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Fernandes KA, Gee EK, Rogers CW, Kittelmann S, Biggs PJ, Bermingham EN, Bolwell CF, Thomas DG. Seasonal Variation in the Faecal Microbiota of Mature Adult Horses Maintained on Pasture in New Zealand. Animals (Basel) 2021; 11:2300. [PMID: 34438757 DOI: 10.3390/ani11082300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/20/2021] [Accepted: 07/28/2021] [Indexed: 12/26/2022] Open
Abstract
Simple Summary Ten horses were kept on pasture for one year, with hay provided from June to October. Each month we measured how much pasture was present and collected pasture and hay samples to assess their nutrient content, and faecal samples from all horses to investigate the diversity of the bacterial species present using next-generation sequencing technology. The population of faecal bacteria was more diverse during the months when the horses were kept exclusively on pasture compared to the months when pasture was supplemented with hay. The diet offered, and the season and the month we sampled the paddock all had a major influence on the diversity of the species of bacteria in the faeces. While there were some differences between the horses, generally the bacterial populations could be grouped together in samples obtained during May, June, and July (late-autumn to winter period), and January, February, and March (a period of drought). More specifically we were able to show an association between specific bacterial species, nutrients (dry matter, protein, and structural carbohydrates), and climatic conditions (rainfall and temperature). Our study showed that the diversity and composition of the bacterial population of horses kept on pasture changes over a 12-month period, and this reflects changes in the nutrient composition of the pasture, which in turn is influenced by climate. The findings of this study may have implications for managing horses on pasture and the use of forages for horses susceptible to digestive problems. Abstract Seasonal variation in the faecal microbiota of forage-fed horses was investigated over a 12-month period to determine whether the bacterial diversity fluctuated over time. Horses (n = 10) were maintained on pasture for one year, with hay supplemented from June to October. At monthly intervals, data were recorded on pasture availability and climate (collected continuously and averaged on monthly basis), pasture and hay samples were collected for nutrient analysis, and faecal samples were collected from all horses to investigate the diversity of faecal microbiota using next-generation sequencing on the Illumina MiSeq platform. The alpha diversity of bacterial genera was high in all samples (n = 118), with significantly higher Simpson’s (p < 0.001) and Shannon-Wiener (p < 0.001) diversity indices observed during the months when horses were kept exclusively on pasture compared to the months when pasture was supplemented with hay. There were significant effects of diet, season, and month (ANOSIM, p < 0.01 for each comparison) on the beta diversity of bacterial genera identified in the faeces. While there was some inter-horse variation, hierarchical clustering of beta diversity indices showed separate clades originating for samples obtained during May, June, and July (late-autumn to winter period), and January, February, and March (a period of drought), with a strong association between bacterial taxa and specific nutrients (dry matter, protein, and structural carbohydrates) and climate variables (rainfall and temperature). Our study supports the hypothesis that the diversity and community structure of the faecal microbiota of horses kept on pasture varied over a 12-month period, and this variation reflects changes in the nutrient composition of the pasture, which in turn is influenced by climatic conditions. The findings of this study may have implications for grazing management and the preparation of conserved forages for those horses susceptible to perturbations of the hindgut microbiota.
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Goto M, Sasaki M, Kobayashi T. The S-Phase Cyclin Clb5 Promotes rRNA Gene (rDNA) Stability by Maintaining Replication Initiation Efficiency in rDNA. Mol Cell Biol 2021; 41:e00324-20. [PMID: 33619126 DOI: 10.1128/MCB.00324-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 02/05/2021] [Indexed: 11/26/2022] Open
Abstract
Regulation of replication origins is important for complete duplication of the genome, but the effect of origin activation on the cellular response to replication stress is poorly understood. The budding yeast rRNA gene (rDNA) forms tandem repeats and undergoes replication fork arrest at the replication fork barrier (RFB), inducing DNA double-strand breaks (DSBs) and genome instability accompanied by copy number alterations. Regulation of replication origins is important for complete duplication of the genome, but the effect of origin activation on the cellular response to replication stress is poorly understood. The budding yeast rRNA gene (rDNA) forms tandem repeats and undergoes replication fork arrest at the replication fork barrier (RFB), inducing DNA double-strand breaks (DSBs) and genome instability accompanied by copy number alterations. Here, we demonstrate that the S-phase cyclin Clb5 promotes rDNA stability. Absence of Clb5 led to reduced efficiency of replication initiation in rDNA but had little effect on the number of replication forks arrested at the RFB, suggesting that arrival of the converging fork is delayed and forks are more stably arrested at the RFB. Deletion of CLB5 affected neither DSB formation nor its repair at the RFB but led to homologous recombination-dependent rDNA instability. Therefore, arrested forks at the RFB may be subject to DSB-independent, recombination-dependent rDNA instability. The rDNA instability in clb5Δ was not completely suppressed by the absence of Fob1, which is responsible for fork arrest at the RFB. Thus, Clb5 establishes the proper interval for active replication origins and shortens the travel distance for DNA polymerases, which may reduce Fob1-independent DNA damage.
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Watada E, Li S, Hori Y, Fujiki K, Shirahige K, Inada T, Kobayashi T. Age-Dependent Ribosomal DNA Variations in Mice. Mol Cell Biol 2020; 40:e00368-20. [PMID: 32900821 DOI: 10.1128/MCB.00368-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/02/2020] [Indexed: 12/22/2022] Open
Abstract
The rRNA gene, which consists of tandem repetitive arrays (ribosomal DNA [rDNA] repeat), is one of the most unstable regions in the genome. The rDNA repeat in the budding yeast Saccharomyces cerevisiae is known to become unstable as the cell ages. However, it is unclear how the rDNA repeat changes in aging mammalian cells. Using quantitative single-cell analyses, we identified age-dependent alterations in rDNA copy number and levels of methylation in mice. The degree of methylation and copy number of rDNA from bone marrow cells of 2-year-old mice were increased by comparison to levels in 4-week-old mice in two mouse strains, BALB/cA and C57BL/6. The rRNA gene, which consists of tandem repetitive arrays (ribosomal DNA [rDNA] repeat), is one of the most unstable regions in the genome. The rDNA repeat in the budding yeast Saccharomyces cerevisiae is known to become unstable as the cell ages. However, it is unclear how the rDNA repeat changes in aging mammalian cells. Using quantitative single-cell analyses, we identified age-dependent alterations in rDNA copy number and levels of methylation in mice. The degree of methylation and copy number of rDNA from bone marrow cells of 2-year-old mice were increased by comparison to levels in 4-week-old mice in two mouse strains, BALB/cA and C57BL/6. Moreover, the level of pre-rRNA transcripts was reduced in older BALB/cA mice. We also identified many sequence variations in the rDNA. Among them, three mutations were unique to old mice, and two of them were found in the conserved region in budding yeast. We established yeast strains with the old-mouse-specific mutations and found that they shortened the life span of the cells. Our findings suggest that rDNA is also fragile in mammalian cells and that alterations within this region have a profound effect on cellular function.
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Shahnazi M, Ebadi M, Abbaspoor Z, Hajialilo E, Javadi A, Heydarian P, Saraei M, Alizadeh SA. Molecular Characterization of Fasciola and Dicrocoelium Species Isolated from Ruminant Livestock in Qazvin, Iran. Infect Disord Drug Targets 2020; 20:737-742. [PMID: 31595853 DOI: 10.2174/1871526519666191009143043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/01/2019] [Accepted: 09/12/2019] [Indexed: 06/10/2023]
Abstract
INTRODUCTION Fascioliasis and dicrocoeliasis are the most frequent zoonotic diseases with increasing human health problems in different parts of Iran. Two species, Fasciola hepatica (F. hepatica) and Fasciola gigantica (F. gigantica), are spread in the country. Molecular approaches have a decisive role in identifying both the species. The aim of this study was to detect Fasciola spp. and Dicrocoelium spp. by amplifying the ITS-2 and 28S rDNA gene sequence. METHODS Overall, 30 infected liver samples were collected from the livestock of Qazvin, Iran. The adult flukes were collected from different livestock. DNA extraction and PCR amplification of ribosomal RNA gene region (ITS2) and 28S rDNA gene fragment were conducted and a phylogenetic tree was constructed. RESULT All the isolates obtained from the cattle (No: 7) and 82.6% (No: 19) of sheep isolates were infected with F. hepatica species, whereas 17.4% (No: 4) of sheep isolates were infected with F. gigantica. It was also shown that F. hepatica was the predominant species of Fasciola present in the region. All the specimens were infected with Dicrocoelium dendriticum (D. dendriticum). CONCLUSION Both the species of Fasciola were found in Qazvin. D. dendriticum was the sole infecting species of the Dicrocoelium genus in the livestock of the city of Qazvin. Further research studies are needed to determine the intermediate host of the parasites in the region.
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Affiliation(s)
- Mojtaba Shahnazi
- Department of Parasitology and Mycology, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Maryam Ebadi
- Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Zahra Abbaspoor
- Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Elham Hajialilo
- Department of Parasitology and Mycology, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Amir Javadi
- Department of Social Sciences, School of Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Peyman Heydarian
- Department of Parasitology and Mycology, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mehrzad Saraei
- Department of Parasitology and Mycology, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Safar Ali Alizadeh
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
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Hosoyamada S, Sasaki M, Kobayashi T. The CCR4-NOT Complex Maintains Stability and Transcription of rRNA Genes by Repressing Antisense Transcripts. Mol Cell Biol 2019; 40:e00320-19. [PMID: 31611247 DOI: 10.1128/MCB.00320-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 09/26/2019] [Indexed: 12/21/2022] Open
Abstract
The rRNA genes (rDNA) in eukaryotes are organized into highly repetitive gene clusters. Each organism maintains a particular number of copies, suggesting that the rDNA is actively stabilized. We previously identified about 700 Saccharomyces cerevisiae genes that could contribute to rDNA maintenance. Here, we further analyzed these deletion mutants with unstable rDNA by measuring the amounts of extrachromosomal rDNA circles (ERCs) that are released as by-products of intrachromosomal recombination. The rRNA genes (rDNA) in eukaryotes are organized into highly repetitive gene clusters. Each organism maintains a particular number of copies, suggesting that the rDNA is actively stabilized. We previously identified about 700 Saccharomyces cerevisiae genes that could contribute to rDNA maintenance. Here, we further analyzed these deletion mutants with unstable rDNA by measuring the amounts of extrachromosomal rDNA circles (ERCs) that are released as by-products of intrachromosomal recombination. We found that extremely high levels of ERCs were formed in the absence of Pop2 (Caf1), which is a subunit of the CCR4-NOT complex, important for the regulation of all stages of gene expression. In the pop2 mutant, transcripts from the noncoding promoter E-pro in the rDNA accumulated, and the amounts of cohesin and condensin were reduced, which could promote recombination events. Moreover, we discovered that the amount of rRNA was decreased in the pop2 mutant. Similar phenotypes were observed in the absence of subunits Ccr4 and Not4 that, like Pop2, convey enzymatic activity to the complex. These findings indicate that lack of any CCR4-NOT-associated enzymatic activity resulted in a severe unstable rDNA phenotype related to the accumulation of noncoding RNA from E-pro.
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Kim SY, Xu D, Jung JH, Choi JK. Phylogeny and Genetic/Morphological Variation of Strombidinopsis minima-like Species (Ciliophora: Choreotrichia). J Eukaryot Microbiol 2019; 67:115-124. [PMID: 31523898 DOI: 10.1111/jeu.12761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 08/19/2019] [Accepted: 08/30/2019] [Indexed: 11/29/2022]
Abstract
Six isolates of mineral-enveloped Strombidinopsis minima-like species were collected from the coastal waters across several regions in Korea. Morphological observations and molecular analyses were performed. The ribosomal DNA sequences (including small subunit ribosomal DNA, internal transcriber spacer 1-5.8S ribosomal DNA-internal transcriber spacer 2; and part of large subunit ribosomal DNA) of these six isolates were compared. Their morphological characteristics were also compared with those of S. minima populations reported. The marked genetic differences (with a similarity range of 96.85-98.48%) in SSU rDNA among these S. minima-like entities suggest the existence of multiple species. This finding is also supported by morphological variations detected in this study and reported in the literature (e.g. 15-32 collar membranelles in different populations). In addition, S. minima-like species are clustered with S. batos and S. sinicum, and therefore, our SSU rDNA results support previous results suggesting that the genus Strombidinopsis is not monophyletic in origin. Further collection of morphological and molecular data may facilitate the determination of a new genus carrying mineral-enveloped Strombidinopsis species.
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Affiliation(s)
- Sun Young Kim
- National Marine Biodiversity Institute of Korea, Seocheon-gun, 33662, Korea
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Jae-Ho Jung
- Department of Biology, Gangneung-Wonju National University, Gangneung, 25457, Korea
| | - Joong Ki Choi
- Department of Oceanography, Inha University, Incheon, 22212, Korea
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Iida T, Kobayashi T. RNA Polymerase I Activators Count and Adjust Ribosomal RNA Gene Copy Number. Mol Cell 2019; 73:645-654.e13. [PMID: 30612878 DOI: 10.1016/j.molcel.2018.11.029] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 10/18/2018] [Accepted: 11/19/2018] [Indexed: 01/08/2023]
Abstract
Ribosome is the most abundant RNA-protein complex in a cell, and many copies of the ribosomal RNA gene (rDNA) have to be maintained. However, arrays of tandemly repeated rDNA genes can lose the copies by intra-repeat recombination. Loss of the rDNA copies of Saccharomyces cerevisiae is counteracted by gene amplification whereby the number of rDNA repeats stabilizes around 150 copies, suggesting the presence of a monitoring mechanism that counts and adjusts the number. Here, we report that, in response to rDNA copy loss, the upstream activating factor (UAF) for RNA polymerase I that transcribes the rDNA is released and directly binds to a RNA polymerase II-transcribed gene, SIR2, whose gene products silence rDNA recombination, to repress. We show that the amount of UAF determines the rDNA copy number that is stably maintained. UAF ensures rDNA production not only by rDNA transcription activation but also by its copy-number maintenance.
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Affiliation(s)
- Tetsushi Iida
- Laboratory of Genome Regeneration, Research Center for Biological Visualization, The Institute for Quantitative Biosciences (IQB), 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
| | - Takehiko Kobayashi
- Laboratory of Genome Regeneration, Research Center for Biological Visualization, The Institute for Quantitative Biosciences (IQB), 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; Collaborative Research Institute for Innovative Microbiology, the University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
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Teschler S, Gotthardt J, Dammann G, Dammann RH. Aberrant DNA Methylation of rDNA and PRIMA1 in Borderline Personality Disorder. Int J Mol Sci 2016; 17:ijms17010067. [PMID: 26742039 PMCID: PMC4730312 DOI: 10.3390/ijms17010067] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/28/2015] [Accepted: 12/29/2015] [Indexed: 12/17/2022] Open
Abstract
Borderline personality disorder (BPD) is a serious psychic disease with a high risk for suicide. DNA methylation is a hallmark for aberrant epigenetic regulation and could be involved in the etiology of BPD. Previously, it has been reported that increased DNA methylation of neuropsychiatric genes is found in the blood of patients with BPD compared to healthy controls. Here, we analyzed DNA methylation patterns of the ribosomal RNA gene (rDNA promoter region and 5′-external transcribed spacer/5′ETS) and the promoter of the proline rich membrane anchor 1 gene (PRIMA1) in peripheral blood samples of 24 female patients (mean age (33 ± 11) years) diagnosed with DSM-IV BPD and in 11 female controls (mean age (32 ± 7) years). A significant aberrant methylation of rDNA and PRIMA1 was revealed for BPD patients using pyrosequencing. For the promoter of PRIMA1, the average methylation of six CpG sites was 1.6-fold higher in BPD patients compared to controls. In contrast, the methylation levels of the rDNA promoter region and the 5′ETS were significantly lower (0.9-fold) in patients with BPD compared to controls. Thus, for nine CpGs located in the rDNA promoter region and for four CpGs at the 5′ETS decreased methylation was found in peripheral blood of patients compared to controls. Our results suggest that aberrant methylation of rDNA and PRIMA1 is associated with the pathogenesis of BPD.
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Affiliation(s)
- Stefanie Teschler
- Institute for Genetics, Justus-Liebig-University Giessen, D-35392 Giessen, Germany.
| | - Julia Gotthardt
- Institute for Genetics, Justus-Liebig-University Giessen, D-35392 Giessen, Germany.
| | - Gerhard Dammann
- Psychiatric Hospital, Psychiatric Services of Thurgovia, CH-8596 Münsterlingen, Switzerland and Department of Psychiatry, Paracelsus Medical University, A-5020 Salzburg, Austria.
| | - Reinhard H Dammann
- Institute for Genetics, Justus-Liebig-University Giessen, D-35392 Giessen, Germany.
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Pontvianne F, Blevins T, Chandrasekhara C, Mozgová I, Hassel C, Pontes OMF, Tucker S, Mokros P, Muchová V, Fajkus J, Pikaard CS. Subnuclear partitioning of rRNA genes between the nucleolus and nucleoplasm reflects alternative epiallelic states. Genes Dev 2013; 27:1545-50. [PMID: 23873938 DOI: 10.1101/gad.221648.113] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Eukaryotes can have thousands of 45S ribosomal RNA (rRNA) genes, many of which are silenced during development. Using fluorescence-activated sorting techniques, we show that active rRNA genes in Arabidopsis thaliana are present within sorted nucleoli, whereas silenced rRNA genes are excluded. DNA methyltransferase (met1), histone deacetylase (hda6), or chromatin assembly (caf1) mutants that disrupt silencing abrogate this nucleoplasmic-nucleolar partitioning. Bisulfite sequencing data indicate that active nucleolar rRNA genes are nearly completely demethylated at promoter CGs, whereas silenced genes are nearly fully methylated. Collectively, the data reveal that rRNA genes occupy distinct but changeable nuclear territories according to their epigenetic state.
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Srikulnath K, Uno Y, Matsubara K, Thongpan A, Suputtitada S, Apisitwanich S, Nishida C, Matsuda Y. Chromosomal localization of the 18S-28S and 5S rRNA genes and (TTAGGG)n sequences of butterfly lizards (Leiolepis belliana belliana and Leiolepis boehmei, Agamidae, Squamata). Genet Mol Biol 2011; 34:582-6. [PMID: 22215961 PMCID: PMC3229112 DOI: 10.1590/s1415-47572011005000042] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 04/29/2011] [Indexed: 11/22/2022] Open
Abstract
Chromosomal mapping of the butterfly lizards Leiolepis belliana belliana and L. boehmei was done using the 18S-28S and 5S rRNA genes and telomeric (TTAGGG)n sequences. The karyotype of L. b. belliana was 2n = 36, whereas that of L. boehmei was 2n = 34. The 18S-28S rRNA genes were located at the secondary constriction of the long arm of chromosome 1, while the 5S rRNA genes were found in the pericentromeric region of chromosome 6 in both species. Hybridization signals for the (TTAGGG)n sequence were observed at the telomeric ends of all chromosomes, as well as interstitially at the same position as the 18S-28S rRNA genes in L. boehmei. This finding suggests that in L. boehmei telomere-to-telomere fusion probably occurred between chromosome 1 and a microchromosome where the 18S-28S rRNA genes were located or, alternatively, at the secondary constriction of chromosome 1. The absence of telomeric sequence signals in chromosome 1 of L. b. belliana suggested that its chromosomes may have only a few copies of the (TTAGGG)n sequence or that there may have been a gradual loss of the repeat sequences during chromosomal evolution.
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Affiliation(s)
- Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
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