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Eynard SE, Klopp C, Canale-Tabet K, Marande W, Vandecasteele C, Roques C, Donnadieu C, Boone Q, Servin B, Vignal A. The black honey bee genome: insights on specific structural elements and a first step towards pangenomes. Genet Sel Evol 2024; 56:51. [PMID: 38943059 PMCID: PMC11212449 DOI: 10.1186/s12711-024-00917-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 06/04/2024] [Indexed: 07/01/2024] Open
Abstract
BACKGROUND The honey bee reference genome, HAv3.1, was produced from a commercial line sample that was thought to have a largely dominant Apis mellifera ligustica genetic background. Apis mellifera mellifera, often referred to as the black bee, has a separate evolutionary history and is the original type in western and northern Europe. Growing interest in this subspecies for conservation and non-professional apicultural practices, together with the necessity of deciphering genome backgrounds in hybrids, triggered the necessity for a specific genome assembly. Moreover, having several high-quality genomes is becoming key for taking structural variations into account in pangenome analyses. RESULTS Pacific Bioscience technology long reads were produced from a single haploid black bee drone. Scaffolding contigs into chromosomes was done using a high-density genetic map. This allowed for re-estimation of the recombination rate, which was over-estimated in some previous studies due to mis-assemblies, which resulted in spurious inversions in the older reference genomes. The sequence continuity obtained was very high and the only limit towards continuous chromosome-wide sequences seemed to be due to tandem repeat arrays that were usually longer than 10 kb and that belonged to two main families, the 371 and 91 bp repeats, causing problems in the assembly process due to high internal sequence similarity. Our assembly was used together with the reference genome to genotype two structural variants by a pangenome graph approach with Graphtyper2. Genotypes obtained were either correct or missing, when compared to an approach based on sequencing depth analysis, and genotyping rates were 89 and 76% for the two variants. CONCLUSIONS Our new assembly for the Apis mellifera mellifera honey bee subspecies demonstrates the utility of multiple high-quality genomes for the genotyping of structural variants, with a test case on two insertions and deletions. It will therefore be an invaluable resource for future studies, for instance by including structural variants in GWAS. Having used a single haploid drone for sequencing allowed a refined analysis of very large tandem repeat arrays, raising the question of their function in the genome. High quality genome assemblies for multiple subspecies such as presented here, are crucial for emerging projects using pangenomes.
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Affiliation(s)
- Sonia E Eynard
- GenPhySE, Université de Toulouse, INRAE, INPT, INP-ENVT, Castanet Tolosan, France
| | | | - Kamila Canale-Tabet
- GenPhySE, Université de Toulouse, INRAE, INPT, INP-ENVT, Castanet Tolosan, France
| | | | | | - Céline Roques
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | | | - Quentin Boone
- GenPhySE, Université de Toulouse, INRAE, INPT, INP-ENVT, Castanet Tolosan, France
- Sigenae, MIAT, INRAE, Castanet Tolosan, France
| | - Bertrand Servin
- GenPhySE, Université de Toulouse, INRAE, INPT, INP-ENVT, Castanet Tolosan, France
| | - Alain Vignal
- GenPhySE, Université de Toulouse, INRAE, INPT, INP-ENVT, Castanet Tolosan, France.
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2
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Law PP, Mikheeva LA, Rodriguez-Algarra F, Asenius F, Gregori M, Seaborne RAE, Yildizoglu S, Miller JRC, Tummala H, Mesnage R, Antoniou MN, Li W, Tan Q, Hillman SL, Rakyan VK, Williams DJ, Holland ML. Ribosomal DNA copy number is associated with body mass in humans and other mammals. Nat Commun 2024; 15:5006. [PMID: 38866738 PMCID: PMC11169392 DOI: 10.1038/s41467-024-49397-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 06/03/2024] [Indexed: 06/14/2024] Open
Abstract
Body mass results from a complex interplay between genetics and environment. Previous studies of the genetic contribution to body mass have excluded repetitive regions due to the technical limitations of platforms used for population scale studies. Here we apply genome-wide approaches, identifying an association between adult body mass and the copy number (CN) of 47S-ribosomal DNA (rDNA). rDNA codes for the 18 S, 5.8 S and 28 S ribosomal RNA (rRNA) components of the ribosome. In mammals, there are hundreds of copies of these genes. Inter-individual variation in the rDNA CN has not previously been associated with a mammalian phenotype. Here, we show that rDNA CN variation associates with post-pubertal growth rate in rats and body mass index in adult humans. rDNA CN is not associated with rRNA transcription rates in adult tissues, suggesting the mechanistic link occurs earlier in development. This aligns with the observation that the association emerges by early adulthood.
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Affiliation(s)
- Pui Pik Law
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King's College London, London, UK
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Liudmila A Mikheeva
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King's College London, London, UK
| | | | - Fredrika Asenius
- UCL EGA Institute for Women's Health, University College London, London, UK
| | - Maria Gregori
- UCL EGA Institute for Women's Health, University College London, London, UK
| | - Robert A E Seaborne
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Centre for Human and Applied Physiological Studies, King's College London, London, UK
| | - Selin Yildizoglu
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - James R C Miller
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Hemanth Tummala
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Robin Mesnage
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Michael N Antoniou
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Weilong Li
- Population Research Unit, University of Helsinki, Helsinki, Finland
| | - Qihua Tan
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Copenhagen, Denmark
| | - Sara L Hillman
- UCL EGA Institute for Women's Health, University College London, London, UK
| | - Vardhman K Rakyan
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - David J Williams
- UCL EGA Institute for Women's Health, University College London, London, UK
| | - Michelle L Holland
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King's College London, London, UK.
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3
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Rodriguez-Algarra F, Evans DM, Rakyan VK. Ribosomal DNA copy number variation associates with hematological profiles and renal function in the UK Biobank. CELL GENOMICS 2024; 4:100562. [PMID: 38749448 PMCID: PMC11228893 DOI: 10.1016/j.xgen.2024.100562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/19/2023] [Accepted: 04/21/2024] [Indexed: 06/15/2024]
Abstract
The phenotypic impact of genetic variation of repetitive features in the human genome is currently understudied. One such feature is the multi-copy 47S ribosomal DNA (rDNA) that codes for rRNA components of the ribosome. Here, we present an analysis of rDNA copy number (CN) variation in the UK Biobank (UKB). From the first release of UKB whole-genome sequencing (WGS) data, a discovery analysis in White British individuals reveals that rDNA CN associates with altered counts of specific blood cell subtypes, such as neutrophils, and with the estimated glomerular filtration rate, a marker of kidney function. Similar trends are observed in other ancestries. A range of analyses argue against reverse causality or common confounder effects, and all core results replicate in the second UKB WGS release. Our work demonstrates that rDNA CN is a genetic influence on trait variance in humans.
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Affiliation(s)
| | - David M Evans
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; Frazer Institute, The University of Queensland, Brisbane, QLD 4102, Australia; MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK
| | - Vardhman K Rakyan
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK.
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4
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Razzaq A, Bejaoui Y, Alam T, Saad M, El Hajj N. Ribosomal DNA Copy Number Variation is Coupled with DNA Methylation Changes at the 45S rDNA Locus. Epigenetics 2023; 18:2229203. [PMID: 37368968 DOI: 10.1080/15592294.2023.2229203] [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: 01/18/2023] [Revised: 06/04/2023] [Accepted: 06/20/2023] [Indexed: 06/29/2023] Open
Abstract
The human ribosomal DNA (rDNA) copy number (CN) has been challenging to analyse, and its sequence has been excluded from reference genomes due to its highly repetitive nature. The 45S rDNA locus encodes essential components of the cell, nevertheless rDNA displays high inter-individual CN variation that could influence human health and disease. CN alterations in rDNA have been hypothesized as a possible factor in autism spectrum disorders (ASD) and were shown to be altered in Schizophrenia patients. We tested whether whole-genome bisulphite sequencing can be used to simultaneously quantify rDNA CN and measure DNA methylation at the 45S rDNA locus. Using this approach, we observed high inter-individual variation in rDNA CN, and limited intra-individual copy differences in several post-mortem tissues. Furthermore, we did not observe any significant alterations in rDNA CN or DNA methylation in Autism Spectrum Disorder (ASD) brains in 16 ASD vs 11 control samples. Similarly, no difference was detected when comparing neurons form 28 Schizophrenia (Scz) patients vs 25 controls or oligodendrocytes from 22 Scz samples vs 20 controls. However, our analysis revealed a strong positive correlation between CN and DNA methylation at the 45S rDNA locus in multiple tissues. This was observed in brain and confirmed in small intestine, adipose tissue, and gastric tissue. This should shed light on a possible dosage compensation mechanism that silences additional rDNA copies to ensure homoeostatic regulation of ribosome biogenesis.
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Affiliation(s)
- Aleem Razzaq
- College of Health and Life Sciences, Qatar Foundation, Hamad Bin Khalifa University, Doha, Qatar
| | - Yosra Bejaoui
- College of Health and Life Sciences, Qatar Foundation, Hamad Bin Khalifa University, Doha, Qatar
| | - Tanvir Alam
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | - Mohamad Saad
- Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Nady El Hajj
- College of Health and Life Sciences, Qatar Foundation, Hamad Bin Khalifa University, Doha, Qatar
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
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5
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Ding X, Chen J, Dai C, Shi P, Pan H, Lin Y, Chen Y, Gong L, Chen L, Wu W, Qiu X, Xu J, Huang Z, Liao B. Developing population identification tool based on polymorphism of rDNA for traditional Chinese medicine: Artemisia annua L. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 116:154882. [PMID: 37210961 DOI: 10.1016/j.phymed.2023.154882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/29/2023] [Accepted: 05/12/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND Artemisia annua, a well-known traditional Chinese medicine, is the main source for production of artemisinin, an anti-malaria drug. A. annua is distributed globally, with great diversity of morphological characteristics and artemisinin contents. Diverse traits among A. annua populations impeded the stable production of artemisinin, which needs an efficient tool to identify strains and assess population genetic homogeneity. PURPOSE In this study, ribosomal DNA (rDNA), were characterized for A. annua for strains identification and population genetic homogeneity assessment. METHODS The ribosomal RNA (rRNA) genes were identified using cmscan and assembled using rDNA unit of LQ-9 as a reference. rDNA among Asteraceae species were compared performing with 45S rDNA. The rDNA copy number was calculated based on sequencing depth. The polymorphisms of rDNA sequences were identified with bam-readcount, and confirmed by Sanger sequencing and restriction enzyme experiment. The ITS2 amplicon sequencing was used to verify the stability of ITS2 haplotype analysis. RESULTS Different from other Asteraceae species, 45S and 5S linked-type rDNA was only found in Artemisia genus. Rich polymorphisms of copy number and sequence of rDNA were identified in A. annua population. The haplotype composition of internal transcribed spacer 2 (ITS2) region which had moderate sequence polymorphism and relative short size was significantly different among A. annua strains. A population discrimination method was developed based on ITS2 haplotype analysis with high-throughput sequencing. CONCLUSION This study provides comprehensive characteristics of rDNA and suggests that ITS2 haplotype analysis is ideal tool for A. annua strain identification and population genetic homogeneity assessment.
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Affiliation(s)
- Xiaoxia Ding
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Jieting Chen
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Chunyan Dai
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Peiqi Shi
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Hengyu Pan
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Yanqi Lin
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Yikang Chen
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Lu Gong
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Linming Chen
- Guangzhou Huibiao Testing Technology Center, Guangzhou 510700, China
| | - Wenguang Wu
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Xiaohui Qiu
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Zhihai Huang
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Baosheng Liao
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
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6
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Morton EA, Hall AN, Cuperus JT, Queitsch C. Substantial rDNA copy number reductions alter timing of development and produce variable tissue-specific phenotypes in C. elegans. Genetics 2023; 224:iyad039. [PMID: 36919976 PMCID: PMC10474940 DOI: 10.1093/genetics/iyad039] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/16/2023] Open
Abstract
The genes that encode ribosomal RNAs are present in several hundred copies in most eukaryotes. These vast arrays of repetitive ribosomal DNA (rDNA) have been implicated not just in ribosome biogenesis, but also aging, cancer, genome stability, and global gene expression. rDNA copy number is highly variable among and within species; this variability is thought to associate with traits relevant to human health and disease. Here we investigate the phenotypic consequences of multicellular life at the lower bounds of rDNA copy number. We use the model Caenorhabditis elegans, which has previously been found to complete embryogenesis using only maternally provided ribosomes. We find that individuals with rDNA copy number reduced to ∼5% of wild type are capable of further development with variable penetrance. Such individuals are sterile and exhibit severe morphological defects, particularly in post-embryonically dividing tissues such as germline and vulva. Developmental completion and fertility are supported by an rDNA copy number ∼10% of wild type, with substantially delayed development. Worms with rDNA copy number reduced to ∼33% of wild type display a subtle developmental timing defect that was absent in worms with higher copy numbers. Our results support the hypothesis that rDNA requirements vary across tissues and indicate that the minimum rDNA copy number for fertile adulthood is substantially less than the lowest naturally observed total copy number. The phenotype of individuals with severely reduced rDNA copy number is highly variable in penetrance and presentation, highlighting the need for continued investigation into the biological consequences of rDNA copy number variation.
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Affiliation(s)
| | - Ashley N Hall
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
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7
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Guaita-Cespedes M, Grillo-Risco R, Hidalgo MR, Fernández-Veledo S, Burks DJ, de la Iglesia-Vayá M, Galán A, Garcia-Garcia F. Deciphering the sex bias in housekeeping gene expression in adipose tissue: a comprehensive meta-analysis of transcriptomic studies. Biol Sex Differ 2023; 14:20. [PMID: 37072826 PMCID: PMC10114345 DOI: 10.1186/s13293-023-00506-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 04/07/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND As the housekeeping genes (HKG) generally involved in maintaining essential cell functions are typically assumed to exhibit constant expression levels across cell types, they are commonly employed as internal controls in gene expression studies. Nevertheless, HKG may vary gene expression profile according to different variables introducing systematic errors into experimental results. Sex bias can indeed affect expression display, however, up to date, sex has not been typically considered as a biological variable. METHODS In this study, we evaluate the expression profiles of six classical housekeeping genes (four metabolic: GAPDH, HPRT, PPIA, and UBC, and two ribosomal: 18S and RPL19) to determine expression stability in adipose tissues (AT) of Homo sapiens and Mus musculus and check sex bias and their overall suitability as internal controls. We also assess the expression stability of all genes included in distinct whole-transcriptome microarrays available from the Gene Expression Omnibus database to identify sex-unbiased housekeeping genes (suHKG) suitable for use as internal controls. We perform a novel computational strategy based on meta-analysis techniques to identify any sexual dimorphisms in mRNA expression stability in AT and to properly validate potential candidates. RESULTS Just above half of the considered studies informed properly about the sex of the human samples, however, not enough female mouse samples were found to be included in this analysis. We found differences in the HKG expression stability in humans between female and male samples, with females presenting greater instability. We propose a suHKG signature including experimentally validated classical HKG like PPIA and RPL19 and novel potential markers for human AT and discarding others like the extensively used 18S gene due to a sex-based variability display in adipose tissue. Orthologs have also been assayed and proposed for mouse WAT suHKG signature. All results generated during this study are readily available by accessing an open web resource ( https://bioinfo.cipf.es/metafun-HKG ) for consultation and reuse in further studies. CONCLUSIONS This sex-based research proves that certain classical housekeeping genes fail to function adequately as controls when analyzing human adipose tissue considering sex as a variable. We confirm RPL19 and PPIA suitability as sex-unbiased human and mouse housekeeping genes derived from sex-specific expression profiles, and propose new ones such as RPS8 and UBB.
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Affiliation(s)
- Maria Guaita-Cespedes
- Bioinformatics and Biostatistics Unit, Principe Felipe Research Center (CIPF), C/ Eduardo Primo Yúfera, 3, 46012, Valencia, Spain
- Hematology Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026, Valencia, Spain
| | - Rubén Grillo-Risco
- Bioinformatics and Biostatistics Unit, Principe Felipe Research Center (CIPF), C/ Eduardo Primo Yúfera, 3, 46012, Valencia, Spain
| | - Marta R Hidalgo
- Bioinformatics and Biostatistics Unit, Principe Felipe Research Center (CIPF), C/ Eduardo Primo Yúfera, 3, 46012, Valencia, Spain
| | - Sonia Fernández-Veledo
- Department of Endocrinology and Nutrition and Research Unit, University Hospital of Tarragona Joan XXIII, Institut d'Investigaciò Sanitària Pere Virgili (IISPV), Tarragona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
| | - Deborah Jane Burks
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
- Molecular Neuroendocrinology Laboratory, Principe Felipe Research Center (CIPF), C/ Eduardo Primo Yúfera, 3, 46012, Valencia, Spain
| | - María de la Iglesia-Vayá
- Imaging Unit FISABIO-CIPF, Fundación Para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana, 46012, Valencia, Spain
| | - Amparo Galán
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain.
- Molecular Neuroendocrinology Laboratory, Principe Felipe Research Center (CIPF), C/ Eduardo Primo Yúfera, 3, 46012, Valencia, Spain.
| | - Francisco Garcia-Garcia
- Bioinformatics and Biostatistics Unit, Principe Felipe Research Center (CIPF), C/ Eduardo Primo Yúfera, 3, 46012, Valencia, Spain.
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8
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Kindelay SM, Maggert KA. Under the magnifying glass: The ups and downs of rDNA copy number. Semin Cell Dev Biol 2023; 136:38-48. [PMID: 35595601 PMCID: PMC9976841 DOI: 10.1016/j.semcdb.2022.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/27/2022] [Accepted: 05/09/2022] [Indexed: 11/22/2022]
Abstract
The ribosomal DNA (rDNA) in Drosophila is found as two additive clusters of individual 35 S cistrons. The multiplicity of rDNA is essential to assure proper translational demands, but the nature of the tandem arrays expose them to copy number variation within and between populations. Here, we discuss means by which a cell responds to insufficient rDNA copy number, including a historical view of rDNA magnification whose mechanism was inferred some 35 years ago. Recent work has revealed that multiple conditions may also result in rDNA loss, in response to which rDNA magnification may have evolved. We discuss potential models for the mechanism of magnification, and evaluate possible consequences of rDNA copy number variation.
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Affiliation(s)
- Selina M Kindelay
- Genetics Graduate Interdisciplinary Program, The University of Arizona, Tucson, AZ 85724, USA
| | - Keith A Maggert
- Genetics Graduate Interdisciplinary Program, The University of Arizona, Tucson, AZ 85724, USA; Department of Cellular and Molecular Medicine, The University of Arizona, Tucson, AZ 85724, USA.
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9
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Sharma D, Denmat SHL, Matzke NJ, Hannan K, Hannan RD, O'Sullivan JM, Ganley ARD. A new method for determining ribosomal DNA copy number shows differences between Saccharomyces cerevisiae populations. Genomics 2022; 114:110430. [PMID: 35830947 DOI: 10.1016/j.ygeno.2022.110430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/23/2022] [Accepted: 07/04/2022] [Indexed: 11/26/2022]
Abstract
Ribosomal DNA genes (rDNA) encode the major ribosomal RNAs and in eukaryotes typically form tandem repeat arrays. Species have characteristic rDNA copy numbers, but there is substantial intra-species variation in copy number that results from frequent rDNA recombination. Copy number differences can have phenotypic consequences, however difficulties in quantifying copy number mean we lack a comprehensive understanding of how copy number evolves and the consequences. Here we present a genomic sequence read approach to estimate rDNA copy number based on modal coverage to help overcome limitations with existing mean coverage-based approaches. We validated our method using Saccharomyces cerevisiae strains with known rDNA copy numbers. Application of our pipeline to a global sample of S. cerevisiae isolates showed that different populations have different rDNA copy numbers. Our results demonstrate the utility of the modal coverage method, and highlight the high level of rDNA copy number variation within and between populations.
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Affiliation(s)
- Diksha Sharma
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Sylvie Hermann-Le Denmat
- School of Biological Sciences, University of Auckland, Auckland, New Zealand; Ecole Normale Supérieure, PSL Research University, F-75005 Paris, France
| | - Nicholas J Matzke
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Katherine Hannan
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, ACT 2601, Australia; Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ross D Hannan
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, ACT 2601, Australia; Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia; Division of Research, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3168, Australia
| | - Justin M O'Sullivan
- Liggins Institute, University of Auckland, Auckland, New Zealand; Maurice Wilkins Center, University of Auckland, New Zealand; MRC Lifecourse Unit, University of Southampton, United Kingdom; Brain Research New Zealand, The University of Auckland, Auckland, New Zealand
| | - Austen R D Ganley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
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10
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Antonarakis SE. Short arms of human acrocentric chromosomes and the completion of the human genome sequence. Genome Res 2022; 32:599-607. [PMID: 35361624 PMCID: PMC8997349 DOI: 10.1101/gr.275350.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The complete, ungapped sequence of the short arms of human acrocentric chromosomes (SAACs) is still unknown almost 20 years after the near completion of the Human Genome Project. Yet these short arms of Chromosomes 13, 14, 15, 21, and 22 contain the ribosomal DNA (rDNA) genes, which are of paramount importance for human biology. The sequences of SAACs show an extensive variation in the copy number of the various repetitive elements, the full extent of which is currently unknown. In addition, the full spectrum of repeated sequences, their organization, and the low copy number functional elements are also unknown. The Telomere-to-Telomere (T2T) Project using mainly long-read sequence technology has recently completed the assembly of the genome from a hydatidiform mole, CHM13, and has thus established a baseline reference for further studies on the organization, variation, functional annotation, and impact in human disorders of all the previously unknown genomic segments, including the SAACs. The publication of the initial results of the T2T Project will update and improve the reference genome for a better understanding of the evolution and function of the human genome.
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Affiliation(s)
- Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, 1211 Geneva, Switzerland.,Foundation Campus Biotech, 1202 Geneva, Switzerland.,Medigenome, Swiss Institute of Genomic Medicine, 1207 Geneva, Switzerland
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11
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Ding Q, Li R, Ren X, Chan LY, Ho VWS, Xie D, Ye P, Zhao Z. Genomic architecture of 5S rDNA cluster and its variations within and between species. BMC Genomics 2022; 23:238. [PMID: 35346033 PMCID: PMC8961926 DOI: 10.1186/s12864-022-08476-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ribosomal DNAs (rDNAs) are arranged in purely tandem repeats, preventing them from being reliably assembled onto chromosomes during generation of genome assembly. The uncertainty of rDNA genomic structure presents a significant barrier for studying their function and evolution. RESULTS Here we generate ultra-long Oxford Nanopore Technologies (ONT) and short NGS reads to delineate the architecture and variation of the 5S rDNA cluster in the different strains of C. elegans and C. briggsae. We classify the individual rDNA's repeating units into 25 types based on the unique sequence variations in each unit of C. elegans (N2). We next perform assembly of the cluster by taking advantage of the long reads that carry these units, which led to an assembly of 5S rDNA cluster consisting of up to 167 consecutive 5S rDNA units in the N2 strain. The ordering and copy number of various rDNA units are consistent with the separation time between strains. Surprisingly, we observed a drastically reduced level of variation in the unit composition in the 5S rDNA cluster in the C. elegans CB4856 and C. briggsae AF16 strains than in the C. elegans N2 strain, suggesting that N2, a widely used reference strain, is likely to be defective in maintaining the 5S rDNA cluster stability compared with other wild isolates of C. elegans or C. briggsae. CONCLUSIONS The results demonstrate that Nanopore DNA sequencing reads are capable of generating assembly of highly repetitive sequences, and rDNA units are highly dynamic both within and between population(s) of the same species in terms of sequence and copy number. The detailed structure and variation of the 5S rDNA units within the rDNA cluster pave the way for functional and evolutionary studies.
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Affiliation(s)
- Qiutao Ding
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Runsheng Li
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
- Department of Infectious Diseases and Public Health, City University of Hong Kong, Hong Kong SAR, China
| | - Xiaoliang Ren
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Lu-Yan Chan
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Vincy W S Ho
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Dongying Xie
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Pohao Ye
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China.
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong SAR, China.
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12
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Hall AN, Morton E, Queitsch C. First discovered, long out of sight, finally visible: ribosomal DNA. Trends Genet 2022; 38:587-597. [PMID: 35272860 PMCID: PMC10132741 DOI: 10.1016/j.tig.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 10/18/2022]
Abstract
With the advent of long-read sequencing, previously unresolvable genomic elements are being revisited in an effort to generate fully complete reference genomes. One such element is ribosomal DNA (rDNA), the highly conserved genomic region that encodes rRNAs. Genomic structure and content of the rDNA are variable in both prokarya and eukarya, posing interesting questions about the biology of rDNA. Here, we consider the types of variation observed in rDNA - including locus structure and number, copy number, and sequence variation - and their known phenotypic consequences. With recent advances in long-read sequencing technology, incorporating the full rDNA sequence into reference genomes is within reach. This knowledge will have important implications for understanding rDNA biology within the context of cell physiology and whole-organism phenotypes.
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13
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Rodriguez-Algarra F, Seaborne RAE, Danson AF, Yildizoglu S, Yoshikawa H, Law PP, Ahmad Z, Maudsley VA, Brew A, Holmes N, Ochôa M, Hodgkinson A, Marzi SJ, Pradeepa MM, Loose M, Holland ML, Rakyan VK. Genetic variation at mouse and human ribosomal DNA influences associated epigenetic states. Genome Biol 2022; 23:54. [PMID: 35164830 PMCID: PMC8842540 DOI: 10.1186/s13059-022-02617-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/24/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Ribosomal DNA (rDNA) displays substantial inter-individual genetic variation in human and mouse. A systematic analysis of how this variation impacts epigenetic states and expression of the rDNA has thus far not been performed. RESULTS Using a combination of long- and short-read sequencing, we establish that 45S rDNA units in the C57BL/6J mouse strain exist as distinct genetic haplotypes that influence the epigenetic state and transcriptional output of any given unit. DNA methylation dynamics at these haplotypes are dichotomous and life-stage specific: at one haplotype, the DNA methylation state is sensitive to the in utero environment, but refractory to post-weaning influences, whereas other haplotypes entropically gain DNA methylation during aging only. On the other hand, individual rDNA units in human show limited evidence of genetic haplotypes, and hence little discernible correlation between genetic and epigenetic states. However, in both species, adjacent units show similar epigenetic profiles, and the overall epigenetic state at rDNA is strongly positively correlated with the total rDNA copy number. Analysis of different mouse inbred strains reveals that in some strains, such as 129S1/SvImJ, the rDNA copy number is only approximately 150 copies per diploid genome and DNA methylation levels are < 5%. CONCLUSIONS Our work demonstrates that rDNA-associated genetic variation has a considerable influence on rDNA epigenetic state and consequently rRNA expression outcomes. In the future, it will be important to consider the impact of inter-individual rDNA (epi)genetic variation on mammalian phenotypes and diseases.
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Affiliation(s)
| | - Robert A E Seaborne
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Amy F Danson
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Present Address: German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Selin Yildizoglu
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Harunori Yoshikawa
- Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
| | - Pui Pik Law
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Zakaryya Ahmad
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Victoria A Maudsley
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Ama Brew
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Nadine Holmes
- DeepSeq, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Mateus Ochôa
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Alan Hodgkinson
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Sarah J Marzi
- UK Dementia Research Institute, Imperial College London, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | - Madapura M Pradeepa
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Matthew Loose
- DeepSeq, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Michelle L Holland
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King's College London, London, UK.
| | - Vardhman K Rakyan
- The Blizard Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK.
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14
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Cockrell AJ, Gerton JL. Nucleolar Organizer Regions as Transcription-Based Scaffolds of Nucleolar Structure and Function. Results Probl Cell Differ 2022; 70:551-580. [PMID: 36348121 DOI: 10.1007/978-3-031-06573-6_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Eukaryotic genomes maintain multiple copies of ribosomal DNA gene repeats in tandem arrays to provide sufficient ribosomal RNAs to make ribosomes. These DNA repeats are the most highly transcribed regions of the genome, with dedicated transcriptional machinery to manage the enormous task of producing more than 50% of the total RNA in a proliferating cell. The arrays are called nucleolar organizer regions (NORs) and constitute the scaffold of the nucleolar compartment, where ribosome biogenesis occurs. Advances in molecular and cellular biology have brought great insights into how these arrays are transcribed and organized within genomes. Much of their biology is driven by their high transcription level, which has also driven the development of unique methods to understand rDNA gene activity, beginning with classic techniques such as silver staining and Miller spreads. However, the application of modern methodologies such as CRISPR gene editing, super-resolution microscopy, and long-read sequencing has enabled recent advances described herein, with many more discoveries possible soon. This chapter highlights what is known about NOR transcription and organization and the techniques applied historically and currently. Given the potential for NORs to impact organismal health and disease, as highlighted at the end of the chapter, the field must continue to develop and apply innovative analysis to understand genetic, epigenetic, and organizer properties of the ribosomal DNA repeats.
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Affiliation(s)
- Alexandria J Cockrell
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Jennifer L Gerton
- Stowers Institute for Medical Research, Kansas City, MO, USA.
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA.
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15
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Analyses of the Updated "Animal rDNA Loci Database" with an Emphasis on Its New Features. Int J Mol Sci 2021; 22:ijms222111403. [PMID: 34768834 PMCID: PMC8584138 DOI: 10.3390/ijms222111403] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/17/2021] [Accepted: 10/20/2021] [Indexed: 11/17/2022] Open
Abstract
We report on a major update to the animal rDNA loci database, which now contains cytogenetic information for 45S and 5S rDNA loci in more than 2600 and 1000 species, respectively. The data analyses show the following: (i) A high variability in 5S and 45S loci numbers, with both showing 50-fold or higher variability. However, karyotypes with an extremely high number of loci were rare, and medians generally converged to two 5S sites and two 45S rDNA sites per diploid genome. No relationship was observed between the number of 5S and 45S loci. (ii) The position of 45S rDNA on sex chromosomes was relatively frequent in some groups, particularly in arthropods (14% of karyotypes). Furthermore, 45S rDNA was almost exclusively located in microchromosomes when these were present (in birds and reptiles). (iii) The proportion of active NORs (positively stained with silver staining methods) progressively decreased with an increasing number of 45S rDNA loci, and karyotypes with more than 12 loci showed, on average, less than 40% of active loci. In conclusion, the updated version of the database provides some new insights into the organization of rRNA genes in chromosomes. We expect that its updated content will be useful for taxonomists, comparative cytogeneticists, and evolutionary biologists.
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Miga KH, Sullivan BA. Expanding studies of chromosome structure and function in the era of T2T genomics. Hum Mol Genet 2021; 30:R198-R205. [PMID: 34302168 PMCID: PMC8631062 DOI: 10.1093/hmg/ddab214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/16/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
The recent accomplishment of a truly complete human genome has afforded a new view of chromosome structure and function that was limited 30 years ago. Here, we discuss the expansion of knowledge from the early cytological studies of the genome to the current high-resolution genomic, epigenetic and functional maps that have been achieved by recent technology and computational advances. These studies have revealed unexpected complexities of genome organization and function and uncovered new views of fundamental chromosomal elements. Comprehensive genomic maps will enable accurate diagnosis of human diseases caused by altered chromosome structure and function, facilitate development of chromosome-based therapies and shape the future of preventative medicine and healthcare.
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Affiliation(s)
- Karen H Miga
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Beth A Sullivan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
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