder
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Alastair Wilson
- Centre for Ecology & Conservation, School of Biosciences, University of Exeter, Exeter, UK
| | - Simon Verhulst
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Tom Tregenza
- Centre for Ecology & Conservation, School of Biosciences, University of Exeter, Exeter, UK
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4
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Teixeira GA, Barros LAC, Silveira LI, Orivel J, Lopes DM, Aguiar HJAC. Karyotype conservation and genomic organization of repetitive sequences in the leaf-cutting ant Atta cephalotes (Linnaeus, 1758) (Formicidae: Myrmicinae). Genome 2022; 65:525-535. [PMID: 35973225 DOI: 10.1139/gen-2021-0129] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Leaf-cutting ants are among the New World's most conspicuous and studied ant species due to their notable ecological and economic role. Cytogenetic studies carried out in Atta show remarkable karyotype conservation among the species. We performed classical cytogenetics and physical mapping of repetitive sequences in the leaf-cutting ant Atta cephalotes, the type species of the genus. Our goal was to test the karyotype conservation in Atta and to start to understand the genomic organization and diversity regarding repetitive sequences in leaf-cutting ants. Atta cephalotes showed 2n=22 (18m+2sm+2st) chromosomes. The heterochromatin followed a centromeric pattern, and the GC-rich regions and 18S rDNA clusters were co-located interstitially in the 4th metacentric pair. These cytogenetic characteristics were observed in other Atta species that had previously been studied, confirming the karyotype conservation in Atta. Evolutionary implications regarding the conservation of the chromosome number in leaf-cutting ants are discussed. Telomeric motif (TTAGG)n was detected in A. cephalotes as observed in other ants. Five out of the 11 microsatellites showed a scattered distribution exclusively on euchromatic areas of the chromosomes. Repetitive sequences mapped on the chromosomes of A. cephalotes are the first insights into genomic organization and diversity in leaf-cutting ants, useful in further comparative studies.
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Vicari MR, Bruschi DP, Cabral-de-Mello DC, Nogaroto V. Telomere organization and the interstitial telomeric sites involvement in insects and vertebrates chromosome evolution. Genet Mol Biol 2022; 45:e20220071. [DOI: 10.1590/1678-4685-gmb-2022-0071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 09/24/2022] [Indexed: 11/16/2022] Open
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6
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Silva AFE, Oliveira TDD, Bertocchi NÁ, Valente VLDS, Zefa E, Deprá M. Study of four Neotropical species of tree crickets Oecanthus Serville, 1831 (Orthoptera, Gryllidae) using cytogenetic and molecular markers. Genet Mol Biol 2022; 45:e20210213. [PMID: 35499272 PMCID: PMC9059253 DOI: 10.1590/1678-4685-gmb-2021-0213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 01/31/2022] [Indexed: 11/28/2022] Open
Abstract
Karyotypes in the worldwide subfamily Oecanthinae show variations in diploid number, chromosome morphology, and sex-chromosome system. This study described the chromosome set and phylogenetic relationships of four Neotropical species, Oecanthus lineolatus, O. valensis, O. pallidus, and O. pictus. We used classical cytogenetics and Bayesian Inference for phylogenetic reconstruction, using the mitochondrial genes COI, 12S rRNA, and 16S rRNA; and analyzed the phylogenetic patterns of changes in chromosome numbers, using ChromEvol. We observed differences in chromosome number among species and two different sex-chromosome systems. Oecanthus pictus showed 2n = 21, X0♂/22, XX♀; O. lineolatus, 2n = 20, XY♂/XX♀; and O. valensis and O. pallidus, 2n = 18, XY♂/XX♀. The karyotype of Oecanthus was asymmetric, one group with large chromosomes and variation in heterochromatin distribution, and another with small acrocentric chromosomes. The phylogenetic tree recovered two main groups: one with the Palearctic species and another with species from different bioregions, but with low posterior probability. The Neotropical species grouped separately, O. valensis and O. pictus with Nearctic and Ethiopian species, and O. pallidus and O. lineolatus in another, well-supported clade. Together, the phylogenic and chromosome data suggest descending dysploidy events during the evolution of the group.
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Affiliation(s)
| | | | | | | | - Edison Zefa
- Universidade Federal de Pelotas, Instituto de Biologia, Brazil
| | - Maríndia Deprá
- Universidade Federal do Rio Grande do Sul, Brazil; Universidade Federal do Rio Grande do Sul, Brazil
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Micolino R, Baldez BCL, Sánchez-Restrepo AF, Calcaterra L, Cristiano MP, Cardoso DC. Karyotype structure and cytogenetic markers of Amoimyrmex bruchi and Amoimyrmex silvestrii: contribution to understanding leaf-cutting ant relationships. Genome 2021; 65:1-9. [PMID: 34520688 DOI: 10.1139/gen-2021-0044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Leaf-cutting ants are considered the most important herbivores in terrestrial environments throughout the Neotropics. Amoimyrmex Cristiano, Cardoso, & Sandoval, 2020 is the sister clade of the remaining leaf-cutting ants from the genera Atta and Acromyrmex. Amoimyrmex striatus was the only species cytogenetically studied within the genus and shares the same chromosomal number as Atta, bearing 22 chromosomes, whereas Acromyrmex bears 38 chromosomes, with the exception of the social parasite Acromyrmex ameliae (2n = 36). Our objective here was to cytogenetically analyze the species of Amoimyrmex bruchi and Amoimyrmex silvestrii, as well as to describe the karyotype of these sister species, using an integrative approach using classical and molecular cytogenetics. We aimed to characterize the cytogenetic markers that contribute to the systematics and taxonomy of the genus. Our results showed that the karyotypes of these two species are very similar, with an identical chromosome number (2n = 22), chromosome morphology (2K = 20m + 2sm), and location of 18S rDNA and telomeric repeat TTAGG on the chromosomes. However, the microsatellite probe GA(15) showed variation across the species and populations studied. We suggest that both species diverged relatively recently and are unmistakably sisters because of the many shared characteristics, including the highly conserved karyotypes.
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Affiliation(s)
- Ricardo Micolino
- Programa de Pós-graduação em Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Brenda Carla Lima Baldez
- Departamento de Biodiversidade, Evolução e Meio Ambiente, Universidade Federal de Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, MG, Brazil
- Programa de Pós-gradução em Ecologia de Biomas Tropicais, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - Andrés F Sánchez-Restrepo
- Fundación para el Estudio de Especies Invasivas (FuEDEI), Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Luis Calcaterra
- Fundación para el Estudio de Especies Invasivas (FuEDEI), Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Maykon Passos Cristiano
- Departamento de Biodiversidade, Evolução e Meio Ambiente, Universidade Federal de Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, MG, Brazil
- Programa de Pós-gradução em Ecologia de Biomas Tropicais, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - Danon Clemes Cardoso
- Programa de Pós-graduação em Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
- Departamento de Biodiversidade, Evolução e Meio Ambiente, Universidade Federal de Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, MG, Brazil
- Programa de Pós-gradução em Ecologia de Biomas Tropicais, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
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8
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Ribeiro T, Nascimento J, Santos A, Félix LP, Guerra M. Origin and evolution of highly polymorphic rDNA sites in Alstroemeria longistaminea (Alstroemeriaceae) and related species. Genome 2021; 64:833-845. [PMID: 33852822 DOI: 10.1139/gen-2020-0159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Alstroemeria (Alstroemeriaceae) displays a conserved and highly asymmetric karyotype, where most rDNA sites can be properly recognized by the size and morphology of the chromosomes. We analyzed the intraspecific variation of rDNA sites in A. longistaminea and compared with their distribution in other species (A. caryophyllaea and A. piauhyensis) and a representative of a sister genus, Bomarea edulis. All three species of Alstroemeria presented 2n = 16, and one to six B chromosomes were found in some individuals of A. longistaminea. There was a set of 12 conserved rDNA sites (four 5S and eight 35S) and up to 11 variable sites. B chromosomes were almost entirely covered by 35S signals, coupled with tiny 5S sites. Noteworthy, most rDNA sites found in A. caryophyllaea and A. piauhyensis were localized in chromosome positions similar to those in A. longistaminea, suggesting the existence of conserved hotspots for rDNA accumulation. Some of these hotspots were absent in Chilean Alstromeria as well in B. edulis. We propose that insertions of rDNA sequences on chromosomes do not occur randomly but rather on preferential sites or hotspots for insertions. The maintenance of these arrays, however, may be favored/constrained by different factors, resulting in stable or polymorphic sites.
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Affiliation(s)
- Tiago Ribeiro
- Laboratório de Citogenética e Evolução Vegetal, Universidade Federal de Pernambuco, Departamento de Botânica, Recife, Pernambuco, Brasil
| | - Jéssica Nascimento
- Laboratório de Citogenética e Evolução Vegetal, Universidade Federal de Pernambuco, Departamento de Botânica, Recife, Pernambuco, Brasil
| | - Amanda Santos
- Laboratório de Citogenética e Evolução Vegetal, Universidade Federal de Pernambuco, Departamento de Botânica, Recife, Pernambuco, Brasil
| | - Leonardo P Félix
- Universidade Federal da Paraíba, Departamento de Biociências, Campus II, Areia, Paraíba, Brasil
| | - Marcelo Guerra
- Laboratório de Citogenética e Evolução Vegetal, Universidade Federal de Pernambuco, Departamento de Botânica, Recife, Pernambuco, Brasil
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Warchałowska-Śliwa E, Grzywacz B, Maryańska-Nadachowska A, Heller KG, Hemp C. Rapid chromosomal evolution in the bush-cricket Gonatoxia helleri Hemp, 2016 (Orthoptera, Phaneropterinae). COMPARATIVE CYTOGENETICS 2020; 14:417-435. [PMID: 32952902 PMCID: PMC7473956 DOI: 10.3897/compcytogen.v14i3.54422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/27/2020] [Indexed: 05/03/2023]
Abstract
Gonatoxia helleri Hemp, 2016 is one of the most widespread bush-crickets of the genus Gonatoxia Karsch, 1889 in East Africa. This species with seven large chromosomes (2n♂ = 7) differs from other representatives of the genus Gonatoxia drastically by its reduced chromosome number, the asymmetrical karyotype including karyomorphs rarely found in tettigoniids, as well as in irregularities in the course of meiosis. To better understand the origin of such an exceptional karyotype, chromosomes of 29 specimens from four populations/localities were studied using classical techniques, such as C-banding, silver impregnation, fluorochrome double staining and fluorescence in situ hybridization (FISH) technique with 18S rDNA and (TTAGG) n telomeric probes. FISH showed many 18S rDNA loci as well as interstitial telomeric sequences, where chromosome morphology varied in these components in terms of quantity and distribution. The 18S rDNA loci coincided with active NORs and C-banding patterns. We suggest that a combination of Robertsonian rearrangements and/or multiple common tandem fusions involving the same chromosomes contributed to the formation of this karyotype/karyomorphs. The results are the first step towards a better understanding of chromosomal reorganization and evolution within the genus Gonatoxia. Low chromosome number, together with the incidence of chromosomal polymorphism that is higher in G. helleri than previously reported in bush-crickets, implies that this species can be a valuable new model for cytogenetic and speciation studies. Our findings suggest that chromosomal translocations lead to diversification and speciation in this species and could be the driving force of adaptive radiation.
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Affiliation(s)
- Elżbieta Warchałowska-Śliwa
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Kraków, PolandPolish Academy of SciencesKrakówPoland
| | - Beata Grzywacz
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Kraków, PolandPolish Academy of SciencesKrakówPoland
| | - Anna Maryańska-Nadachowska
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Kraków, PolandPolish Academy of SciencesKrakówPoland
| | | | - Claudia Hemp
- University of Bayreuth, Dept. Plant Systematics, Bayreuth, GermanyUniversity of BayreuthBayreuthGermany
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10
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Mora P, Vela J, Ruiz-Mena A, Palomeque T, Lorite P. Isolation of a Pericentromeric Satellite DNA Family in Chnootriba argus ( Henosepilachna argus) with an Unusual Short Repeat Unit (TTAAAA) for Beetles. INSECTS 2019; 10:insects10090306. [PMID: 31546864 PMCID: PMC6780895 DOI: 10.3390/insects10090306] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/11/2019] [Accepted: 09/17/2019] [Indexed: 12/30/2022]
Abstract
Ladybird beetles (Coccinellidae) are one of the largest groups of beetles. Among them, some species are of economic interest since they can act as a biological control for some agricultural pests whereas other species are phytophagous and can damage crops. Chnootriba argus (Coccinellidae, Epilachnini) has large heterochromatic pericentromeric blocks on all chromosomes, including both sexual chromosomes. Classical digestion of total genomic DNA using restriction endonucleases failed to find the satellite DNA located on these heterochromatic regions. Cloning of C0t-1 DNA resulted in the isolation of a repetitive DNA with a repeat unit of six base pairs, TTAAAA. The amount of TTAAAA repeat in the C. argus genome was about 20%. Fluorescence in situ hybridization (FISH) analysis and digestion of chromosomes with the endonuclease Tru9I revealed that this repetitive DNA could be considered as the putative pericentromeric satellite DNA (satDNA) in this species. The presence of this satellite DNA was tested in other species of the tribe Epilachnini and it is also present in Epilachna paenulata. In both species, the TTAAAA repeat seems to be the main satellite DNA and it is located on the pericentromeric region on all chromosomes. The size of this satDNA, which has only six base pairs is unusual in Coleoptera satellite DNAs, where satDNAs usually have repeat units of a much larger size. Southern hybridization and FISH proved that this satDNA is conserved in some Epilachnini species but not in others. This result is in concordance with the controversial phylogenetic relationships among the genera of the tribe Epilachnini, where the limits between genera are unclear.
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Affiliation(s)
- Pablo Mora
- Department of Experimental Biology, Genetic Area, University of Jaén, 23071 Jaén, Spain.
| | - Jesús Vela
- Department of Experimental Biology, Genetic Area, University of Jaén, 23071 Jaén, Spain.
| | - Areli Ruiz-Mena
- Department of Experimental Biology, Genetic Area, University of Jaén, 23071 Jaén, Spain.
| | - Teresa Palomeque
- Department of Experimental Biology, Genetic Area, University of Jaén, 23071 Jaén, Spain.
| | - Pedro Lorite
- Department of Experimental Biology, Genetic Area, University of Jaén, 23071 Jaén, Spain.
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11
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Palacios-Gimenez OM, Bardella VB, Lemos B, Cabral-de-Mello DC. Satellite DNAs are conserved and differentially transcribed among Gryllus cricket species. DNA Res 2018; 25:137-147. [PMID: 29096008 PMCID: PMC5909420 DOI: 10.1093/dnares/dsx044] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/19/2017] [Indexed: 11/21/2022] Open
Abstract
Satellite DNA (satDNA) is an abundant class of non-coding repetitive DNA that is preferentially found as tandemly repeated arrays in gene-poor heterochromatin but is also present in gene-rich euchromatin. Here, we used DNA- and RNA-seq from Gryllus assimilis to address the content and transcriptional patterns of satDNAs. We also mapped RNA-seq libraries for other Gryllus species against the satDNAs found in G. assimilis and G. bimaculatus genomes to investigate their evolutionary conservation and transcriptional profiles in Gryllus. Through DNA-seq read clustering analysis using RepeatExplorer, dotplots analysis and fluorescence in situ hybridization mapping, we found that ∼4% of the G. assimilis genome is represented by 11 well-defined A + T-rich satDNA families. These are mainly located in heterochromatic areas, with some repeats able to form high-order repeat structures. By in silico transcriptional analysis we identified satDNAs that are conserved in Gryllus but differentially transcribed. The data regarding satDNA presence in G. assimilis genome were discussed in an evolutionary context, with transcriptional data enabling comparisons between sexes and across tissues when possible. We discuss hypotheses for the conservation and transcription of satDNAs in Gryllus, which might result from their role in sexual differentiation at the chromatin level, heterochromatin formation and centromeric function.
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Affiliation(s)
- Octavio Manuel Palacios-Gimenez
- Departamento de Biologia, Instituto de Biociências/IB, UNESP-Univ Estadual Paulista, Rio Claro, São Paulo, Brazil.,Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard University T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Vanessa Bellini Bardella
- Departamento de Biologia, Instituto de Biociências/IB, UNESP-Univ Estadual Paulista, Rio Claro, São Paulo, Brazil
| | - Bernardo Lemos
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard University T. H. Chan School of Public Health, Boston, MA 02115, USA
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12
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Palacios-Gimenez OM, Milani D, Lemos B, Castillo ER, Martí DA, Ramos E, Martins C, Cabral-de-Mello DC. Uncovering the evolutionary history of neo-XY sex chromosomes in the grasshopper Ronderosia bergii (Orthoptera, Melanoplinae) through satellite DNA analysis. BMC Evol Biol 2018; 18:2. [PMID: 29329524 PMCID: PMC5767042 DOI: 10.1186/s12862-017-1113-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 12/08/2017] [Indexed: 03/26/2023] Open
Abstract
BACKGROUND Neo-sex chromosome systems arose independently multiple times in evolution, presenting the remarkable characteristic of repetitive DNAs accumulation. Among grasshoppers, occurrence of neo-XY was repeatedly noticed in Melanoplinae. Here we analyzed the most abundant tandem repeats of R. bergii (2n = 22, neo-XY♂) using deep Illumina sequencing and graph-based clustering in order to address the neo-sex chromosomes evolution. RESULTS The analyses revealed ten families of satDNAs comprising about ~1% of the male genome, which occupied mainly C-positive regions of autosomes. Regarding the sex chromosomes, satDNAs were recorded within centromeric or interstitial regions of the neo-X chromosome and four satDNAs occurred in the neo-Y, two of them being exclusive (Rber248 and Rber299). Using a combination of probes we uncovered five well-defined cytological variants for neo-Y, originated by multiple paracentric inversions and satDNA amplification, besides fragmented neo-Y. These neo-Y variants were distinct in frequency between embryos and adult males. CONCLUSIONS The genomic data together with cytogenetic mapping enabled us to better understand the neo-sex chromosome dynamics in grasshoppers, reinforcing differentiation of neo-X and neo-Y and revealing the occurrence of multiple additional rearrangements involved in the neo-Y evolution of R. bergii. We discussed the possible causes that led to differences in frequency for the neo-Y variants between embryos and adults. Finally we hypothesize about the role of DNA satellites in R. bergii as well as putative historical events involved in the evolution of the R. bergii neo-XY.
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Affiliation(s)
- Octavio M. Palacios-Gimenez
- Departamento de Biologia, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, São Paulo 13506-900 Brazil
| | - Diogo Milani
- Departamento de Biologia, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, São Paulo 13506-900 Brazil
| | - Bernardo Lemos
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard University T. H. Chan School of Public Health, Boston, Massachusetts 02115 USA
| | | | | | - Erica Ramos
- Departamento de Morfologia, UNESP – Univ Estadual Paulista, Instituto de Biociências/IB, Botucatu, São Paulo Brazil
| | - Cesar Martins
- Departamento de Morfologia, UNESP – Univ Estadual Paulista, Instituto de Biociências/IB, Botucatu, São Paulo Brazil
| | - Diogo C. Cabral-de-Mello
- Departamento de Biologia, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, São Paulo 13506-900 Brazil
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Anjos A, Paladini A, Mariguela TC, Cabral-de-Mello DC. U1 snDNA chromosomal mapping in ten spittlebug species (Cercopidade, Auchenorrhyncha, Hemiptera). Genome 2018; 61:59-62. [DOI: 10.1139/gen-2017-0151] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Spittlebugs, which belong to the family Cercopidae (Auchenorrhyncha, Hemiptera), form a large group of xylem-feeding insects that are best known for causing damage to plantations and pasture grasses. The holocentric chromosomes of these insects remain poorly studied in regards to the organization of different classes of repetitive DNA. To improve chromosomal maps based on repetitive DNAs and to better understand the chromosomal organization and evolutionary dynamics of multigene families in spittlebugs, we physically mapped the U1 snRNA gene with fluorescence in situ hybridization (FISH) in 10 species of Cercopidae belonging to three different genera. All the U1 snDNA clusters were autosomal and located in interstitial position. In seven species, they were restricted to one autosome per haploid genome, while three species of the genus Mahanarva showed two clusters in two different autosomes. Although it was not possible to precisely define the ancestral location of this gene, it was possible to observe the presence of at least one cluster located in a small bivalent in all karyotypes. The karyotype stability observed in Cercopidae is also observed in respect to the distribution of U1 snDNA. Our data are discussed in light of possible mechanisms for U1 snDNA conservation and compared with the available data from other species.
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Affiliation(s)
- Allison Anjos
- Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, SP, Brazil
| | - Andressa Paladini
- Departamento de Ecologia e Evolução, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Tatiane C. Mariguela
- Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, SP, Brazil
| | - Diogo C. Cabral-de-Mello
- Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, SP, Brazil
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Liehr T, Buleu O, Karamysheva T, Bugrov A, Rubtsov N. New Insights into Phasmatodea Chromosomes. Genes (Basel) 2017; 8:genes8110327. [PMID: 29149047 PMCID: PMC5704240 DOI: 10.3390/genes8110327] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/13/2017] [Accepted: 11/13/2017] [Indexed: 12/15/2022] Open
Abstract
Currently, approximately 3000 species of stick insects are known; however, chromosome numbers, which range between 21 and 88, are known for only a few of these insects. Also, centromere banding staining (C-banding) patterns were described for fewer than 10 species, and fluorescence in situ hybridization (FISH) was applied exclusively in two Leptynia species. Interestingly, 10–25% of stick insects (Phasmatodea) are obligatory or facultative parthenogenetic. As clonal and/or bisexual reproduction can affect chromosomal evolution, stick insect karyotypes need to be studied more intensely. Chromosome preparation from embryos of five Phasmatodea species (Medauroidea extradentata, Sungaya inexpectata, Sipyloidea sipylus, Phaenopharos khaoyaiensis, and Peruphasma schultei) from four families were studied here by C-banding and FISH applying ribosomal deoxyribonucleic acid (rDNA) and telomeric repeat probes. For three species, data on chromosome numbers and structure were obtained here for the first time, i.e., S. inexpectata, P. khaoyaiensis, and P. schultei. Large C-positive regions enriched with rDNA were identified in all five studied, distantly related species. Some of these C-positive blocks were enriched for telomeric repeats, as well. Chromosomal evolution of stick insects is characterized by variations in chromosome numbers as well as transposition and amplification of repetitive DNA sequences. Here, the first steps were made towards identification of individual chromosomes in Phasmatodea.
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Affiliation(s)
- Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Am Klinikum 1, D-07747 Jena, Germany.
| | - Olesya Buleu
- Novosibirsk State University, 630090 Novosibirsk, Russia.
| | - Tatyana Karamysheva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia.
| | - Alexander Bugrov
- Novosibirsk State University, 630090 Novosibirsk, Russia.
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia.
| | - Nikolai Rubtsov
- Novosibirsk State University, 630090 Novosibirsk, Russia.
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia.
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15
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Palacios-Gimenez OM, Dias GB, de Lima LG, Kuhn GCES, Ramos É, Martins C, Cabral-de-Mello DC. High-throughput analysis of the satellitome revealed enormous diversity of satellite DNAs in the neo-Y chromosome of the cricket Eneoptera surinamensis. Sci Rep 2017; 7:6422. [PMID: 28743997 PMCID: PMC5527012 DOI: 10.1038/s41598-017-06822-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/19/2017] [Indexed: 12/31/2022] Open
Abstract
Satellite DNAs (satDNAs) constitute large portion of eukaryote genomes, comprising non-protein-coding sequences tandemly repeated. They are mostly found in heterochromatic regions of chromosomes such as around centromere or near telomeres, in intercalary heterochromatin, and often in non-recombining segments of sex chromosomes. We examined the satellitome in the cricket Eneoptera surinamensis (2n = 9, neo-X1X2Y, males) to characterize the molecular evolution of its neo-sex chromosomes. To achieve this, we analyzed illumina reads using graph-based clustering and complementary analyses. We found an unusually high number of 45 families of satDNAs, ranging from 4 bp to 517 bp, accounting for about 14% of the genome and showing different modular structures and high diversity of arrays. FISH mapping revealed that satDNAs are located mostly in C-positive pericentromeric regions of the chromosomes. SatDNAs enrichment was also observed in the neo-sex chromosomes in comparison to autosomes. Especially astonishing accumulation of satDNAs loci was found in the highly differentiated neo-Y, including 39 satDNAs over-represented in this chromosome, which is the greatest satDNAs diversity yet reported for sex chromosomes. Our results suggest possible involvement of satDNAs in genome increasing and in molecular differentiation of the neo-sex chromosomes in this species, contributing to the understanding of sex chromosome composition and evolution in Orthoptera.
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Affiliation(s)
| | - Guilherme Borges Dias
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Leonardo Gomes de Lima
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Érica Ramos
- UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Departamento de Morfologia, Botucatu, São Paulo, Brazil
| | - Cesar Martins
- UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Departamento de Morfologia, Botucatu, São Paulo, Brazil
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16
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Discovery of the youngest sex chromosomes reveals first case of convergent co-option of ancestral autosomes in turtles. Chromosoma 2016; 126:105-113. [DOI: 10.1007/s00412-016-0576-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 01/21/2016] [Accepted: 01/22/2016] [Indexed: 11/27/2022]
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