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Frydrychová RČ, Konopová B, Peska V, Brejcha M, Sábová M. Telomeres and telomerase: active but complex players in life-history decisions. Biogerontology 2024; 25:205-226. [PMID: 37610666 DOI: 10.1007/s10522-023-10060-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 08/24/2023]
Abstract
Studies on human telomeres have established that telomeres exert a significant influence on lifespan and health of organisms. However, recent research has indicated that the original idea that telomeres affect lifespan in a universal and central manner across all eukaryotic species is an oversimplification. Indeed, findings from a variety of animal species revealed that the role of telomere biology in aging is more subtle and intricate than previously recognized. Here, we show how telomere biology varies depending on the taxon. We also show how telomere biology corresponds to basic life history traits and affects the life table of a species and investments in growth, body size, reproduction, and lifespan; telomeres are hypothesized to shape evolutionary perspectives for species in an active but complex manner. Our evaluation is based on telomere biology data from many examples from throughout the animal kingdom that vary according to the degree of organismal complexity and life history strategies.
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Affiliation(s)
- Radmila Čapková Frydrychová
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, Ceske Budejovice, Czech Republic.
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, Ceske Budejovice, Czech Republic.
| | - Barbora Konopová
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, Ceske Budejovice, Czech Republic
| | - Vratislav Peska
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00, Brno, Czech Republic
| | - Miloslav Brejcha
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, Ceske Budejovice, Czech Republic
| | - Michala Sábová
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, Ceske Budejovice, Czech Republic
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Kwak Y, Hansen AK. Unveiling metabolic integration in psyllids and their nutritional endosymbionts through comparative transcriptomics analysis. iScience 2023; 26:107930. [PMID: 37810228 PMCID: PMC10558732 DOI: 10.1016/j.isci.2023.107930] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/23/2023] [Accepted: 09/12/2023] [Indexed: 10/10/2023] Open
Abstract
Psyllids, a group of insects that feed on plant sap, have a symbiotic relationship with an endosymbiont called Carsonella. Carsonella synthesizes essential amino acids and vitamins for its psyllid host, but lacks certain genes required for this process, suggesting a compensatory role of psyllid host genes. To investigate this, gene expression was compared between two psyllid species, Bactericera cockerelli and Diaphorina citri, in specialized cells where Carsonella resides (bacteriomes). Collaborative psyllid genes, including horizontally transferred genes, showed patterns of conserved gene expression; however, species-specific patterns were also observed, suggesting differences in the nutritional metabolism between psyllid species. Also, the recycling of nitrogen in bacteriomes may primarily rely on glutamate dehydrogenase (GDH). Additionally, lineage-specific gene clusters were differentially expressed in B. cockerelli and D. citri bacteriomes and are highlighted here. These findings shed light on potential host adaptations for the regulation of this symbiosis due to host, microbiome, and environmental differences.
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Affiliation(s)
- Younghwan Kwak
- Department of Life and Environmental Sciences, University of California, Merced, 5200 Lake Road, Merced, CA 95343, USA
| | - Allison K Hansen
- Department of Entomology, University of California, Riverside, 900 University Avenue, Riverside, CA 92521, USA
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Luo X, He Z, Liu J, Wu H, Gong X. FISH Mapping of Telomeric and Non-Telomeric (AG3T3)3 Reveal the Chromosome Numbers and Chromosome Rearrangements of 41 Woody Plants. Genes (Basel) 2022; 13:genes13071239. [PMID: 35886022 PMCID: PMC9323580 DOI: 10.3390/genes13071239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/12/2022] [Accepted: 07/12/2022] [Indexed: 02/05/2023] Open
Abstract
Data for the chromosomal FISH mapping localization of (AG3T3)3 are compiled for 37 species belonging 27 families; for 24 species and 14 families, this is the first such report. The chromosome number and length ranged from 14–136 and 0.56–14.48 μm, respectively. A total of 23 woody plants presented chromosome length less than 3 μm, thus belonging to the small chromosome group. Telomeric signals were observed at each chromosome terminus in 38 plants (90.5%) and were absent at several chromosome termini in only four woody plants (9.5%). Non-telomeric signals were observed in the chromosomes of 23 plants (54.8%); in particular, abundant non-telomeric (AG3T3)3 was obviously observed in Chimonanthus campanulatus. Telomeric signals outside of the chromosome were observed in 11 woody plants (26.2%). Overall, ten (AG3T3)3 signal pattern types were determined, indicating the complex genome architecture of the 37 considered species. The variation in signal pattern was likely due to chromosome deletion, duplication, inversion, and translocation. In addition, large primary constriction was observed in some species, probably due to or leading to chromosome breakage and the formation of new chromosomes. The presented results will guide further research focused on determining the chromosome number and disclosing chromosome rearrangements of woody plants.
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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: 9] [Impact Index Per Article: 4.5] [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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Nath S, Shaw DE, White MA. Improved contiguity of the threespine stickleback genome using long-read sequencing. G3-GENES GENOMES GENETICS 2021; 11:6114463. [PMID: 33598708 PMCID: PMC8022941 DOI: 10.1093/g3journal/jkab007] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/27/2020] [Indexed: 12/28/2022]
Abstract
While the cost and time for assembling a genome has drastically decreased, it still remains a challenge to assemble a highly contiguous genome. These challenges are rapidly being overcome by the integration of long-read sequencing technologies. Here, we use long-read sequencing to improve the contiguity of the threespine stickleback fish (Gasterosteus aculeatus) genome, a prominent genetic model species. Using Pacific Biosciences sequencing, we assembled a highly contiguous genome of a freshwater fish from Paxton Lake. Using contigs from this genome, we were able to fill over 76.7% of the gaps in the existing reference genome assembly, improving contiguity over fivefold. Our gap filling approach was highly accurate, validated by 10X Genomics long-distance linked-reads. In addition to closing a majority of gaps, we were able to assemble segments of telomeres and centromeres throughout the genome. This highlights the power of using long sequencing reads to assemble highly repetitive and difficult to assemble regions of genomes. This latest genome build has been released through a newly designed community genome browser that aims to consolidate the growing number of genomics datasets available for the threespine stickleback fish.
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Affiliation(s)
- Shivangi Nath
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Daniel E Shaw
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Michael A White
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
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Prušáková D, Peska V, Pekár S, Bubeník M, Čížek L, Bezděk A, Čapková Frydrychová R. Telomeric DNA sequences in beetle taxa vary with species richness. Sci Rep 2021; 11:13319. [PMID: 34172809 PMCID: PMC8233369 DOI: 10.1038/s41598-021-92705-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/14/2021] [Indexed: 02/06/2023] Open
Abstract
Telomeres are protective structures at the ends of eukaryotic chromosomes, and disruption of their nucleoprotein composition usually results in genome instability and cell death. Telomeric DNA sequences have generally been found to be exceptionally conserved in evolution, and the most common pattern of telomeric sequences across eukaryotes is (TxAyGz)n maintained by telomerase. However, telomerase-added DNA repeats in some insect taxa frequently vary, show unusual features, and can even be absent. It has been speculated about factors that might allow frequent changes in telomere composition in Insecta. Coleoptera (beetles) is the largest of all insect orders and based on previously available data, it seemed that the telomeric sequence of beetles varies to a great extent. We performed an extensive mapping of the (TTAGG)n sequence, the ancestral telomeric sequence in Insects, across the main branches of Coleoptera. Our study indicates that the (TTAGG)n sequence has been repeatedly or completely lost in more than half of the tested beetle superfamilies. Although the exact telomeric motif in most of the (TTAGG)n-negative beetles is unknown, we found that the (TTAGG)n sequence has been replaced by two alternative telomeric motifs, the (TCAGG)n and (TTAGGG)n, in at least three superfamilies of Coleoptera. The diversity of the telomeric motifs was positively related to the species richness of taxa, regardless of the age of the taxa. The presence/absence of the (TTAGG)n sequence highly varied within the Curculionoidea, Chrysomeloidea, and Staphylinoidea, which are the three most diverse superfamilies within Metazoa. Our data supports the hypothesis that telomere dysfunctions can initiate rapid genomic changes that lead to reproductive isolation and speciation.
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Affiliation(s)
- Daniela Prušáková
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Vratislav Peska
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Michal Bubeník
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Lukáš Čížek
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Aleš Bezděk
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Radmila Čapková Frydrychová
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic.
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
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Peska V, Garcia S. Origin, Diversity, and Evolution of Telomere Sequences in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:117. [PMID: 32153618 PMCID: PMC7046594 DOI: 10.3389/fpls.2020.00117] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/27/2020] [Indexed: 05/18/2023]
Abstract
Telomeres are basic structures of eukaryote genomes. They distinguish natural chromosome ends from double-stranded breaks in DNA and protect chromosome ends from degradation or end-to-end fusion with other chromosomes. Telomere sequences are usually tandemly arranged minisatellites, typically following the formula (TxAyGz)n. Although they are well conserved across large groups of organisms, recent findings in plants imply that their diversity has been underestimated. Changes in telomeres are of enormous evolutionary importance as they can affect whole-genome stability. Even a small change in the telomere motif of each repeat unit represents an important interference in the system of sequence-specific telomere binding proteins. Here, we provide an overview of telomere sequences, considering the latest phylogenomic evolutionary framework of plants in the broad sense (Archaeplastida), in which new telomeric sequences have recently been found in diverse and economically important families such as Solanaceae and Amaryllidaceae. In the family Lentibulariaceae and in many groups of green algae, deviations from the typical plant telomeric sequence have also been detected recently. Ancestry and possible homoplasy in telomeric motifs, as well as extant gaps in knowledge are discussed. With the increasing availability of genomic approaches, it is likely that more telomeric diversity will be uncovered in the future. We also discuss basic methods used for telomere identification and we explain the implications of the recent discovery of plant telomerase RNA on further research about the role of telomerase in eukaryogenesis or on the molecular causes and consequences of telomere variability.
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Affiliation(s)
- Vratislav Peska
- Department of Cell Biology and Radiobiology, The Czech Academy of Sciences, Institute of Biophysics, Brno, Czechia
| | - Sònia Garcia
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
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A telomerase with novel non-canonical roles: TERT controls cellular aggregation and tissue size in Dictyostelium. PLoS Genet 2019; 15:e1008188. [PMID: 31237867 PMCID: PMC6592521 DOI: 10.1371/journal.pgen.1008188] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/10/2019] [Indexed: 11/19/2022] Open
Abstract
Telomerase, particularly its main subunit, the reverse transcriptase, TERT, prevents DNA erosion during eukaryotic chromosomal replication, but also has poorly understood non-canonical functions. Here, in the model social amoeba Dictyostelium discoideum, we show that the protein encoded by tert has telomerase-like motifs, and regulates, non-canonically, important developmental processes. Expression levels of wild-type (WT) tert were biphasic, peaking at 8 and 12 h post-starvation, aligning with developmental events, such as the initiation of streaming (~7 h) and mound formation (~10 h). In tert KO mutants, however, aggregation was delayed until 16 h. Large, irregular streams formed, then broke up, forming small mounds. The mound-size defect was not induced when a KO mutant of countin (a master size-regulating gene) was treated with TERT inhibitors, but anti-countin antibodies did rescue size in the tert KO. Although, conditioned medium (CM) from countin mutants failed to rescue size in the tert KO, tert KO CM rescued the countin KO phenotype. These and additional observations indicate that TERT acts upstream of smlA/countin: (i) the observed expression levels of smlA and countin, being respectively lower and higher (than WT) in the tert KO; (ii) the levels of known size-regulation intermediates, glucose (low) and adenosine (high), in the tert mutant, and the size defect's rescue by supplemented glucose or the adenosine-antagonist, caffeine; (iii) the induction of the size defect in the WT by tert KO CM and TERT inhibitors. The tert KO's other defects (delayed aggregation, irregular streaming) were associated with changes to cAMP-regulated processes (e.g. chemotaxis, cAMP pulsing) and their regulatory factors (e.g. cAMP; acaA, carA expression). Overexpression of WT tert in the tert KO rescued these defects (and size), and restored a single cAMP signaling centre. Our results indicate that TERT acts in novel, non-canonical and upstream ways, regulating key developmental events in Dictyostelium.
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Telomere maintenance during anterior regeneration and aging in the freshwater annelid Aeolosoma viride. Sci Rep 2018; 8:18078. [PMID: 30584242 PMCID: PMC6305377 DOI: 10.1038/s41598-018-36396-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/20/2018] [Indexed: 12/13/2022] Open
Abstract
Aging is a complex process involving declines in various cellular and physical functionalities, including regenerative ability. Telomere maintenance is thought to be necessary for regeneration, and telomere attrition is one mechanism that contributes to aging. However, it is unclear if aging affects regeneration owing to deterioration of telomeric maintenance. We introduce Aeolosoma viride—a freshwater annelid with strong regenerative abilities—as a new model for studying the effects of aging on telomere functions and regeneration. We show that the anterior regenerative ability of A. viride declines with age. We characterized the A. viride telomere sequence as being composed of TTAGGG repeats and identifyied the telomerase gene Avi-tert. In adult A. viride, telomerase was constantly active and telomere lengths were similar among different body sections and stably maintained with age. Notably, we found that regeneration did not result in telomere shortening at regenerating sites. Moreover, transient up-regulation of Avi-tert expression and telomerase activity was observed at regenerating sites, which might promote telomere lengthening to counteract telomere erosion resulting from cell proliferation. Our study suggests that although aging affects A. viride regeneration independent of steady-state telomere length, timely regulation of telomerase functions is critical for the regeneration process in A. viride.
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Anokhin BA, Kuznetsova VG. FISH-based karyotyping of Pelmatohydraoligactis (Pallas, 1766), Hydraoxycnida Schulze, 1914, and H.magnipapillata Itô, 1947 (Cnidaria, Hydrozoa). COMPARATIVE CYTOGENETICS 2018; 12:539-548. [PMID: 30613371 PMCID: PMC6308218 DOI: 10.3897/compcytogen.v12i2.32120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 12/12/2018] [Indexed: 06/09/2023]
Abstract
An account is given of the karyotypes of Hydramagnipapillata Itô, 1947, H.oxycnida Schulze, 1914, and Pelmatohydraoligactis (Pallas, 1766) (Cnidaria, Hydrozoa, Hydridae). A number of different techniques were used: conventional karyotype characterization by standard staining, DAPI-banding and C-banding was complemented by the physical mapping of the ribosomal RNA (18S rDNA probe) and H3 histone genes, and the telomeric (TTAGGG) n sequence by fluorescence in situ hybridization (FISH). We found that the species studied had 2n = 30; constitutive heterochromatin was present in the centromeric regions of the chromosomes; the "vertebrate" telomeric (TTAGGG) n motif was located on both ends of each chromosome and no interstitial sites were detected; 18S rDNA was mapped on the largest chromosome pair in H.magnipapillata and on one of the largest chromosome pairs in H.oxycnida and P.oligactis; in H.magnipapillata, the major rRNA and H3 histone multigene families were located on the largest pair of chromosomes, on their long arms and in the centromeric areas respectively. This is the first chromosomal mapping of H3 in hydras.
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Affiliation(s)
- Boris A. Anokhin
- Zoological Institute of Russian Academy of Sciences, St. Petersburg, 199034, RussiaZoological Institute of Russian Academy of SciencesSt. PetersburgRussia
| | - Valentina G. Kuznetsova
- Zoological Institute of Russian Academy of Sciences, St. Petersburg, 199034, RussiaZoological Institute of Russian Academy of SciencesSt. PetersburgRussia
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Guo L, Accorsi A, He S, Guerrero-Hernández C, Sivagnanam S, McKinney S, Gibson M, Sánchez Alvarado A. An adaptable chromosome preparation methodology for use in invertebrate research organisms. BMC Biol 2018; 16:25. [PMID: 29482548 PMCID: PMC5828064 DOI: 10.1186/s12915-018-0497-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/07/2018] [Indexed: 12/16/2022] Open
Abstract
Background The ability to efficiently visualize and manipulate chromosomes is fundamental to understanding the genome architecture of organisms. Conventional chromosome preparation protocols developed for mammalian cells and those relying on species-specific conditions are not suitable for many invertebrates. Hence, a simple and inexpensive chromosome preparation protocol, adaptable to multiple invertebrate species, is needed. Results We optimized a chromosome preparation protocol and applied it to several planarian species (phylum Platyhelminthes), the freshwater apple snail Pomacea canaliculata (phylum Mollusca), and the starlet sea anemone Nematostella vectensis (phylum Cnidaria). We demonstrated that both mitotically active adult tissues and embryos can be used as sources of metaphase chromosomes, expanding the potential use of this technique to invertebrates lacking cell lines and/or with limited access to the complete life cycle. Simple hypotonic treatment with deionized water was sufficient for karyotyping; growing cells in culture was not necessary. The obtained karyotypes allowed the identification of differences in ploidy and chromosome architecture among otherwise morphologically indistinguishable organisms, as in the case of a mixed population of planarians collected in the wild. Furthermore, we showed that in all tested organisms representing three different phyla this protocol could be effectively coupled with downstream applications, such as chromosome fluorescent in situ hybridization. Conclusions Our simple and inexpensive chromosome preparation protocol can be readily adapted to new invertebrate research organisms to accelerate the discovery of novel genomic patterns across the branches of the tree of life.
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Affiliation(s)
- Longhua Guo
- University of California, Los Angeles, CA, USA
| | - Alice Accorsi
- Stowers Institute for Medical Research, Kansas City, MO, USA.,Howard Hughes Medical Institute, Kansas City, MO, USA
| | - Shuonan He
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | | | | | - Sean McKinney
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Matthew Gibson
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Alejandro Sánchez Alvarado
- Stowers Institute for Medical Research, Kansas City, MO, USA. .,Howard Hughes Medical Institute, Kansas City, MO, USA.
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12
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Chirino MG, Dalíková M, Marec FR, Bressa MJ. Chromosomal distribution of interstitial telomeric sequences as signs of evolution through chromosome fusion in six species of the giant water bugs (Hemiptera, Belostoma). Ecol Evol 2017; 7:5227-5235. [PMID: 28770061 PMCID: PMC5528210 DOI: 10.1002/ece3.3098] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 04/26/2017] [Accepted: 04/27/2017] [Indexed: 11/11/2022] Open
Abstract
Tandem arrays of TTAGG repeats show a highly conserved location at the telomeres across the phylogenetic tree of arthropods. In giant water bugs Belostoma, the chromosome number changed during speciation by fragmentation of the single ancestral X chromosome, resulting in a multiple sex chromosome system. Several autosome–autosome fusions and a fusion between the sex chromosome pair and an autosome pair resulted in the reduced number in several species. We mapped the distribution of telomeric sequences and interstitial telomeric sequences (ITSs) in Belostoma candidulum (2n = 12 + XY/XX; male/female), B. dentatum (2n = 26 + X1X2Y/X1X1X2X2), B. elegans (2n = 26 + X1X2Y/X1X1X2X2), B. elongatum (2n = 26 + X1X2Y/X1X1X2X2), B. micantulum (2n = 14 + XY/XX), and B. oxyurum (2n = 6 + XY/XX) by FISH with the (TTAGG)n probes. Hybridization signals confirmed the presence of TTAGG repeats in the telomeres of all species examined. The three species with reduced chromosome numbers showed additional hybridization signals in interstitial positions, indicating the occurrence of ITS. From the comparison of all species here analyzed, we observed inverse relationships between chromosome number and chromosome size, and between presence/absence of ITS and chromosome number. The ITS distribution between these closely related species supports the hypothesis that several telomere–telomere fusions of the chromosomes from an ancestral diploid chromosome number 2n = 26 + XY/XX played a major role in the karyotype evolution of Belostoma. Consequently, our study provide valuable features that can be used to understand the karyotype evolution, may contribute to a better understanding of taxonomic relationships, and also elucidate the high plasticity of nuclear genomes at the chromosomal level during the speciation processes.
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Affiliation(s)
- Mónica G Chirino
- Grupo de Citogenética de Insectos Instituto de Ecología, Genética y Evolución de Buenos Aires Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Ciudad Autónoma de Buenos Aires Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas Ciudad Autónoma de Buenos Aires Argentina
| | - Martina Dalíková
- Laboratory of Molecular Cytogenetics Institute of Entomology Biology Centre ASCR České Budějovice Czech Republic
| | - František R Marec
- Laboratory of Molecular Cytogenetics Institute of Entomology Biology Centre ASCR České Budějovice Czech Republic
| | - María J Bressa
- Grupo de Citogenética de Insectos Instituto de Ecología, Genética y Evolución de Buenos Aires Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Ciudad Autónoma de Buenos Aires Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas Ciudad Autónoma de Buenos Aires Argentina
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13
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Kuznetsova VG, Khabiev GN, Anokhin BA. Cytogenetic study on antlions (Neuroptera, Myrmeleontidae): first data on telomere structure and rDNA location. COMPARATIVE CYTOGENETICS 2016; 10:647-656. [PMID: 28123685 PMCID: PMC5240515 DOI: 10.3897/compcytogen.v10i4.10775] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/08/2016] [Indexed: 06/06/2023]
Abstract
Myrmeleontidae, commonly known as "antlions", are the most diverse family of the insect order Neuroptera, with over 1700 described species (in 191 genera) of which 37 species (in 21 genera) have so far been studied in respect to standard karyotypes. In the present paper we provide first data on the occurrence of the "insect-type" telomeric repeat (TTAGG) n and location of 18S rDNA clusters in the antlion karyotypes studied using fluorescence in situ hybridization (FISH). We show that males of Palpares libelluloides (Linnaeus, 1764) (Palparinae), Acanthaclisis occitanica (Villers, 1789) (Acanthaclisinae) and Distoleon tetragrammicus (Fabricius, 1798) (Nemoleontinae) have rDNA clusters on a large bivalent, two last species having an additional rDNA cluster on one of the sex chromosomes, most probably the X. (TTAGG) n - containing telomeres are clearly characteristic of Palpares libelluloides and Acanthaclisis occitanica; the presence of this telomeric motif in Distoleon tetragrammicus is questionable. In addition, we detected the presence of the (TTAGG) n telomeric repeat in Libelloides macaronius (Scopoli, 1763) from the family Ascalaphidae (owlflies), a sister group to the Myrmeleontidae. We presume that the "insect" motif (TTAGG) n was present in a common ancestor of the families Ascalaphidae and Myrmeleontidae within the neuropteran suborder Myrmeleontiformia.
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Affiliation(s)
- Valentina G. Kuznetsova
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, 199034, St. Petersburg, Russia
| | - Gadzhimurad N. Khabiev
- Prikaspiyskiy Institute of Biological Resources, Dagestan Scientific Centre, Russian Academy of Sciences, ul. M. Gadzhieva 45, 367025 Makhachkala, Russia
| | - Boris A. Anokhin
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, 199034, St. Petersburg, Russia
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Věchtová P, Dalíková M, Sýkorová M, Žurovcová M, Füssy Z, Zrzavá M. CpSAT-1, a transcribed satellite sequence from the codling moth, Cydia pomonella. Genetica 2016; 144:385-95. [PMID: 27236660 DOI: 10.1007/s10709-016-9907-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 05/23/2016] [Indexed: 10/21/2022]
Abstract
Satellite DNA (satDNA) is a non-coding component of eukaryotic genomes, located mainly in heterochromatic regions. Relevance of satDNA began to emerge with accumulating evidence of its potential yet hardly comprehensible role that it can play in the genome of many organisms. We isolated the first satDNA of the codling moth (Cydia pomonella, Tortricidae, Lepidoptera), a species with holokinetic chromosomes and a single large heterochromatic element, the W chromosome in females. The satDNA, called CpSAT-1, is located on all chromosomes of the complement, although in different amounts. Surprisingly, the satellite is almost missing in the heterochromatic W chromosome. Additionally, we isolated mRNA from all developmental stages (1st-5th instar larva, pupa, adult), both sexes (adult male and female) and several tissues (Malpighian tubules, gut, heart, testes, and ovaries) of the codling moth and showed the CpSAT-1 sequence was transcribed in all tested samples. Using CpSAT-1 specific primers we amplified, cloned and sequenced 40 monomers from cDNA and gDNA, respectively. The sequence analysis revealed a high mutation rate and the presence of potentially functional motifs, mainly in non-conserved regions of the monomers. Both the chromosomal distribution and the sequence analysis suggest that CPSAT-1 has no function in the C. pomonella genome.
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Affiliation(s)
- Pavlína Věchtová
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, Ceske Budejovice, Czech Republic.,Institute of Entomology, Biology Centre CAS, Ceske Budejovice, Czech Republic.,Institute of Parasitology, Biology Centre CAS, Ceske Budejovice, Czech Republic
| | - Martina Dalíková
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, Ceske Budejovice, Czech Republic.,Institute of Entomology, Biology Centre CAS, Ceske Budejovice, Czech Republic
| | - Miroslava Sýkorová
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, Ceske Budejovice, Czech Republic.,Institute of Entomology, Biology Centre CAS, Ceske Budejovice, Czech Republic
| | - Martina Žurovcová
- Institute of Entomology, Biology Centre CAS, Ceske Budejovice, Czech Republic
| | - Zoltán Füssy
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, Ceske Budejovice, Czech Republic.,Institute of Parasitology, Biology Centre CAS, Ceske Budejovice, Czech Republic
| | - Magda Zrzavá
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, Ceske Budejovice, Czech Republic. .,Institute of Entomology, Biology Centre CAS, Ceske Budejovice, Czech Republic.
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15
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Kuznetsova V, Aguin-Pombo D. Comparative cytogenetics of Auchenorrhyncha (Hemiptera, Homoptera): a review. Zookeys 2015:63-93. [PMID: 26807037 PMCID: PMC4722918 DOI: 10.3897/zookeys.538.6724] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 10/25/2015] [Indexed: 11/12/2022] Open
Abstract
A comprehensive review of cytogenetic features is provided for the large hemipteran suborder Auchenorrhyncha, which currently contains approximately 42,000 valid species. This review is based on the analysis of 819 species, 483 genera, and 31 families representing all presently recognized Auchenorrhyncha superfamilies, e.i. Cicadoidea (cicadas), Cercopoidea (spittle bugs), Membracoidea (leafhoppers and treehoppers), Myerslopioidea (ground-dwelling leafhoppers), and Fulgoroidea (planthoppers). History and present status of chromosome studies are described, as well as the structure of chromosomes, chromosome counts, trends and mechanisms of evolution of karyotypes and sex determining systems, their variation at different taxonomic levels and most characteristic (modal) states, occurrence of parthenogenesis, polyploidy, B-chromosomes and chromosome rearrangements, and methods used for cytogenetic analysis of Auchenorrhyncha.
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Affiliation(s)
- Valentina Kuznetsova
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, Universitetskaya nab. 1, 199034 St. Petersburg, Russia; Saint Petersburg Scientific Center, Universitetskaya nab. 5, 199034, St. Petersburg, Russia
| | - Dora Aguin-Pombo
- University of Madeira, 9000-390 Funchal, Madeira Il., Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), Vairão, Portugal
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16
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Kuznetsova VG, Grozeva SM, Hartung V, Anokhin BA. First evidence for (TTAGG)n telomeric sequence and sex chromosome post-reduction in Coleorrhyncha (Insecta, Hemiptera). COMPARATIVE CYTOGENETICS 2015; 9:523-32. [PMID: 26753072 PMCID: PMC4698568 DOI: 10.3897/compcytogen.v9i4.5609] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 08/10/2015] [Indexed: 05/24/2023]
Abstract
Telomeric repeats are general and significant structures of eukaryotic chromosomes. However, nothing is known about the molecular structure of telomeres in the enigmatic hemipteran suborder Coleorrhyncha (moss bugs) commonly considered as the sister group to the suborder Heteroptera (true bugs). The true bugs are known to differ from the rest of the Hemiptera in that they display an inverted sequence of sex chromosome divisions in male meiosis, the so-called sex chromosome post-reduction. To date, there has been no information about meiosis in Coleorrhyncha. Here we report a cytogenetic observation of Peloridium pomponorum, a representative of the single extant coleorrhynchan family Peloridiidae, using the standard chromosome staining and fluorescence in situ hybridization (FISH) with a (TTAGG) n telomeric probe. We show that Peloridium pomponorum displays 2n = 31 (30A + X) in males, the classical insect (TTAGG) n telomere organization and sex chromosome post-reduction during spermatocyte meiosis. The plesiomorphic insect-type (TTAGG) n telomeric sequence is suggested to be preserved in Coleorrhyncha and in a basal heteropteran infraorder Nepomorpha, but absent (lost) in the advanced heteropteran lineages Cimicomorpha and Pentatomomorpha. The telomere structure in other true bug infraorders is currently unknown. We consider here the inverted sequence of sex chromosome divisions as a synapomorphy of the group Coleorrhyncha + Heteroptera.
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Affiliation(s)
- Valentina G Kuznetsova
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, St. Petersburg 199034, Russia
| | - Snejana M Grozeva
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Blvd Tsar Osvoboditel 1, Sofia 1000, Bulgaria
| | - Viktor Hartung
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany; Staatliches Museum für Naturkunde Karlsruhe, Erbprinzenstraße 13, 76133 Karlsruhe, Germany
| | - Boris A Anokhin
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, St. Petersburg 199034, Russia
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17
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Vershinina AO, Anokhin BA, Lukhtanov VA. Ribosomal DNA clusters and telomeric (TTAGG)n repeats in blue butterflies (Lepidoptera, Lycaenidae) with low and high chromosome numbers. COMPARATIVE CYTOGENETICS 2015; 9:161-71. [PMID: 26140159 PMCID: PMC4488964 DOI: 10.3897/compcytogen.v9i2.4715] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 03/20/2015] [Indexed: 05/24/2023]
Abstract
Ribosomal DNA clusters and telomeric repeats are important parts of eukaryotic genome. However, little is known about their organization and localization in karyotypes of organisms with holocentric chromosomes. Here we present first cytogenetic study of these molecular structures in seven blue butterflies of the genus Polyommatus Latreille, 1804 with low and high chromosome numbers (from n=10 to n=ca.108) using fluorescence in situ hybridization (FISH) with 18S rDNA and (TTAGG) n telomeric probes. FISH with the 18S rDNA probe showed the presence of two different variants of the location of major rDNA clusters in Polyommatus species: with one or two rDNA-carrying chromosomes in haploid karyotype. We discuss evolutionary trends and possible mechanisms of changes in the number of ribosomal clusters. We also demonstrate that Polyommatus species have the classical insect (TTAGG) n telomere organization. This chromosome end protection mechanism probably originated de novo in small chromosomes that evolved via fragmentations.
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Affiliation(s)
- Alisa O. Vershinina
- Zoological Institute, Russian Academy of Sciences, Universitetskaya emb. 1, St. Petersburg 199034, Russia
| | - Boris A. Anokhin
- Zoological Institute, Russian Academy of Sciences, Universitetskaya emb. 1, St. Petersburg 199034, Russia
| | - Vladimir A. Lukhtanov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya emb. 1, St. Petersburg 199034, Russia
- Department of Entomology, St. Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg 199034, Russia
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18
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Vershinina AO, Anokhin BA, Lukhtanov VA. Ribosomal DNA clusters and telomeric (TTAGG)n repeats in blue butterflies (Lepidoptera, Lycaenidae) with low and high chromosome numbers. COMPARATIVE CYTOGENETICS 2015; 9:161-171. [PMID: 26140159 DOI: 10.3897/compcytogen.v.9i2.4751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 03/20/2015] [Indexed: 05/21/2023]
Abstract
Ribosomal DNA clusters and telomeric repeats are important parts of eukaryotic genome. However, little is known about their organization and localization in karyotypes of organisms with holocentric chromosomes. Here we present first cytogenetic study of these molecular structures in seven blue butterflies of the genus Polyommatus Latreille, 1804 with low and high chromosome numbers (from n=10 to n=ca.108) using fluorescence in situ hybridization (FISH) with 18S rDNA and (TTAGG) n telomeric probes. FISH with the 18S rDNA probe showed the presence of two different variants of the location of major rDNA clusters in Polyommatus species: with one or two rDNA-carrying chromosomes in haploid karyotype. We discuss evolutionary trends and possible mechanisms of changes in the number of ribosomal clusters. We also demonstrate that Polyommatus species have the classical insect (TTAGG) n telomere organization. This chromosome end protection mechanism probably originated de novo in small chromosomes that evolved via fragmentations.
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Affiliation(s)
- Alisa O Vershinina
- Zoological Institute, Russian Academy of Sciences, Universitetskaya emb. 1, St. Petersburg 199034, Russia
| | - Boris A Anokhin
- Zoological Institute, Russian Academy of Sciences, Universitetskaya emb. 1, St. Petersburg 199034, Russia
| | - Vladimir A Lukhtanov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya emb. 1, St. Petersburg 199034, Russia ; Department of Entomology, St. Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg 199034, Russia
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Schaible R, Sussman M, Kramer BH. Aging and potential for self-renewal: hydra living in the age of aging - a mini-review. Gerontology 2014; 60:548-56. [PMID: 25012456 DOI: 10.1159/000360397] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 02/06/2014] [Indexed: 11/19/2022] Open
Abstract
Hydra present an interesting deviation from typical life histories: they have an extensive capacity to regenerate and self-renew and seem to defy the aging process. Hydra have the ability to decouple the aging process from their life history and therefore provide us with a unique opportunity to gain insight into the aging process not only for basal hydrozoans but also for other species across the tree of life. We argue that under steady feeding and asexual reproduction Hydra species are able to escape aging as a result of high levels of cell proliferation and regenerative ability. We further highlight cellular processes for stem cell maintenance, such as the telomere dynamic, which prevent the accumulation of damage and protect against diseases and pathogens that mediate this condition. In addition, we discuss the causes of aging in other Hydra species.
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Affiliation(s)
- Ralf Schaible
- Max Planck Institute for Demographic Research, Rostock, Germany
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20
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Fulnecková J, Sevcíková T, Fajkus J, Lukesová A, Lukes M, Vlcek C, Lang BF, Kim E, Eliás M, Sykorová E. A broad phylogenetic survey unveils the diversity and evolution of telomeres in eukaryotes. Genome Biol Evol 2013; 5:468-83. [PMID: 23395982 PMCID: PMC3622300 DOI: 10.1093/gbe/evt019] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Telomeres, ubiquitous and essential structures of eukaryotic chromosomes, are known to come in a variety of forms, but knowledge about their actual diversity and evolution across the whole phylogenetic breadth of the eukaryotic life remains fragmentary. To fill this gap, we employed a complex experimental approach to probe telomeric minisatellites in various phylogenetically diverse groups of algae. Our most remarkable results include the following findings: 1) algae of the streptophyte class Klebsormidiophyceae possess the Chlamydomonas-type telomeric repeat (TTTTAGGG) or, in at least one species, a novel TTTTAGG repeat, indicating an evolutionary transition from the Arabidopsis-type repeat (TTTAGGG) ancestral for Chloroplastida; 2) the Arabidopsis-type repeat is also present in telomeres of Xanthophyceae, in contrast to the presence of the human-type repeat (TTAGGG) in other ochrophytes studied, and of the photosynthetic alveolate Chromera velia, consistent with its phylogenetic position close to apicomplexans and dinoflagellates; 3) glaucophytes and haptophytes exhibit the human-type repeat in their telomeres; and 4) ulvophytes and rhodophytes have unusual telomere structures recalcitrant to standard analysis. To obtain additional details on the distribution of different telomere types in eukaryotes, we performed in silico analyses of genomic data from major eukaryotic lineages, utilizing also genome assemblies from our on-going genome projects for representatives of three hitherto unsampled lineages (jakobids, malawimonads, and goniomonads). These analyses confirm the human-type repeat as the most common and possibly ancestral in eukaryotes, but alternative motifs replaced it along the phylogeny of diverse eukaryotic lineages, some of them several times independently.
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Affiliation(s)
- Jana Fulnecková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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21
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Salvadori S, Coluccia E, Deidda F, Cau A, Cannas R, Deiana AM. Comparative cytogenetics in four species of Palinuridae: B chromosomes, ribosomal genes and telomeric sequences. Genetica 2012; 140:429-37. [PMID: 23224906 DOI: 10.1007/s10709-012-9691-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 11/20/2012] [Indexed: 10/27/2022]
Abstract
The evolutionary pathway of Palinuridae (Crustacea, Decapoda) is still controversial, uncertain and unexplored, expecially from a karyological point of view. Here we describe the South African spiny lobster Jasus lalandii karyotype: n and 2n values, heterochromatin distribution, nucleolar organizer region (NOR) location and telomeric repeat structure and location. To compare the genomic and chromosomal organization in Palinuridae we located NORs in Panulirus regius, Palinurus gilchristi and Palinurus mauritanicus: all species showed multiple NORs. In J. lalandii NORs were located on three chromosome pairs, with interindividual polymorphism. In P. regius and in the two Palinurus species NORs were located on two chromosome pairs. In the two last species 45S ribosomal gene loci were also found on B chromosomes. In addition, the nature and location of telomeric repeats were investigated by FISH in J. lalandii, P. gilchristi, P. mauritanicus Palinurus elephas, and P. regius (Palinuridae, Achelata), and in Scyllarus arctus (Scyllaridae, Achelata): all these Achelata species showed the (TTAGG)n pentameric repeats. Furthermore, in J. lalandii these repeats occurred in all the telomeres and in some interstitial chromosomal sites, associated with NORs.
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Affiliation(s)
- Susanna Salvadori
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Via T. Fiorelli 1, 09126, Cagliari, Italy.
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22
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Drosopoulou E, Nakou I, Síchová J, Kubíčková S, Marec F, Mavragani-Tsipidou P. Sex chromosomes and associated rDNA form a heterochromatic network in the polytene nuclei of Bactrocera oleae (Diptera: Tephritidae). Genetica 2012; 140:169-80. [PMID: 22825842 DOI: 10.1007/s10709-012-9668-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 07/11/2012] [Indexed: 10/28/2022]
Abstract
The olive fruit fly, Bactrocera oleae, has a diploid set of 2n = 12 chromosomes including a pair of sex chromosomes, XX in females and XY in males, but polytene nuclei show only five polytene chromosomes, obviously formed by five autosome pairs. Here we examined the fate of the sex chromosomes in the polytene complements of this species using fluorescence in situ hybridization (FISH) with the X and Y chromosome-derived probes, prepared by laser microdissection of the respective chromosomes from mitotic metaphases. Specificity of the probes was verified by FISH in preparations of mitotic chromosomes. In polytene nuclei, both probes hybridized strongly to a granular heterochromatic network, indicating thus underreplication of the sex chromosomes. The X chromosome probe (in both female and male nuclei) highlighted most of the granular mass, whereas the Y chromosome probe (in male nuclei) identified a small compact body of this heterochromatic network. Additional hybridization signals of the X probe were observed in the centromeric region of polytene chromosome II and in the telomeres of six polytene arms. We also examined distribution of the major ribosomal DNA (rDNA) using FISH with an 18S rDNA probe in both mitotic and polytene chromosome complements of B. oleae. In mitotic metaphases, the probe hybridized exclusively to the sex chromosomes. The probe signals localized a discrete rDNA site at the end of the short arm of the X chromosome, whereas they appeared dispersed over the entire dot-like Y chromosome. In polytene nuclei, the rDNA was found associated with the heterochromatic network representing the sex chromosomes. Only in nuclei with preserved nucleolar structure, the probe signals were scattered in the restricted area of the nucleolus. Thus, our study clearly shows that the granular heterochromatic network of polytene nuclei in B. oleae is formed by the underreplicated sex chromosomes and associated rDNA.
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Affiliation(s)
- Elena Drosopoulou
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Telomere maintenance and telomerase activity are differentially regulated in asexual and sexual worms. Proc Natl Acad Sci U S A 2012; 109:4209-14. [PMID: 22371573 DOI: 10.1073/pnas.1118885109] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In most sexually reproducing animals, replication and maintenance of telomeres occurs in the germ line and during early development in embryogenesis through the use of telomerase. Somatic cells generally do not maintain telomere sequences, and these cells become senescent in adults as telomeres shorten to a critical length. Some animals reproduce clonally and must therefore require adult somatic mechanisms for maintaining their chromosome ends. Here we study the telomere biology of planarian flatworms with apparently limitless regenerative capacity fueled by a population of highly proliferative adult stem cells. We show that somatic telomere maintenance is different in asexual and sexual animals. Asexual animals maintain telomere length somatically during reproduction by fission or when regeneration is induced by amputation, whereas sexual animals only achieve telomere elongation through sexual reproduction. We demonstrate that this difference is reflected in the expression and alternate splicing of the protein subunit of the telomerase enzyme. Asexual adult planarian stem cells appear to maintain telomere length over evolutionary timescales without passage through a germ-line stage. The adaptations we observe demonstrate indefinite somatic telomerase activity in proliferating stem cells during regeneration or reproduction by fission, and establish planarians as a pertinent model for studying telomere structure, function, and maintenance.
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NAKAMICHI H, OJIMI MC, ISOMURA N, HIDAKA M. Somatic tissues of the coral Galaxea fascicularis possess telomerase activity. ACTA ACUST UNITED AC 2012. [DOI: 10.3755/galaxea.14.1_53] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hirotoshi NAKAMICHI
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus
| | - Michiko C. OJIMI
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus
| | - Naoko ISOMURA
- Department of Bioresources Engineering, Okinawa National College of Technology
| | - Michio HIDAKA
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus
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Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon. BMC Genomics 2011; 12:242. [PMID: 21575266 PMCID: PMC3124438 DOI: 10.1186/1471-2164-12-242] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 05/17/2011] [Indexed: 11/28/2022] Open
Abstract
Background The black tiger shrimp (Penaeus monodon) is one of the most important aquaculture species in the world, representing the crustacean lineage which possesses the greatest species diversity among marine invertebrates. Yet, we barely know anything about their genomic structure. To understand the organization and evolution of the P. monodon genome, a fosmid library consisting of 288,000 colonies and was constructed, equivalent to 5.3-fold coverage of the 2.17 Gb genome. Approximately 11.1 Mb of fosmid end sequences (FESs) from 20,926 non-redundant reads representing 0.45% of the P. monodon genome were obtained for repetitive and protein-coding sequence analyses. Results We found that microsatellite sequences were highly abundant in the P. monodon genome, comprising 8.3% of the total length. The density and the average length of microsatellites were evidently higher in comparison to those of other taxa. AT-rich microsatellite motifs, especially poly (AT) and poly (AAT), were the most abundant. High abundance of microsatellite sequences were also found in the transcribed regions. Furthermore, via self-BlastN analysis we identified 103 novel repetitive element families which were categorized into four groups, i.e., 33 WSSV-like repeats, 14 retrotransposons, 5 gene-like repeats, and 51 unannotated repeats. Overall, various types of repeats comprise 51.18% of the P. monodon genome in length. Approximately 7.4% of the FESs contained protein-coding sequences, and the Inhibitor of Apoptosis Protein (IAP) gene and the Innexin 3 gene homologues appear to be present in high abundance in the P. monodon genome. Conclusions The redundancy of various repeat types in the P. monodon genome illustrates its highly repetitive nature. In particular, long and dense microsatellite sequences as well as abundant WSSV-like sequences highlight the uniqueness of genome organization of penaeid shrimp from those of other taxa. These results provide substantial improvement to our current knowledge not only for shrimp but also for marine crustaceans of large genome size.
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TCAGG, an alternative telomeric sequence in insects. Chromosoma 2011; 120:367-76. [PMID: 21499744 DOI: 10.1007/s00412-011-0317-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 03/06/2011] [Accepted: 03/06/2011] [Indexed: 10/18/2022]
Abstract
The TTAGG repeat, the only determined telomerase-dependent sequence in the Insecta, is generally reputed to be the canonical telomeric motif within the class. By studying the distribution of telomeric DNAs in 30 coleopteran beetles using Southern hybridization, BAL 31 DNA end-degradation assay and fluorescence in situ hybridization, we showed that arrays built of a TCAGG repeat substitute for (TTAGG)n sequences in all tested species within the superfamily Tenebrionoidea. We also provided the experimental evidence that (TCAGG)n repeats represent the terminal sequences on all chromosomes of the model species Tribolium castaneum. (TCAGG)n repeats are therefore promoted as the first sequence-motif alternative to TTAGG-type chromosome ends in insects. Detection of species negative for both TTAGG and TCAGG reveals that, although widespread, these motifs are not ubiquitous telomeric sequences within the order Coleoptera. In addition, Timarcha balearica proved to be a species that harbors (TTAGG)n repeats, but not at telomeric positions, thus further increasing the complexity of telomeric DNAs. Our experiments discarded CTAGG, CTGGG, TTGGG, and TTAGGG variants as potential replacements in TTAGG/TCAGG-negative species, indicating that chromosome termini of these beetles comprise other form(s) of telomeric sequences and telomere maintenance mechanisms.
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Steele RE, David CN, Technau U. A genomic view of 500 million years of cnidarian evolution. Trends Genet 2010; 27:7-13. [PMID: 21047698 DOI: 10.1016/j.tig.2010.10.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Revised: 09/23/2010] [Accepted: 10/08/2010] [Indexed: 01/29/2023]
Abstract
Cnidarians (corals, anemones, jellyfish and hydras) are a diverse group of animals of interest to evolutionary biologists, ecologists and developmental biologists. With the publication of the genome sequences of Hydra and Nematostella, whose last common ancestor was the stem cnidarian, researchers are beginning to see the genomic underpinnings of cnidarian biology. Cnidarians are known for the remarkable plasticity of their morphology and life cycles. This plasticity is reflected in the Hydra and Nematostella genomes, which differ to an exceptional degree in size, base composition, transposable element content and gene conservation. It is now known what cnidarian genomes, given 500 million years, are capable of; as we discuss here, the next challenge is to understand how this genomic history has led to the striking diversity seen in this group.
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Affiliation(s)
- Robert E Steele
- Department of Biological Chemistry and the Developmental Biology Center, University of California, Irvine, CA 92697, USA.
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Castagnone-Sereno P, Danchin EGJ, Deleury E, Guillemaud T, Malausa T, Abad P. Genome-wide survey and analysis of microsatellites in nematodes, with a focus on the plant-parasitic species Meloidogyne incognita. BMC Genomics 2010; 11:598. [PMID: 20973953 PMCID: PMC3091743 DOI: 10.1186/1471-2164-11-598] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Accepted: 10/25/2010] [Indexed: 11/13/2022] Open
Abstract
Background Microsatellites are the most popular source of molecular markers for studying population genetic variation in eukaryotes. However, few data are currently available about their genomic distribution and abundance across the phylum Nematoda. The recent completion of the genomes of several nematode species, including Meloidogyne incognita, a major agricultural pest worldwide, now opens the way for a comparative survey and analysis of microsatellites in these organisms. Results Using MsatFinder, the total numbers of 1-6 bp perfect microsatellites detected in the complete genomes of five nematode species (Brugia malayi, Caenorhabditis elegans, M. hapla, M. incognita, Pristionchus pacificus) ranged from 2,842 to 61,547, and covered from 0.09 to 1.20% of the nematode genomes. Under our search criteria, the most common repeat motifs for each length class varied according to the different nematode species considered, with no obvious relation to the AT-richness of their genomes. Overall, (AT)n, (AG)n and (CT)n were the three most frequent dinucleotide microsatellite motifs found in the five genomes considered. Except for two motifs in P. pacificus, all the most frequent trinucleotide motifs were AT-rich, with (AAT)n and (ATT)n being the only common to the five nematode species. A particular attention was paid to the microsatellite content of the plant-parasitic species M. incognita. In this species, a repertoire of 4,880 microsatellite loci was identified, from which 2,183 appeared suitable to design markers for population genetic studies. Interestingly, 1,094 microsatellites were identified in 801 predicted protein-coding regions, 99% of them being trinucleotides. When compared against the InterPro domain database, 497 of these CDS were successfully annotated, and further assigned to Gene Ontology terms. Conclusions Contrasted patterns of microsatellite abundance and diversity were characterized in five nematode genomes, even in the case of two closely related Meloidogyne species. 2,245 di- to hexanucleotide loci were identified in the genome of M. incognita, providing adequate material for the future development of a wide range of microsatellite markers in this major plant parasite.
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Gomes NM, Shay JW, Wright WE. Telomere biology in Metazoa. FEBS Lett 2010; 584:3741-51. [PMID: 20655915 PMCID: PMC2928394 DOI: 10.1016/j.febslet.2010.07.031] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 07/19/2010] [Accepted: 07/20/2010] [Indexed: 12/22/2022]
Abstract
In this review we present critical overview of some of the available literature on the fundamental biology of telomeres and telomerase in Metazoan. With the exception of Nematodes and Arthropods, the (TTAGGG)(n) sequence is conserved in most Metazoa. Available data show that telomerase-based end maintenance is a very ancient mechanism in unicellular and multicellular organisms. In invertebrates, fish, amphibian, and reptiles persistent telomerase activity in somatic tissues might allow the maintenance of the extensive regenerative potentials of these species. Telomerase repression among birds and many mammals suggests that, as humans, they may use replicative aging as a tumor protection mechanism.
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Affiliation(s)
- Nuno M.V. Gomes
- Department of Cell Biology. The University of Texas Southwestern Medical Center at Dallas. 5323 Harry Hines Boulevard, Dallas, Texas, 75390-9039
| | - Jerry W. Shay
- Department of Cell Biology. The University of Texas Southwestern Medical Center at Dallas. 5323 Harry Hines Boulevard, Dallas, Texas, 75390-9039
| | - Woodring E. Wright
- Department of Cell Biology. The University of Texas Southwestern Medical Center at Dallas. 5323 Harry Hines Boulevard, Dallas, Texas, 75390-9039
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Senthilkumar R, Sabarinathan R, Hameed BS, Banerjee N, Chidambarathanu N, Karthik R, Sekar K. FAIR: A server for internal sequence repeats. Bioinformation 2010; 4:271-5. [PMID: 20978598 PMCID: PMC2957760 DOI: 10.6026/97320630004271] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Revised: 11/16/2009] [Accepted: 11/16/2009] [Indexed: 11/23/2022] Open
Abstract
UNLABELLED An Internet computing server has been developed to identify all the occurrences of the internal sequence repeats in a protein and DNA sequences. Further, an option is provided for the users to check the occurrence(s) of the resultant sequence repeats in the other sequence and structure (Protein Data Bank) databases. The databases deployed in the proposed computing engine are up-to-date and thus the users will get the latest information available in the respective databases. The server is freely accessible over the World Wide Web (WWW). AVAILABILITY http://bioserver1.physics.iisc.ernet.in/fair/
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Affiliation(s)
- Ramaswamy Senthilkumar
- Bioinformatics Centre, Centre of Excellence in Structural Biology and Bio-computing, Indian Institute of Science, Bangalore 560 012, India
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Robertson HM. The choanoflagellate Monosiga brevicollis karyotype revealed by the genome sequence: telomere-linked helicase genes resemble those of some fungi. Chromosome Res 2009; 17:873-82. [PMID: 19789987 DOI: 10.1007/s10577-009-9078-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 08/06/2009] [Accepted: 08/13/2009] [Indexed: 12/01/2022]
Abstract
The approximately 42 Mbp assembled genome sequence for the choanoflagellate Monosiga brevicollis reveals that most of the large scaffolds of 300-2,600 kb represent entire chromosomes or chromosome arms. Telomeres are partially assembled at the termini of 37 scaffolds, while another 43 scaffolds end in telomere-associated regions containing distinctive gene sets. Potential centromeric regions were identified on 39 scaffolds. Together, these observations suggest a karyotype of approximately 40 metacentric and submetacentric chromosomes averaging 1 Mbp in size. Genes encoding RecQ family DNA helicases, along with ankyrin-domain proteins and serine/threonine kinases, are associated with most telomeres, a feature shared with some fungi. This telomere-linked helicase gene arrangement might be ancestral to both fungi and choanoflagellates in the super-kingdom Opisthokonta; however, the great lability of telomere architecture suggests that it could also be a convergent feature.
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Affiliation(s)
- Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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Simple telomeres in a simple animal: absence of subtelomeric repeat regions in the placozoan Trichoplax adhaerens. Genetics 2008; 181:323-5. [PMID: 18984569 DOI: 10.1534/genetics.108.096289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Simple telomeres were identified in the genome assembly of the basal placozoan animal Trichoplax adhaerens. They have 1-2 kb of TTAGGG telomeric repeats, which are preceded by a subtelomeric region of 1.5-13 kb. Unlike subtelomeric regions in most animals examined, these subtelomeric regions are unique to each telomere.
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Voigt O, Erpenbeck D, Wörheide G. A fragmented metazoan organellar genome: the two mitochondrial chromosomes of Hydra magnipapillata. BMC Genomics 2008; 9:350. [PMID: 18655725 PMCID: PMC2518934 DOI: 10.1186/1471-2164-9-350] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2008] [Accepted: 07/26/2008] [Indexed: 01/30/2023] Open
Abstract
Background Animal mitochondrial (mt) genomes are characteristically circular molecules of ~16–20 kb. Medusozoa (Cnidaria excluding Anthozoa) are exceptional in that their mt genomes are linear and sometimes subdivided into two to presumably four different molecules. In the genus Hydra, the mt genome comprises one or two mt chromosomes. Here, we present the whole mt genome sequence from the hydrozoan Hydra magnipapillata, comprising the first sequence of a fragmented metazoan mt genome encoded on two linear mt chromosomes (mt1 and mt2). Results The H. magnipapillata mt chromosomes contain the typical metazoan set of 13 genes for respiratory proteins, the two rRNA genes and two tRNA genes. All genes are unidirectionally oriented on mt1 and mt2, and several genes overlap. The gene arrangement suggests that the two mt chromosomes originated from one linear molecule that separated between nd5 and rns. Strong correlations between the AT content of rRNA genes (rns and rnl) and the AT content of protein-coding genes among 24 cnidarian genomes imply that base composition is mainly determined by mt genome-wide constraints. We show that identical inverted terminal repeats (ITR) occur on both chromosomes; these ITR contain a partial copy or part of the 3' end of cox1 (54 bp). Additionally, both mt chromosomes possess identical oriented sequences (IOS) at the 5' and 3' ends (5' and 3' IOS) adjacent to the ITR. The 5' IOS contains trnM and non-coding sequences (119 bp), whereas the 3' IOS comprises a larger part (mt2) with a larger partial copy of cox1 (243 bp). Conclusion ITR are also documented in the two other available medusozoan mt genomes (Aurelia aurita and Hydra oligactis). In H. magnipapillata, the arrangement of ITR and 5' IOS and 3' IOS suggest that these regions are crucial for mt DNA replication and/or transcription initiation. An analogous organization occurs in a highly fragmented ichthyosporean mt genome. With our data, we can reject a model of mt replication that has previously been proposed for Hydra. This raises new questions regarding replication mechanisms probably employed by all medusozoans, and also has general implications for the expected organization of fragmented linear mt chromosomes of other taxa.
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Affiliation(s)
- Oliver Voigt
- Courant Research Center Geobiology, Georg-August-Universität Göttingen, Goldschmidtstr, 3, 37077 Göttingen, Germany.
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Barthélémy RM, Casanova JP, Faure E. Transcriptome Analysis of ESTs from a Chaetognath Reveals a Deep-Branching Clade of Retrovirus-Like Retrotransposons. Open Virol J 2008; 2:44-60. [PMID: 19440464 PMCID: PMC2678813 DOI: 10.2174/1874357900802010044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 04/08/2008] [Accepted: 04/09/2008] [Indexed: 01/04/2023] Open
Abstract
Chaetognaths constitute a small marine phylum exhibiting several characteristic which are highly unusual in animal genomes, including two classes of both rRNA and protein ribosomal genes. As in this phylum presence of retrovirus-like elements has never been documented, analysis of a published expressed sequence tag (EST) collection of the chaetognath Spadella cephaloptera has been made. Twelve sequences representing transcript sections of reverse transcriptase domain of active retrotransposons were isolated from~11,000 ESTs. Five of them are originated from Gypsy retrovirus-like elements, whereas the other are transcripts from a Bel-Pao LTR-retrotransposon, a Penelope-like element and LINE retrotransposons. Moreover, a part of a putative integrase has also been found. Phylogenetic analyses suggest a deep-branching clade of the retrovirus-like elements, which is in agreement with the probably Cambrian origin of the phylum. Moreover, retrotransposons have not been found in telomeric-like transcripts which are probably constituted by both vertebrate and arthropod canonical repeats.
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Affiliation(s)
- Roxane M Barthélémy
- LATP, CNRS-UMR 6632, Evolution biologique et modélisation, case 5, Université de Provence, Place Victor Hugo, 13331 Marseille cedex 3, France
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