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Wang H, Wu P, Xiong L, Kim HS, Kim JH, Ki JS. Nuclear genome of dinoflagellates: Size variation and insights into evolutionary mechanisms. Eur J Protistol 2024; 93:126061. [PMID: 38394997 DOI: 10.1016/j.ejop.2024.126061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024]
Abstract
Recent progress in high-throughput sequencing technologies has dramatically increased availability of genome data for prokaryotes and eukaryotes. Dinoflagellates have distinct chromosomes and a huge genome size, which make their genomic analysis complicated. Here, we reviewed the nuclear genomes of core dinoflagellates, focusing on the genome and cell size. Till now, the genome sizes of several dinoflagellates (more than 25) have been measured by certain methods (e.g., flow cytometry), showing a range of 3-250 pg of genomic DNA per cell. In contrast to their relatively small cell size, their genomes are huge (about 1-80 times the human haploid genome). In the present study, we collected the genome and cell size data of dinoflagellates and compared their relationships. We found that dinoflagellate genome size exhibits a positive correlation with cell size. On the other hand, we recognized that the genome size is not correlated with phylogenetic relatedness. These may be caused by genome duplication, increased gene copy number, repetitive non-coding DNA, transposon expansion, horizontal gene transfer, organelle-to-nucleus gene transfer, and/or mRNA reintegration into the genome. Ultimate verification of these factors as potential causative mechanisms would require sequencing of more dinoflagellate genomes in the future.
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Affiliation(s)
- Hui Wang
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China; Department of Life Science, Sangmyung University, Seoul 03016, Republic of Korea
| | - Peiling Wu
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Lu Xiong
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Han-Sol Kim
- Department of Life Science, Sangmyung University, Seoul 03016, Republic of Korea
| | - Jin Ho Kim
- Department of Earth and Marine Science, College of Ocean Sciences, Jeju National University, Jeju 63243, Republic of Korea
| | - Jang-Seu Ki
- Department of Life Science, Sangmyung University, Seoul 03016, Republic of Korea; Department of Biotechnology, Sangmyung University, Seoul 03016, Republic of Korea.
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2
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Bi YH, Li Z, Zhou ZG. Karyotype analysis of the brown seaweed Saccharina (or Laminaria) japonica. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.103081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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3
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Telomeres and Their Neighbors. Genes (Basel) 2022; 13:genes13091663. [PMID: 36140830 PMCID: PMC9498494 DOI: 10.3390/genes13091663] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/21/2022] Open
Abstract
Telomeres are essential structures formed from satellite DNA repeats at the ends of chromosomes in most eukaryotes. Satellite DNA repeat sequences are useful markers for karyotyping, but have a more enigmatic role in the eukaryotic cell. Much work has been done to investigate the structure and arrangement of repetitive DNA elements in classical models with implications for species evolution. Still more is needed until there is a complete picture of the biological function of DNA satellite sequences, particularly when considering non-model organisms. Celebrating Gregor Mendel’s anniversary by going to the roots, this review is designed to inspire and aid new research into telomeres and satellites with a particular focus on non-model organisms and accessible experimental and in silico methods that do not require specialized equipment or expensive materials. We describe how to identify telomere (and satellite) repeats giving many examples of published (and some unpublished) data from these techniques to illustrate the principles behind the experiments. We also present advice on how to perform and analyse such experiments, including details of common pitfalls. Our examples are a selection of recent developments and underexplored areas of research from the past. As a nod to Mendel’s early work, we use many examples from plants and insects, especially as much recent work has expanded beyond the human and yeast models traditional in telomere research. We give a general introduction to the accepted knowledge of telomere and satellite systems and include references to specialized reviews for the interested reader.
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Cuadrado Á, Figueroa RI, Sixto M, Bravo I, De Bustos A. First record of the spatial organization of the nucleosome-less chromatin of dinoflagellates: The nonrandom distribution of microsatellites and bipolar arrangement of telomeres in the nucleus of Gambierdiscus australes (Dinophyceae). JOURNAL OF PHYCOLOGY 2022; 58:297-307. [PMID: 35038777 DOI: 10.1111/jpy.13236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
Dinoflagellates are a group of protists whose exceptionally large genome is organized in permanently condensed nucleosome-less chromosomes. In this study, we examined the potential role of repetitive DNAs in both the structure of dinoflagellate chromosomes and the architecture of the dinoflagellate nucleus. Non-denaturing fluorescent in situ hybridization (ND-FSH) was used to determine the abundance and physical distribution of telomeric DNA and 16 microsatellites (1- to 4-bp repeats) in the nucleus of Gambierdiscus australes. The results showed an increased relative abundance of the different microsatellite motifs with increasing GC content. Two ND-FISH probes, (A)20 and (AAT)5 , did not yield signals whereas the remainder revealed a dispersed but nonrandom distribution of the microsatellites, mostly in clusters. The bean-shaped interphase nucleus of G. australes contained a region with a high density of trinucleotides. This nuclear compartment was located between the nucleolar organizer region (NOR), located on the concave side of the nucleus, and the convex side. Telomeric DNA was grouped in multiple foci and distributed in two polarized compartments: one associated with the NOR and the other peripherally located along the convex side of the nucleus. Changes in the position of the telomeres during cell division evidenced their dynamic distribution and thus that of the chromosomes during dinomitosis. These insights into the spatial organization of microsatellites and telomeres and thus into the nuclear architecture of G. australes will open up new lines of research into the structure and function of the nucleosome-less chromatin of dinoflagellates.
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Affiliation(s)
- Ángeles Cuadrado
- Departamento de Biomedicina y Biotecnología, Universidad de Alcalá (UAH), Alcalá de Henares, Madrid, 28805, Spain
| | - Rosa I Figueroa
- Centro Oceanográfico de Vigo, Instituto Español de Oceanografía (IEO-CSIC), Subida a Radio Faro 50, Vigo, 36390, Spain
| | - Marta Sixto
- Centro Oceanográfico de Vigo, Instituto Español de Oceanografía (IEO-CSIC), Subida a Radio Faro 50, Vigo, 36390, Spain
- Campus do Mar, Facultad de Ciencias del Mar, Universidad de Vigo, Vigo, 36311, Spain
| | - Isabel Bravo
- Centro Oceanográfico de Vigo, Instituto Español de Oceanografía (IEO-CSIC), Subida a Radio Faro 50, Vigo, 36390, Spain
| | - Alfredo De Bustos
- Departamento de Biomedicina y Biotecnología, Universidad de Alcalá (UAH), Alcalá de Henares, Madrid, 28805, Spain
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Gornik SG, Hu I, Lassadi I, Waller RF. The Biochemistry and Evolution of the Dinoflagellate Nucleus. Microorganisms 2019; 7:microorganisms7080245. [PMID: 31398798 PMCID: PMC6723414 DOI: 10.3390/microorganisms7080245] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/05/2019] [Accepted: 08/07/2019] [Indexed: 12/14/2022] Open
Abstract
Dinoflagellates are known to possess a highly aberrant nucleus-the so-called dinokaryon-that exhibits a multitude of exceptional biological features. These include: (1) Permanently condensed chromosomes; (2) DNA in a cholesteric liquid crystalline state, (3) extremely large DNA content (up to 200 pg); and, perhaps most strikingly, (4) a deficit of histones-the canonical building blocks of all eukaryotic chromatin. Dinoflagellates belong to the Alveolata clade (dinoflagellates, apicomplexans, and ciliates) and, therefore, the biological oddities observed in dinoflagellate nuclei are derived character states. Understanding the sequence of changes that led to the dinokaryon has been difficult in the past with poor resolution of dinoflagellate phylogeny. Moreover, lack of knowledge of their molecular composition has constrained our understanding of the molecular properties of these derived nuclei. However, recent advances in the resolution of the phylogeny of dinoflagellates, particularly of the early branching taxa; the realization that divergent histone genes are present; and the discovery of dinoflagellate-specific nuclear proteins that were acquired early in dinoflagellate evolution have all thrown new light nature and evolution of the dinokaryon.
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Affiliation(s)
- Sebastian G Gornik
- Centre for Organismal Studies (COS), Universität Heidelberg, 69120 Heidelberg, Germany.
| | - Ian Hu
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Imen Lassadi
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
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Cuadrado Á, De Bustos A, Figueroa RI. Chromosomal markers in the genus Karenia: Towards an understanding of the evolution of the chromosomes, life cycle patterns and phylogenetic relationships in dinoflagellates. Sci Rep 2019; 9:3072. [PMID: 30816125 PMCID: PMC6395649 DOI: 10.1038/s41598-018-35785-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 11/07/2018] [Indexed: 12/12/2022] Open
Abstract
Dinoflagellates are a group of protists whose genome is unique among eukaryotes in terms of base composition, chromosomal structure and gene expression. Even after decades of research, the structure and behavior of their amazing chromosomes-which without nucleosomes exist in a liquid crystalline state-are still poorly understood. We used flow cytometry and fluorescence in situ hybridization (FISH) to analyze the genome size of three species of the toxic dinoflagellate genus Karenia as well the organization and behavior of the chromosomes in different cell-cycle stages. FISH was also used to study the distribution patterns of ribosomal DNA (45S rDNA), telomeric and microsatellites repeats in order to develop chromosomal markers. The results revealed several novel and important features regarding dinoflagellate chromosomes during mitosis, including their telocentric behavior and radial arrangement along the nuclear envelope. Additionally, using the (AG)10 probe we identified an unusual chromosome in K. selliformis and especially in K. mikimotoi that is characterized by AG repeats along its entire length. This feature was employed to easily differentiate morphologically indistinguishable life-cycle stages. The evolutionary relationship between Karenia species is discussed with respect to differences in both DNA content and the chromosomal distribution patterns of the DNA sequences analyzed.
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Affiliation(s)
- Ángeles Cuadrado
- Universidad de Alcala (UAH), Dpto Biomedicina y Biotecnología, 28805 Alcalá de Henares, Madrid, Spain.
| | - Alfredo De Bustos
- Universidad de Alcala (UAH), Dpto Biomedicina y Biotecnología, 28805 Alcalá de Henares, Madrid, Spain
| | - Rosa I Figueroa
- Instituto Español de Oceanografia (IEO), Subida a Radio Faro 50, 36390, Vigo, Spain.
- Aquatic Ecology, Biology Building, Lund University, 22362, Lund, Sweden.
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Figueroa RI, de Bustos A, Cuadrado Á. A novel FISH technique for labeling the chromosomes of dinoflagellates in suspension. PLoS One 2018; 13:e0204382. [PMID: 30356238 PMCID: PMC6200182 DOI: 10.1371/journal.pone.0204382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 10/11/2018] [Indexed: 11/19/2022] Open
Abstract
Dinoflagellates possess some of the largest known genomes. However, the study of their chromosomes is complicated by their similar size and their inability to be distinguished by traditional banding techniques. Dinoflagellate chromosomes lack nucleosomes and are present in a liquid crystalline state. In addition, approaches such as fluorescent in situ hybridization (FISH) are problematic because chromosomes are difficult to isolate from the nuclear membrane, which in dinoflagellates remains intact, also during mitosis. Here we describe a novel, reliable and effective technique to study dinoflagellate chromosomes by physical mapping of repetitive DNA sequences in chromosomes in suspension (FISH-IS), rather than on a microscope slide. A suspension of non-fixed chromosomes was achieved by lysing the cells and destabilizing the nuclear envelope. This treatment resulted in the release of the permanently condensed chromosomes in a high-quality chromosomal suspension. Nevertheless, slide preparations of the chromosomes were not suitable for conventional FISH because the nuclear integrity and chromosomal morphology was destroyed. Our newly developed, simple and efficient FISH-IS technique employs fluorescently labeled, synthetic short sequence repeats that are hybridized with suspended, acetic-acid-pretreated chromosomes for 1 h at room temperature. The method can be successfully used to discriminate single chromosomes or specific chromosomal regions, depending on the specificity of the repeat sequences used as probes. The combination of FISH-IS and flow sorting will improve genomic studies of dinoflagellates, overcoming the difficulties posed by their huge genomes, including long stretches of non-coding sequences in multiple copies and the presence of high-copy-number tandem gene arrays.
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Affiliation(s)
- Rosa I Figueroa
- Instituto Español de Oceanografia (IEO), Subida a Radio Faro 50, Vigo, Spain
| | - Alfredo de Bustos
- Universidad de Alcala (UAH), Dpto Biomedicina y Biotecnología, Alcalá de Henares, Madrid, Spain
| | - Ángeles Cuadrado
- Universidad de Alcala (UAH), Dpto Biomedicina y Biotecnología, Alcalá de Henares, Madrid, Spain
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Sováková PP, Magdolenová A, Konečná K, Rájecká V, Fajkus J, Fojtová M. Telomere elongation upon transfer to callus culture reflects the reprogramming of telomere stability control in Arabidopsis. PLANT MOLECULAR BIOLOGY 2018; 98:81-99. [PMID: 30128721 DOI: 10.1007/s11103-018-0765-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/12/2018] [Indexed: 05/23/2023]
Abstract
KEY MESSAGE Standard pathways involved in the regulation of telomere stability do not contribute to gradual telomere elongation observed in the course of A. thaliana calli propagation. Genetic and epigenetic changes accompanying the culturing of plant cells have frequently been reported. Here we aimed to characterize the telomere homeostasis during long term callus propagation. While in Arabidopsis thaliana calli gradual telomere elongation was observed, telomeres were stable in Nicotiana tabacum and N. sylvestris cultures. Telomere elongation during callus propagation is thus not a general feature of plant cells. The long telomere phenotype in Arabidopsis calli was correlated neither with changes in telomerase activity nor with activation of alternative mechanisms of telomere elongation. The dynamics of telomere length changes was maintained in mutant calli with loss of function of important epigenetic modifiers but compromised in the presence of epigenetically active drug zebularine. To examine whether the cell culture-induced disruption of telomere homeostasis is associated with the modulated structure of chromosome ends, epigenetic properties of telomere chromatin were analysed. Albeit distinct changes in epigenetic modifications of telomere histones were observed, these were broadly stochastic. Our results show that contrary to animal cells, the structure and function of plant telomeres is not determined significantly by the epigenetic character of telomere chromatin. Set of differentially transcribed genes was identified in calli, but considering the known telomere- or telomerase-related functions of respective proteins, none of these changes per se was apparently related to the elongated telomere phenotype. Based on our data, we propose that the disruption in telomere homeostasis in Arabidopsis calli arises from the interplay of multiple factors, as a part of reprogramming of plant cells to long-term culture conditions.
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Affiliation(s)
- Pavla Polanská Sováková
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic
| | - Alžbeta Magdolenová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic v.v.i., Prague, Czech Republic
| | - Klára Konečná
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic
| | - Veronika Rájecká
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic
| | - Jiří Fajkus
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., 612 65, Brno, Czech Republic
| | - Miloslava Fojtová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 625 00, Brno, Czech Republic.
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 625 00, Brno, Czech Republic.
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9
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Yang QF, Liu L, Liu Y, Zhou ZG. Telomeric localization of the Arabidopsis-type heptamer repeat, (TTTAGGG) n , at the chromosome ends in Saccharina japonica (Phaeophyta). JOURNAL OF PHYCOLOGY 2017; 53:235-240. [PMID: 27885670 DOI: 10.1111/jpy.12497] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 09/12/2016] [Indexed: 06/06/2023]
Abstract
Telomeres generally consist of short repeats of minisatellite DNA sequences and are useful in chromosome identification and karyotype analysis. To date, telomeres have not been characterized in the economically important brown seaweed Saccharina japonica, thus its full cytogenetic research and genetic breeding potential has not been realized. Herein, the tentative sequence of telomeres in S. japonica was identified by PCR amplification with primers designed based on the Arabidopsis-type telomere sequence (TTTAGGG)n , which was chosen out of three possible telomeric repeat DNA sequences typically present in plants and algae. After PCR optimization and cloning, sequence analysis of the amplified products from S. japonica genomic DNA showed that they were composed of repeat units, (TTTAGGG)n , in which the repeat number ranged from 15 to 63 (n = 46). This type of repeat sequence was verified by a Southern blot assay with the Arabidopsis-type telomere sequence as a probe. The digestion of S. japonica genomic DNA with the exonuclease Bal31 illustrated that the target sequence corresponding to the Arabidopsis-type telomere sequence was susceptible to Bal31 digestion, suggesting that the repeat sequence was likely located at the outermost ends of the kelp chromosomes. Fluorescence in situ hybridizations with the aforementioned probe provided the initial cytogenetic evidence that the hybridization signals were principally localized at both ends of S. japonica chromosomes. This study indicates that the telomeric repeat of the kelp chromosomes is (TTTAGGG)n which differs from the previously reported (TTAGGG)n sequence in Ectocarpus siliculosus through genome sequencing, thereby suggesting distinct telomeres in brown seaweeds.
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Affiliation(s)
- Qi-Fan Yang
- College of Aqua-Life Sciences and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Li Liu
- College of Aqua-Life Sciences and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Yu Liu
- College of Aqua-Life Sciences and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Zhi-Gang Zhou
- College of Aqua-Life Sciences and Technology, Shanghai Ocean University, Shanghai, 201306, China
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10
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Uzlíková M, Fulnečková J, Weisz F, Sýkorová E, Nohýnková E, Tůmová P. Characterization of telomeres and telomerase from the single-celled eukaryote Giardia intestinalis. Mol Biochem Parasitol 2017; 211:31-38. [DOI: 10.1016/j.molbiopara.2016.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/08/2016] [Accepted: 09/12/2016] [Indexed: 10/21/2022]
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11
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Lin S, Cheng S, Song B, Zhong X, Lin X, Li W, Li L, Zhang Y, Zhang H, Ji Z, Cai M, Zhuang Y, Shi X, Lin L, Wang L, Wang Z, Liu X, Yu S, Zeng P, Hao H, Zou Q, Chen C, Li Y, Wang Y, Xu C, Meng S, Xu X, Wang J, Yang H, Campbell DA, Sturm NR, Dagenais-Bellefeuille S, Morse D. The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and coral symbiosis. Science 2015; 350:691-4. [PMID: 26542574 DOI: 10.1126/science.aad0408] [Citation(s) in RCA: 278] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Dinoflagellates are important components of marine ecosystems and essential coral symbionts, yet little is known about their genomes. We report here on the analysis of a high-quality assembly from the 1180-megabase genome of Symbiodinium kawagutii. We annotated protein-coding genes and identified Symbiodinium-specific gene families. No whole-genome duplication was observed, but instead we found active (retro)transposition and gene family expansion, especially in processes important for successful symbiosis with corals. We also documented genes potentially governing sexual reproduction and cyst formation, novel promoter elements, and a microRNA system potentially regulating gene expression in both symbiont and coral. We found biochemical complementarity between genomes of S. kawagutii and the anthozoan Acropora, indicative of host-symbiont coevolution, providing a resource for studying the molecular basis and evolution of coral symbiosis.
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Affiliation(s)
- Senjie Lin
- State Key Laboratory of Marine Environmental Science and Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen 361101, China. Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA.
| | - Shifeng Cheng
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Hong Kong University (HKU)-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The Computer Science Department, The University of Hong Kong, Hong Kong, China. School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Bo Song
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Xiao Zhong
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science and Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen 361101, China
| | - Wujiao Li
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science and Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen 361101, China
| | - Yaqun Zhang
- State Key Laboratory of Marine Environmental Science and Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen 361101, China
| | - Huan Zhang
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
| | - Zhiliang Ji
- State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiamen 361101, China
| | - Meichun Cai
- State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiamen 361101, China
| | - Yunyun Zhuang
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
| | - Xinguo Shi
- State Key Laboratory of Marine Environmental Science and Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen 361101, China
| | - Lingxiao Lin
- State Key Laboratory of Marine Environmental Science and Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen 361101, China
| | - Lu Wang
- State Key Laboratory of Marine Environmental Science and Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen 361101, China
| | - Zhaobao Wang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Xin Liu
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Sheng Yu
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Peng Zeng
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Han Hao
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - Quan Zou
- State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiamen 361101, China
| | - Chengxuan Chen
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Yanjun Li
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Ying Wang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Chunyan Xu
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Shanshan Meng
- State Key Laboratory of Marine Environmental Science and Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen 361101, China
| | - Xun Xu
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Jun Wang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Huanming Yang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia. James D. Watson Institute of Genome Science, Hangzhou, China
| | - David A Campbell
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Nancy R Sturm
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Steve Dagenais-Bellefeuille
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal, Canada
| | - David Morse
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal, Canada
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12
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Tran TD, Cao HX, Jovtchev G, Neumann P, Novák P, Fojtová M, Vu GTH, Macas J, Fajkus J, Schubert I, Fuchs J. Centromere and telomere sequence alterations reflect the rapid genome evolution within the carnivorous plant genus Genlisea. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:1087-99. [PMID: 26485466 DOI: 10.1111/tpj.13058] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 10/07/2015] [Accepted: 10/15/2015] [Indexed: 05/25/2023]
Abstract
Linear chromosomes of eukaryotic organisms invariably possess centromeres and telomeres to ensure proper chromosome segregation during nuclear divisions and to protect the chromosome ends from deterioration and fusion, respectively. While centromeric sequences may differ between species, with arrays of tandemly repeated sequences and retrotransposons being the most abundant sequence types in plant centromeres, telomeric sequences are usually highly conserved among plants and other organisms. The genome size of the carnivorous genus Genlisea (Lentibulariaceae) is highly variable. Here we study evolutionary sequence plasticity of these chromosomal domains at an intrageneric level. We show that Genlisea nigrocaulis (1C = 86 Mbp; 2n = 40) and G. hispidula (1C = 1550 Mbp; 2n = 40) differ as to their DNA composition at centromeres and telomeres. G. nigrocaulis and its close relative G. pygmaea revealed mainly 161 bp tandem repeats, while G. hispidula and its close relative G. subglabra displayed a combination of four retroelements at centromeric positions. G. nigrocaulis and G. pygmaea chromosome ends are characterized by the Arabidopsis-type telomeric repeats (TTTAGGG); G. hispidula and G. subglabra instead revealed two intermingled sequence variants (TTCAGG and TTTCAGG). These differences in centromeric and, surprisingly, also in telomeric DNA sequences, uncovered between groups with on average a > 9-fold genome size difference, emphasize the fast genome evolution within this genus. Such intrageneric evolutionary alteration of telomeric repeats with cytosine in the guanine-rich strand, not yet known for plants, might impact the epigenetic telomere chromatin modification.
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Affiliation(s)
- Trung D Tran
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Hieu X Cao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Gabriele Jovtchev
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Pavel Neumann
- Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, Branišovská 31/1160, 37005, České Budějovice, Czech Republic
| | - Petr Novák
- Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, Branišovská 31/1160, 37005, České Budějovice, Czech Republic
| | - Miloslava Fojtová
- Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Giang T H Vu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Jiří Macas
- Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, Branišovská 31/1160, 37005, České Budějovice, Czech Republic
| | - Jiří Fajkus
- Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 61265, Brno, Czech Republic
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466, Stadt Seeland, Germany
- Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Joerg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466, Stadt Seeland, Germany
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Figueroa RI, Cuadrado A, Stüken A, Rodríguez F, Fraga S. Ribosomal DNA Organization Patterns within the Dinoflagellate Genus Alexandrium as Revealed by FISH: Life Cycle and Evolutionary Implications. Protist 2014; 165:343-63. [DOI: 10.1016/j.protis.2014.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 04/03/2014] [Accepted: 04/08/2014] [Indexed: 10/25/2022]
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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: 70] [Impact Index Per Article: 6.4] [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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15
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Ševčíková T, Bišová K, Fojtová M, Lukešová A, Hrčková K, Sýkorová E. Completion of cell division is associated with maximum telomerase activity in naturally synchronized cultures of the green alga Desmodesmus quadricauda. FEBS Lett 2013; 587:743-8. [PMID: 23395610 DOI: 10.1016/j.febslet.2013.01.058] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 01/17/2013] [Accepted: 01/23/2013] [Indexed: 10/27/2022]
Abstract
Telomerase maintains the ends of eukaryotic chromosomes, and its activity is an important parameter correlating with the proliferative capacity of cells. We have investigated cell cycle-specific changes in telomerase activity using cultures of Desmodesmus quadricauda, a model alga naturally synchronized by light/dark entrainment. A quantitative telomerase assay revealed high activity in algal cultures, with slight changes during the light period. Significantly increased telomerase activity was observed at the end of the dark phase, when cell division was complete. In contrast to other models, a natural separation between nuclear and cellular division typical for the cell cycle in D. quadricauda made this observation possible.
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Affiliation(s)
- Tereza Ševčíková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, vvi, 612 65 Brno, Czech Republic
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Fulnečková J, Hasíková T, Fajkus J, Lukešová A, Eliáš M, Sýkorová E. Dynamic evolution of telomeric sequences in the green algal order Chlamydomonadales. Genome Biol Evol 2012; 4:248-64. [PMID: 22247428 PMCID: PMC3318450 DOI: 10.1093/gbe/evs007] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Telomeres, which form the protective ends of eukaryotic chromosomes, are a ubiquitous and conserved structure of eukaryotic genomes but the basic structural unit of most telomeres, a repeated minisatellite motif with the general consensus sequence TnAmGo, may vary between eukaryotic groups. Previous studies on several species of green algae revealed that this group exhibits at least two types of telomeric sequences, a presumably ancestral type shared with land plants (Arabidopsis type, TTTAGGG) and conserved in, for example, Ostreococcus and Chlorella species, and a novel type (Chlamydomonas type, TTTTAGGG) identified in Chlamydomonas reinhardtii. We have employed several methodical approaches to survey the diversity of telomeric sequences in a phylogenetically wide array of green algal species, focusing on the order Chlamydomonadales. Our results support the view that the Arabidopsis-type telomeric sequence is ancestral for green algae and has been conserved in most lineages, including Mamiellophyceae, Chlorodendrophyceae, Trebouxiophyceae, Sphaeropleales, and most Chlamydomonadales. However, within the Chlamydomonadales, at least two independent evolutionary changes to the Chlamydomonas type occurred, specifically in a subgroup of the Reinhardtinia clade (including C. reinhardtii and Volvox carteri) and in the Chloromonadinia clade. Furthermore, a complex structure of telomeric repeats, including a mix of the ancestral Arabidopsis-type motifs and derived motifs identical to the human-type telomeric repeats (TTAGGG), was found in the chlamydomonadalean clades Dunaliellinia and Stephanosphaeria. Our results indicate that telomere evolution in green algae, particularly in the order Chlamydomonadales, is far more dynamic and complex than thought before. General implications of our findings for the mode of telomere evolution are discussed.
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Affiliation(s)
- Jana Fulnečková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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