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Zhou Y, Wang Y, Xiong X, Appel AG, Zhang C, Wang X. Profiles of telomeric repeats in Insecta reveal diverse forms of telomeric motifs in Hymenopterans. Life Sci Alliance 2022; 5:5/7/e202101163. [PMID: 35365574 PMCID: PMC8977481 DOI: 10.26508/lsa.202101163] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 12/23/2022] Open
Abstract
Telomeres consist of highly conserved simple tandem telomeric repeat motif (TRM): (TTAGG)n in arthropods, (TTAGGG)n in vertebrates, and (TTTAGGG)n in most plants. TRM can be detected from chromosome-level assembly, which typically requires long-read sequencing data. To take advantage of short-read data, we developed an ultra-fast Telomeric Repeats Identification Pipeline and evaluated its performance on 91 species. With proven accuracy, we applied Telomeric Repeats Identification Pipeline in 129 insect species, using 7 Tbp of short-read sequences. We confirmed (TTAGG)n as the TRM in 19 orders, suggesting it is the ancestral form in insects. Systematic profiling in Hymenopterans revealed a diverse range of TRMs, including the canonical 5-bp TTAGG (bees, ants, and basal sawflies), three independent losses of tandem repeat form TRM (Ichneumonoids, hunting wasps, and gall-forming wasps), and most interestingly, a common 8-bp (TTATTGGG)n in Chalcid wasps with two 9-bp variants in the miniature wasp (TTACTTGGG) and fig wasps (TTATTGGGG). Our results identified extraordinary evolutionary fluidity of Hymenopteran TRMs, and rapid evolution of TRM and repeat abundance at all evolutionary scales, providing novel insights into telomere evolution.
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Affiliation(s)
- Yihang Zhou
- Fundamental Research Center, Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), School of Life Sciences and Technology, Tongji University, Shanghai, China.,Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA.,Auburn University Center for Advanced Science, Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn, AL, USA
| | - Yi Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Xiao Xiong
- Fundamental Research Center, Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), School of Life Sciences and Technology, Tongji University, Shanghai, China.,Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA.,Auburn University Center for Advanced Science, Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn, AL, USA
| | - Arthur G Appel
- Auburn University Center for Advanced Science, Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn, AL, USA.,Department of Entomology and Plant Pathology, Auburn University, AL, USA
| | - Chao Zhang
- Fundamental Research Center, Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xu Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA.,Auburn University Center for Advanced Science, Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn, AL, USA.,Department of Entomology and Plant Pathology, Auburn University, AL, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
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2
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Kuznetsova VG, Gavrilov-Zimin IA, Grozeva SM, Golub NV. Comparative analysis of chromosome numbers and sex chromosome systems in Paraneoptera (Insecta). COMPARATIVE CYTOGENETICS 2021; 15:279-327. [PMID: 34616525 PMCID: PMC8490342 DOI: 10.3897/compcytogen.v15.i3.71866] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/06/2021] [Indexed: 05/28/2023]
Abstract
This article is part (the 4th article) of the themed issue (a monograph) "Aberrant cytogenetic and reproductive patterns in the evolution of Paraneoptera". The purpose of this article is to consider chromosome structure and evolution, chromosome numbers and sex chromosome systems, which all together constitute the chromosomal basis of reproduction and are essential for reproductive success. We are based on our own observations and literature data available for all major lineages of Paraneoptera including Zoraptera (angel insects), Copeognatha (=Psocoptera; bark lice), Parasita (=Phthiraptera s. str; true lice), Thysanoptera (thrips), Homoptera (scale insects, aphids, jumping plant-lice, whiteflies, and true hoppers), Heteroptera (true bugs), and Coleorrhyncha (moss bugs). Terminology, nomenclature, classification, and the study methods are given in the first paper of the issue (Gavrilov-Zimin et al. 2021).
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Affiliation(s)
- Valentina G. Kuznetsova
- Zoological Institute, Russian Academy of Sciences, Universitetskaya emb. 1, St. Petersburg, 199034, RussiaZoological Institute, Russian Academy of SciencesSt. PetersburgRussia
| | - Ilya A. Gavrilov-Zimin
- Zoological Institute, Russian Academy of Sciences, Universitetskaya emb. 1, St. Petersburg, 199034, RussiaZoological Institute, Russian Academy of SciencesSt. PetersburgRussia
| | - Snejana M. Grozeva
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Blvd Tsar Osvoboditel 1, Sofia 1000, BulgariaInstitute of Biodiversity and Ecosystem Research, Bulgarian Academy of SciencesSofiaBulgaria
| | - Natalia V. Golub
- Zoological Institute, Russian Academy of Sciences, Universitetskaya emb. 1, St. Petersburg, 199034, RussiaZoological Institute, Russian Academy of SciencesSt. PetersburgRussia
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3
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Cavalcante MG, Nagamachi CY, Pieczarka JC, Noronha RCR. Evolutionary insights in Amazonian turtles (Testudines, Podocnemididae): co-location of 5S rDNA and U2 snRNA and wide distribution of Tc1/Mariner. Biol Open 2020; 9:bio049817. [PMID: 32229487 PMCID: PMC7197720 DOI: 10.1242/bio.049817] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/18/2020] [Indexed: 12/29/2022] Open
Abstract
Eukaryotic genomes exhibit substantial accumulation of repetitive DNA sequences. These sequences can participate in chromosomal reorganization events and undergo molecular cooption to interfere with the function and evolution of genomes. In turtles, repetitive DNA sequences appear to be accumulated at probable break points and may participate in events such as non-homologous recombination and chromosomal rearrangements. In this study, repeated sequences of 5S rDNA, U2 snRNA and Tc1/Mariner transposons were amplified from the genomes of the turtles, Podocnemis expansa and Podocnemis unifilis, and mapped by fluorescence in situ hybridization. Our data confirm the 2n=28 chromosomes for these species (the second lowest 2n in the order Testudines). We observe high conservation of the co-located 5S rDNA and U2 snRNA genes on a small chromosome pair (pair 13), and surmise that this represents the ancestral condition. Our analysis reveals a wide distribution of the Tc1/Mariner transposons and we discuss how the mobility of these transposons can act on karyotypic reorganization events (contributing to the 2n decrease of those species). Our data add new information for the order Testudines and provide important insights into the dynamics and organization of these sequences in the chelonian genomes.
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Affiliation(s)
- Manoella Gemaque Cavalcante
- Centro de Estudos Avançados da Biodiversidade, Cytogenetics Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Cleusa Yoshiko Nagamachi
- Centro de Estudos Avançados da Biodiversidade, Cytogenetics Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Julio Cesar Pieczarka
- Centro de Estudos Avançados da Biodiversidade, Cytogenetics Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Renata Coelho Rodrigues Noronha
- Centro de Estudos Avançados da Biodiversidade, Cytogenetics Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
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4
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Kuznetsova V, Grozeva S, Gokhman V. Telomere structure in insects: A review. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12332] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Valentina Kuznetsova
- Department of Karyosystematics, Zoological Institute Russian Academy of Sciences St. Petersburg Russia
| | - Snejana Grozeva
- Cytotaxonomy and Evolution Research Group, Institute of Biodiversity and Ecosystem Research Bulgarian Academy of Sciences Sofia Bulgaria
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5
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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: 1.0] [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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6
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Traldi JB, Ziemniczak K, de Fátima Martinez J, Blanco DR, Lui RL, Schemberger MO, Nogaroto V, Moreira-Filho O, Vicari MR. Chromosome Mapping of H1 and H4 Histones in Parodontidae (Actinopterygii: Characiformes): Dispersed and/or Co-Opted Transposable Elements? Cytogenet Genome Res 2019; 158:106-113. [PMID: 31203273 DOI: 10.1159/000500987] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2019] [Indexed: 01/22/2023] Open
Abstract
The karyotypes of the family Parodontidae consist of 2n = 54 chromosomes. The main chromosomal evolutionary changes of its species are attributed to chromosome rearrangements in repetitive DNA regions in their genomes. Physical mapping of the H1 and H4 histones was performed in 7 Parodontidae species to analyze the chromosome rearrangements involved in karyotype diversification in the group. In parallel, the observation of a partial sequence of an endogenous retrovirus (ERV) retrotransposon in the H1 histone sequence was evaluated to verify molecular co-option of the transposable elements (TEs) and to assess paralogous sequence dispersion in the karyotypes. Six of the studied species had an interstitial histone gene cluster in the short arm of the autosomal pair 13. Besides this interstitial cluster, in Apareiodon davisi, a probable further site was detected in the terminal region of the long arm in the same chromosome pair. The H1/H4 clusters in Parodon cf. pongoensis were located in the smallest chromosomes (pair 20). In addition, scattered H1 signals were observed on the chromosomes in all species. The H1 sequence showed an ERV in the open reading frame (ORF), and the scattered H1 signals on the chromosomes were attributed to the ERV's location. The H4 sequence had no similarity to the TEs and displayed no dispersed signals. Furthermore, the degeneration of the inner ERV in the H1 sequence (which overlapped a stretch of the H1 ORF) was discussed regarding the likelihood of molecular co-option of this retroelement in histone gene function in Parodontidae.
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7
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Sadílek D, Urfus T, Vilímová J, Hadrava J, Suda J. Nuclear Genome Size in Contrast to Sex Chromosome Number Variability in the Human Bed Bug, Cimex lectularius (Heteroptera: Cimicidae). Cytometry A 2019; 95:746-756. [PMID: 30729668 DOI: 10.1002/cyto.a.23729] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 01/02/2019] [Accepted: 01/21/2019] [Indexed: 11/12/2022]
Abstract
The human bed bug Cimex lectularius is one of the most prevalent human ectoparasites in temperate climate zones. The cytogenetic features of this resilient pest include holokinetic chromosomes, special chromosome behavior in meiosis, and numerical variation of chromosomes, where the diploid number ranges from 26 + X1 X2 Y to 26 + X1-20 Y. It is desirable to assess the nuclear DNA content of various cytotypes for a further detailed study of the C. lectularius genome. Detailed knowledge of the DNA content of this parasite could also clarify the origin of additional chromosomes. The average nuclear genome size C. lectularius with 2n = 26 + X1 X2 Y is 2C = 1.94 pg for males and 1.95 pg for females. There is a significant correlation between genome size and the number of chromosomes, but in some specimens with additional chromosomes, nuclear genome size decreases or remains average. Several species used as the internal reference standard were tested for further investigations of genome size in C. lectularius, and the plant Solanum pseudocaspicum turned out to be the most suitable. © 2019 International Society for Advancement of Cytometry.
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Affiliation(s)
- David Sadílek
- Faculty of Science, Department of Zoology, Charles University, Praha, Czech Republic
| | - Tomáš Urfus
- Faculty of Science, Department of Botany, Charles University, Praha, Czech Republic
| | - Jitka Vilímová
- Faculty of Science, Department of Zoology, Charles University, Praha, Czech Republic
| | - Jiří Hadrava
- Faculty of Science, Department of Zoology, Charles University, Praha, Czech Republic.,Institute of Entomology, Biological Centre, Czech Academy of Science, České Budějovice, Czech Republic
| | - Jan Suda
- Faculty of Science, Department of Botany, Charles University, Praha, Czech Republic
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8
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Burger NFV, Botha AM. Genome of Russian wheat aphid an economically important cereal aphid. Stand Genomic Sci 2017; 12:90. [PMID: 29299110 PMCID: PMC5745598 DOI: 10.1186/s40793-017-0307-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 12/08/2017] [Indexed: 02/07/2023] Open
Abstract
Although the hemipterans (Aphididae) are comprised of roughly 50,000 extant insect species, only four have sequenced genomes that are publically available, namely Acyrthosiphon pisum (pea aphid), Rhodnius prolixus (Kissing bug), Myzus persicae (Green peach aphid) and Diuraphis noxia (Russian wheat aphid). As a significant proportion of agricultural pests are phloem feeding aphids, it is crucial for sustained global food security that a greater understanding of the genomic and molecular functioning of this family be elucidated. Recently, the genome of US D. noxia biotype US2 was sequenced but its assembly only incorporated ~ 32% of produced reads and contained a surprisingly low gene count when compared to that of the model/first sequenced aphid, A. pisum. To this end, we present here the genomes of two South African Diuraphis noxia (Kurdjumov, Hemiptera: Aphididae) biotypes (SA1 and SAM), obtained after sequencing the genomes of the only two D. noxia biotypes with documented linked genealogy. To better understand overall targets and patterns of heterozygosity, we also sequenced a pooled sample of 9 geographically separated D. noxia populations (MixIX). We assembled a 399 Mb reference genome (PRJNA297165, representing 64% of the projected genome size 623 Mb) using ± 28 Gb of 101 bp paired-end HiSeq2000 reads from the D. noxia biotype SAM, whilst ± 13 Gb 101 bp paired-end HiSeq2000 reads from the D. noxia biotype SA1 were generated to facilitate genomic comparisons between the two biotypes. Sequencing the MixIX sample yielded ±26 Gb 50 bp paired-end SOLiD reads which facilitated SNP detection when compared to the D. noxia biotype SAM assembly. Ab initio gene calling produced a total of 31,885 protein coding genes from the assembled contigs spanning ~ 399 Mb (GCA_001465515.1).
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Affiliation(s)
| | - Anna-Maria Botha
- University of Stellenbosch, Private Bag X1, Matieland, Stellenbosch, Western Cape 7602 South Africa
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9
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Pita S, Panzera F, Mora P, Vela J, Palomeque T, Lorite P. The presence of the ancestral insect telomeric motif in kissing bugs (Triatominae) rules out the hypothesis of its loss in evolutionarily advanced Heteroptera (Cimicomorpha). COMPARATIVE CYTOGENETICS 2016; 10:427-437. [PMID: 27830050 PMCID: PMC5088353 DOI: 10.3897/compcytogen.v10i3.9960] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 08/22/2016] [Indexed: 05/27/2023]
Abstract
Next-generation sequencing data analysis on Triatoma infestans Klug, 1834 (Heteroptera, Cimicomorpha, Reduviidae) revealed the presence of the ancestral insect (TTAGG)n telomeric motif in its genome. Fluorescence in situ hybridization confirms that chromosomes bear this telomeric sequence in their chromosomal ends. Furthermore, motif amount estimation was about 0.03% of the total genome, so that the average telomere length in each chromosomal end is almost 18 kb long. We also detected the presence of (TTAGG)n telomeric repeat in mitotic and meiotic chromosomes in other three species of Triatominae: Triatoma dimidiata Latreille, 1811, Dipetalogaster maxima Uhler, 1894, and Rhodnius prolixus Ståhl, 1859. This is the first report of the (TTAGG)n telomeric repeat in the infraorder Cimicomorpha, contradicting the currently accepted hypothesis that evolutionarily recent heteropterans lack this ancestral insect telomeric sequence.
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Affiliation(s)
- Sebastián Pita
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Francisco Panzera
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Pablo Mora
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Jaen, Spain
| | - Jesús Vela
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Jaen, Spain
| | - Teresa Palomeque
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Jaen, Spain
| | - Pedro Lorite
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Jaen, Spain
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10
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Chromosomal evolutionary dynamics of four multigene families in Coreidae and Pentatomidae (Heteroptera) true bugs. Mol Genet Genomics 2016; 291:1919-25. [DOI: 10.1007/s00438-016-1229-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 06/22/2016] [Indexed: 12/31/2022]
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11
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Mason JM, Randall TA, Capkova Frydrychova R. Telomerase lost? Chromosoma 2016; 125:65-73. [PMID: 26162505 PMCID: PMC6512322 DOI: 10.1007/s00412-015-0528-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 06/25/2015] [Accepted: 06/29/2015] [Indexed: 01/22/2023]
Abstract
Telomerase and telomerase-generated telomeric DNA sequences are widespread throughout eukaryotes, yet they are not universal. Neither telomerase nor the simple DNA repeats associated with telomerase have been found in some plant and animal species. Telomerase was likely lost from Diptera before the divergence of Diptera and Siphonaptera, some 260 million years ago. Even so, Diptera is one of the most successful animal orders, making up 11% of known animal species. In addition, many species of Coleoptera and Hemiptera seem to lack canonical telomeric repeats at their chromosome ends. These and other insects that appear to lack canonical terminal repeat sequences account for another 10-15% of animal species. Conversely, the silk moth Bombyx mori maintains canonical telomeric sequences at its chromosome ends but seems to lack a functional telomerase. We speculate that a telomere-specific capping complex that recognizes the telomeric repeats and protects chromosome ends is the determining factor in maintaining canonical telomeric sequences and that telomerase is an early and efficacious mechanism for satisfying the needs of capping complex. There are alternate mechanisms for maintaining chromosome ends that do not depend on telomerase, such as recombination found in some human cancer cells and yeast mutants. These mechanisms may maintain the canonical telomeric repeats or allow the terminal sequence to evolve when specificity of the capping complex for terminal repeat sequences is weak.
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Affiliation(s)
- James M Mason
- Laboratory of Genome Integrity and Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Thomas A Randall
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
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12
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Sadílek D, Angus RB, Šťáhlavský F, Vilímová J. Comparison of different cytogenetic methods and tissue suitability for the study of chromosomes in Cimex lectularius (Heteroptera, Cimicidae). COMPARATIVE CYTOGENETICS 2016; 10:731-752. [PMID: 28123691 PMCID: PMC5240521 DOI: 10.3897/compcytogen.v10i4.10681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 10/30/2016] [Indexed: 05/14/2023]
Abstract
In the article we summarize the most common recent cytogenetic methods used in analysis of karyotypes in Heteroptera. We seek to show the pros and cons of the spreading method compared with the traditional squashing method. We discuss the suitability of gonad, midgut and embryo tissue in Cimex lectularius Linnaeus, 1758 chromosome research and production of figures of whole mitosis and meiosis, using the spreading method. The hotplate spreading technique has many advantages in comparison with the squashing technique. Chromosomal slides prepared from the testes tissue gave the best results, tissues of eggs and midgut epithelium are not suitable. Metaphase II is the only division phase in which sex chromosomes can be clearly distinguished. Chromosome number determination is easy during metaphase I and metaphase II. Spreading of gonad tissue is a suitable method for the cytogenetic analysis of holokinetic chromosomes of Cimex lectularius.
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Affiliation(s)
- David Sadílek
- Charles University in Prague, Faculty of Science, Department of Zoology, Viničná 7, CZ-12844 Praha, Czech Republic
| | - Robert B. Angus
- Department of Life Sciences (Entomology), The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - František Šťáhlavský
- Charles University in Prague, Faculty of Science, Department of Zoology, Viničná 7, CZ-12844 Praha, Czech Republic
| | - Jitka Vilímová
- Charles University in Prague, Faculty of Science, Department of Zoology, Viničná 7, CZ-12844 Praha, Czech Republic
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13
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Bhowmick BK, Yamamoto M, Jha S. Chromosomal localization of 45S rDNA, sex-specific C values, and heterochromatin distribution in Coccinia grandis (L.) Voigt. PROTOPLASMA 2016; 253:201-209. [PMID: 25795278 DOI: 10.1007/s00709-015-0797-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 03/05/2015] [Indexed: 06/04/2023]
Abstract
Coccinia grandis is a widely distributed dioecious cucurbit in India, with heteromorphic sex chromosomes and X-Y sex determination mode. The present study aids in the cytogenetic characterization of four native populations of this plant employing distribution patterns of 45S rDNA on chromosomes and guanine-cytosine (GC)-rich heterochromatin in the genome coupled with flow cytometric determination of genome sizes. Existence of four nucleolar chromosomes could be confirmed by the presence of four telomeric 45S rDNA signals in both male and female plants. All four 45S rDNA sites are rich in heterochromatin evident from the co-localization of telomeric chromomycin A (CMA)(+ve) signals. The size of 45S rDNA signal was found to differ between the homologues of one nucleolar chromosome pair. The distribution of heterochromatin is found to differ among the male and female populations. The average GC-rich heterochromatin content of male and female populations is 23.27 and 29.86 %, respectively. Moreover, the male plants have a genome size of 0.92 pg/2C while the female plants have a size of 0.73 pg/2C, reflecting a huge genomic divergence between the genders. The great variation in genome size is owing to the presence of Y chromosome in the male populations, playing a multifaceted role in sexual divergence in C. grandis.
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Affiliation(s)
- Biplab Kumar Bhowmick
- Center of Advanced Study, Department of Botany, University of Calcutta 35, Ballygunge Circular Road, Kolkata, West Bengal, 700019, India.
| | - Masashi Yamamoto
- Faculty of Agriculture, Kagoshima University, 1-21-24, Korimoto, Kagoshima, 890-0065, Japan.
| | - Sumita Jha
- Center of Advanced Study, Department of Botany, University of Calcutta 35, Ballygunge Circular Road, Kolkata, West Bengal, 700019, India.
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14
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Nicholson SJ, Nickerson ML, Dean M, Song Y, Hoyt PR, Rhee H, Kim C, Puterka GJ. The genome of Diuraphis noxia, a global aphid pest of small grains. BMC Genomics 2015; 16:429. [PMID: 26044338 PMCID: PMC4561433 DOI: 10.1186/s12864-015-1525-1] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 04/11/2015] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The Russian wheat aphid, Diuraphis noxia Kurdjumov, is one of the most important pests of small grains throughout the temperate regions of the world. This phytotoxic aphid causes severe systemic damage symptoms in wheat, barley, and other small grains as a direct result of the salivary proteins it injects into the plant while feeding. RESULTS We sequenced and de novo assembled the genome of D. noxia Biotype 2, the strain most virulent to resistance genes in wheat. The assembled genomic scaffolds span 393 MB, equivalent to 93% of its 421 MB genome, and contains 19,097 genes. D. noxia has the most AT-rich insect genome sequenced to date (70.9%), with a bimodal CpG(O/E) distribution and a complete set of methylation related genes. The D. noxia genome displays a widespread, extensive reduction in the number of genes per ortholog group, including defensive, detoxification, chemosensory, and sugar transporter groups in comparison to the Acyrthosiphon pisum genome, including a 65% reduction in chemoreceptor genes. Thirty of 34 known D. noxia salivary genes were found in this assembly. These genes exhibited less homology with those salivary genes commonly expressed in insect saliva, such as glucose dehydrogenase and trehalase, yet greater conservation among genes that are expressed in D. noxia saliva but not detected in the saliva of other insects. Genes involved in insecticide activity and endosymbiont-derived genes were also found, as well as genes involved in virus transmission, although D. noxia is not a viral vector. CONCLUSIONS This genome is the second sequenced aphid genome, and the first of a phytotoxic insect. D. noxia's reduced gene content of may reflect the influence of phytotoxic feeding in shaping the D. noxia genome, and in turn in broadening its host range. The presence of methylation-related genes, including cytosine methylation, is consistent with other parthenogenetic and polyphenic insects. The D. noxia genome will provide an important contrast to the A. pisum genome and advance functional and comparative genomics of insects and other organisms.
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Affiliation(s)
- Scott J Nicholson
- USDA Agricultural Research Service, Stillwater, OK, 74075, USA.
- Department of Molecular Biology and Biochemistry, Oklahoma State University, Stillwater, OK, 74078, USA.
| | - Michael L Nickerson
- National Institutes of Health, National Cancer Institute, Bethesda, MD, 20892, USA.
| | - Michael Dean
- National Institutes of Health, National Cancer Institute, Bethesda, MD, 20892, USA.
| | - Yan Song
- Department of Molecular Biology and Biochemistry, Oklahoma State University, Stillwater, OK, 74078, USA.
| | - Peter R Hoyt
- Department of Molecular Biology and Biochemistry, Oklahoma State University, Stillwater, OK, 74078, USA.
| | | | | | - Gary J Puterka
- USDA Agricultural Research Service, Stillwater, OK, 74075, USA.
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Gavrilov-Zimin IA, Stekolshchikov AV, Gautam D. General trends of chromosomal evolution in Aphidococca (Insecta, Homoptera, Aphidinea + Coccinea). COMPARATIVE CYTOGENETICS 2015; 9:335-422. [PMID: 26312130 PMCID: PMC4547034 DOI: 10.3897/compcytogen.v9i3.4930] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 05/14/2015] [Indexed: 05/08/2023]
Abstract
Parallel trends of chromosomal evolution in Aphidococca are discussed, based on the catalogue of chromosomal numbers and genetic systems of scale insects by Gavrilov (2007) and the new catalogue for aphids provided in the present paper. To date chromosome numbers have been reported for 482 species of scale insects and for 1039 species of aphids, thus respectively comprising about 6% and 24% of the total number of species. Such characters as low modal numbers of chromosomes, heterochromatinization of part of chromosomes, production of only two sperm instead of four from each primary spermatocyte, physiological sex determination, "larval" meiosis, wide distribution of parthenogenesis and chromosomal races are considered as a result of homologous parallel changes of the initial genotype of Aphidococca ancestors. From a cytogenetic point of view, these characters separate Aphidococca from all other groups of Paraneoptera insects and in this sense can be considered as additional taxonomic characters. In contrast to available paleontological data the authors doubt that Coccinea with their very diverse (and partly primitive) genetic systems may have originated later then Aphidinea with their very specialised and unified genetic system.
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Affiliation(s)
- Ilya A. Gavrilov-Zimin
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, St. Petersburg 199034, Russia
| | - Andrey V. Stekolshchikov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, St. Petersburg 199034, Russia
| | - D.C. Gautam
- Department of Bio-Sciences, Himachal Pradesh University, Shimla, India
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Botha AM, Burger NFV, Van Eck L. Hypervirulent Diuraphis noxia (Hemiptera: Aphididae) biotype SAM avoids triggering defenses in its host (Triticum aestivum) (Poales: Poaceae) during feeding. ENVIRONMENTAL ENTOMOLOGY 2014; 43:672-81. [PMID: 24874154 DOI: 10.1603/en13331] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In the molecular arms race between aphids and plants, both organisms rely on adaptive strategies to outcompete their evolutionary rival. In the current study, we investigated the difference in elicited defense responses of wheat (Triticum aestivum L.) near-isogenic lines with different Dn resistance genes, upon feeding by an avirulent and hypervirulent Diuraphis noxia Kurdjumov biotype. After measuring the activity of a suite of enzymes associated with plant defense, it became apparent that the host does not recognize the invasion by the hypervirulent aphid because none of these were induced, while feeding by the avirulent biotype did result in induction of enzyme activity. Genomic plasticity in D. noxia may be a likely explanation for the observed differences in virulence between D. noxia biotype SA1 and SAM, as demonstrated in the current study.
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Affiliation(s)
- Anna-Maria Botha
- Genetics Department, Stellenbosch University, Private Bag X1, Matieland, 7601, South Africa
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Král J, Kořínková T, Krkavcová L, Musilová J, Forman M, Herrera IMÁ, Haddad CR, Vítková M, Henriques S, Vargas JGP, Hedin M. Evolution of karyotype, sex chromosomes, and meiosis in mygalomorph spiders (Araneae: Mygalomorphae). Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12056] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jiří Král
- Laboratory of Arachnid Cytogenetics; Department of Genetics and Microbiology; Faculty of Science; Charles University in Prague; CZ-128 44 Prague 2 Czech Republic
| | - Tereza Kořínková
- Laboratory of Arachnid Cytogenetics; Department of Genetics and Microbiology; Faculty of Science; Charles University in Prague; CZ-128 44 Prague 2 Czech Republic
| | - Lenka Krkavcová
- Laboratory of Arachnid Cytogenetics; Department of Genetics and Microbiology; Faculty of Science; Charles University in Prague; CZ-128 44 Prague 2 Czech Republic
| | - Jana Musilová
- Laboratory of Arachnid Cytogenetics; Department of Genetics and Microbiology; Faculty of Science; Charles University in Prague; CZ-128 44 Prague 2 Czech Republic
| | - Martin Forman
- Laboratory of Arachnid Cytogenetics; Department of Genetics and Microbiology; Faculty of Science; Charles University in Prague; CZ-128 44 Prague 2 Czech Republic
| | - Ivalú M. Ávila Herrera
- Laboratory of Arachnid Cytogenetics; Department of Genetics and Microbiology; Faculty of Science; Charles University in Prague; CZ-128 44 Prague 2 Czech Republic
| | - Charles R. Haddad
- Department of Zoology and Entomology; University of the Free State; Bloemfontein 9300 South Africa
| | - Magda Vítková
- Faculty of Science; University of South Bohemia; CZ-370 05 České Budějovice Czech Republic
- Department of Molecular Biology and Genetics; Institute of Entomology; Biology Centre ASCR; CZ-370 05 České Budějovice Czech Republic
| | - Sergio Henriques
- Centro de Investigação em Biodiversidade e Recursos Genéticos; Campus Agrário de Vairão; P-4485-661 Vila do Conde Portugal
| | - José G. Palacios Vargas
- Departamento de Ecología y Recursos Naturales; Universidad Nacional Autónoma de México; Facultad de Ciencias; Ciudad Universitaria; C. P. 04510 México
| | - Marshal Hedin
- Department of Biology; San Diego State University; San Diego CA 92182-4614 USA
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Hashimoto D, Ferguson-Smith M, Rens W, Prado F, Foresti F, Porto-Foresti F. Cytogenetic Mapping of H1 Histone and Ribosomal RNA Genes in Hybrids between Catfish SpeciesPseudoplatystoma corruscansandPseudoplatystoma reticulatum. Cytogenet Genome Res 2013. [DOI: 10.1159/000345299] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Cabral-de-Mello DC, Oliveira SG, de Moura RC, Martins C. Chromosomal organization of the 18S and 5S rRNAs and histone H3 genes in Scarabaeinae coleopterans: insights into the evolutionary dynamics of multigene families and heterochromatin. BMC Genet 2011. [PMID: 21999519 DOI: 10.1186/14712156-12-88] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2023] Open
Abstract
BACKGROUND Scarabaeinae beetles show a high level of macro-chromosomal variability, although the karyotypic organization of heterochromatin and multigene families (rDNAs and histone genes) is poorly understood in this group. To better understand the chromosomal organization and evolution in this group, we analyzed the karyotypes, heterochromatin distribution and chromosomal locations of the rRNAs and histone H3 genes in beetles belonging to eight tribes from the Scarabaeinae subfamily (Coleoptera, Scarabaeidae). RESULTS The number of 18S rRNA gene (a member of the 45S rDNA unit) sites varied from one to 16 and were located on the autosomes, sex chromosomes or both, although two clusters were most common. Comparison of the 45S rDNA cluster number and the diploid numbers revealed a low correlation value. However, a comparison between the number of 45S rDNA sites per genome and the quantity of heterochromatin revealed (i) species presenting heterochromatin restricted to the centromeric/pericentromeric region that contained few rDNA sites and (ii) species with a high quantity of heterochromatin and a higher number of rDNA sites. In contrast to the high variability for heterochromatin and 45S rDNA cluster, the presence of two clusters (one bivalent cluster) co-located on autosomal chromosomes with the 5S rRNA and histone H3 genes was highly conserved. CONCLUSIONS Our results indicate that the variability of the 45S rDNA chromosomal clusters is not associated with macro-chromosomal rearrangements but are instead related to the spread of heterochromatin. The data obtained also indicate that both heterochromatin and the 45S rDNA loci could be constrained by similar evolutionary forces regulating spreading in the distinct Scarabaeinae subfamily lineages. For the 5S rRNA and the histone H3 genes, a similar chromosomal organization could be attributed to their association/co-localization in the Scarabaeinae karyotypes. These data provide evidence that different evolutionary forces act at the heterochromatin and the 45S rDNA loci compared to the 5S rRNA and histone H3 genes during the evolution of the Scarabainae karyotypes.
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Affiliation(s)
- Diogo C Cabral-de-Mello
- UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Departamento de Biologia, Rio Claro, São Paulo, Brazil.
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Cabral-de-Mello DC, Oliveira SG, de Moura RC, Martins C. Chromosomal organization of the 18S and 5S rRNAs and histone H3 genes in Scarabaeinae coleopterans: insights into the evolutionary dynamics of multigene families and heterochromatin. BMC Genet 2011; 12:88. [PMID: 21999519 PMCID: PMC3209441 DOI: 10.1186/1471-2156-12-88] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 10/15/2011] [Indexed: 11/22/2022] Open
Abstract
Background Scarabaeinae beetles show a high level of macro-chromosomal variability, although the karyotypic organization of heterochromatin and multigene families (rDNAs and histone genes) is poorly understood in this group. To better understand the chromosomal organization and evolution in this group, we analyzed the karyotypes, heterochromatin distribution and chromosomal locations of the rRNAs and histone H3 genes in beetles belonging to eight tribes from the Scarabaeinae subfamily (Coleoptera, Scarabaeidae). Results The number of 18S rRNA gene (a member of the 45S rDNA unit) sites varied from one to 16 and were located on the autosomes, sex chromosomes or both, although two clusters were most common. Comparison of the 45S rDNA cluster number and the diploid numbers revealed a low correlation value. However, a comparison between the number of 45S rDNA sites per genome and the quantity of heterochromatin revealed (i) species presenting heterochromatin restricted to the centromeric/pericentromeric region that contained few rDNA sites and (ii) species with a high quantity of heterochromatin and a higher number of rDNA sites. In contrast to the high variability for heterochromatin and 45S rDNA cluster, the presence of two clusters (one bivalent cluster) co-located on autosomal chromosomes with the 5S rRNA and histone H3 genes was highly conserved. Conclusions Our results indicate that the variability of the 45S rDNA chromosomal clusters is not associated with macro-chromosomal rearrangements but are instead related to the spread of heterochromatin. The data obtained also indicate that both heterochromatin and the 45S rDNA loci could be constrained by similar evolutionary forces regulating spreading in the distinct Scarabaeinae subfamily lineages. For the 5S rRNA and the histone H3 genes, a similar chromosomal organization could be attributed to their association/co-localization in the Scarabaeinae karyotypes. These data provide evidence that different evolutionary forces act at the heterochromatin and the 45S rDNA loci compared to the 5S rRNA and histone H3 genes during the evolution of the Scarabainae karyotypes.
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Affiliation(s)
- Diogo C Cabral-de-Mello
- UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Departamento de Biologia, Rio Claro, São Paulo, Brazil.
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Monti V, Manicardi GC, Mandrioli M. Cytogenetic and molecular analysis of the holocentric chromosomes of the potato aphid Macrosiphum euphorbiae (Thomas, 1878). COMPARATIVE CYTOGENETICS 2011; 5:163-72. [PMID: 24260627 PMCID: PMC3833776 DOI: 10.3897/compcytogen.v5i3.1724] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Accepted: 07/19/2011] [Indexed: 05/08/2023]
Abstract
Cytogenetic and molecular investigations on the holocentric chromosomes of the aphid Macrosiphum euphorbiae (Thomas, 1878)have been carried out using silver staining and C-banding (followed by chromomycin A3 and DAPI staining) in order to improve our knowledge about the structure of aphid chromosomes. The C-banding pattern is peculiar since only the two X chromosomes and a single pair of autosomes presented heterochromatic bands. Silver staining and FISH with the 28S rDNA probe localized the rDNA genes on one telomere of each X chromosome that were also brightly fluorescent after chromomycin A3 staining of C-banded chromosomes, whereas all other heterochromatic bands were DAPI positive. Interestingly, a remarkable nucleolar organizing region (NOR) heteromorphism was present making the two X chromosomes easily distinguishable. Southern blotting and FISH assessed the presence of the (TTAGG)n repeat at the ends of all the Macrosiphum euphorbiae chromosomes. Karyotype analysis showed that all males possessed the X chromosome with the larger amount of rDNA suggesting a non-Mendelian inheritance of the two X chromosomes.
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Affiliation(s)
- Valentina Monti
- Dipartimento di Biologia, Università di Modena e Reggio Emilia, Via Campi 213/D, 41125 Modena, Italy
- Dipartimento di Scienze Agrarie e degli Alimenti, Università di Modena e Reggio Emilia, Via Amendola 2, 42100 Reggio Emilia, Italy
| | - Gian Carlo Manicardi
- Dipartimento di Scienze Agrarie e degli Alimenti, Università di Modena e Reggio Emilia, Via Amendola 2, 42100 Reggio Emilia, Italy
| | - Mauro Mandrioli
- Dipartimento di Biologia, Università di Modena e Reggio Emilia, Via Campi 213/D, 41125 Modena, Italy
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