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Guo J, Zhang Z, Li Q, Chang X, Liu X. TeCD: The eccDNA Collection Database for extrachromosomal circular DNA. BMC Genomics 2023; 24:47. [PMID: 36707765 PMCID: PMC9881285 DOI: 10.1186/s12864-023-09135-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 01/13/2023] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Extrachromosomal circular DNA (eccDNA) is a kind of DNA that widely exists in eukaryotic cells. Studies in recent years have shown that eccDNA is often enriched during tumors and aging, and participates in the development of cell physiological activities in a special way, so people have paid more and more attention to the eccDNA, and it has also become a critical new topic in modern biological research. DESCRIPTION We built a database to collect eccDNA, including animals, plants and fungi, and provide researchers with an eccDNA retrieval platform. The collected eccDNAs were processed in a uniform format and classified according to the species to which it belongs and the chromosome of the source. Each eccDNA record contained sequence length, start and end sites on the corresponding chromosome, order of the bases, genomic elements such as genes and transposons, and other information in the respective sequencing experiment. All the data were stored into the TeCD (The eccDNA Collection Database) and the BLAST (Basic Local Alignment Search Tool) sequence alignment function was also added into the database for analyzing the potential eccDNA sequences. CONCLUSION We built TeCD, a platform for users to search and obtain eccDNA data, and analyzed the possible potential functions of eccDNA. These findings may provide a basis and direction for researchers to further explore the biological significance of eccDNA in the future.
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Affiliation(s)
- Jing Guo
- grid.410726.60000 0004 1797 8419Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310013 China ,grid.410726.60000 0004 1797 8419Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310013 China ,grid.464226.00000 0004 1760 7263Institute of Statistics and Applied Mathematics, Anhui University of Finance & Economics, Bengbu, 233030 China ,grid.27255.370000 0004 1761 1174School of Mathematics and Statistics, Shandong University, Weihai, 264209 Shandong China
| | - Ze Zhang
- grid.410726.60000 0004 1797 8419Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310013 China ,grid.410726.60000 0004 1797 8419Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310013 China ,grid.410726.60000 0004 1797 8419School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310013 China
| | - Qingcui Li
- grid.410726.60000 0004 1797 8419School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310013 China
| | - Xiao Chang
- grid.464226.00000 0004 1760 7263Institute of Statistics and Applied Mathematics, Anhui University of Finance & Economics, Bengbu, 233030 China
| | - Xiaoping Liu
- grid.410726.60000 0004 1797 8419Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310013 China ,grid.410726.60000 0004 1797 8419Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310013 China ,grid.27255.370000 0004 1761 1174School of Mathematics and Statistics, Shandong University, Weihai, 264209 Shandong China
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Ivković S, Dey LS, Maria Buzzetti F, Puskás G, Warchałowska‑Śliwa E, Horvat L, Chobanov D, Hochkirch A. Strong intraspecific phylogenetic and karyotypic diversification in Isophya modestior (Orthoptera: Tettigoniidae: Phaneropterinae). Biol J Linn Soc Lond 2023. [DOI: 10.1093/biolinnean/blac142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Abstract
Isophya modestior (Orthoptera: Tettigoniidae) is a species distributed in central and south-eastern Europe, where its distribution is largely separated by two large rivers (Sava and Danube). Since previous studies on the song and morphology of the stridulatory file across its complete geographic range showed that the species is separated into two main groups, we decided to use phylogenetic and karyological analyses in order to evaluate the status of the previously analysed populations.
Phylogenetic analyses showed the existence of two major clades within I. modestior with very high bootstrap values and posterior probabilities—Clade A: present on the Balkan Peninsula, Slovenia (Inner Carniola), Italy, Pannonian Serbia (Vršac Mts and Deronje) and Austria (Burgenland and Lower Austria); Clade B: present in Slovenia (Upper Carniola), Croatia and Austria (Carinthia), Pannonian Serbia (Fruška Gora Mt.) and Hungary.
A comparison of chromosomes of 51 specimens revealed discrete differences between their karyotypes. The physical characteristics of the karyotypes included chromosome number (2n), sex chromosome (X) morphology and C-banding patterns. The standard chromosome complement of 50 specimens from different localities is characterized by 2n = 30 + X0 in males. In one male collected in Fruška Gora Mt. (Andrevlje), the chromosome number was reduced to 2n = 28 + neo-XY. Therefore, further cytogenetic studies involving larger samples, especially from Fruška Gora Mt., are needed in order to gain a more comprehensive view of the chromosome evolution in this group of Isophya species.
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Affiliation(s)
- Slobodan Ivković
- Department of Biogeography, Trier University, Universitätsring 15 , 54296 Trier , Germany
| | - Lara-Sophie Dey
- Leibniz Institute for the Analysis of Biodiversity (LIB), University of Hamburg, Martin-Luther-King Platz 3 , 20146 Hamburg , Germany
| | | | | | - Elżbieta Warchałowska‑Śliwa
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences , Sławkowska 17, 31-016 Kraków , Poland
| | | | - Dragan Chobanov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences , 1 Tsar Osvoboditel Boulevard, 1000 Sofia , Bulgaria
| | - Axel Hochkirch
- Department of Biogeography, Trier University, Universitätsring 15 , 54296 Trier , Germany
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Wang Y, Chen Y, Wei Q, Chen X, Wan H, Sun C. Characterization of repetitive sequences in Dendrobium officinale and comparative chromosomal structures in Dendrobium species using FISH. Gene 2022; 846:146869. [PMID: 36075328 DOI: 10.1016/j.gene.2022.146869] [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: 06/10/2022] [Revised: 08/26/2022] [Accepted: 09/01/2022] [Indexed: 11/04/2022]
Abstract
Tandem repeats are one of the most conserved features in the eukaryote genomes. Dendrobium is the third largest genus in family Orchidaceae compromising over 1,200 species. However, the organization of repetitive sequences in Dendrobium species remains unclear. In this study, we performed the identification and characterization of the tandem repeats in D. officinale genome using graph-based clustering and Fluorescence in situ hybridization (FISH). Six major clusters including five satellite DNAs (DofSat1-5) and one 5S rDNA repeat (Dof5S) were identified as tandem repeats. The tandem organization of DofSat5 was verified by PCR amplification and southern blotting. The chromosomal locations of the repetitive DNAs in D. officinale were investigated by FISH using the tandem repeats and oligos probes. The results showed that each of the DofSat5, 5S and 45S rDNA had one pair of strong signals on D. officinale chromosomes. The distribution of repetitive DNAs along chromosomes was also investigated based on genomic in situ hybridization (GISH) among four Dendrobium species. The results suggested complex chromosomal fusion/segmentation and rearrangements during the evolution of Dendrobium species. In conclusion, the present study provides new landmarks for unequival differentiation of the Dendrobium chromosomes and facilitate the understanding the chromosome evolution in Dendrobium speceis.
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Affiliation(s)
- Yunzhu Wang
- Institute of Horticulture Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Yue Chen
- Institute of Horticulture Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Qingzhen Wei
- Institute of Vegetable Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Xiaoyang Chen
- Seed Management Terminal of Zhejiang, Hangzhou 310021, China.
| | - Hongjian Wan
- Institute of Vegetable Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Chongbo Sun
- Institute of Horticulture Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
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Amutkan Mutlu D, Suludere Z. Ultrastructural Changes in the Ovariole of Isophya nervosa Ramme, 1931 (Orthoptera: Tettigoniidae) and Egg Morphology. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-7. [PMID: 35285436 DOI: 10.1017/s1431927622000319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This study was conducted to assess the morphology of eggs and histology of the ovaries in female Isophya nervosa Ramme, 1931 (Orthoptera: Tettigoniidae). While the egg morphology of I. nervosa was studied and examined by a stereomicroscope, a light microscope, and a scanning electron microscope, respectively, the morphology and histology of the ovary of this species were studied and examined by a stereomicroscope, a light microscope, a scanning electron microscope, and a transmission electron microscope, respectively. We found that the adult female had two pairs of ovaries, lateral oviduct, common oviduct, and spermatheca. Morphological study of the ovariole revealed that it is categorized under panoistic type of ovariole which is divided into three regions, the terminal filament, the germarium, and the vitellarium. We also observed that the eggs in I. nervosa have an ellipsoidal shape and are brown in color. Three different layers such as extrachorion, exochorion, and endochorion were observed. When the egg morphology is examined, it is understood that the surface pattern of the egg and the features of the micropylar areas may be distinguishing characters at the subfamily level, in addition to known classical taxonomic characters.
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Affiliation(s)
- Damla Amutkan Mutlu
- Faculty of Science, Department of Biology, Gazi University, Ankara06500, Turkey
| | - Zekiye Suludere
- Faculty of Science, Department of Biology, Gazi University, Ankara06500, Turkey
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Highly divergent karyotypes and barcoding of the East African genus Gonatoxia Karsch (Orthoptera: Phaneropterinae). Sci Rep 2021; 11:22781. [PMID: 34815452 PMCID: PMC8610994 DOI: 10.1038/s41598-021-02110-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 10/20/2021] [Indexed: 11/09/2022] Open
Abstract
East Africa is a hotspot of biodiversity of many orthopteran taxa, including bushcrickets. Gonatoxia Karsch, 1889 species are fully alate Phaneropterinae, which are perfectly adapted to the foliage of forests. We examined five species using combined cytogenetic and molecular data to determine the inter- and intraspecific genetic diversity. The variation in the diploid number of chromosomes in males ranged from 2n = 28 + X0 and 26 + X0 to 2n = 6 + X0. Fluorescence in situ hybridization showed from one to many 18S rDNA loci as well as interstitial sequences, especially in G. helleri. 18S rDNA loci coincided with active NOR and C-banding patterns. The isolation of populations of the species explains differences in the number of chromosomes (G. maculata), chromosomal polymorphism and chromosomal heterozygosity (G. helleri). Our molecular phylogeny based on the COI locus supported the monophyly of the genus Gonatoxia and separateness of the five examined species in accordance with their morphological features and chromosome numbers as well as the species' distribution.
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Warchałowska-Śliwa E, Grzywacz B, Maryańska-Nadachowska A, Heller KG, Hemp C. Rapid chromosomal evolution in the bush-cricket Gonatoxia helleri Hemp, 2016 (Orthoptera, Phaneropterinae). COMPARATIVE CYTOGENETICS 2020; 14:417-435. [PMID: 32952902 PMCID: PMC7473956 DOI: 10.3897/compcytogen.v14i3.54422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/27/2020] [Indexed: 05/03/2023]
Abstract
Gonatoxia helleri Hemp, 2016 is one of the most widespread bush-crickets of the genus Gonatoxia Karsch, 1889 in East Africa. This species with seven large chromosomes (2n♂ = 7) differs from other representatives of the genus Gonatoxia drastically by its reduced chromosome number, the asymmetrical karyotype including karyomorphs rarely found in tettigoniids, as well as in irregularities in the course of meiosis. To better understand the origin of such an exceptional karyotype, chromosomes of 29 specimens from four populations/localities were studied using classical techniques, such as C-banding, silver impregnation, fluorochrome double staining and fluorescence in situ hybridization (FISH) technique with 18S rDNA and (TTAGG) n telomeric probes. FISH showed many 18S rDNA loci as well as interstitial telomeric sequences, where chromosome morphology varied in these components in terms of quantity and distribution. The 18S rDNA loci coincided with active NORs and C-banding patterns. We suggest that a combination of Robertsonian rearrangements and/or multiple common tandem fusions involving the same chromosomes contributed to the formation of this karyotype/karyomorphs. The results are the first step towards a better understanding of chromosomal reorganization and evolution within the genus Gonatoxia. Low chromosome number, together with the incidence of chromosomal polymorphism that is higher in G. helleri than previously reported in bush-crickets, implies that this species can be a valuable new model for cytogenetic and speciation studies. Our findings suggest that chromosomal translocations lead to diversification and speciation in this species and could be the driving force of adaptive radiation.
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Affiliation(s)
- Elżbieta Warchałowska-Śliwa
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Kraków, PolandPolish Academy of SciencesKrakówPoland
| | - Beata Grzywacz
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Kraków, PolandPolish Academy of SciencesKrakówPoland
| | - Anna Maryańska-Nadachowska
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Kraków, PolandPolish Academy of SciencesKrakówPoland
| | | | - Claudia Hemp
- University of Bayreuth, Dept. Plant Systematics, Bayreuth, GermanyUniversity of BayreuthBayreuthGermany
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Cytogenetic markers reveal a reinforcement of variation in the tension zone between chromosome races in the brachypterous grasshopper Podisma sapporensis Shir. on Hokkaido Island. Sci Rep 2019; 9:16860. [PMID: 31728044 PMCID: PMC6856175 DOI: 10.1038/s41598-019-53416-7] [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: 07/31/2019] [Accepted: 10/31/2019] [Indexed: 11/12/2022] Open
Abstract
The cytogenetic characteristics of the grasshopper Podisma sapporensis (two races 2n = 23♂ X0/XX and 2n = 22♂ neo-XY/neo-XX) were analysed through fluorescence in situ hybridization with rDNA and telomeric DNA probes, C-banding, fluorochrome and silver staining. For the first time, samples from the neighbourhood of a hybrid population (i.e., Mikuni Pass population) were studied. Our results indicated a significant degree of chromosomal differentiation between P. sapporensis races when comparing the number and position of the rDNA sites, as well as the heterochromatin composition and distribution obtained by C-banding and DAPI/CMA3 staining. Telomeric signals were usually detected at the distal and/or subdistal position of the autosomes; however, some chromosome ends lacked signals, probably due to a low number of telomeric repeats. On the other hand, telomeric DNA sequences were found as interstitial telomeric repeats in some autosomes, which can trigger a variety of genome instability. B chromosomes were found in specimens belonging to both main races from nine out of 22 localities. Four types of X chromosomes in the X0/XX race were identified. It was concluded that the physical mapping of rDNA sequences and heterochromatin are useful as additional markers for understanding the phylogeographic patterns of cytogenetic differentiation in P. sapporensis populations.
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Miao Y, Wang JS, Hua BZ. Molecular phylogeny of the scorpionflies Panorpidae (Insecta: Mecoptera) and chromosomal evolution. Cladistics 2019; 35:385-400. [PMID: 34633699 DOI: 10.1111/cla.12357] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/30/2018] [Indexed: 11/29/2022] Open
Abstract
Panorpidae is the most species-rich family in Mecoptera with ca. 470 species in the Northern Hemisphere. However, the intergeneric phylogenetic relationships of Panorpidae remain unsatisfactorily resolved to date. Here, we used molecular and cytogenetic approaches to determine the phylogenetic relationships of Panorpidae in the evolutionary scenario of chromosomes, and estimated their divergence times using fossil-calibrated Bayesian analysis. In total, 89 species representing all seven genera of Panorpidae were used to reconstruct the phylogenetic trees using maximum parsimony, maximum likelihood and Bayesian inference based on the nuclear 28S rRNA and mitochondrial cox1 and cox2 genes. The results reveal that Panorpidae is a well-supported monophyletic group that can be categorized into two major clades. Major Clade I comprises Neopanorpa and Leptopanorpa, and Major Clade II consists of all the other genera (Cerapanorpa, Dicerapanorpa, Furcatopanorpa, Panorpa and Sinopanorpa). Neopanorpa and Cerapanorpa are regarded as paraphyletic groups for the first time. BEAST analysis indicates that Panorpidae originated in the Lower Cretaceous approximately 122.5 Ma (96.8-149.3 Ma), and that most diversification occurred from the Selandian (59.8 Ma) to the Middle Pleistocene (0.6 Ma) in the Cenozoic. Cytogenetic data plotted on the cladogram show that the lineage differentiation of Panorpidae is closely related to the chromosomal evolution, especially the reduction of chromosome number. Our study suggests that a taxonomic revision of Panorpidae is urgently needed at the generic level.
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Affiliation(s)
- Ying Miao
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ji-Shen Wang
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Bao-Zhen Hua
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
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Grzywacz B, Lehmann AW, Chobanov DP, Lehmann GU. Multiple origin of flightlessness in Phaneropterinae bushcrickets and redefinition of the tribus Odonturini (Orthoptera: Tettigonioidea: Phaneropteridae). ORG DIVERS EVOL 2018. [DOI: 10.1007/s13127-018-0370-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Winterfeld G, Becher H, Voshell S, Hilu K, Röser M. Karyotype evolution in Phalaris (Poaceae): The role of reductional dysploidy, polyploidy and chromosome alteration in a wide-spread and diverse genus. PLoS One 2018; 13:e0192869. [PMID: 29462207 PMCID: PMC5819788 DOI: 10.1371/journal.pone.0192869] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 01/31/2018] [Indexed: 11/24/2022] Open
Abstract
Karyotype characteristics can provide valuable information on genome evolution and speciation, in particular in taxa with varying basic chromosome numbers and ploidy levels. Due to its worldwide distribution, remarkable variability in morphological traits and the fact that ploidy change plays a key role in its evolution, the canary grass genus Phalaris (Poaceae) is an excellent study system to investigate the role of chromosomal changes in species diversification and expansion. Phalaris comprises diploid species with two basic chromosome numbers of x = 6 and 7 as well as polyploids based on x = 7. To identify distinct karyotype structures and to trace chromosome evolution within the genus, we apply fluorescence in situ hybridisation (FISH) of 5S and 45S rDNA probes in four diploid and four tetraploid Phalaris species of both basic numbers. The data agree with a dysploid reduction from x = 7 to x = 6 as the result of reciprocal translocations between three chromosomes of an ancestor with a diploid chromosome complement of 2n = 14. We recognize three different genomes in the genus: (1) the exclusively Mediterranean genome A based on x = 6, (2) the cosmopolitan genome B based on x = 7 and (3) a genome C based on x = 7 and with a distribution in the Mediterranean and the Middle East. Both auto- and allopolyploidy of genomes B and C are suggested for the formation of tetraploids. The chromosomal divergence observed in Phalaris can be explained by the occurrence of dysploidy, the emergence of three different genomes, and the chromosome rearrangements accompanied by karyotype change and polyploidization. Mapping the recognized karyotypes on the existing phylogenetic tree suggests that genomes A and C are restricted to sections Phalaris and Bulbophalaris, respectively, while genome B occurs across all taxa with x = 7.
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Affiliation(s)
- Grit Winterfeld
- Institute of Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Hannes Becher
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephanie Voshell
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Khidir Hilu
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Martin Röser
- Institute of Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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Yang S, Qin X, Cheng C, Li Z, Lou Q, Li J, Chen J. Organization and evolution of four differentially amplified tandem repeats in the Cucumis hystrix genome. PLANTA 2017; 246:749-761. [PMID: 28668977 DOI: 10.1007/s00425-017-2716-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 05/29/2017] [Indexed: 05/18/2023]
Abstract
Three subtelomeric satellites and one interstitial 5S rDNA were characterized in Cucumis hystrix, and the pericentromeric signals of two C. hystrix subtelomeric satellites along C. sativus chromosomes supported the hypothesis of chromosome fusion in Cucumis. Tandem repeats are chromosome structural fractions consisting of highly repetitive sequences organized in large tandem arrays in most eukaryotes. Differentiation of tandem repeats directly affects the chromosome structure, which contributes to species formation and evolution. Cucumis hystrix (2n = 2x = 24) is the only wild Cucumis species grouped into the same subgenus with C. sativus (2n = 2x = 14), hence its phylogenetic position confers a vital role for C. hystrix to understand the chromosome evolution in Cucumis. However, our knowledge of C. hystrix tandem repeats is insufficient for a detailed understanding of the chromosome evolution in Cucumis. Based on de novo tandem repeat characterization using bioinformatics and in situ hybridization (ISH), we identified and characterized four differentially amplified tandem repeats, Cucumis hystrix satellite 1-3 (CuhySat1-CuhySat3) located at the subtelomeric regions of all chromosomes, and Cucumis hystrix 5S (Cuhy5S) located at the interstitial regions of one single chromosome pair. Comparative ISH mapping using CuhySat1-3 and Cuhy5S revealed high homology of tandem repeats between C. hystrix and C. sativus. Intriguingly, we found signal distribution variations of CuhySat2 and CuhySat3 on C. sativus chromosomes. In comparison to their subtelomeric signal distribution on C. hystrix chromosomes, CuhySat3 showed a pericentromeric signal distribution and CuhySat2 showed both subtelomeric and pericentromeric signal distributions on C. sativus chromosomes. This detailed characterization of four C. hystrix tandem repeats significantly widens our knowledge of the C. hystrix chromosome structure, and the observed signal distribution variations will be helpful for understanding the chromosome evolution of Cucumis.
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Affiliation(s)
- Shuqiong Yang
- State Key Lab of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaodong Qin
- State Key Lab of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chunyan Cheng
- State Key Lab of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ziang Li
- State Key Lab of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qunfeng Lou
- State Key Lab of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ji Li
- State Key Lab of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinfeng Chen
- State Key Lab of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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Warchałowska-Śliwa E, Grzywacz B, Heller KG, Chobanov DP. Comparative analysis of chromosomes in the Palaearctic bush-crickets of tribe Pholidopterini (Orthoptera, Tettigoniinae). COMPARATIVE CYTOGENETICS 2017; 11:309-324. [PMID: 28919967 PMCID: PMC5596980 DOI: 10.3897/compcytogen.v11i2.12070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/28/2017] [Indexed: 06/07/2023]
Abstract
The present study focused on the evolution of the karyotype in four genera of the tribe Pholidopterini: Eupholidoptera Mařan, 1953, Parapholidoptera Mařan, 1953, Pholidoptera Wesmaël, 1838, Uvarovistia Mařan, 1953. Chromosomes were analyzed using fluorescence in situ hybridization (FISH) with 18S rDNA and (TTAGG) n telomeric probes, and classical techniques, such as C-banding, silver impregnation and fluorochrome DAPI/CMA3 staining. Most species retained the ancestral diploid chromosome number 2n = 31 (male) or 32 (female), while some of the taxa, especially a group of species within genus Pholidoptera, evolved a reduced chromosome number 2n = 29. All species show the same sex determination system X0/XX. In some taxa, a pericentric inversion has changed the morphology of the ancestral acrocentric X chromosome to the biarmed X. The rDNA loci coincided with active NORs and C-band/CG-rich segments. A comparison of the location of the single rDNA/NOR in the genus Pholidoptera suggests that reduced chromosome number results from Robertsonian translocation between two pairs of autosomes, one carrying the rDNA/NOR. The results constitute a step towards better understanding of the chromosomal reorganization and evolution within the tribe Phaneropterini and the whole subfamily Tettigoniinae.
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Affiliation(s)
- Elżbieta Warchałowska-Śliwa
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Krakow, Poland
| | - Beata Grzywacz
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Krakow, Poland
| | | | - Dragan P. Chobanov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Boul., 1000 Sofia, Bulgaria
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Chamorro-Rengifo J, Olivier RDS, Araujo D. Bucrates lanista Rehn 1918 (Tettigoniidae: Conocephalinae): The First Record from the Brazilian Pantanal, the First Description of the Male, the First Karyotypic Report for the Genus, and the First Telomeric Hybridization of the Subfamily. Zoolog Sci 2016; 33:537-544. [PMID: 27715412 DOI: 10.2108/zs150176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Bucrates lanista, the most southerly distributed species in the genus Bucrates Burmeister, was originally described from Brazil based on a female collected in the state of Rio Grande do Sul, but the species has not been recorded since 1918. In this work, we report that B. lanista inhabits the Pantanal Wetland in the state of Mato Grosso do Sul and, for the first time, describe the male. Individuals of B. lanista are gregarious and present a brown/green color dimorphism; this behavior and color variation are also observed in species of closely related genera. Individuals from the Pantanal vary slightly from those of Rio Grande do Sul. The karyotype was determined to be 2n♂ = 21 = 20 + X0 and 2n♀ = 22 = 20 + XX. The X chromosome is metacentric and the largest of the complement, and all of the autosomes are submetacentrics. All chromosomes solely present telomeric (TTAGG)n repeats at their ends, and some chromosomes present positive and negative DAPI bands.
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Affiliation(s)
- Juliana Chamorro-Rengifo
- 1 Programa de Pós-Graduação em Biologia Animal, Centro de Ciências Biológicas e da Saúde,Universidade Federal de Mato Grosso do Sul. Campo Grande, Mato Grosso do Sul, Brasil
| | - Renan da Silva Olivier
- 2 Laboratório de Sistemática, Ecologia e Evolução, Programa de Pós-Graduação em Biologia Animal,Centro de Ciências Biológicas e da Saúde, Universidade Federal de Mato Grosso do Sul.Campo Grande, Mato Grosso do Sul, Brasil
| | - Douglas Araujo
- 3 Laboratório de Citogenética Molecular Animal, Programa de Pós-Graduação em Biologia Animal,Centro de Ciências Biológicas e da Saúde, Universidade Federal de Mato Grosso do Sul.Campo Grande, Mato Grosso do Sul, Brasil
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Review of the East African species of the phaneropterine genus Parapyrrhicia Brunner von Wattenwyl, 1891 (Insecta: Orthoptera): secret communication of a forest-bound taxon. ORG DIVERS EVOL 2016. [DOI: 10.1007/s13127-016-0303-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Chobanov DP, Kaya S, Grzywacz B, Warchałowska-Śliwa E, Çıplak B. The Anatolio-Balkan phylogeographic fault: a snapshot from the genusIsophya(Orthoptera, Tettigoniidae). ZOOL SCR 2016. [DOI: 10.1111/zsc.12194] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dragan P. Chobanov
- Institute of Biodiversity and Ecosystem Research; Bulgarian Academy of Sciences; 1 Tsar Osvoboditel Blvd. 1000 Sofia Bulgaria
| | - Sarp Kaya
- Mehmet Akif Ersoy University; Health Services; Vocational Schools; 15030 Burdur Turkey
| | - Beata Grzywacz
- Institute of Systematics and Evolution of Animals; Polish Academy of Sciences; Sławkowska 17 31-016 Krakow Poland
| | - Elżbieta Warchałowska-Śliwa
- Institute of Systematics and Evolution of Animals; Polish Academy of Sciences; Sławkowska 17 31-016 Krakow Poland
| | - Battal Çıplak
- Faculty of Sciences; Akdeniz University; 07058 Antalya Turkey
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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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Grzywacz B, Hemp C, Heller KG, Hemp A, Chobanov DP, Warchałowska-Śliwa E. Cytogenetics and molecular differentiation in the African armoured ground bushcrickets (Orthoptera: Tettigoniidae: Hetrodinae). ZOOL ANZ 2015. [DOI: 10.1016/j.jcz.2015.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Zhang Y, Cheng C, Li J, Yang S, Wang Y, Li Z, Chen J, Lou Q. Chromosomal structures and repetitive sequences divergence in Cucumis species revealed by comparative cytogenetic mapping. BMC Genomics 2015; 16:730. [PMID: 26407707 PMCID: PMC4583154 DOI: 10.1186/s12864-015-1877-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 08/24/2015] [Indexed: 12/23/2022] Open
Abstract
Background Differentiation and copy number of repetitive sequences affect directly chromosome structure which contributes to reproductive isolation and speciation. Comparative cytogenetic mapping has been verified an efficient tool to elucidate the differentiation and distribution of repetitive sequences in genome. In present study, the distinct chromosomal structures of five Cucumis species were revealed through genomic in situ hybridization (GISH) technique and comparative cytogenetic mapping of major satellite repeats. Results Chromosome structures of five Cucumis species were investigated using GISH and comparative mapping of specific satellites. Southern hybridization was employed to study the proliferation of satellites, whose structural characteristics were helpful for analyzing chromosome evolution. Preferential distribution of repetitive DNAs at the subtelomeric regions was found in C. sativus, C hystrix and C. metuliferus, while majority was positioned at the pericentromeric heterochromatin regions in C. melo and C. anguria. Further, comparative GISH (cGISH) through using genomic DNA of other species as probes revealed high homology of repeats between C. sativus and C. hystrix. Specific satellites including 45S rDNA, Type I/II, Type III, Type IV, CentM and telomeric repeat were then comparatively mapped in these species. Type I/II and Type IV produced bright signals at the subtelomeric regions of C. sativus and C. hystrix simultaneously, which might explain the significance of their amplification in the divergence of Cucumis subgenus from the ancient ancestor. Unique positioning of Type III and CentM only at the centromeric domains of C. sativus and C. melo, respectively, combining with unique southern bands, revealed rapid evolutionary patterns of centromeric DNA in Cucumis. Obvious interstitial telomeric repeats were observed in chromosomes 1 and 2 of C. sativus, which might provide evidence of the fusion hypothesis of chromosome evolution from x = 12 to x = 7 in Cucumis species. Besides, the significant correlation was found between gene density along chromosome and GISH band intensity in C. sativus and C. melo. Conclusions In summary, comparative cytogenetic mapping of major satellites and GISH revealed the distinct differentiation of chromosome structure during species formation. The evolution of repetitive sequences was the main force for the divergence of Cucumis species from common ancestor. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1877-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yunxia Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Chunyan Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Ji Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Shuqiong Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Yunzhu Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Ziang Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jinfeng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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Hemp C, Heller KG, Warchałowska-Śliwa E, Grzywacz B, Hemp A. Review of the Plangia graminea (Serville) complex and the description of new Plangia species from East Africa (Orthoptera: Phaneropteridae, Phaneropterinae) with data on habitat, bioacoustics, and chromosomes. ORG DIVERS EVOL 2015. [DOI: 10.1007/s13127-015-0216-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Cytogenetics of Aspidogaster limacoides (Trematoda, Aspidogastrea): karyotype, spermatocyte division, and genome size. Parasitol Res 2015; 114:1473-83. [DOI: 10.1007/s00436-015-4330-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 01/19/2015] [Indexed: 10/24/2022]
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Hemp C, Heller KG, Warchałowska-Śliwa E, Grzywacz B, Hemp A. Ecology, acoustics and chromosomes of the East African genus Afroanthracites Hemp & Ingrisch (Orthoptera, Tettigoniidae, Conocephalinae, Agraeciini) with the description of new species. ORG DIVERS EVOL 2014. [DOI: 10.1007/s13127-014-0194-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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