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Mandrioli M. From Environmental Epigenetics to the Inheritance of Acquired Traits: A Historian and Molecular Perspective on an Unnecessary Lamarckian Explanation. Biomolecules 2023; 13:1077. [PMID: 37509113 PMCID: PMC10377537 DOI: 10.3390/biom13071077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/16/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
In the last decade, it has been suggested that epigenetics may enhance the adaptive possibilities of animals and plants to novel environments and/or habitats and that such epigenetic changes may be inherited from parents to offspring, favoring their adaptation. As a consequence, several Authors called for a shift in the Darwinian paradigm, asking for a neo-Lamarckian view of evolution. Regardless of what will be discovered about the mechanisms of rapid adaptation to environmental changes, the description of epigenetic inheritance as a Lamarckian process is incorrect from a historical point of view and useless at a scientific level. At the same time, even if some examples support the presence of adaptation without the involvement of changes in DNA sequences, in the current scenario no revolution is actually occurring, so we are simply working on a stimulating research program that needs to be developed but that is, at present, completely Darwinian.
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Affiliation(s)
- Mauro Mandrioli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 213/D, 41125 Modena, Italy
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2
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Kalinka A, Achrem M. The distribution pattern of 5-methylcytosine in rye (Secale L.) chromosomes. PLoS One 2020; 15:e0240869. [PMID: 33057421 PMCID: PMC7561101 DOI: 10.1371/journal.pone.0240869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/04/2020] [Indexed: 12/02/2022] Open
Abstract
The rye (Secale L.) genome is large, and it contains many classes of repetitive sequences. Secale species differ in terms of genome size, heterochromatin content, and global methylation level; however, the organization of individual types of sequences in chromosomes is relatively similar. The content of the abundant subtelomeric heterochromatin fraction in rye do not correlate with the global level of cytosine methylation, hence immunofluorescence detection of 5-methylcytosine (5-mC) distribution in metaphase chromosomes was performed. The distribution patterns of 5-methylcytosine in the chromosomes of Secale species/subspecies were generally similar. 5-methylcytosine signals were dispersed along the entire length of the chromosome arms of all chromosomes, indicating high levels of methylation, especially at retrotransposon sequences. 5-mC signals were absent in the centromeric and telomeric regions, as well as in subtelomeric blocks of constitutive heterochromatin, in each of the taxa studied. Pericentromeric domains were methylated, however, there was a certain level of polymorphism in these areas, as was the case with the nucleolus organizer region. Sequence methylation within the region of the heterochromatin intercalary bands were also demonstrated to be heterogenous. Unexpectedly, there was a lack of methylation in rye subtelomeres, indicating that heterochromatin is a very diverse fraction of chromatin, and its epigenetic regulation or potential influence on adjacent regions can be more complex than has conventionally been thought. Like telomeres and centromeres, subtelomeric heterochromatin can has a specific role, and the absence of 5-mC is required to maintain the heterochromatin state.
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Affiliation(s)
- Anna Kalinka
- Institute of Biology, University of Szczecin, Szczecin, Poland
- Molecular Biology and Biotechnology Center, University of Szczecin, Szczecin, Poland
- * E-mail:
| | - Magdalena Achrem
- Institute of Biology, University of Szczecin, Szczecin, Poland
- Molecular Biology and Biotechnology Center, University of Szczecin, Szczecin, Poland
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3
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Abstract
Holocentric chromosomes possess multiple kinetochores along their length rather than the single centromere typical of other chromosomes [1]. They have been described for the first time in cytogenetic experiments dating from 1935 and, since this first observation, the term holocentric chromosome has referred to chromosomes that: i. lack the primary constriction corresponding to centromere observed in monocentric chromosomes [2]; ii. possess multiple kinetochores dispersed along the chromosomal axis so that microtubules bind to chromosomes along their entire length and move broadside to the pole from the metaphase plate [3]. These chromosomes are also termed holokinetic, because, during cell division, chromatids move apart in parallel and do not form the classical V-shaped figures typical of monocentric chromosomes [4–6]. Holocentric chromosomes evolved several times during both animal and plant evolution and are currently reported in about eight hundred diverse species, including plants, insects, arachnids and nematodes [7,8]. As a consequence of their diffuse kinetochores, holocentric chromosomes may stabilize chromosomal fragments favouring karyotype rearrangements [9,10]. However, holocentric chromosome may also present limitations to crossing over causing a restriction of the number of chiasma in bivalents [11] and may cause a restructuring of meiotic divisions resulting in an inverted meiosis [12].
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Affiliation(s)
- Mauro Mandrioli
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Modena, Italy
- * E-mail:
| | - Gian Carlo Manicardi
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Modena, Italy
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Bioinformatics analysis of the network of histone H3 lysine 9 trimethylation in acute myeloid leukaemia. Oncol Rep 2020; 44:543-554. [PMID: 32468066 PMCID: PMC7336454 DOI: 10.3892/or.2020.7627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/06/2020] [Indexed: 12/20/2022] Open
Abstract
Changes in histone H3 lysine 9 trimethylation (H3K9me3) may be related to the development of drug-resistant acute myeloid leukaemia (AML); insights into the network of H3K9me3 may improve patient prognosis. Patient data were derived from the Gene Expression Omnibus (GEO) database and data from AML cells treated with chidamide, a novel benzamide chemical class of histone deacetylase inhibitor (HDACi), in vitro were derived from ChIP-seq. Patients and AML cell data were analysed using GEO2R, GOseq, KOBAS, the STRING database and Cytoscape 3.5.1. We identified several genes related to the upregulation or downregulation of H3K9me3 in AML patients; some of these genes were related to apoptosis, autophagy, and the pathway of cell longevity. AML cells treated with chidamide in vitro showed the same gene changes. The protein interactions in the network did not have significantly more interactions than expected, suggesting the need for more research to identify these interactions. One compelling result from the protein interaction study was that sirtuin 1 (SIRT1) may have an indirect interaction with lysine-specific demethylase 4A (KDM4A). These results help explain alterations of H3K9me3 in AML that may direct further studies aimed at improving patient prognosis. These results may also provide a basis for chidamide as a treatment strategy for AML patients in the future.
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Comparative Analysis of Intra- and Inter-Specific Genomic Variability in the Peach Potato Aphid, Myzus persicae. INSECTS 2019; 10:insects10100368. [PMID: 31652640 PMCID: PMC6835256 DOI: 10.3390/insects10100368] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/09/2019] [Accepted: 10/17/2019] [Indexed: 12/20/2022]
Abstract
The availability of genomic data in the last decade relating to different aphid species has allowed the analysis of the genomic variability occurring among such species, whereas intra-specific variability has hitherto very largely been neglected. In order to analyse the intra-genomic variability in the peach potato aphid, Myzus persicae, comparative analyses were performed revealing several clone-specific gene duplications, together with numerous deletions/rearrangements. Our comparative approach also allowed us to evaluate the synteny existing between the two M. persicae clones tested and between the peach potato aphid and the pea aphid, Acyrthosiphon pisum. Even if part of the observed rearrangements are related to a low quality of some assembled contigs and/or to the high number of contigs present in these aphid genomes, our evidence reveals that aphid clones are genetically more different than expected. These results suggest that the choice of performing genomes sequencing combining different biotypes/populations, as revealed in the case of the soybean aphid, Aphis glycines, is unlikely to be very informative in aphids. Interestingly, it is possible that the holocentric nature of aphid chromosomes favours genome rearrangements that can be successively inherited transgenerationally via the aphid's apomictic (parthenogenetic) mode of reproduction. Lastly, we evaluated the structure of the cluster of genes coding for the five histones (H1, H2A, H2B, H3 and H4) in order to better understand the quality of the two M. persicae genomes and thereby to improve our knowledge of this functionally important gene family.
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Mandrioli M, Melchiori G, Panini M, Chiesa O, Giordano R, Mazzoni E, Manicardi GC. Analysis of the extent of synteny and conservation in the gene order in aphids: A first glimpse from the Aphis glycines genome. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 113:103228. [PMID: 31446034 DOI: 10.1016/j.ibmb.2019.103228] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 07/03/2019] [Accepted: 08/21/2019] [Indexed: 06/10/2023]
Abstract
In the last decade several insect genomes have been sequenced, but for most the chromosomal mapping of the identified scaffolds/annotated genes is not available. The lack of this information makes it difficult to analyse various genetic aspects, including the presence of genome rearrangements and the extent of synteny within and across species. We mapped five multigenic DNA families (major and minor rDNAs, histone gene cluster, esterases and carotenoid desaturases) and seven scaffolds corresponding to 9 Mb of the soybean aphid, Aphis glycines, genome and identified loci spanning the four soybean aphid chromosomes. A comparative analysis of the localization of the annotated A. glycines genes with respect to the peach potato aphid, Myzus persicae, and the fly, Drosophila melanogaster, evidenced a lower degree of synteny between the two aphid species than in the aphid-fly comparison. Only 1.4 genes per syntenic block were observed in aphids in contrast to 2.3 genes per block in flies. This higher chromosomal rearrangement rate in aphids could be explained considering that they possess holocentric chromosomes that can favour the stabilization and inheritance of chromosomal rearrangements. Lastly, our experiments did not detect the presence of chimeric assemblies in the newly available A. glycines biotype 1 genome, differently from what reported in assembled genome of other aphid species, suggesting that chromosomal mapping can be used to ascertain the quality of assembled genomes.
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Affiliation(s)
- Mauro Mandrioli
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Via Campi 213/D, 41125, Modena, Italy.
| | - Giulia Melchiori
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Via Campi 213/D, 41125, Modena, Italy
| | - Michela Panini
- Dipartimento di Scienze delle produzioni vegetali sostenibili, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Olga Chiesa
- Dipartimento di Scienze delle produzioni vegetali sostenibili, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Rosanna Giordano
- Puerto Rico Science, Technology & Research Trust, San Juan, PR, USA; Know Your Bee, Inc., San Juan, PR, USA
| | - Emanuele Mazzoni
- Dipartimento di Scienze delle produzioni vegetali sostenibili, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Gian Carlo Manicardi
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Via Campi 213/D, 41125, Modena, Italy
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Jaquiéry J, Peccoud J, Ouisse T, Legeai F, Prunier-Leterme N, Gouin A, Nouhaud P, Brisson JA, Bickel R, Purandare S, Poulain J, Battail C, Lemaitre C, Mieuzet L, Le Trionnaire G, Simon JC, Rispe C. Disentangling the Causes for Faster-X Evolution in Aphids. Genome Biol Evol 2018; 10:507-520. [PMID: 29360959 PMCID: PMC5798017 DOI: 10.1093/gbe/evy015] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2018] [Indexed: 12/22/2022] Open
Abstract
The faster evolution of X chromosomes has been documented in several species, and results from the increased efficiency of selection on recessive alleles in hemizygous males and/or from increased drift due to the smaller effective population size of X chromosomes. Aphids are excellent models for evaluating the importance of selection in faster-X evolution because their peculiar life cycle and unusual inheritance of sex chromosomes should generally lead to equivalent effective population sizes for X and autosomes. Because we lack a high-density genetic map for the pea aphid, whose complete genome has been sequenced, we first assigned its entire genome to the X or autosomes based on ratios of sequencing depth in males (X0) to females (XX). Then, we computed nonsynonymous to synonymous substitutions ratios (dN/dS) for the pea aphid gene set and found faster evolution of X-linked genes. Our analyses of substitution rates, together with polymorphism and expression data, showed that relaxed selection is likely to be the greatest contributor to faster-X because a large fraction of X-linked genes are expressed at low rates and thus escape selection. Yet, a minor role for positive selection is also suggested by the difference between substitution rates for X and autosomes for male-biased genes (but not for asexual female-biased genes) and by lower Tajima’s D for X-linked compared with autosomal genes with highly male-biased expression patterns. This study highlights the relevance of organisms displaying alternative chromosomal inheritance to the understanding of forces shaping genome evolution.
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Affiliation(s)
- Julie Jaquiéry
- INRA UMR IGEPP Domaine de la Motte, Le Rheu, France.,CNRS UMR 6553 ECOBIO, Université de Rennes 1, France
| | - Jean Peccoud
- CNRS UMR 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, France
| | | | - Fabrice Legeai
- INRA UMR IGEPP Domaine de la Motte, Le Rheu, France.,INRIA Centre Rennes - Bretagne Atlantique, GenOuest, Rennes, France
| | | | - Anais Gouin
- INRA UMR IGEPP Domaine de la Motte, Le Rheu, France.,INRIA Centre Rennes - Bretagne Atlantique, GenOuest, Rennes, France
| | - Pierre Nouhaud
- Institute of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | | | - Ryan Bickel
- Department of Biology, University of Rochester
| | - Swapna Purandare
- Multidisciplinary Center for Advance Research and Studies (MCARS), Jamia Millia Islamia, New Delhi, India
| | - Julie Poulain
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Christophe Battail
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Centre National de Génotypage (CNG), Evry, France
| | - Claire Lemaitre
- INRIA Centre Rennes - Bretagne Atlantique, GenOuest, Rennes, France
| | | | | | | | - Claude Rispe
- BIOEPAR, INRA, ONIRIS, La Chantrerie, Nantes, France
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Alvarenga EM, Rodrigues VL, Moraes AS, Naves LS, Mondin M, Felisbino MB, Mello MLS. Histone epigenetic marks in heterochromatin and euchromatin of the Chagas' disease vector, Triatoma infestans. Acta Histochem 2016; 118:401-12. [PMID: 27079857 DOI: 10.1016/j.acthis.2016.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 03/31/2016] [Accepted: 04/05/2016] [Indexed: 01/23/2023]
Abstract
Triatoma infestans, a vector of Chagas' disease, shows several particular cell biology characteristics, including the presence of conspicuous heterochromatic bodies (chromocenters) where DNA methylation has not been previously detected. Whether histone modifications contribute to the condensed state of these bodies has not yet been studied. Here, we investigated epigenetic modifications of histones H3 and H4 and presence of the non-histone heterochromatin protein (HP1-α) in the chromocenters and euchromatin of T. infestans cell nuclei, using immunocytochemistry. The effect of different concentrations of the histone deacetylase inhibitors valproic acid (VPA) and sodium butyrate (NaBt) on chromocenter condensation was visually examined; in VPA-treated specimens, this effect was also analyzed by image analysis. Trimethylated H3K9 signals, which were revealed in chromocenter and non-chromocenter areas, were strongest in chromocenters, whereas selected acetylated histone marks and mono- and dimethylated H3K9 and H4K20 signals were detected only in euchromatin. Weak trimethylated H4K20 signals and variable distribution of HP1-α were detected in chromocenters of part of the cellular population analyzed. Although specific VPA and NaBt treatment conditions affected the heterochromatin condensation pattern, they did not induce a decrease in survival and molting rates of the T. infestans nymphs. The VPA-induced chromatin remodeling was not accompanied by induction of H3K9 acetylation in chromocenters. Present findings regarding histone modifications and effects following VPA or NaBt treatments did not yet solve the question of which factors are responsible for maintenance of the condensed state of chromocenters in T. infestans. A possibility requiring further investigation remains on histone methylation marks and/or non-histone proteins.
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Kuznetsova V, Aguin-Pombo D. Comparative cytogenetics of Auchenorrhyncha (Hemiptera, Homoptera): a review. Zookeys 2015:63-93. [PMID: 26807037 PMCID: PMC4722918 DOI: 10.3897/zookeys.538.6724] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 10/25/2015] [Indexed: 11/12/2022] Open
Abstract
A comprehensive review of cytogenetic features is provided for the large hemipteran suborder Auchenorrhyncha, which currently contains approximately 42,000 valid species. This review is based on the analysis of 819 species, 483 genera, and 31 families representing all presently recognized Auchenorrhyncha superfamilies, e.i. Cicadoidea (cicadas), Cercopoidea (spittle bugs), Membracoidea (leafhoppers and treehoppers), Myerslopioidea (ground-dwelling leafhoppers), and Fulgoroidea (planthoppers). History and present status of chromosome studies are described, as well as the structure of chromosomes, chromosome counts, trends and mechanisms of evolution of karyotypes and sex determining systems, their variation at different taxonomic levels and most characteristic (modal) states, occurrence of parthenogenesis, polyploidy, B-chromosomes and chromosome rearrangements, and methods used for cytogenetic analysis of Auchenorrhyncha.
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Affiliation(s)
- Valentina Kuznetsova
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, Universitetskaya nab. 1, 199034 St. Petersburg, Russia; Saint Petersburg Scientific Center, Universitetskaya nab. 5, 199034, St. Petersburg, Russia
| | - Dora Aguin-Pombo
- University of Madeira, 9000-390 Funchal, Madeira Il., Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), Vairão, Portugal
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Fablet M, Vieira C. Evolvability, epigenetics and transposable elements. Biomol Concepts 2015; 2:333-41. [PMID: 25962041 DOI: 10.1515/bmc.2011.035] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 07/11/2011] [Indexed: 12/31/2022] Open
Abstract
Evolvability can be defined as the capacity of an individual to evolve and thus to capture adaptive mutations. Transposable elements (TE) are an important source of mutations in organisms. Their capacity to transpose within a genome, sometimes at a high rate, and their copy number regulation are environment-sensitive, as are the epigenetic pathways that mediate TE regulation in a genome. In this review we revisit the way we see evolvability with regard to transposable elements and epigenetics.
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Integrative Genomic Approaches to Studying Epigenetic Mechanisms of Phenotypic Plasticity in the Aphid. SHORT VIEWS ON INSECT GENOMICS AND PROTEOMICS 2015. [DOI: 10.1007/978-3-319-24235-4_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Manicardi GC, Mandrioli M, Blackman RL. The cytogenetic architecture of the aphid genome. Biol Rev Camb Philos Soc 2014; 90:112-25. [PMID: 24593177 DOI: 10.1111/brv.12096] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 02/04/2014] [Accepted: 02/07/2014] [Indexed: 12/28/2022]
Abstract
In recent years aphids, with their well-defined polyphenism, have become favoured as model organisms for the study of epigenetic processes. The availability of the pea aphid (Acyrthosiphon pisum) genome sequence has engendered much research aimed at elucidating the mechanisms by which the phenotypic plasticity of aphids is inherited and controlled. Yet so far this research effort has paid little attention to the cytogenetic processes that play a vital part in the organisation, expression and inheritance of the aphid genome. Aphids have holocentric chromosomes, which have very different properties from the chromosomes with localised centromeres that are found in most other organisms. Here we review the diverse forms of aphid chromosome behaviour that occur during sex determination and male and female meiosis, often in response to environmental changes and mediated by endocrine factors. Remarkable differences occur, even between related species, that could have significant effects on the inheritance of all or parts of the genome. In relation to this, we review the particular features of the distribution of heterochromatin, rDNA genes and other repetitive DNA in aphid chromosomes, and discuss the part that these may play in the epigenetic modification of chromatin structure and function.
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Affiliation(s)
- Gian Carlo Manicardi
- Department of Life Sciences, University of Modena and Reggio Emilia, Besta Building, via Amendola 2, 42122, Reggio Emilia, Italy
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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: 1.3] [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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Mon H, Lee JM, Mita K, Goldsmith MR, Kusakabe T. Chromatin-induced spindle assembly plays an important role in metaphase congression of silkworm holocentric chromosomes. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2014; 45:40-50. [PMID: 24291286 DOI: 10.1016/j.ibmb.2013.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 11/19/2013] [Accepted: 11/21/2013] [Indexed: 06/02/2023]
Abstract
The kinetochore plays important roles in cell cycle progression. Interactions between chromosomes and spindle microtubules allow chromosomes to congress to the middle of the cell and to segregate the sister chromatids into daughter cells in mitosis. The chromosome passenger complex (CPC), composed of the Aurora B kinase and its regulatory subunits INCENP, Survivin, and Borealin, plays multiple roles in these chromosomal events. In the genome of the silkworm, Bombyx mori, which has holocentric chromosomes, the CPC components and their molecular interactions were highly conserved. In contrast to monocentric species, however, the silkworm CPC co-localized with the chromatin-driven spindles on the upper side of prometaphase chromosomes without forming bipolar mitotic spindles. Depletion of the CPC by RNAi arrested the cell cycle progression at prometaphase and disrupted the microtubule network of the chromatin-driven spindles. Interestingly, depletion of mitotic centromere-associated kinesin (MCAK) recovered formation of the microtubule network but did not overcome the cell cycle arrest at prometaphase. These results suggest that the CPC modulates the chromatin-induced spindle assembly and metaphase congression of silkworm holocentric chromosomes.
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Affiliation(s)
- Hiroaki Mon
- Laboratory of Silkworm Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Hakozaki 6-10-1, Higashi-ku, Fukuoka 812-8581, Japan
| | - Jae Man Lee
- Laboratory of Silkworm Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Hakozaki 6-10-1, Higashi-ku, Fukuoka 812-8581, Japan
| | - Kazuei Mita
- Laboratory of Molecular Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500001, India
| | - Marian R Goldsmith
- Biological Sciences Department, University of Rhode Island, Kingston, RI 02881, USA
| | - Takahiro Kusakabe
- Laboratory of Silkworm Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Hakozaki 6-10-1, Higashi-ku, Fukuoka 812-8581, Japan.
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Jaquiéry J, Rispe C, Roze D, Legeai F, Le Trionnaire G, Stoeckel S, Mieuzet L, Da Silva C, Poulain J, Prunier-Leterme N, Ségurens B, Tagu D, Simon JC. Masculinization of the x chromosome in the pea aphid. PLoS Genet 2013; 9:e1003690. [PMID: 23950732 PMCID: PMC3738461 DOI: 10.1371/journal.pgen.1003690] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 06/17/2013] [Indexed: 11/18/2022] Open
Abstract
Evolutionary theory predicts that sexually antagonistic mutations accumulate differentially on the X chromosome and autosomes in species with an XY sex-determination system, with effects (masculinization or feminization of the X) depending on the dominance of mutations. Organisms with alternative modes of inheritance of sex chromosomes offer interesting opportunities for studying sexual conflicts and their resolution, because expectations for the preferred genomic location of sexually antagonistic alleles may differ from standard systems. Aphids display an XX/X0 system and combine an unusual inheritance of the X chromosome with the alternation of sexual and asexual reproduction. In this study, we first investigated theoretically the accumulation of sexually antagonistic mutations on the aphid X chromosome. Our results show that i) the X is always more favourable to the spread of male-beneficial alleles than autosomes, and should thus be enriched in sexually antagonistic alleles beneficial for males, ii) sexually antagonistic mutations beneficial for asexual females accumulate preferentially on autosomes, iii) in contrast to predictions for standard systems, these qualitative results are not affected by the dominance of mutations. Under the assumption that sex-biased gene expression evolves to solve conflicts raised by the spread of sexually antagonistic alleles, one expects that male-biased genes should be enriched on the X while asexual female-biased genes should be enriched on autosomes. Using gene expression data (RNA-Seq) in males, sexual females and asexual females of the pea aphid, we confirm these theoretical predictions. Although other mechanisms than the resolution of sexual antagonism may lead to sex-biased gene expression, we argue that they could hardly explain the observed difference between X and autosomes. On top of reporting a strong masculinization of the aphid X chromosome, our study highlights the relevance of organisms displaying an alternative mode of sex chromosome inheritance to understanding the forces shaping chromosome evolution.
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Affiliation(s)
- Julie Jaquiéry
- INRA, UMR 1349, Institute of Genetics, Environment and Plant Protection, Domaine de la Motte, Le Rheu, France.
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16
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Bickel RD, Dunham JP, Brisson JA. Widespread selection across coding and noncoding DNA in the pea aphid genome. G3 (BETHESDA, MD.) 2013; 3:993-1001. [PMID: 23589520 PMCID: PMC3689810 DOI: 10.1534/g3.113.005793] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 04/08/2013] [Indexed: 12/03/2022]
Abstract
Genome-wide patterns of diversity and selection are critical measures for understanding how evolution has shaped the genome. Yet, these population genomic estimates are available for only a limited number of model organisms. Here we focus on the population genomics of the pea aphid (Acyrthosiphon pisum). The pea aphid is an emerging model system that exhibits a range of intriguing biological traits not present in classic model systems. We performed low-coverage genome resequencing of 21 clonal pea aphid lines collected from alfalfa host plants in North America to characterize genome-wide patterns of diversity and selection. We observed an excess of low-frequency polymorphisms throughout coding and noncoding DNA, which we suggest is the result of a founding event and subsequent population expansion in North America. Most gene regions showed lower levels of Tajima's D than synonymous sites, suggesting that the majority of the genome is not evolving neutrally but rather exhibits significant constraint. Furthermore, we used the pea aphid's unique manner of X-chromosome inheritance to assign genomic scaffolds to either autosomes or the X chromosome. Comparing autosomal vs. X-linked sequence variation, we discovered that autosomal genes show an excess of low frequency variants indicating that purifying selection acts more efficiently on the X chromosome. Overall, our results provide a critical first step in characterizing the genetic diversity and evolutionary pressures on an aphid genome.
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Affiliation(s)
- Ryan D Bickel
- University of Nebraska, School of Biological Sciences, Lincoln, Nebraska 68588, USA.
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17
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Srinivasan DG, Brisson JA. Aphids: a model for polyphenism and epigenetics. GENETICS RESEARCH INTERNATIONAL 2012; 2012:431531. [PMID: 22567389 PMCID: PMC3335499 DOI: 10.1155/2012/431531] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 12/01/2011] [Indexed: 01/21/2023]
Abstract
Environmental conditions can alter the form, function, and behavior of organisms over short and long timescales, and even over generations. Aphid females respond to specific environmental cues by transmitting signals that have the effect of altering the development of their offspring. These epigenetic phenomena have positioned aphids as a model for the study of phenotypic plasticity. The molecular basis for this epigenetic inheritance in aphids and how this type of inheritance system could have evolved are still unanswered questions. With the availability of the pea aphid genome sequence, new genomics technologies, and ongoing genomics projects in aphids, these questions can now be addressed. Here, we review epigenetic phenomena in aphids and recent progress toward elucidating the molecular basis of epigenetics in aphids. The discovery of a functional DNA methylation system, functional small RNA system, and expanded set of chromatin modifying genes provides a platform for analyzing these pathways in the context of aphid plasticity. With these tools and further research, aphids are an emerging model system for studying the molecular epigenetics of polyphenisms.
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Affiliation(s)
| | - Jennifer A. Brisson
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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18
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Maryańska-Nadachowska A, Kuznetsova VG, Lachowska D, Drosopoulos S. Mediterranean species of the spittlebug genus Philaenus: modes of chromosome evolution. JOURNAL OF INSECT SCIENCE (ONLINE) 2012; 12:54. [PMID: 22963598 PMCID: PMC3476953 DOI: 10.1673/031.012.5401] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 08/26/2011] [Indexed: 05/08/2023]
Abstract
The evolution of karyotypes and sex determination system of Philaenus Stål (Auchenorrhyncha: Aphrophoridae) species is studied here in detail. The most plausible scenario of chromosomal rearrangements accompanying phylogenetic differentiation in Philaenus is advanced. It is postulated that the ancestral karyotype of Philaenus was 2n = 24 + X0. Karyotype changes occurred several times independently in the genus. The karyotype of 2n = 22 + X0 (P. spumarius and P. tesselatus) originated from 2n = 24 + X0 by fusion between two autosomal pairs. The neo-XY system (P. arslani, P. loukasi, P. signatus, P. maghresignus, and P. tarifa) also originated from the 24 + X0 karyotype by means of independent fusions between autosomes and the original X chromosome. The neo-X(1)X(2)Y system (P. italosignus) evolved from the 2n = 22 + neo-XY karyotype by an additional fusion between the Y chromosome and one more autosomal pair. The neo-X(n)Y system of P. italosignus is the first reported case of an evolutionarily fixed multiple sex chromosome system in Auchenorrhyncha.
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Affiliation(s)
| | | | - Dorota Lachowska
- Department of Entomology, Institute of Zoology, Jagiellonian University, Poland
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19
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Jaquiéry J, Stoeckel S, Rispe C, Mieuzet L, Legeai F, Simon JC. Accelerated evolution of sex chromosomes in aphids, an x0 system. Mol Biol Evol 2011; 29:837-47. [PMID: 21998277 DOI: 10.1093/molbev/msr252] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Sex chromosomes play a role in many important biological processes, including sex determination, genomic conflicts, imprinting, and speciation. In particular, they exhibit several unusual properties such as inheritance pattern, hemizygosity, and reduced recombination, which influence their response to evolutionary factors (e.g., drift, selection, and demography). Here, we examine the evolutionary forces driving X chromosome evolution in aphids, an XO system where females are homozygous (XX) and males are hemizygous (X0) at sex chromosomes. We show by simulations that the unusual mode of transmission of the X chromosome in aphids, coupled with cyclical parthenogenesis, results in similar effective population sizes and predicted levels of genetic diversity for X chromosomes and autosomes under neutral evolution. These results contrast with expectations from standard XX/XY or XX/X0 systems (where the effective population size of the X is three-fourths that of autosomes) and have deep consequences for aphid X chromosome evolution. We then localized 52 microsatellite markers on the X and 351 on autosomes. We genotyped 167 individuals with 356 of these loci and found similar levels of allelic richness on the X and on the autosomes, as predicted by our simulations. In contrast, we detected higher dN and dN/dS ratio for X-linked genes compared with autosomal genes, a pattern compatible with either positive or relaxed selection. Given that both types of chromosomes have similar effective population sizes and that the single copy of the X chromosome of male aphids exposes its recessive genes to selection, some degree of positive selection seems to best explain the higher rates of evolution of X-linked genes. Overall, this study highlights the particular relevance of aphids to study the evolutionary factors driving sex chromosomes and genome evolution.
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Affiliation(s)
- Julie Jaquiéry
- Institut National de Recherche Agronomique (INRA), Unité Mixte de Recherche 1099, Biology of Organisms and Populations Applied to Plant Protection, Le Rheu, France.
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20
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Stanojcic S, Gimenez S, Permal E, Cousserans F, Quesneville H, Fournier P, d'Alençon E. Correlation of LNCR rasiRNAs expression with heterochromatin formation during development of the holocentric insect Spodoptera frugiperda. PLoS One 2011; 6:e24746. [PMID: 21980354 PMCID: PMC3184123 DOI: 10.1371/journal.pone.0024746] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Accepted: 08/16/2011] [Indexed: 01/30/2023] Open
Abstract
Repeat-associated small interfering RNAs (rasiRNAs) are derived from various genomic repetitive elements and ensure genomic stability by silencing endogenous transposable elements. Here we describe a novel subset of 46 rasiRNAs named LNCR rasiRNAs due to their homology with one long non-coding RNA (LNCR) of Spodoptera frugiperda. LNCR operates as the intermediate of an unclassified transposable element (TE-LNCR). TE-LNCR is a very invasive transposable element, present in high copy numbers in the S. frugiperda genome. LNCR rasiRNAs are single-stranded RNAs without a prominent nucleotide motif, which are organized in two distinct, strand-specific clusters. The expression of LNCR and LNCR rasiRNAs is developmentally regulated. Formation of heterochromatin in the genomic region where three copies of the TE-LNCR are embedded was followed by chromatin immunoprecipitation (ChIP) and we observed this chromatin undergo dynamic changes during development. In summary, increased LNCR expression in certain developmental stages is followed by the appearance of a variety of LNCR rasiRNAs which appears to correlate with subsequent accumulation of a heterochromatic histone mark and silencing of the genomic region with TE-LNCR. These results support the notion that a repeat-associated small interfering RNA pathway is linked to heterochromatin formation and/or maintenance during development to establish repression of the TE-LNCR transposable element. This study provides insights into the rasiRNA silencing pathway and its role in the formation of fluctuating heterochromatin during the development of one holocentric organism.
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Affiliation(s)
| | - Sylvie Gimenez
- UMR1333 INRA, Université Montpellier II, Montpellier, France
| | - Emmanuelle Permal
- UR1164, INRA, Centre de Recherche de Versailles, bât.18, RD10, Versailles, France
| | | | - Hadi Quesneville
- UR1164, INRA, Centre de Recherche de Versailles, bât.18, RD10, Versailles, France
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21
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Mandrioli M, Azzoni P, Lombardo G, Manicardi GC. Composition and epigenetic markers of heterochromatin in the aphid Aphis nerii (Hemiptera: Aphididae). Cytogenet Genome Res 2011; 133:67-77. [PMID: 21273762 DOI: 10.1159/000323510] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2010] [Indexed: 11/19/2022] Open
Abstract
A detailed karyotype analysis of the oleander aphid Aphis nerii focusing on the distribution, molecular composition and epigenetic modifications of heterochromatin was done in order to better understand the structure and evolution of holocentric/holokinetic chromosomes in aphids. The female karyotype (2n = 8) consisted of 3 pairs of autosomes and a pair of X chromosomes that were the longest elements in the karyotype and carried a single, terminally located nucleolar organizer region. Males showed 2n = 7 chromosomes due to the presence of a single X chromosome. Heterochromatin was located in the X chromosomes only and consisted of 4 satellite DNAs that have been identified. A. nerii constitutive heterochromatin was enriched in mono-, di- and tri-methylated H3 histones and HP1 proteins but, interestingly, it lacked DNA methylation that was widespread in euchromatic chromosomal regions. These results suggest that aphid heterochromatin is assembled and condensed without any involvement of DNA methylation.
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Affiliation(s)
- M Mandrioli
- Dipartimento di Biologia, Università di Modena e Reggio Emilia, Modena, Italia.
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22
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Single base-resolution methylome of the silkworm reveals a sparse epigenomic map. Nat Biotechnol 2010; 28:516-20. [PMID: 20436463 DOI: 10.1038/nbt.1626] [Citation(s) in RCA: 236] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Accepted: 03/23/2010] [Indexed: 12/30/2022]
Abstract
Epigenetic regulation in insects may have effects on diverse biological processes. Here we survey the methylome of a model insect, the silkworm Bombyx mori, at single-base resolution using Illumina high-throughput bisulfite sequencing (MethylC-Seq). We conservatively estimate that 0.11% of genomic cytosines are methylcytosines, all of which probably occur in CG dinucleotides. CG methylation is substantially enriched in gene bodies and is positively correlated with gene expression levels, suggesting it has a positive role in gene transcription. We find that transposable elements, promoters and ribosomal DNAs are hypomethylated, but in contrast, genomic loci matching small RNAs in gene bodies are densely methylated. This work contributes to our understanding of epigenetics in insects, and in contrast to previous studies of the highly methylated genomes of Arabidopsis and human, demonstrates a strategy for sequencing the epigenomes of organisms such as insects that have low levels of methylation.
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Walsh TK, Brisson JA, Robertson HM, Gordon K, Jaubert-Possamai S, Tagu D, Edwards OR. A functional DNA methylation system in the pea aphid, Acyrthosiphon pisum. INSECT MOLECULAR BIOLOGY 2010; 19 Suppl 2:215-28. [PMID: 20482652 DOI: 10.1111/j.1365-2583.2009.00974.x] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Methylation of cytosine is one of the main epigenetic mechanisms involved in controlling gene expression. Here we show that the pea aphid (Acyrthosiphon pisum) genome possesses homologues to all the DNA methyltransferases found in vertebrates, and that 0.69% (+/-0.25%) of all cytosines are methylated. Identified methylation sites are predominantly restricted to the coding sequence of genes at CpG sites. We identify twelve methylated genes, including genes that interact with juvenile hormone, a key endocrine signal in insects. Bioinformatic prediction using CpG ratios for all predicted genes suggest that a large proportion of genes are methylated within the pea aphid.
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Affiliation(s)
- T K Walsh
- CSIRO Entomology, Centre for Environment and Life Sciences, Floreat Park, WA, Australia.
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24
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Krauss V, Eisenhardt C, Unger T. The genome of the stick insect Medauroidea extradentata is strongly methylated within genes and repetitive DNA. PLoS One 2009; 4:e7223. [PMID: 19787064 PMCID: PMC2747282 DOI: 10.1371/journal.pone.0007223] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Accepted: 09/05/2009] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Cytosine DNA methylation has been detected in many eukaryotic organisms and has been shown to play an important role in development and disease of vertebrates including humans. Molecularly, DNA methylation appears to be involved in the suppression of initiation or of elongation of transcription. Resulting organismal functions are suggested to be the regulation of gene silencing, the suppression of transposon activity and the suppression of initiation of transcription within genes. However, some data concerning the distribution of methylcytosine in insect species appear to contradict such roles. PRINCIPAL FINDINGS By comparison of MspI and HpaII restriction patterns in genomic DNA of several insects we show that stick insects (Phasmatodea) have highly methylated genomes. We isolated methylated DNA fragments from the Vietnamese Walking Stick Medauroidea extradentata (formerly known as Baculum extradentatum) and demonstrated that most of the corresponding sequences are repetitive. Bisulfite sequencing of one of these fragments and of parts of conserved protein-coding genes revealed a methylcytosine content of 12.6%, mostly found at CpG, but also at CpT and CpA dinucleotides. Corresponding depletions of CpG and enrichments of TpG and CpA dinucleotides in some highly conserved protein-coding genes of Medauroidea reach a similar degree as in vertebrates and show that CpG methylation has occurred in the germline of these insects. CONCLUSIONS Using four different methods, we demonstrate that the genome of Medauroidea extradentata is strongly methylated. Both repetitive DNA and coding genes appear to contain high levels of methylcytosines. These results argue for similar functions of DNA methylation in stick insects as those already known for vertebrates.
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Affiliation(s)
- Veiko Krauss
- Department of Genetics, Institute of Biology II, University of Leipzig, Leipzig, Germany.
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