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Grishanin A. Chromatin diminution as a tool to study some biological problems. COMPARATIVE CYTOGENETICS 2024; 18:27-49. [PMID: 38369988 PMCID: PMC10870232 DOI: 10.3897/compcytogen.17.112152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 01/21/2024] [Indexed: 02/20/2024]
Abstract
This work reveals the opportunities to obtain additional information about some biological problems through studying species that possess chromatin diminution. A brief review of the hypothesized biological significance of chromatin diminution is discussed. This article analyzes the biological role of chromatin diminution as it relates to the C-value enigma. It is proposed to consider chromatin diminution as a universal mechanism of genome reduction, reducing the frequency of recombination events in the genome, which leads to specialization and adaptation of the species to more narrow environmental conditions. A hypothesis suggesting the role of non-coding DNA in homologous recombination in eukaryotes is proposed. Cyclopskolensis Lilljeborg, 1901 (Copepoda, Crustacea) is proposed as a model species for studying the mechanisms of transformation of the chromosomes and interphase nuclei structure of somatic line cells due to chromatin diminution. Chromatin diminution in copepods is considered as a stage of irreversible differentiation of embryonic cells during ontogenesis. The process of speciation in cyclopoids with chromatin diminution is considered.
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Affiliation(s)
- Andrey Grishanin
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, 152742 Borok, Yaroslavl Prov., RussiaRussian Academy of SciencesBorokRussia
- Department of Biophisics, Faculty of Natural and Engineering Sciences, Dubna State University, Universitetskaya 19, 141980, Dubna, Moscow Prov., RussiaDubna State UniversityDubnaRussia
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Wyngaard GA, Skern-Mauritzen R, Malde K, Prendergast R, Peruzzi S. The salmon louse genome may be much larger than sequencing suggests. Sci Rep 2022; 12:6616. [PMID: 35459797 PMCID: PMC9033869 DOI: 10.1038/s41598-022-10585-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 04/08/2022] [Indexed: 12/30/2022] Open
Abstract
The genome size of organisms impacts their evolution and biology and is often assumed to be characteristic of a species. Here we present the first published estimates of genome size of the ecologically and economically important ectoparasite, Lepeophtheirus salmonis (Copepoda, Caligidae). Four independent L. salmonis genome assemblies of the North Atlantic subspecies Lepeophtheirus salmonis salmonis, including two chromosome level assemblies, yield assemblies ranging from 665 to 790 Mbps. These genome assemblies are congruent in their findings, and appear very complete with Benchmarking Universal Single-Copy Orthologs analyses finding > 92% of expected genes and transcriptome datasets routinely mapping > 90% of reads. However, two cytometric techniques, flow cytometry and Feulgen image analysis densitometry, yield measurements of 1.3-1.6 Gb in the haploid genome. Interestingly, earlier cytometric measurements reported genome sizes of 939 and 567 Mbps in L. salmonis salmonis samples from Bay of Fundy and Norway, respectively. Available data thus suggest that the genome sizes of salmon lice are variable. Current understanding of eukaryotic genome dynamics suggests that the most likely explanation for such variability involves repetitive DNA, which for L. salmonis makes up ≈ 60% of the genome assemblies.
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Affiliation(s)
- Grace A Wyngaard
- Department of Biology, James Madison University, Harrisonburg, VA, USA
| | | | - Ketil Malde
- Institute of Marine Research, Bergen, Norway
- Department of Informatics, University of Bergen, Bergen, Norway
| | | | - Stefano Peruzzi
- Department of Arctic Marine Biology, UiT-the Arctic University of Norway, Tromsø, Norway.
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Drotos KH, Zagoskin MV, Kess T, Gregory TR, Wyngaard GA. Throwing away DNA: programmed downsizing in somatic nuclei. Trends Genet 2022; 38:483-500. [DOI: 10.1016/j.tig.2022.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/30/2022] [Accepted: 02/01/2022] [Indexed: 11/25/2022]
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Banerji A, Deshpande R, Elk M, Shoemaker JA, Tettenhorst DR, Bagley M, Santo Domingo JW. Highlighting the promise of qPCR-based environmental monitoring: response of the ribosomal RNA:DNA ratio of calanoid copepods to toxic cyanobacteria. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:411-420. [PMID: 33675450 PMCID: PMC8237716 DOI: 10.1007/s10646-021-02366-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/06/2021] [Indexed: 06/12/2023]
Abstract
Calanoid copepods are integral to aquatic food webs and may drive the bioaccumulation of toxins and heavy metals, spread of infectious diseases, and occurrence of toxic cyanobacterial harmful algal blooms (HABs) in freshwater aquatic systems. However, interrelationships between copepod and cyanobacterial population dynamics and ecophysiology remain unclear. Insights into these relationships are important to aquatic resource management, as they may help guide mitigation efforts. We developed a calanoid copepod qPCR assay to investigate how copepod abundance and physiological status relate to the abundance of cyanobacteria and the concentration of total microcystin in a HAB-prone freshwater multi-use eutrophic lake. Through in silico and in vitro validation of primers and analyses of time series, we demonstrate that our assay can be used as a reliable tool for environmental monitoring. Importantly, copepod RNA:DNA ratios on and shortly after the day when microcystin concentration was at its highest within the lake were not significantly lower (or higher) than before or after this period, suggesting that copepods may have been tolerant of microcystin levels observed and capable of perpetuating bloom events by consuming competitors of toxic cyanobacteria.
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Affiliation(s)
- Aabir Banerji
- Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | | | - Michael Elk
- Biology Department, University of La Verne, La Verne, CA, USA
| | - Jody A Shoemaker
- Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Dan R Tettenhorst
- Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Mark Bagley
- Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Jorge W Santo Domingo
- Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA.
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The Whole Genome Sequence and mRNA Transcriptome of the Tropical Cyclopoid Copepod Apocyclops royi. G3-GENES GENOMES GENETICS 2019; 9:1295-1302. [PMID: 30923136 PMCID: PMC6505139 DOI: 10.1534/g3.119.400085] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Copepoda is one of the most ecologically important animal groups on Earth, yet very few genetic resources are available for this Subclass. Here, we present the first whole genome sequence (WGS, acc. UYDY01) and the first mRNA transcriptome assembly (TSA, Acc. GHAJ01) for the tropical cyclopoid copepod species Apocyclops royi. Until now, only the 18S small subunit of ribosomal RNA gene and the COI gene has been available from A. royi, and WGS resources was only available from one other cyclopoid copepod species. Overall, the provided resources are the 8th copepod species to have WGS resources available and the 19th copepod species with TSA information available. We analyze the length and GC content of the provided WGS scaffolds as well as the coverage and gene content of both the WGS and the TSA assembly. Finally, we place the resources within the copepod order Cyclopoida as a member of the Apocyclops genus. We estimate the total genome size of A. royi to 450 Mb, with 181 Mb assembled nonrepetitive sequence, 76 Mb assembled repeats and 193 Mb unassembled sequence. The TSA assembly consists of 29,737 genes and an additional 45,756 isoforms. In the WGS and TSA assemblies, >80% and >95% of core genes can be found, though many in fragmented versions. The provided resources will allow researchers to conduct physiological experiments on A. royi, and also increase the possibilities for copepod gene set analysis, as it adds substantially to the copepod datasets available.
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Walczyńska A, Labecka AM, Sobczyk M. What may a fussy creature reveal about body/cell size integration under stressful conditions? Dev Genes Evol 2018; 228:179-188. [PMID: 29728762 PMCID: PMC6013519 DOI: 10.1007/s00427-018-0613-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 04/23/2018] [Indexed: 11/30/2022]
Abstract
There is a growing amount of empirical evidence on the important role of cell size in body size adjustment in ambient or changing conditions. Though the adaptive significance of their correspondence is well understood and demonstrated, the proximate mechanisms are still in a phase of speculation. We made interesting observations on body/cell size adjustment under stressful conditions during an experiment designed for another purpose. We found that the strength of the body/cell size match is condition-dependent. Specifically, it is stronger under more stressful conditions, and it changes depending on exposure to lower temperature vs. exposure to higher temperature. The question whether these observations are of limiting or adaptive character remains open; yet, according to our results, both versions are possible but may differ in response to stress caused by too low vs. too high temperatures. Our results suggest that testing the hypotheses on body/cell size match may be a promising study system for the recent scientific dispute on the evolutionary meaning of developmental noise as opposed to phenotypic plasticity.
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Affiliation(s)
- Aleksandra Walczyńska
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland.
| | - Anna Maria Labecka
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Mateusz Sobczyk
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
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Madoui MA, Poulain J, Sugier K, Wessner M, Noel B, Berline L, Labadie K, Cornils A, Blanco-Bercial L, Stemmann L, Jamet JL, Wincker P. New insights into global biogeography, population structure and natural selection from the genome of the epipelagic copepodOithona. Mol Ecol 2017. [DOI: 10.1111/mec.14214] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Mohammed-Amin Madoui
- Commissariat à l'Energie Atomique (CEA); Institut de Biologie François Jacob, Genoscope; Evry France
- Centre National de la Recherche Scientifique; UMR 8030 Université d'Evry val d'Essonne; Evry France
- Université d'Evry Val D'Essonne; Evry France
| | - Julie Poulain
- Commissariat à l'Energie Atomique (CEA); Institut de Biologie François Jacob, Genoscope; Evry France
| | - Kevin Sugier
- Commissariat à l'Energie Atomique (CEA); Institut de Biologie François Jacob, Genoscope; Evry France
- Centre National de la Recherche Scientifique; UMR 8030 Université d'Evry val d'Essonne; Evry France
- Université d'Evry Val D'Essonne; Evry France
| | - Marc Wessner
- Commissariat à l'Energie Atomique (CEA); Institut de Biologie François Jacob, Genoscope; Evry France
| | - Benjamin Noel
- Commissariat à l'Energie Atomique (CEA); Institut de Biologie François Jacob, Genoscope; Evry France
| | - Leo Berline
- CNRS/INSU/IRD; Mediterranean Institute of Oceanography (MIO); Aix-Marseille Université; Marseille France
| | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA); Institut de Biologie François Jacob, Genoscope; Evry France
| | - Astrid Cornils
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung; Polar Biological Oceanography; Bremerhaven Germany
| | | | - Lars Stemmann
- INSU-CNRS; Laboratoire D'Océanographie de Villefranche; UPMC Univ Paris 06; Sorbonne Universités; Villefranche-Sur-Mer France
| | - Jean-Louis Jamet
- Laboratoire PROTEE-EBMA E.A. 3819; Université de Toulon; La Garde Cedex France
| | - Patrick Wincker
- Commissariat à l'Energie Atomique (CEA); Institut de Biologie François Jacob, Genoscope; Evry France
- Centre National de la Recherche Scientifique; UMR 8030 Université d'Evry val d'Essonne; Evry France
- Université d'Evry Val D'Essonne; Evry France
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Teterina VI, Galimova YA, Sheveleva NG, Sukhanova LV, Mayor TY, Zaitseva AN, Kirilchik SV. A simple and effective method for assessing chromatin diminution values in copepods using qPCR. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416110168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Clower MK, Holub AS, Smith RT, Wyngaard GA. EMBRYONIC DEVELOPMENT AND A QUANTITATIVE MODEL OF PROGRAMMED DNA ELIMINATION IN MESOCYCLOPS EDAX (S. A. FORBES, 1891) (COPEPODA: CYCLOPOIDA). JOURNAL OF CRUSTACEAN BIOLOGY : A QUARTERLY OF THE CRUSTACEAN SOCIETY FOR THE PUBLICATION OF RESEARCH ON ANY ASPECT OF THE BIOLOGY OF CRUSTACEA 2016; 36:661-674. [PMID: 27857452 PMCID: PMC5110247 DOI: 10.1163/1937240x-00002473] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The highly programmed fragmentation of chromosomes and elimination of large amounts of nuclear DNA from the presomatic cell lineages (i.e., chromatin diminution), occurs in the embryos of the freshwater zooplankton Mesocyclops edax (S. A. Forbes, 1891) (Crustacea: Copepoda). The somatic genome is reorganized and reduced to a size five times smaller even though the germline genome remains intact. We present the first comprehensive, quantitative model of DNA content throughout embryogenesis in a copepod that possesses embryonic DNA elimination. We used densitometric image analysis to measure the DNA content of polar bodies, germline and somatic nuclei, and excised DNA "droplets." We report: 1) variable DNA contents of polar bodies, some of which do not contain the amount corresponding to the haploid germline genome size; 2) presence of pronuclei in newly laid embryo sacs; 3) gonomeric chromosomes in the second to fourth cleavage divisions and in the primordial germ cell and primordial endoderm cell during the fifth cleavage division; 4) timing of early embryonic cell stages, elimination of DNA, and divisions of the primordial germ cell and primordial endoderm cell at 22°C; and 5) persistence of a portion of the excised DNA "droplets" throughout embryogenesis. DNA elimination is a trait that spans multiple embryonic stages and a knowledge of the timing and variability of the associated cytological events with DNA elimination will promote the study of the molecular mechanisms involved in this trait. We propose the "genome yolk hypothesis" as a functional explanation for the persistence of the eliminated DNA that might serve as a resource during postdiminution cleavage divisions.
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Affiliation(s)
- Michelle K. Clower
- North Carolina Coastal Federation, 128 Grenville St., Manteo, NC 27954, USA
| | - Ashton S. Holub
- Department of Biology, MSC 7801, James Madison University, Harrisonburg, VA 22807, USA
| | - Rebecca T. Smith
- Eastern Shore Laboratory, Virginia Institute of Marine Science, Wachapreague, VA 23480, USA
| | - Grace A. Wyngaard
- Department of Biology, MSC 7801, James Madison University, Harrisonburg, VA 22807, USA
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Cheng W, Lei J, Fox CW, Johnston JS, Zhu-Salzman K. Comparison of life history and genetic properties of cowpea bruchid strains and their response to hypoxia. JOURNAL OF INSECT PHYSIOLOGY 2015; 75:5-11. [PMID: 25733404 DOI: 10.1016/j.jinsphys.2015.02.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 02/22/2015] [Accepted: 02/24/2015] [Indexed: 06/04/2023]
Abstract
The cowpea bruchid (Callosobruchus maculatus) is the most important storage pest of grain legumes and comprises geographically distinct strains. Storage under a modified atmosphere with decreased O2 content represents an alternative to chemical fumigants for pest control of stored grains. In this study, we compared reproduction, development and survival, as well as genome size of bruchid strains from South India (SI), Burkina Faso (BF), Niger (CmNnC) and the United States (OH), reared on mung bean (Vigna radiata). Fecundity and egg-to-adult duration varied significantly among these strains. Notably, strain BF had the highest fecundity, and strain SI displayed the fastest development whereas strain OH was the slowest. Differences in adult lifespan among strains were only detected in unmated but not in the mated group. Genome size of SI females was significantly larger than that of OH females, and for all four strains, the female genomes were larger than those of their corresponding males. Furthermore, we studied effects of exposure to 1% O2+99% N2 on strains SI and BF. Mortality caused by hypoxia was influenced by not only developmental stage but also by insect strain. Eggs were most sensitive, particularly at the early stage, whereas the 3rd and 4th instar larvae were most tolerant and could survive up to 15 days of low O2. Strain SI was slightly more resistant than BF in egg and larval stages. Proteolytic activity prior to, during and after hypoxia treatment revealed remarkable metabolic plasticity of cowpea bruchids in response to modified atmosphere.
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Affiliation(s)
- Weining Cheng
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China; Department of Entomology, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics & Biotechnology, Texas A&M University, College Station, TX 77843, USA.
| | - Jiaxin Lei
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics & Biotechnology, Texas A&M University, College Station, TX 77843, USA
| | - Charles W Fox
- Entomology Department, University of Kentucky, Lexington, KY 40546, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Keyan Zhu-Salzman
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics & Biotechnology, Texas A&M University, College Station, TX 77843, USA.
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Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development. BMC Genomics 2014; 15:186. [PMID: 24618421 PMCID: PMC4029161 DOI: 10.1186/1471-2164-15-186] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 03/03/2014] [Indexed: 12/15/2022] Open
Abstract
Background Chromatin diminution is the programmed deletion of DNA from presomatic cell or nuclear lineages during development, producing single organisms that contain two different nuclear genomes. Phylogenetically diverse taxa undergo chromatin diminution — some ciliates, nematodes, copepods, and vertebrates. In cyclopoid copepods, chromatin diminution occurs in taxa with massively expanded germline genomes; depending on species, germline genome sizes range from 15 – 75 Gb, 12–74 Gb of which are lost from pre-somatic cell lineages at germline – soma differentiation. This is more than an order of magnitude more sequence than is lost from other taxa. To date, the sequences excised from copepods have not been analyzed using large-scale genomic datasets, and the processes underlying germline genomic gigantism in this clade, as well as the functional significance of chromatin diminution, have remained unknown. Results Here, we used high-throughput genomic sequencing and qPCR to characterize the germline and somatic genomes of Mesocyclops edax, a freshwater cyclopoid copepod with a germline genome of ~15 Gb and a somatic genome of ~3 Gb. We show that most of the excised DNA consists of repetitive sequences that are either 1) verifiable transposable elements (TEs), or 2) non-simple repeats of likely TE origin. Repeat elements in both genomes are skewed towards younger (i.e. less divergent) elements. Excised DNA is a non-random sample of the germline repeat element landscape; younger elements, and high frequency DNA transposons and LINEs, are disproportionately eliminated from the somatic genome. Conclusions Our results suggest that germline genome expansion in M. edax reflects explosive repeat element proliferation, and that billions of base pairs of such repeats are deleted from the somatic genome every generation. Thus, we hypothesize that chromatin diminution is a mechanism that controls repeat element load, and that this load can evolve to be divergent between tissue types within single organisms.
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Ivankina EA, Alekseeva AL, Semeshin VF, Omelyanchuk LV, Palchikova IG, Sheveleva NG, Kirilchik SV, Zhimulev IF. Cytophotometric determination of genome size in two species of Cyclops of Lake Baikal (Crustacea: Copepoda, Cyclopoida) in ontogenetic development. ACTA ACUST UNITED AC 2013. [DOI: 10.1134/s1990519x13020053] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Collares-Pereira M, Matos I, Morgado-Santos M, Coelho M. Natural Pathways towards Polyploidy in Animals: TheSqualius alburnoidesFish Complex as a Model System to Study Genome Size and Genome Reorganization in Polyploids. Cytogenet Genome Res 2013; 140:97-116. [DOI: 10.1159/000351729] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Hessen DO, Daufresne M, Leinaas HP. Temperature-size relations from the cellular-genomic perspective. Biol Rev Camb Philos Soc 2012; 88:476-89. [DOI: 10.1111/brv.12006] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Revised: 11/08/2012] [Accepted: 11/20/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Dag O. Hessen
- Department of Biology; University of Oslo, CEES; PO Box 1066 Blindern; 0316; Oslo; Norway
| | - Martin Daufresne
- HYAX-EL; Irstea; 3275 Route de Cézanne; 13182; Aix-en-Provence; France
| | - Hans P. Leinaas
- Department of Biology; University of Oslo, Integrative Biology; PO Box 1066 Blindern; 0316; Oslo; Norway
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Unusual augmentation of germline genome size in Cyclops kolensis (Crustacea, Copepoda): further evidence in support of a revised model of chromatin diminution. Chromosome Res 2012; 19:911-23. [PMID: 21953028 DOI: 10.1007/s10577-011-9234-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Embryonic chromatin diminution, the selective excision of large amounts of heterochromatic DNA from presomatic cell lineages, provides an example of an unusually large augmentation of the germline genome and raises questions regarding the source of the increased amount of DNA and its relevance to the biology of the organism. DNA levels in adult germ cell nuclei of the copepod Cyclops kolensis were determined by DNA-Feulgen cytophotometry and compared with those of somatic nuclei of adults and both pre- and postdiminuted embryos from the same mothers. Almost 75 pg DNA/nucleus is excised by diminution, resulting in the return of each generation to the approximately 1 pg DNA/nucleus level found for adult soma. To account for the increase in DNA levels of germ cells observed here, we propose alternative hypotheses to the original model of chromatin diminution: (1) repetitive endocycles or (2) proliferation of genetic elements. Specific tests for these hypotheses using next-generation sequencing and quantitative cytophotometry, as well as the functional significance of germ cell DNA augmentation to the copepod, are discussed.
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HESSEN DAGO, PERSSON JONAS. Genome size as a determinant of growth and life-history traits in crustaceans. Biol J Linn Soc Lond 2009. [DOI: 10.1111/j.1095-8312.2009.01285.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Bonnivard E, Catrice O, Ravaux J, Brown SC, Higuet D. Survey of genome size in 28 hydrothermal vent species covering 10 families. Genome 2009; 52:524-36. [PMID: 19483771 DOI: 10.1139/g09-027] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Knowledge of genome size is a useful and necessary prerequisite for the development of many genomic resources. To better understand the origins and effects of DNA gains and losses among species, it is important to collect data from a broad taxonomic base, but also from particular ecosystems. Oceanic thermal vents are an interesting model to investigate genome size in very unstable environments. Here we provide data estimated by flow cytometry for 28 vent-living species among the most representative from different hydrothermal vents. We also report the genome size of closely related coastal decapods. Haploid C-values were compared with those previously reported for species from corresponding orders or infraorders. This is the first broad survey of 2C values in vent organisms. Contrary to expectations, it shows that certain hydrothermal vent species have particularly large genomes. The vent squat lobster Munidopsis recta has the largest genome yet reported for any anomuran: 2C=31.1 pg=30.4x10(9) bp. In several groups, such as Brachyura, Phyllodocida, and Veneroida, vent species have genomes that clearly rank at the high end of published values for each group. We also describe the highest DNA content yet recorded for the Brachyura (coastal crabs Xantho pilipes and Necora puber). Finally, analysis of genome size variation across populations revealed unexpected intraspecific variation in the vent shrimp Mirocaris fortunata that could not be attributed simply to ploidy changes.
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Affiliation(s)
- Eric Bonnivard
- Equipe Génétique et Evolution, UMR Systématique Adaptation et Evolution (7138), Université Paris VI, 7 quai St. Bernard, 75252 Paris, France.
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Hessen DO, Ventura M, Elser JJ. Do phosphorus requirements for RNA limit genome size in crustacean zooplankton? Genome 2008; 51:685-91. [DOI: 10.1139/g08-053] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
As for most other organisms, genome size in zooplankton differs widely. This may have a range of consequences for growth rate, development, and life history strategies, yet the causes of this pronounced variability are not settled. Here we propose that small genome size may be an evolutionary consequence of phosphorus (P) allocation from DNA to RNA under P deficiency. To test this hypothesis we have compared the two major groups of zooplankton, copepods and cladocerans, that have overlapping niches and body size. Relative to the cladocerans, copepods have a more complex life history and a lower mass-specific P content, while cladocerans tend to have higher P and RNA contents and higher specific growth rates and frequently experience P-limited growth, likely due to a shortage of P for ribosome synthesis. Cladocerans also generally have smaller genomes than copepods (1C = 0.17–0.63 pg DNA·cell–1vs. 1C = 0.10–10 pg DNA·cell–1). Furthermore, cladocerans have a higher slope of the relationship of body size with DNA content (1.5 vs. 0.28 in copepods) and present almost 15-fold higher RNA:DNA ratios (24.8 in cladocerans vs. 1.6 in copepods). Hence, small genome size in cladocerans could reflect an evolutionary pressure towards “efficient” genomes to conserve a key element needed to maximize growth rate. We do not claim that this is a universal cause of genome size variability, but propose that streamlining of genomes could be related to P conservation rather than energy conservation. This could be relevant for a range of organisms that may suffer P-limited growth rates.
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Affiliation(s)
- Dag O. Hessen
- University of Oslo, Department of Biology, CEES, P.O. Box 1066, Blindern, 0316 Oslo, Norway
- Department of Freshwater Ecology, National Environmental Research Institute (NERI), Vejlsøvej 25, DK-8600 Silkeborg, Denmark
- Limnology Group (CSIC-UB), Centre for Advanced Studies of Blanes (CEAB), Spanish Research Council (CSIC), Accés a la Cala Sant Francesc, 14, 17300 Blanes, Girona, Spain
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
| | - Marc Ventura
- University of Oslo, Department of Biology, CEES, P.O. Box 1066, Blindern, 0316 Oslo, Norway
- Department of Freshwater Ecology, National Environmental Research Institute (NERI), Vejlsøvej 25, DK-8600 Silkeborg, Denmark
- Limnology Group (CSIC-UB), Centre for Advanced Studies of Blanes (CEAB), Spanish Research Council (CSIC), Accés a la Cala Sant Francesc, 14, 17300 Blanes, Girona, Spain
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
| | - James J. Elser
- University of Oslo, Department of Biology, CEES, P.O. Box 1066, Blindern, 0316 Oslo, Norway
- Department of Freshwater Ecology, National Environmental Research Institute (NERI), Vejlsøvej 25, DK-8600 Silkeborg, Denmark
- Limnology Group (CSIC-UB), Centre for Advanced Studies of Blanes (CEAB), Spanish Research Council (CSIC), Accés a la Cala Sant Francesc, 14, 17300 Blanes, Girona, Spain
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
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Rasch EM, Wyngaard GA, Connelly BA. Heterochromatin endoreduplication prior to gametogenesis and chromatin diminution during early embryogenesis in Mesocyclops edax (Copepoda: Crustacea). J Morphol 2008; 269:387-97. [PMID: 17932949 DOI: 10.1002/jmor.10576] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The segregation of progenitor somatic cells from those of the primordial germ cells that sequester and retain elevated levels of DNA during subsequent developmental events, poses an interesting, alternative pathway of chromosome behavior during the reproductive cycle of certain species of cyclopoid copepods and several other organisms. Separation of maternal and paternal chromosome sets during very early cleavages (gonomery) is often a feature following marked elevations of DNA levels in germ cells for some of these species. Here, we report on the accumulation of large amounts of DNA in germ line nuclei of both female and male juveniles and adults of a freshwater copepod, Mesocyclops edax (Forbes, 1890). We also report the robust uptake of 3H-thymidine by germ cells prior to gametogenesis in this species. By using cytophotometric analysis of the DNA levels in both germ line cells and somatic cells from the same specimens we demonstrate that germ cell nuclei accumulate high levels of DNA prior to the onset of gametogenesis. These elevated amounts coincide with the levels of heterochromatic DNA discarded during chromatin diminution. A new model is proposed of major cytological events accompanying the process of chromatin diminution in M. edax.
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Affiliation(s)
- Ellen M Rasch
- Department of Anatomy and Cell Biology, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614-0582, USA.
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