1
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English AC, Dolzhenko E, Ziaei Jam H, McKenzie SK, Olson ND, De Coster W, Park J, Gu B, Wagner J, Eberle MA, Gymrek M, Chaisson MJP, Zook JM, Sedlazeck FJ. Analysis and benchmarking of small and large genomic variants across tandem repeats. Nat Biotechnol 2024:10.1038/s41587-024-02225-z. [PMID: 38671154 DOI: 10.1038/s41587-024-02225-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/28/2024] [Indexed: 04/28/2024]
Abstract
Tandem repeats (TRs) are highly polymorphic in the human genome, have thousands of associated molecular traits and are linked to over 60 disease phenotypes. However, they are often excluded from at-scale studies because of challenges with variant calling and representation, as well as a lack of a genome-wide standard. Here, to promote the development of TR methods, we created a catalog of TR regions and explored TR properties across 86 haplotype-resolved long-read human assemblies. We curated variants from the Genome in a Bottle (GIAB) HG002 individual to create a TR dataset to benchmark existing and future TR analysis methods. We also present an improved variant comparison method that handles variants greater than 4 bp in length and varying allelic representation. The 8.1% of the genome covered by the TR catalog holds ~24.9% of variants per individual, including 124,728 small and 17,988 large variants for the GIAB HG002 'truth-set' TR benchmark. We demonstrate the utility of this pipeline across short-read and long-read technologies.
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Affiliation(s)
- Adam C English
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
| | | | - Helyaneh Ziaei Jam
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | | | - Nathan D Olson
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Wouter De Coster
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Applied and Translational Neurogenomics Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Jonghun Park
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Bida Gu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Justin Wagner
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | - Melissa Gymrek
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mark J P Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Justin M Zook
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Department of Computer Science, Rice University, Houston, TX, USA.
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2
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Lorig-Roach R, Meredith M, Monlong J, Jain M, Olsen HE, McNulty B, Porubsky D, Montague TG, Lucas JK, Condon C, Eizenga JM, Juul S, McKenzie SK, Simmonds SE, Park J, Asri M, Koren S, Eichler EE, Axel R, Martin B, Carnevali P, Miga KH, Paten B. Phased nanopore assembly with Shasta and modular graph phasing with GFAse. Genome Res 2024; 34:454-468. [PMID: 38627094 DOI: 10.1101/gr.278268.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 03/19/2024] [Indexed: 04/30/2024]
Abstract
Reference-free genome phasing is vital for understanding allele inheritance and the impact of single-molecule DNA variation on phenotypes. To achieve thorough phasing across homozygous or repetitive regions of the genome, long-read sequencing technologies are often used to perform phased de novo assembly. As a step toward reducing the cost and complexity of this type of analysis, we describe new methods for accurately phasing Oxford Nanopore Technologies (ONT) sequence data with the Shasta genome assembler and a modular tool for extending phasing to the chromosome scale called GFAse. We test using new variants of ONT PromethION sequencing, including those using proximity ligation, and show that newer, higher accuracy ONT reads substantially improve assembly quality.
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Affiliation(s)
- Ryan Lorig-Roach
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA;
| | - Melissa Meredith
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA
| | - Jean Monlong
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA
| | - Miten Jain
- Department of Bioengineering, Department of Physics, Northeastern University, Boston, Massachusetts 02120, USA
| | - Hugh E Olsen
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA
| | - Brandy McNulty
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Tessa G Montague
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, New York 10027, USA
- Howard Hughes Medical Institute, Columbia University, New York, New York 10032, USA
| | - Julian K Lucas
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA
| | - Chris Condon
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA
| | - Jordan M Eizenga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA
| | - Sissel Juul
- Oxford Nanopore Technologies Incorporated, New York, New York 10013, USA
| | - Sean K McKenzie
- Oxford Nanopore Technologies Incorporated, New York, New York 10013, USA
| | - Sara E Simmonds
- Chan Zuckerberg Initiative Foundation, Redwood City, California 94063, USA
| | - Jimin Park
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA
| | - Mobin Asri
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
| | - Richard Axel
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, New York 10027, USA
- Howard Hughes Medical Institute, Columbia University, New York, New York 10032, USA
| | - Bruce Martin
- Chan Zuckerberg Initiative Foundation, Redwood City, California 94063, USA
| | - Paolo Carnevali
- Chan Zuckerberg Initiative Foundation, Redwood City, California 94063, USA;
| | - Karen H Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA;
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3
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Anders KR, Abeyta A, Andrade CC, Bonilla CY, Braley AB, Bratt AG, Duncan KA, Hayes SG, Robinson CJ, Smith-Flores H, Ettinger ASH, Ettinger WF, Fay MM, Haydock J, McKenzie SK, Garlena RA, Russell DA, Poxleitner MK. Genome sequences of 31 mycobacteriophages isolated on Mycobacterium smegmatis mc 2155 at room temperature. Microbiol Resour Announc 2024; 13:e0108623. [PMID: 38099681 DOI: 10.1128/mra.01086-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 11/29/2023] [Indexed: 01/18/2024] Open
Abstract
We report the genome sequences of 31 mycobacteriophages isolated on Mycobacterium smegmatis mc2155 at room temperature. The genomes add to the diversity of Clusters A, B, C, G, and K. Collectively, the genomes include 70 novel protein-coding genes that have no close relatives among the actinobacteriophages.
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Affiliation(s)
- Kirk R Anders
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Antonio Abeyta
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Christy C Andrade
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Carla Y Bonilla
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Amanda B Braley
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Alexandra G Bratt
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Kaya A Duncan
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Stephen G Hayes
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Ciara J Robinson
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | | | | | | | - Marta M Fay
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Joseph Haydock
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Sean K McKenzie
- Department of Biology, Gonzaga University , Spokane, Washington, USA
| | - Rebecca A Garlena
- Department of Biological Sciences, University of Pittsburgh , Pittsburgh, Pennsylvania, USA
| | - Daniel A Russell
- Department of Biological Sciences, University of Pittsburgh , Pittsburgh, Pennsylvania, USA
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4
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Kay T, Liberti J, Richardson TO, McKenzie SK, Weitekamp CA, La Mendola C, Rüegg M, Kesner L, Szombathy N, McGregor S, Romiguier J, Engel P, Keller L. Social network position is a major predictor of ant behavior, microbiota composition, and brain gene expression. PLoS Biol 2023; 21:e3002203. [PMID: 37486940 PMCID: PMC10399779 DOI: 10.1371/journal.pbio.3002203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 08/03/2023] [Accepted: 06/16/2023] [Indexed: 07/26/2023] Open
Abstract
The physiology and behavior of social organisms correlate with their social environments. However, because social environments are typically confounded by age and physical environments (i.e., spatial location and associated abiotic factors), these correlations are usually difficult to interpret. For example, associations between an individual's social environment and its gene expression patterns may result from both factors being driven by age or behavior. Simultaneous measurement of pertinent variables and quantification of the correlations between these variables can indicate whether relationships are direct (and possibly causal) or indirect. Here, we combine demographic and automated behavioral tracking with a multiomic approach to dissect the correlation structure among the social and physical environment, age, behavior, brain gene expression, and microbiota composition in the carpenter ant Camponotus fellah. Variations in physiology and behavior were most strongly correlated with the social environment. Moreover, seemingly strong correlations between brain gene expression and microbiota composition, physical environment, age, and behavior became weak when controlling for the social environment. Consistent with this, a machine learning analysis revealed that from brain gene expression data, an individual's social environment can be more accurately predicted than any other behavioral metric. These results indicate that social environment is a key regulator of behavior and physiology.
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Affiliation(s)
- Tomas Kay
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Joanito Liberti
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Thomas O. Richardson
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Sean K. McKenzie
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Chelsea A. Weitekamp
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Christine La Mendola
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Matthias Rüegg
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Lucie Kesner
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Natasha Szombathy
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Sean McGregor
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Jonathan Romiguier
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology and Ecology, University of Montpellier, Montpellier, France
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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5
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Trible W, Chandra V, Lacy KD, Limón G, McKenzie SK, Olivos-Cisneros L, Arsenault SV, Kronauer DJC. A caste differentiation mutant elucidates the evolution of socially parasitic ants. Curr Biol 2023; 33:1047-1058.e4. [PMID: 36858043 PMCID: PMC10050096 DOI: 10.1016/j.cub.2023.01.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/31/2022] [Accepted: 01/31/2023] [Indexed: 03/03/2023]
Abstract
Most ant species have two distinct female castes-queens and workers-yet the developmental and genetic mechanisms that produce these alternative phenotypes remain poorly understood. Working with a clonal ant, we discovered a variant strain that expresses queen-like traits in individuals that would normally become workers. The variants show changes in morphology, behavior, and fitness that cause them to rely on workers in wild-type (WT) colonies for survival. Overall, they resemble the queens of many obligately parasitic ants that have evolutionarily lost the worker caste and live inside colonies of closely related hosts. The prevailing theory for the evolution of these workerless social parasites is that they evolve from reproductively isolated populations of facultative intermediates that acquire parasitic phenotypes in a stepwise fashion. However, empirical evidence for such facultative ancestors remains weak, and it is unclear how reproductive isolation could gradually arise in sympatry. In contrast, we isolated these variants just a few generations after they arose within their WT parent colony, implying that the complex phenotype reported here was induced in a single genetic step. This suggests that a single genetic module can decouple the coordinated mechanisms of caste development, allowing an obligately parasitic variant to arise directly from a free-living ancestor. Consistent with this hypothesis, the variants have lost one of the two alleles of a putative supergene that is heterozygous in WTs. These findings provide a plausible explanation for the evolution of ant social parasites and implicate new candidate molecular mechanisms for ant caste differentiation.
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Affiliation(s)
- Waring Trible
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; John Harvard Distinguished Science Fellowship Program, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
| | - Vikram Chandra
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Department of Organismic and Evolutionary Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Kip D Lacy
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Gina Limón
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Department of Microbiology, New York University School of Medicine, 430 E. 29th Street, New York, NY 10016, USA
| | - Sean K McKenzie
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Oxford Nanopore Technologies, Oxford OX4 4DQ, UK
| | - Leonora Olivos-Cisneros
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Samuel V Arsenault
- John Harvard Distinguished Science Fellowship Program, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA; Department of Organismic and Evolutionary Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Daniel J C Kronauer
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Howard Hughes Medical Institute, New York, NY 10065, USA.
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6
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McKenzie SK, Winston ME, Grewe F, Vargas Asensio G, Rodríguez-Hernández N, Rubin BER, Murillo-Cruz C, von Beeren C, Moreau CS, Suen G, Pinto-Tomás AA, Kronauer DJC. The genomic basis of army ant chemosensory adaptations. Mol Ecol 2021; 30:6627-6641. [PMID: 34582590 PMCID: PMC9292994 DOI: 10.1111/mec.16198] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 05/25/2020] [Revised: 09/06/2021] [Accepted: 09/15/2021] [Indexed: 12/23/2022]
Abstract
The evolution of mass raiding has allowed army ants to become dominant arthropod predators in the tropics. Although a century of research has led to many discoveries about behavioural, morphological and physiological adaptations in army ants, almost nothing is known about the molecular basis of army ant biology. Here we report the genome of the iconic New World army ant Eciton burchellii, and show that it is unusually compact, with a reduced gene complement relative to other ants. In contrast to this overall reduction, a particular gene subfamily (9‐exon ORs) expressed predominantly in female antennae is expanded. This subfamily has previously been linked to the recognition of hydrocarbons, key olfactory cues used in insect communication and prey discrimination. Confocal microscopy of the brain showed a corresponding expansion in a putative hydrocarbon response centre within the antennal lobe, while scanning electron microscopy of the antenna revealed a particularly high density of hydrocarbon‐sensitive sensory hairs. E. burchellii shares these features with its predatory and more cryptic relative, the clonal raider ant. By integrating genomic, transcriptomic and anatomical analyses in a comparative context, our work thus provides evidence that army ants and their relatives possess a suite of modifications in the chemosensory system that may be involved in behavioural coordination and prey selection during social predation. It also lays the groundwork for future studies of army ant biology at the molecular level.
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Affiliation(s)
- Sean K McKenzie
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, New York, USA.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | - Felix Grewe
- Grainger Bioinformatics Center, Science and Education, Field Museum of Natural History, Chicago, Illinois, USA
| | - Gabriel Vargas Asensio
- Centro de Investigación en Biología Molecular y Celular (CIBCM), Universidad de Costa Rica, San José, Costa Rica.,Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Natalia Rodríguez-Hernández
- Centro de Investigación en Estructuras Microscópicas (CIEMIC), Universidad de Costa Rica, San José, Costa Rica
| | - Benjamin E R Rubin
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Catalina Murillo-Cruz
- Centro de Investigación en Estructuras Microscópicas (CIEMIC), Universidad de Costa Rica, San José, Costa Rica
| | - Christoph von Beeren
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, New York, USA.,Ecological Networks, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Corrie S Moreau
- Departments of Entomology and Ecology & Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Adrian A Pinto-Tomás
- Centro de Investigación en Biología Molecular y Celular (CIBCM), Universidad de Costa Rica, San José, Costa Rica.,Centro de Investigación en Estructuras Microscópicas (CIEMIC), Universidad de Costa Rica, San José, Costa Rica.,Escuela de Medicina, Departamento de Bioquímica, Universidad de Costa Rica, San José, Costa Rica
| | - Daniel J C Kronauer
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, New York, USA
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7
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Ryba AR, McKenzie SK, Olivos-Cisneros L, Clowney EJ, Pires PM, Kronauer DJC. Comparative Development of the Ant Chemosensory System. Curr Biol 2020; 30:3223-3230.e4. [PMID: 32559450 DOI: 10.1016/j.cub.2020.05.072] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/24/2020] [Accepted: 05/21/2020] [Indexed: 12/15/2022]
Abstract
The insect antennal lobe (AL) contains the first synapses of the olfactory system, where olfactory sensory neurons (OSNs) contact second-order projection neurons (PNs). In Drosophila melanogaster, OSNs expressing specific receptor genes send stereotyped projections to one or two of about 50 morphologically defined glomeruli [1-3]. The mechanisms for this precise matching between OSNs and PNs have been studied extensively in D. melanogaster, where development is deterministic and independent of neural activity [4-6]. However, a number of insect lineages, most notably the ants, have receptor gene repertoires many times larger than D. melanogaster and exhibit more structurally complex antennal lobes [7-12]. Moreover, perturbation of OSN function via knockout of the odorant receptor (OR) co-receptor, Orco, results in drastic AL reductions in ants [13, 14], but not in Drosophila [15]. Here, we characterize AL development in the clonal raider ant, Ooceraea biroi. We find that, unlike in Drosophila, ORs and Orco are expressed before the onset of glomerulus formation, and Orco protein is trafficked to developing axon terminals, raising the possibility that ORs play a role during ant AL development. Additionally, ablating ant antennae at the onset of pupation results in AL defects that recapitulate the Orco mutant phenotype. Thus, early loss of functional OSN innervation reveals latent structure in the AL that develops independently of peripheral input, suggesting that the AL is initially pre-patterned and later refined in an OSN-dependent manner. This two-step process might increase developmental flexibility and thereby facilitate the rapid evolution and expansion of the ant chemosensory system.
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Affiliation(s)
- Anna R Ryba
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY 10065, USA
| | - Sean K McKenzie
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY 10065, USA; Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
| | - Leonora Olivos-Cisneros
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY 10065, USA
| | - E Josephine Clowney
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter Mussells Pires
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY 10065, USA
| | - Daniel J C Kronauer
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY 10065, USA.
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8
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McKenzie SK, Walston RF, Allen JL. Complete, high-quality genomes from long-read metagenomic sequencing of two wolf lichen thalli reveals enigmatic genome architecture. Genomics 2020; 112:3150-3156. [PMID: 32504651 DOI: 10.1016/j.ygeno.2020.06.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 04/23/2020] [Revised: 05/20/2020] [Accepted: 06/02/2020] [Indexed: 02/08/2023]
Abstract
Fungal genomes display incredible levels of complexity and diversity, and are exceptional study systems for genome evolution. Here we used the Oxford Nanopore MinION sequencing platform to generate high-quality fungal genomes from complex metagenomic samples of lichen thalli. We sequenced two wolf lichens using one flow cell per sample, generating 17.1 Gbps for Letharia lupina and 14.3 Gbps for Letharia columbiana. The resulting L. lupina genome is one of the most contiguous lichen genomes available to date, with 49.2 Mbp contained on 31 contigs. The L. columbiana genome, while less contiguous, is still relatively high quality, with 52.3 Mbp on a total of 161 contigs. Each thallus for both species contained multiple distinct haplotypes, a phenomenon that has rarely been empirically demonstrated. The Oxford Nanopore sequencing technologies are robust and effective when applied to complex symbioses, and have the potential to fundamentally transform our understanding of fungal genetics.
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Affiliation(s)
- Sean K McKenzie
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland; Current affiliation: Emory Integrated Computational Core, Emory University, Atlanta, GA, USA.
| | - Ridge F Walston
- Department of Biology, Eastern Washington University, Cheney, WA, USA
| | - Jessica L Allen
- Department of Biology, Eastern Washington University, Cheney, WA, USA
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9
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Trible W, McKenzie SK, Kronauer DJC. Globally invasive populations of the clonal raider ant are derived from Bangladesh. Biol Lett 2020; 16:20200105. [PMID: 32544382 PMCID: PMC7336853 DOI: 10.1098/rsbl.2020.0105] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/13/2020] [Indexed: 12/14/2022] Open
Abstract
Identifying the native range of invasive species is useful to understand their evolution and natural history, as well as to develop new methods to control potentially harmful introduced organisms. The clonal raider ant, Ooceraea biroi, is an introduced species and an increasingly important social insect model organism, but its native range remains unknown. Here, we report a new series of O. biroi collections from Bangladesh, Singapore, Vietnam and China. We use a molecular phylogeny constructed with five gene fragments from 27 samples to determine that invasive lineages of O. biroi originated in Bangladesh. These lineages may have spread from Bangladesh via the historically significant Bay of Bengal shipping ports. Ooceraea biroi shares multiple features of its biology with other introduced ants, including parthenogenesis, retention of heterozygosity and presence of multiple egg-layers in the colony. Using laboratory rearing and microsatellite markers, we show that colonies collected from disturbed habitat in Bangladesh have these traits in common with colonies from the invasive range. Ancestral populations with sexual reproduction in primary habitats either remain to be discovered or have gone extinct. Our findings advance our understanding of the global spread of the clonal raider ant and highlight a suite of general traits that make certain ants prone to becoming invasive.
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Affiliation(s)
- Waring Trible
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
- Center for Systems Biology, Harvard University, 52 Oxford Street, NW 369.20, Cambridge, MA 02138, USA
| | - Sean K. McKenzie
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
- Department of Ecology and Evolution, University of Lausanne, Lausanne CH-1015, Switzerland
| | - Daniel J. C. Kronauer
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
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10
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Abstract
The massive expansions of odorant receptor (OR) genes in ant genomes are notable examples of rapid genome evolution and adaptive gene duplication. However, the molecular mechanisms leading to gene family expansion remain poorly understood, partly because available ant genomes are fragmentary. Here, we present a highly contiguous, chromosome-level assembly of the clonal raider ant genome, revealing the largest known OR repertoire in an insect. While most ant ORs originate via local tandem duplication, we also observe several cases of dispersed duplication followed by tandem duplication in the most rapidly evolving OR clades. We found that areas of unusually high transposable element density (TE islands) were depauperate in ORs in the clonal raider ant, and found no evidence for retrotransposition of ORs. However, OR loci were enriched for transposons relative to the genome as a whole, potentially facilitating tandem duplication by unequal crossing over. We also found that ant OR genes are highly AT-rich compared to other genes. In contrast, in flies, OR genes are dispersed and largely isolated within the genome, and we find that fly ORs are not AT-rich. The genomic architecture and composition of ant ORs thus show convergence with the unrelated vertebrate ORs rather than the related fly ORs. This might be related to the greater gene numbers and/or potential similarities in gene regulation between ants and vertebrates as compared to flies.
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Affiliation(s)
- Sean K McKenzie
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, New York 10065, USA
| | - Daniel J C Kronauer
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, New York 10065, USA
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11
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Allen JL, McKenzie SK, Sleith RS, Alter SE. First genome-wide analysis of the endangered, endemic lichen Cetradonia linearis reveals isolation by distance and strong population structure. Am J Bot 2018; 105:1556-1567. [PMID: 30157288 DOI: 10.1002/ajb2.1150] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/14/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Lichenized fungi are evolutionarily diverse and ecologically important, but little is known about the processes that drive their diversification and genetic differentiation. Distributions are often assumed to be wholly shaped by ecological requirements rather than dispersal limitations. Furthermore, although asexual and sexual reproductive structures are observable, the lack of information about recombination rates makes inferences about reproductive strategies difficult. We investigated the population genomics of Cetradonia linearis, a federally endangered lichen in the southern Appalachians of eastern North America, to test the relative contributions of environmental and geographic distance in shaping genetic structure, and to characterize the mating system and genome-wide recombination. METHODS Whole-genome shotgun sequencing was conducted to generate data for 32 individuals of C. linearis. A reference genome was assembled, and reads from all samples were aligned to generate a set of single-nucleotide polymorphisms for further analyses. KEY RESULTS We found evidence for low rates of recombination and for isolation by distance, but not for isolation by environment. The species is putatively unisexual, given that only one mating-type locus was found. Hindcast species distribution models and the distribution of genetic diversity support C. linearis having a larger range during the Last Glacial Maximum in the southern portion of its current extent. CONCLUSIONS Our findings contribute to the understanding of factors that shape genetic diversity in C. linearis and in fungi more broadly. Because all populations are highly genetically differentiated, the extirpation of any population would mean the loss of unique genetic diversity; therefore, our results support the continued conservation of this species.
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Affiliation(s)
- Jessica L Allen
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York, 10458, USA
- The Graduate Center, City University of New York, 365 5th Avenue, New York, New York, 10016, USA
| | - Sean K McKenzie
- Rockefeller University, 1230 York Avenue, New York, New York, 10065, USA
| | - Robin S Sleith
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York, 10458, USA
- The Graduate Center, City University of New York, 365 5th Avenue, New York, New York, 10016, USA
| | - S Elizabeth Alter
- The Graduate Center, City University of New York, 365 5th Avenue, New York, New York, 10016, USA
- Biology Department, York College, 94-20 Guy R Brewer Blvd., Jamaica, New York, 11451, USA
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Chandra V, Fetter-Pruneda I, Oxley PR, Ritger AL, McKenzie SK, Libbrecht R, Kronauer DJC. Social regulation of insulin signaling and the evolution of eusociality in ants. Science 2018; 361:398-402. [PMID: 30049879 PMCID: PMC6178808 DOI: 10.1126/science.aar5723] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 04/01/2018] [Accepted: 05/30/2018] [Indexed: 12/15/2022]
Abstract
Queens and workers of eusocial Hymenoptera are considered homologous to the reproductive and brood care phases of an ancestral subsocial life cycle. However, the molecular mechanisms underlying the evolution of reproductive division of labor remain obscure. Using a brain transcriptomics screen, we identified a single gene, insulin-like peptide 2 (ilp2), which is always up-regulated in ant reproductives, likely because they are better nourished than their nonreproductive nestmates. In clonal raider ants (Ooceraea biroi), larval signals inhibit adult reproduction by suppressing ilp2, thus producing a colony reproductive cycle reminiscent of ancestral subsociality. However, increasing ILP2 peptide levels overrides larval suppression, thereby breaking the colony cycle and inducing a stable division of labor. These findings suggest a simple model for the origin of ant eusociality via nutritionally determined reproductive asymmetries potentially amplified by larval signals.
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Affiliation(s)
- Vikram Chandra
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - Ingrid Fetter-Pruneda
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - Peter R Oxley
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
- Samuel J. Wood Library, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Amelia L Ritger
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Sean K McKenzie
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Romain Libbrecht
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany
| | - Daniel J C Kronauer
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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13
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Trible W, Olivos-Cisneros L, McKenzie SK, Saragosti J, Chang NC, Matthews BJ, Oxley PR, Kronauer DJC. orco Mutagenesis Causes Loss of Antennal Lobe Glomeruli and Impaired Social Behavior in Ants. Cell 2017; 170:727-735.e10. [PMID: 28802042 DOI: 10.1016/j.cell.2017.07.001] [Citation(s) in RCA: 160] [Impact Index Per Article: 22.9] [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: 03/24/2017] [Revised: 05/24/2017] [Accepted: 06/29/2017] [Indexed: 11/25/2022]
Abstract
Life inside ant colonies is orchestrated with diverse pheromones, but it is not clear how ants perceive these social signals. It has been proposed that pheromone perception in ants evolved via expansions in the numbers of odorant receptors (ORs) and antennal lobe glomeruli. Here, we generate the first mutant lines in the clonal raider ant, Ooceraea biroi, by disrupting orco, a gene required for the function of all ORs. We find that orco mutants exhibit severe deficiencies in social behavior and fitness, suggesting they are unable to perceive pheromones. Surprisingly, unlike in Drosophila melanogaster, orco mutant ants also lack most of the ∼500 antennal lobe glomeruli found in wild-type ants. These results illustrate that ORs are essential for ant social organization and raise the possibility that, similar to mammals, receptor function is required for the development and/or maintenance of the highly complex olfactory processing areas in the ant brain. VIDEO ABSTRACT.
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Affiliation(s)
- Waring Trible
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY 10065, USA.
| | - Leonora Olivos-Cisneros
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY 10065, USA
| | - Sean K McKenzie
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY 10065, USA
| | - Jonathan Saragosti
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY 10065, USA
| | - Ni-Chen Chang
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY 10065, USA
| | - Benjamin J Matthews
- Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, Chevy Chase, MD 23930, USA
| | - Peter R Oxley
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY 10065, USA
| | - Daniel J C Kronauer
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY 10065, USA.
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14
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McKenzie SK, Oxley PR, Kronauer DJC. Comparative genomics and transcriptomics in ants provide new insights into the evolution and function of odorant binding and chemosensory proteins. BMC Genomics 2014; 15:718. [PMID: 25159315 PMCID: PMC4161878 DOI: 10.1186/1471-2164-15-718] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 08/14/2014] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The complex societies of ants and other social insects rely on sophisticated chemical communication. Two families of small soluble proteins, the odorant binding and chemosensory proteins (OBPs and CSPs), are believed to be important in insect chemosensation. To better understand the role of these proteins in ant olfaction, we examined their evolution and expression across the ants using phylogenetics and sex- and tissue-specific RNA-seq. RESULTS We find that subsets of both OBPs and CSPs are expressed in the antennae, contradicting the previous hypothesis that CSPs have replaced OBPs in ant olfaction. Both protein families have several highly conserved clades with a single ortholog in all eusocial hymenopterans, as well as clades with more dynamic evolution and many taxon-specific radiations. The dynamically evolving OBPs and CSPs have been hypothesized to function in chemical communication. Intriguingly, we find that seven members of the conserved clades are expressed specifically in the antennae of the clonal raider ant Cerapachys biroi, whereas only one dynamically evolving CSP is antenna specific. The orthologs of the conserved, antenna-specific C. biroi genes are also expressed in antennae of the ants Camponotus floridanus and Harpegnathos saltator, indicating that antenna-specific expression of these OBPs and CSPs is conserved across ants. Most members of the dynamically evolving clades in both protein families are expressed primarily in non-chemosensory tissues and thus likely do not fulfill chemosensory functions. CONCLUSIONS Our results identify candidate OBPs and CSPs that are likely involved in conserved aspects of ant olfaction, and suggest that OBPs and CSPs may not rapidly evolve to recognize species-specific signals.
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Affiliation(s)
- Sean K McKenzie
- Laboratory of Insect Social Evolution, The Rockefeller University, 1230 York Avenue, 10065 New York, NY, USA.
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Oxley PR, Ji L, Fetter-Pruneda I, McKenzie SK, Li C, Hu H, Zhang G, Kronauer DJC. The genome of the clonal raider ant Cerapachys biroi. Curr Biol 2014; 24:451-8. [PMID: 24508170 DOI: 10.1016/j.cub.2014.01.018] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 11/26/2013] [Accepted: 01/09/2014] [Indexed: 11/17/2022]
Abstract
Social insects are important models for social evolution and behavior. However, in many species, experimental control over important factors that regulate division of labor, such as genotype and age, is limited. Furthermore, most species have fixed queen and worker castes, making it difficult to establish causality between the molecular mechanisms that underlie reproductive division of labor, the hallmark of insect societies. Here we present the genome of the queenless clonal raider ant Cerapachys biroi, a powerful new study system that does not suffer from these constraints. Using cytology and RAD-seq, we show that C. biroi reproduces via automixis with central fusion and that heterozygosity is lost extremely slowly. As a consequence, nestmates are almost clonally related (r = 0.996). Workers in C. biroi colonies synchronously alternate between reproduction and brood care, and young workers eclose in synchronized cohorts. We show that genes associated with division of labor in other social insects are conserved in C. biroi and dynamically regulated during the colony cycle. With unparalleled experimental control over an individual's genotype and age, and the ability to induce reproduction and brood care, C. biroi has great potential to illuminate the molecular regulation of division of labor.
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Affiliation(s)
- Peter R Oxley
- Laboratory of Insect Social Evolution, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - Lu Ji
- China National Genebank, BGI-Shenzhen, Shenzhen 518083, China
| | - Ingrid Fetter-Pruneda
- Laboratory of Insect Social Evolution, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Sean K McKenzie
- Laboratory of Insect Social Evolution, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Cai Li
- China National Genebank, BGI-Shenzhen, Shenzhen 518083, China
| | - Haofu Hu
- China National Genebank, BGI-Shenzhen, Shenzhen 518083, China
| | - Guojie Zhang
- China National Genebank, BGI-Shenzhen, Shenzhen 518083, China; Centre for Social Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Daniel J C Kronauer
- Laboratory of Insect Social Evolution, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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Duffull SB, McKenzie SK. Interaction between amiodarone and phenytoin. Am J Cardiol 1991; 67:328-9. [PMID: 1990811 DOI: 10.1016/0002-9149(91)90588-c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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