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Pepke ML, Ringsby TH, Eisenberg DTA. The evolution of early-life telomere length, pace-of-life and telomere-chromosome length dynamics in birds. Mol Ecol 2023; 32:2898-2912. [PMID: 36847070 DOI: 10.1111/mec.16907] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 02/09/2023] [Accepted: 02/21/2023] [Indexed: 03/01/2023]
Abstract
Telomeres, the short DNA sequences that protect chromosome ends, are an ancient molecular structure, which is highly conserved across most eukaryotes. Species differ in their telomere lengths, but the causes of this variation are not well understood. Here, we demonstrate that mean early-life telomere length is an evolutionary labile trait across 57 bird species (representing 35 families in 12 orders) with the greatest trait diversity found among passerines. Among these species, telomeres are significantly shorter in fast-lived than in slow-lived species, suggesting that telomere length may have evolved to mediate trade-offs between physiological requirements underlying the diversity of pace-of-life strategies in birds. This association was attenuated when excluding studies that may include interstitial telomeres in the estimation of mean telomere length. Curiously, within some species, larger individual chromosome size predicts longer telomere lengths on that chromosome, leading to the hypothesis that telomere length also covaries with chromosome length across species. We show that longer mean chromosome length or genome size tends to be associated with longer mean early-life telomere length (measured across all chromosomes) within a phylogenetic framework constituting up to 31 bird species. These associations were strengthened when excluding highly influential outliers. However, sensitivity analyses suggested that they were susceptible to sample size effects and not robust to the exclusion of studies that may include interstitial telomeres. Combined, our analyses generalize patterns previously found within a few species and provide potential adaptive explanations for the 10-fold variation in telomere lengths observed among birds.
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Affiliation(s)
- Michael Le Pepke
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Thor Harald Ringsby
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Dan T A Eisenberg
- Department of Anthropology, University of Washington, Seattle, Washington, USA
- Centre for Studies in Demography and Ecology, University of Washington, Seattle, Washington, USA
- Department of Biology, University of Washington, Seattle, Washington, USA
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2
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Glugoski L, Deon GA, Nogaroto V, Moreira-Filho O, Vicari MR. Robertsonian Fusion Site in Rineloricaria pentamaculata (Siluriformes: Loricariidae): Involvement of 5S Ribosomal DNA and Satellite Sequences. Cytogenet Genome Res 2023; 162:657-664. [PMID: 37054691 DOI: 10.1159/000530636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 04/07/2023] [Indexed: 04/15/2023] Open
Abstract
Cytogenetic studies demonstrated that unstable chromosomal sites in armored catfishes (Loricariidae) triggered intense karyotypic diversification, mainly derived from Robertsonian rearrangements. In Loricariinae, the presence of ribosomal DNA (rDNA) clusters and their flanking repeated regions (such as microsatellites or partial transposable element sequences) was proposed to facilitate chromosomal rearrangements. Hence, this study aimed to characterize the numerical chromosomal polymorphism observed in Rineloricaria pentamaculata and evaluate the chromosomal rearrangements which originated diploid chromosome number (2n) variation, from 56 to 54. Our data indicate a centric fusion event between acrocentric chromosomes of pairs 15 and 18, bearing 5S rDNA sites on their short (p) arms. This chromosome fusion established the numerical polymorphism, decreasing the 2n from original 56 (karyomorph A) to 55 in karyomorph B and 54 in karyomorph C. Although vestiges of telomeric sequences were evidenced at the fusion point, no 5S rDNA was detected in this region. The acrocentric chromosomes involved in the origin of the fusion were enriched with (CA)n and (GA)n microsatellites. Repetitive sequences in the acrocentric chromosomes subtelomeres have facilitated the rearrangement. Our study thus reinforces the view on the important role of particular repetitive DNA classes in promoting chromosome fusions which frequently drive Rineloricaria karyotype evolution.
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Affiliation(s)
- Larissa Glugoski
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Geize A Deon
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Viviane Nogaroto
- Department of Structural Biology, Molecular and Genetics, State University of Ponta Grossa, Ponta Grossa, Brazil
| | - Orlando Moreira-Filho
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Marcelo Ricardo Vicari
- Department of Structural Biology, Molecular and Genetics, State University of Ponta Grossa, Ponta Grossa, Brazil
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3
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Glugoski L, Nogaroto V, Deon GA, Azambuja M, Moreira-Filho O, Vicari MR. Enriched tandemly repeats in chromosomal fusion points of Rineloricaria latirostris (Boulenger, 1900) (Siluriformes: Loricariidae). Genome 2022; 65:479-489. [PMID: 35939838 DOI: 10.1139/gen-2022-0043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cytogenetic data showed the enrichment of repetitive DNAs in chromosomal rearrangement points between closely related species in armored catfishes. Still, few studies integrated cytogenetic and genomic data aiming to identify their prone-to-break DNA sites. Here, we aimed to obtain the repetitive fraction in Rineloricaria latirostris to recognize the microsatellite and homopolymers flanking the regions previously described as chromosomal fusion points. The results indicated that repetitive DNAs in R. latirostris are predominantly DNA transposons, and considering the microsatellite and homopolymers, A/T-rich expansions were the most abundant. The in situ localization demonstrated the A/T-rich repetitive sequences are scattered on the chromosomes, while A/G-rich microsatellites units were accumulated in some regions. The DNA transposon hAT, the 5S rDNA, and 45S rDNA (previously identified in Robertsonian fusion points in R. latirostris) are clusterized with some microsatellites, especially (CA)n, (GA)n, and poly-A, which also are enriched in regions of chromosomal fusions. Our findings demonstrated that repetitive sequences such as rDNAs, hAT transposon, and microsatellite units flank probable evolutionary breakpoint regions in R. latirostris. However, due to the sequence unit homologies in different chromosomal sites, these repeat DNAs only may have facilitated chromosome fusion events in R. latirostris rather than work as a double-strand breakpoint site.
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Affiliation(s)
- Larissa Glugoski
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Sao Carlos, São Paulo, Brazil;
| | - Viviane Nogaroto
- Universidade Estadual de Ponta Grossa, Departamento de Biologia Estrutural, Molecular e Genética, Ponta Grossa, Paraná, Brazil;
| | - Geize Aparecida Deon
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Sao Carlos, São Paulo, Brazil;
| | - Matheus Azambuja
- Universidade Federal do Paraná, Departamento de Genética, Curitiba, PR, Brazil;
| | - Orlando Moreira-Filho
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Sao Carlos, São Paulo, Brazil;
| | - Marcelo Ricardo Vicari
- Universidade Estadual de Ponta Grossa, Departamento de Biologia Estrutural, Molecular e Genética, Ponta Grossa, Paraná, Brazil.,Universidade Federal do Paraná, Departamento de Genética, Curitiba, PR, Brazil;
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4
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Deon GA, Glugoski L, Sassi FDMC, Hatanaka T, Nogaroto V, Bertollo LAC, Liehr T, Al-Rikabi A, Moreira-Filho O, Cioffi MDB, Vicari MR. Chromosomal Rearrangements and Origin of the Multiple XX/XY 1Y 2 Sex Chromosome System in Harttia Species (Siluriformes: Loricariidae). Front Genet 2022; 13:877522. [PMID: 35386289 PMCID: PMC8977651 DOI: 10.3389/fgene.2022.877522] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/03/2022] [Indexed: 11/13/2022] Open
Abstract
The Neotropical genus Harttia comprises species with extensive chromosomal remodeling and distinct sex chromosome systems (SCSs). So far, three different SCSs with male heterogamety have been characterized in the group. In some species, the presence of the XX/XY1Y2 SCS is associated with a decrease in diploid numbers and several chromosomal rearrangements, although a direct relation to sex chromosome differentiation has not been shown yet. Here, we aimed to investigate the differentiation processes that have led to the establishment of the rare XX/XY1Y2 SCS and track its evolutionary history among other Harttia species. For that, four whole chromosome painting probes derived from chromosome 1 of H. torrenticola (HTO-1), chromosomes 9 and X of H. carvalhoi (HCA-9 and HCA-X), and chromosome X from H. intermontana (HIN-X) were applied in nine Harttia species. Homeologous chromosome blocks were located in Harttia species and demonstrated that Robertsonian (Rb) fusions originated HTO-1, HCA-9, and HCA-X chromosomes, while Rb fissions explain Y1 and Y2 sex chromosomes. Specifically, in H. intermontana, HCA-X, HCA-9, and the NOR-bearing chromosome demonstrated that homeologous blocks were used in the HIN-X and metacentric pair 2 origins. Consequently, diploid numbers changed between the studied species. Overall, the data also reinforce the existence of unstable genomic sites promoting chromosomal differentiation and remodeling within the genus Harttia.
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Affiliation(s)
- Geize Aparecida Deon
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo, Brazil.,Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Paraná, Brazil
| | - Larissa Glugoski
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo, Brazil.,Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Paraná, Brazil
| | | | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo, Brazil
| | - Viviane Nogaroto
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Paraná, Brazil
| | | | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | - Ahmed Al-Rikabi
- Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | - Orlando Moreira-Filho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo, Brazil
| | | | - Marcelo Ricardo Vicari
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Paraná, Brazil
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Vicari MR, Bruschi DP, Cabral-de-Mello DC, Nogaroto V. Telomere organization and the interstitial telomeric sites involvement in insects and vertebrates chromosome evolution. Genet Mol Biol 2022; 45:e20220071. [DOI: 10.1590/1678-4685-gmb-2022-0071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 09/24/2022] [Indexed: 11/16/2022] Open
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6
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Cytogenetic, morphological and molecular characterization of two cryptic species of the genus Omophoita Chevrolat, 1837 (Coleoptera: Chrysomelidae: Galerucinae). Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00715-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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7
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Slijepcevic P. Serial Endosymbiosis Theory: From biology to astronomy and back to the origin of life. Biosystems 2021; 202:104353. [PMID: 33453317 DOI: 10.1016/j.biosystems.2021.104353] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 12/20/2022]
Abstract
Serial Endosymbiosis Theory, or SET, was conceived and developed by Lynn Margulis, to explain the greatest discontinuity in the history of life, the origin of eukaryotic cells. Some predictions of SET, namely the origin of mitochondria and chloroplasts, withstood the test of the most recent evidence from a variety of disciplines including phylogenetics, biochemistry, and cell biology. Even though some other predictions fared less well, SET remains a seminal theory in biology. In this paper, I focus on two aspects of SET. First, using the concept of "universal symbiogenesis", developed by Freeman Dyson to search for commonalities in astronomy and biology, I propose that SET can be extended beyond eukaryogenesis. The extension refers to the possibility that even prokaryotic organisms, themselves subject to the process of symbiogenesis in SET, could have emerged symbiotically. Second, I contrast a recent "viral eukaryogenesis" hypothesis, according to which the nucleus evolved from a complex DNA virus, with a view closer to SET, according to which the nucleus evolved through the interplay of the archaeal host, the eubacterial symbiont, and a non-LTR transposon, or telomerase. Viruses joined in later, through the process of viral endogenization, to shape eukaryotic chromosomes in the process of karyotype evolution. These two proposals based on SET are a testament to its longevity as a scientific theory.
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Affiliation(s)
- Predrag Slijepcevic
- Department of Life Sciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UB8 3PH, United Kingdom.
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8
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Highly Rearranged Karyotypes and Multiple Sex Chromosome Systems in Armored Catfishes from the Genus Harttia (Teleostei, Siluriformes). Genes (Basel) 2020; 11:genes11111366. [PMID: 33218104 PMCID: PMC7698909 DOI: 10.3390/genes11111366] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 11/16/2022] Open
Abstract
Harttia comprises an armored catfish genus endemic to the Neotropical region, including 27 valid species with low dispersion rates that are restricted to small distribution areas. Cytogenetics data point to a wide chromosomal diversity in this genus due to changes that occurred in isolated populations, with chromosomal fusions and fissions explaining the 2n number variation. In addition, different multiple sex chromosome systems and rDNA loci location are also found in some species. However, several Harttia species and populations remain to be investigated. In this study, Harttia intermontana and two still undescribed species, morphologically identified as Harttia sp. 1 and Harttia sp. 2, were cytogenetically analyzed. Harttia intermontana has 2n = 52 and 2n = 53 chromosomes, while Harttia sp. 1 has 2n = 56 and 2n = 57 chromosomes in females and males, respectively, thus highlighting the occurrence of an XX/XY1Y2 multiple sex chromosome system in both species. Harttia sp. 2 presents 2n = 62 chromosomes for both females and males, with fission events explaining its karyotype diversification. Chromosomal locations of the rDNA sites were also quite different among species, reinforcing that extensive rearrangements had occurred in their karyotype evolution. Comparative genomic hybridization (CGH) experiments among some Harttia species evidenced a shared content of the XY1Y2 sex chromosomes in three of them, thus pointing towards their common origin. Therefore, the comparative analysis among all Harttia species cytogenetically studied thus far allowed us to provide an evolutionary scenario related to the speciation process of this fish group.
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9
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10
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Leo L, Marchetti M, Giunta S, Fanti L. Epigenetics as an Evolutionary Tool for Centromere Flexibility. Genes (Basel) 2020; 11:genes11070809. [PMID: 32708654 PMCID: PMC7397245 DOI: 10.3390/genes11070809] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/11/2020] [Accepted: 07/13/2020] [Indexed: 12/31/2022] Open
Abstract
Centromeres are the complex structures responsible for the proper segregation of chromosomes during cell division. Structural or functional alterations of the centromere cause aneuploidies and other chromosomal aberrations that can induce cell death with consequences on health and survival of the organism as a whole. Because of their essential function in the cell, centromeres have evolved high flexibility and mechanisms of tolerance to preserve their function following stress, whether it is originating from within or outside the cell. Here, we review the main epigenetic mechanisms of centromeres’ adaptability to preserve their functional stability, with particular reference to neocentromeres and holocentromeres. The centromere position can shift in response to altered chromosome structures, but how and why neocentromeres appear in a given chromosome region are still open questions. Models of neocentromere formation developed during the last few years will be hereby discussed. Moreover, we will discuss the evolutionary significance of diffuse centromeres (holocentromeres) in organisms such as nematodes. Despite the differences in DNA sequences, protein composition and centromere size, all of these diverse centromere structures promote efficient chromosome segregation, balancing genome stability and adaptability, and ensuring faithful genome inheritance at each cellular generation.
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Affiliation(s)
- Laura Leo
- Istituto Pasteur Italia, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, “Sapienza” University of Rome, 00185 Rome, Italy; (L.L.); (M.M.); (S.G.)
| | - Marcella Marchetti
- Istituto Pasteur Italia, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, “Sapienza” University of Rome, 00185 Rome, Italy; (L.L.); (M.M.); (S.G.)
| | - Simona Giunta
- Istituto Pasteur Italia, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, “Sapienza” University of Rome, 00185 Rome, Italy; (L.L.); (M.M.); (S.G.)
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Laura Fanti
- Istituto Pasteur Italia, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, “Sapienza” University of Rome, 00185 Rome, Italy; (L.L.); (M.M.); (S.G.)
- Correspondence:
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11
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Tomaska L, Nosek J, Kar A, Willcox S, Griffith JD. A New View of the T-Loop Junction: Implications for Self-Primed Telomere Extension, Expansion of Disease-Related Nucleotide Repeat Blocks, and Telomere Evolution. Front Genet 2019; 10:792. [PMID: 31475042 PMCID: PMC6702307 DOI: 10.3389/fgene.2019.00792] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/26/2019] [Indexed: 12/12/2022] Open
Abstract
Telomere loops (t-loops) are formed at the ends of chromosomes in species ranging from humans to worms, plants, and with genetic manipulation, some yeast. Recent in vitro studies demonstrated that transcription of telomeric DNA leads to highly efficient t-loop formation. It was also shown that both DNA termini are inserted into the preceding DNA to generate a highly stable t-loop junction. Furthermore, some telomeric RNA remains present at the junction, potentially acting as a plug to further protect and stabilize the t-loop. Modeling the loop junction reveals two mechanisms by which the canonical chromosomal replication factors could extend the telomere in the absence of telomerase. One mechanism would utilize the annealed 3’ terminus as a de novo replication origin. In vitro evidence for the ability of the t-loop to prime telomere extension using the T7 replication factors is presented. A second mechanism would involve resolution of the Holliday junction present in the t-loop bubble by factors such as GEN1 to generate a rolling circle template at the extreme terminus of the telomere. This could lead to large expansions of the telomeric tract. Here, we propose that telomeres evolved as terminal elements containing long arrays of short nucleotide repeats due to the ability of such arrays to fold back into loops and self-prime their replicative extension. In this view, telomerase may have evolved later to provide a more precise mechanism of telomere maintenance. Both pathways have direct relevance to the alternative lengthening of telomeres (ALT) pathway. This view also provides a possible mechanism for the very large repeat expansions observed in nucleotide repeat diseases such as Fragile X syndrome, myotonic dystrophy, familial amyotrophic lateral sclerosis (ALS), and frontotemporal dementia (FTD). The evolution of telomeres is discussed in the framework of these models.
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Affiliation(s)
- Lubomir Tomaska
- Departments of Genetics and Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Jozef Nosek
- Departments of Genetics and Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Anirban Kar
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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12
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Slijepcevic P. Genome dynamics over evolutionary time: “C-value enigma” in light of chromosome structure. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2018; 836:22-27. [DOI: 10.1016/j.mrgentox.2018.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 03/28/2018] [Accepted: 05/03/2018] [Indexed: 12/15/2022]
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13
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Klegarth AR, Eisenberg DTA. Mammalian chromosome-telomere length dynamics. ROYAL SOCIETY OPEN SCIENCE 2018; 5:180492. [PMID: 30109098 PMCID: PMC6083700 DOI: 10.1098/rsos.180492] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 06/19/2018] [Indexed: 06/08/2023]
Abstract
Individual chromosome arms have specific individual telomere lengths (TLs). Past studies within species have shown strong positive correlations between individual chromosome length and TL at that chromosome. While the reasons for these associations are unclear, the strength and consistency of the associations across disparate taxa suggest that this is important to telomere biology and should be explored further. If TL is primarily determined by chromosome length, then chromosome length should be considered and controlled for in cross-species analyses of TL. Here, we employ a cross-species approach to explore whether the chromosome length-TL association observed intraspecifically is a determinant of mean TL across species. Data were compiled from two studies characterizing TL across a range of mammalian taxa and analysed in a phylogenetic framework. We found no significant relationship between TL and chromosome size across mammals or within mammalians orders. The pattern trends in the expected direction and we suggest may be masked by evolutionary lag effects.
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Affiliation(s)
- Amy R. Klegarth
- Department of Anthropology, University of Washington, 314 Denny Hall, Seattle, WA 98105, USA
- Center for Studies in Demography and Ecology, University of Washington, 230 Raitt Hall, Seattle, WA 98105, USA
| | - Dan T. A. Eisenberg
- Department of Anthropology, University of Washington, 314 Denny Hall, Seattle, WA 98105, USA
- Center for Studies in Demography and Ecology, University of Washington, 230 Raitt Hall, Seattle, WA 98105, USA
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14
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Glugoski L, Giuliano-Caetano L, Moreira-Filho O, Vicari MR, Nogaroto V. Co-located hAT transposable element and 5S rDNA in an interstitial telomeric sequence suggest the formation of Robertsonian fusion in armored catfish. Gene 2018; 650:49-54. [DOI: 10.1016/j.gene.2018.01.099] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/23/2018] [Accepted: 01/31/2018] [Indexed: 01/12/2023]
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15
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Slijepcevic P. Evolutionary epistemology: Reviewing and reviving with new data the research programme for distributed biological intelligence. Biosystems 2017; 163:23-35. [PMID: 29199093 DOI: 10.1016/j.biosystems.2017.11.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/27/2017] [Accepted: 11/27/2017] [Indexed: 02/06/2023]
Abstract
Numerous studies in microbiology, eukaryotic cell biology, plant biology, biomimetics, synthetic biology, and philosophy of science appear to support the principles of the epistemological theory inspired by evolution, also known as "Evolutionary Epistemology", or EE. However, that none of the studies acknowledged EE suggests that its principles have not been formulated with sufficient clarity and depth to resonate with the interests of the empirical research community. In this paper I review evidence in favor of EE, and also reformulate EE principles to better inform future research. The revamped programme may be tentatively called Research Programme for Distributed Biological Intelligence. Intelligence I define as the capacity of organisms to gain information about their environment, process that information internally, and translate it into phenotypic forms. This multistage progression may be expressed through the acronym IGPT (information-gain-process-translate). The key principles of the programme may be summarized as follows. (i) Intelligence, a universal biological phenomenon promoting individual fitness, is required for effective organism-environment interactions. Given that animals represent less than 0.01% of the planetary biomass, neural intelligence is not the evolutionary norm. (ii) The basic unit of intelligence is a single cell prokaryote. All other forms of intelligence are derived. (iii) Intelligence is hierarchical. It ranges from bacteria to the biosphere or Gaia. (iv) The concept of "information" acquires a new meaning because information processing is at the heart of biological intelligence. All biological systems, from bacteria to Gaia, are intelligent, open thermodynamic systems that exchange information, matter and energy with the environment. (v) The organism-environment interaction is cybernetic. As much as the organism changes due to the influence of the environment, the organism's responses to induced changes affect the environment and subsequent organism-environment interactions. Based on the above principles a new research agenda can be formulated to explore different forms of biological intelligence.
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Affiliation(s)
- Predrag Slijepcevic
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UB8 3PH, United Kingdom.
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16
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Villa N, Conconi D, Benussi DG, Tornese G, Crosti F, Sala E, Dalprà L, Pecile V. A complete duplication of X chromosome resulting in a tricentric isochromosome originated by centromere repositioning. Mol Cytogenet 2017. [PMID: 28630649 PMCID: PMC5470200 DOI: 10.1186/s13039-017-0323-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Neocentromeres are rare and considered chromosomal aberrations, because a non-centromeric region evolves in an active centromere by mutation. The literature reported several structural anomalies of X chromosome and they influence the female reproductive capacity or are associated to Turner syndrome in the presence of monosomy X cell line. CASE PRESENTATION We report a case of chromosome X complex rearrangement found in a prenatal diagnosis. The fetal karyotype showed a mosaicism with a 45,X cell line and a 46 chromosomes second line with a big marker, instead of a sex chromosome. The marker morphology and fluorescence in situ hybridization (FISH) characterization allowed us to identify a tricentric X chromosome constituted by two complete X chromosome fused at the p arms telomere and an active neocentromere in the middle, at the union of the two Xp arms, where usually are the telomeric regions. FISH also showed the presence of a paracentric inversion of both Xp arms. Furthermore, fragility figures were found in 56% of metaphases from peripheral blood lymphocytes culture at birth: a shorter marker chromosome and an apparently acentric fragment frequently lost. CONCLUSIONS At our knowledge, this is the first isochromosome of an entire non-acrocentric chromosome. The neocentromere is constituted by canonical sequences but localized in an unusual position and the original centromeres are inactivated. We speculated that marker chromosome was the result of a double rearrangement: firstly, a paracentric inversion which involved the Xp arm, shifting a part of the centromere at the p end and subsequently a duplication of the entire X chromosome, which gave rise to an isochromosome. It is possible to suppose that the first event could be a result of a non-allelic homologous recombination mediated by inverted low-copy repeats. As expected, our case shows a Turner phenotype with mild facial features and no major skeletal deformity, normal psychomotor development and a spontaneous development of puberty and menarche, although with irregular menses since the last follow-up.
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Affiliation(s)
- N Villa
- Medical Genetics Laboratory, Clinical Pathology Department, S. Gerardo Hospital, Monza, Italy
| | - D Conconi
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - D Gambel Benussi
- Medical Genetics, Institute for Maternal and Child Health I.R.C.C.S. "Burlo Garofolo", Trieste, Italy
| | - G Tornese
- Department of Pediatrics, Institute for Maternal and Child Health I.R.C.C.S. "Burlo Garofolo", Trieste, Italy
| | - F Crosti
- Medical Genetics Laboratory, Clinical Pathology Department, S. Gerardo Hospital, Monza, Italy
| | - E Sala
- Medical Genetics Laboratory, Clinical Pathology Department, S. Gerardo Hospital, Monza, Italy
| | - L Dalprà
- Medical Genetics Laboratory, Clinical Pathology Department, S. Gerardo Hospital, Monza, Italy.,School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - V Pecile
- Medical Genetics, Institute for Maternal and Child Health I.R.C.C.S. "Burlo Garofolo", Trieste, Italy
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Bolzán AD. Interstitial telomeric sequences in vertebrate chromosomes: Origin, function, instability and evolution. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 773:51-65. [PMID: 28927537 DOI: 10.1016/j.mrrev.2017.04.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 03/13/2017] [Accepted: 04/17/2017] [Indexed: 12/21/2022]
Abstract
By definition, telomeric sequences are located at the very ends or terminal regions of chromosomes. However, several vertebrate species show blocks of (TTAGGG)n repeats present in non-terminal regions of chromosomes, the so-called interstitial telomeric sequences (ITSs), interstitial telomeric repeats or interstitial telomeric bands, which include those intrachromosomal telomeric-like repeats located near (pericentromeric ITSs) or within the centromere (centromeric ITSs) and those telomeric repeats located between the centromere and the telomere (i.e., truly interstitial telomeric sequences) of eukaryotic chromosomes. According with their sequence organization, localization and flanking sequences, ITSs can be classified into four types: 1) short ITSs, 2) subtelomeric ITSs, 3) fusion ITSs, and 4) heterochromatic ITSs. The first three types have been described mainly in the human genome, whereas heterochromatic ITSs have been found in several vertebrate species but not in humans. Several lines of evidence suggest that ITSs play a significant role in genome instability and evolution. This review aims to summarize our current knowledge about the origin, function, instability and evolution of these telomeric-like repeats in vertebrate chromosomes.
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Affiliation(s)
- Alejandro D Bolzán
- Laboratorio de Citogenética y Mutagénesis, Instituto Multidisciplinario de Biología Celular (IMBICE, CICPBA-UNLP-CONICET La Plata), C.C. 403, 1900 La Plata, Argentina; Facultad de Ciencias Naturales y Museo, UNLP, Calle 60 y 122, 1900 La Plata, Argentina.
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Barros AV, Wolski MAV, Nogaroto V, Almeida MC, Moreira-Filho O, Vicari MR. Fragile sites, dysfunctional telomere and chromosome fusions: What is 5S rDNA role? Gene 2017; 608:20-27. [DOI: 10.1016/j.gene.2017.01.013] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 01/04/2017] [Accepted: 01/18/2017] [Indexed: 11/29/2022]
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