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Viljakainen L, Fürst MA, Grasse AV, Jurvansuu J, Oh J, Tolonen L, Eder T, Rattei T, Cremer S. Antiviral immune response reveals host-specific virus infections in natural ant populations. Front Microbiol 2023; 14:1119002. [PMID: 37007485 PMCID: PMC10060816 DOI: 10.3389/fmicb.2023.1119002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/23/2023] [Indexed: 03/18/2023] Open
Abstract
Hosts can carry many viruses in their bodies, but not all of them cause disease. We studied ants as a social host to determine both their overall viral repertoire and the subset of actively infecting viruses across natural populations of three subfamilies: the Argentine ant (Linepithema humile, Dolichoderinae), the invasive garden ant (Lasius neglectus, Formicinae) and the red ant (Myrmica rubra, Myrmicinae). We used a dual sequencing strategy to reconstruct complete virus genomes by RNA-seq and to simultaneously determine the small interfering RNAs (siRNAs) by small RNA sequencing (sRNA-seq), which constitute the host antiviral RNAi immune response. This approach led to the discovery of 41 novel viruses in ants and revealed a host ant-specific RNAi response (21 vs. 22 nt siRNAs) in the different ant species. The efficiency of the RNAi response (sRNA/RNA read count ratio) depended on the virus and the respective ant species, but not its population. Overall, we found the highest virus abundance and diversity per population in Li. humile, followed by La. neglectus and M. rubra. Argentine ants also shared a high proportion of viruses between populations, whilst overlap was nearly absent in M. rubra. Only one of the 59 viruses was found to infect two of the ant species as hosts, revealing high host-specificity in active infections. In contrast, six viruses actively infected one ant species, but were found as contaminants only in the others. Disentangling spillover of disease-causing infection from non-infecting contamination across species is providing relevant information for disease ecology and ecosystem management.
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Affiliation(s)
- Lumi Viljakainen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
- *Correspondence: Lumi Viljakainen,
| | - Matthias A. Fürst
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Anna V. Grasse
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Jaana Jurvansuu
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Jinook Oh
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Lassi Tolonen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Thomas Eder
- Centre for Microbiology and Environmental Systems Science, Division of Computational System Biology, University of Vienna, Vienna, Austria
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science, Division of Computational System Biology, University of Vienna, Vienna, Austria
| | - Sylvia Cremer
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
- Sylvia Cremer,
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de Paula Freitas FC, Lourenço AP, Nunes FMF, Paschoal AR, Abreu FCP, Barbin FO, Bataglia L, Cardoso-Júnior CAM, Cervoni MS, Silva SR, Dalarmi F, Del Lama MA, Depintor TS, Ferreira KM, Gória PS, Jaskot MC, Lago DC, Luna-Lucena D, Moda LM, Nascimento L, Pedrino M, Oliveira FR, Sanches FC, Santos DE, Santos CG, Vieira J, Barchuk AR, Hartfelder K, Simões ZLP, Bitondi MMG, Pinheiro DG. The nuclear and mitochondrial genomes of Frieseomelitta varia - a highly eusocial stingless bee (Meliponini) with a permanently sterile worker caste. BMC Genomics 2020; 21:386. [PMID: 32493270 PMCID: PMC7268684 DOI: 10.1186/s12864-020-06784-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 05/14/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Most of our understanding on the social behavior and genomics of bees and other social insects is centered on the Western honey bee, Apis mellifera. The genus Apis, however, is a highly derived branch comprising less than a dozen species, four of which genomically characterized. In contrast, for the equally highly eusocial, yet taxonomically and biologically more diverse Meliponini, a full genome sequence was so far available for a single Melipona species only. We present here the genome sequence of Frieseomelitta varia, a stingless bee that has, as a peculiarity, a completely sterile worker caste. RESULTS The assembly of 243,974,526 high quality Illumina reads resulted in a predicted assembled genome size of 275 Mb composed of 2173 scaffolds. A BUSCO analysis for the 10,526 predicted genes showed that these represent 96.6% of the expected hymenopteran orthologs. We also predicted 169,371 repetitive genomic components, 2083 putative transposable elements, and 1946 genes for non-coding RNAs, largely long non-coding RNAs. The mitochondrial genome comprises 15,144 bp, encoding 13 proteins, 22 tRNAs and 2 rRNAs. We observed considerable rearrangement in the mitochondrial gene order compared to other bees. For an in-depth analysis of genes related to social biology, we manually checked the annotations for 533 automatically predicted gene models, including 127 genes related to reproductive processes, 104 to development, and 174 immunity-related genes. We also performed specific searches for genes containing transcription factor domains and genes related to neurogenesis and chemosensory communication. CONCLUSIONS The total genome size for F. varia is similar to the sequenced genomes of other bees. Using specific prediction methods, we identified a large number of repetitive genome components and long non-coding RNAs, which could provide the molecular basis for gene regulatory plasticity, including worker reproduction. The remarkable reshuffling in gene order in the mitochondrial genome suggests that stingless bees may be a hotspot for mtDNA evolution. Hence, while being just the second stingless bee genome sequenced, we expect that subsequent targeting of a selected set of species from this diverse clade of highly eusocial bees will reveal relevant evolutionary signals and trends related to eusociality in these important pollinators.
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Affiliation(s)
- Flávia C. de Paula Freitas
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Alfenas, MG Brazil
| | - Anete P. Lourenço
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
- Departamento de Ciências Biológicas, Faculdade de Ciências Biológicas e da Saúde, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, MG Brazil
| | - Francis M. F. Nunes
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | | | - Fabiano C. P. Abreu
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Fábio O. Barbin
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Luana Bataglia
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Carlos A. M. Cardoso-Júnior
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-900 Brazil
| | - Mário S. Cervoni
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-900 Brazil
| | - Saura R. Silva
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, SP Brazil
| | - Fernanda Dalarmi
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Marco A. Del Lama
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Thiago S. Depintor
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Kátia M. Ferreira
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Paula S. Gória
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Michael C. Jaskot
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Denyse C. Lago
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Danielle Luna-Lucena
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Livia M. Moda
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Alfenas, MG Brazil
| | - Leonardo Nascimento
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Matheus Pedrino
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Franciene Rabiço Oliveira
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Fernanda C. Sanches
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Douglas E. Santos
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-900 Brazil
| | - Carolina G. Santos
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-900 Brazil
| | - Joseana Vieira
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Alfenas, MG Brazil
| | - Angel R. Barchuk
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Alfenas, MG Brazil
| | - Klaus Hartfelder
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-900 Brazil
| | - Zilá L. P. Simões
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Márcia M. G. Bitondi
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Daniel G. Pinheiro
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, SP Brazil
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Near-Complete Genome Sequences of New Strains of Nylanderia Fulva Virus 1 from Solenopsis invicta. Microbiol Resour Announc 2020; 9:9/15/e00798-19. [PMID: 32273367 PMCID: PMC7380534 DOI: 10.1128/mra.00798-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Nylanderia fulva virus 1 (NfV-1) is a single-stranded positive-sense RNA virus that infects the tawny crazy ant. Three near-complete genomes of NfV-1SI (92% to 94% nucleotide identity to reference strain NfV-1) found infecting the red imported fire ant were determined. The genomes have 10,904 to 10,918 nucleotides and include most of the coding region for the polyprotein. Nylanderia fulva virus 1 (NfV-1) is a single-stranded positive-sense RNA virus that infects the tawny crazy ant. Three near-complete genomes of NfV-1SI (92% to 94% nucleotide identity to reference strain NfV-1) found infecting the red imported fire ant were determined. The genomes have 10,904 to 10,918 nucleotides and include most of the coding region for the polyprotein.
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Abril S, Jurvansuu J. Season- and caste-specific variation in RNA viruses in the invasive Argentine ant European supercolony. J Gen Virol 2020; 101:322-333. [PMID: 31985392 DOI: 10.1099/jgv.0.001384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The Argentine ant (Linepithema humile, Mayr) is a highly invasive species. Recently, several RNA viruses have been identified in samples from invasive Argentine ant colonies. Using quantitative PCR, we investigated variation in the levels of these viruses in the main European supercolony over the course of a year. We discovered that virus prevalence and amounts of viral RNA were affected by season and caste: ants had more virus types during warm versus cold months, and queens had more virus types and higher virus prevalence than did workers or males. This seasonal variation was largely due to the appearance of positive-strand RNA viruses in the summer and their subsequent disappearance in the winter. The prevalences of positive-strand RNA viruses were positively correlated with worker foraging activity. We hypothesise that during warmer months, ants are more active and more numerous and, as a result, they have more conspecific and heterospecific interactions that promote virus transmission.
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Affiliation(s)
- Sílvia Abril
- Department of Environmental Sciences, University of Girona, Girona, Spain
| | - Jaana Jurvansuu
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
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Hsu HW, Chiu MC, Shih CJ, Matsuura K, Yang CCS. Apoptosis as a primary defense mechanism in response to viral infection in invasive fire ant Solenopsis invicta. Virology 2019; 531:255-259. [DOI: 10.1016/j.virol.2019.03.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 03/25/2019] [Accepted: 03/25/2019] [Indexed: 10/27/2022]
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Eyer PA, McDowell B, Johnson LNL, Calcaterra LA, Fernandez MB, Shoemaker D, Puckett RT, Vargo EL. Supercolonial structure of invasive populations of the tawny crazy ant Nylanderia fulva in the US. BMC Evol Biol 2018; 18:209. [PMID: 30594137 PMCID: PMC6310932 DOI: 10.1186/s12862-018-1336-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 12/17/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Social insects are among the most serious invasive pests in the world, particularly successful at monopolizing environmental resources to outcompete native species and achieve ecological dominance. The invasive success of some social insects is enhanced by their unicolonial structure, under which the presence of numerous queens and the lack of aggression against non-nestmates allow high worker densities, colony growth, and survival while eliminating intra-specific competition. In this study, we investigated the population genetics, colony structure and levels of aggression in the tawny crazy ant, Nylanderia fulva, which was recently introduced into the United States from South America. RESULTS We found that this species experienced a genetic bottleneck during its invasion lowering its genetic diversity by 60%. Our results show that the introduction of N. fulva is associated with a shift in colony structure. This species exhibits a multicolonial organization in its native range, with colonies clearly separated from one another, whereas it displays a unicolonial system with no clear boundaries among nests in its invasive range. We uncovered an absence of genetic differentiation among populations across the entire invasive range, and a lack of aggressive behaviors towards conspecifics from different nests, even ones separated by several hundreds of kilometers. CONCLUSIONS Overall, these results suggest that across its entire invasive range in the U.S.A., this species forms a single supercolony spreading more than 2000 km. In each invasive nest, we found several, up to hundreds, of reproductive queens, each being mated with a single male. The many reproductive queens per nests, together with the free movement of individuals between nests, leads to a relatedness coefficient among nestmate workers close to zero in introduced populations, calling into question the stability of this unicolonial system in which indirect fitness benefits to workers is apparently absent.
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Affiliation(s)
- Pierre-André Eyer
- Department of Entomology, 2143 TAMU, Texas A&M University, College Station, TX, 77843-2143, USA.
| | - Bryant McDowell
- Department of Entomology, 2143 TAMU, Texas A&M University, College Station, TX, 77843-2143, USA
| | - Laura N L Johnson
- Department of Entomology, 2143 TAMU, Texas A&M University, College Station, TX, 77843-2143, USA
| | - Luis A Calcaterra
- Fundación para el Estudio de Especies Invasivas (FuEDEI) and CONICET, Bolívar 1559, B1686EFA, Hurlingham, Buenos Aires, Argentina
| | - Maria Belen Fernandez
- Fundación para el Estudio de Especies Invasivas (FuEDEI) and CONICET, Bolívar 1559, B1686EFA, Hurlingham, Buenos Aires, Argentina
| | - DeWayne Shoemaker
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996-4560, USA
| | - Robert T Puckett
- Department of Entomology, 2143 TAMU, Texas A&M University, College Station, TX, 77843-2143, USA
| | - Edward L Vargo
- Department of Entomology, 2143 TAMU, Texas A&M University, College Station, TX, 77843-2143, USA
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Meta-Omics Tools in the World of Insect-Microorganism Interactions. BIOLOGY 2018; 7:biology7040050. [PMID: 30486337 PMCID: PMC6316257 DOI: 10.3390/biology7040050] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/16/2018] [Accepted: 11/22/2018] [Indexed: 02/07/2023]
Abstract
Microorganisms are able to influence several aspects of insects’ life, and this statement is gaining increasing strength, as research demonstrates it daily. At the same time, new sequencing technologies are now available at a lower cost per base, and bioinformatic procedures are becoming more user-friendly. This is triggering a huge effort in studying the microbial diversity associated to insects, and especially to economically important insect pests. The importance of the microbiome has been widely acknowledged for a wide range of animals, and also for insects this topic is gaining considerable importance. In addition to bacterial-associates, the insect-associated fungal communities are also gaining attention, especially those including plant pathogens. The use of meta-omics tools is not restricted to the description of the microbial world, but it can be also used in bio-surveillance, food safety assessment, or even to bring novelties to the industry. This mini-review aims to give a wide overview of how meta-omics tools are fostering advances in research on insect-microorganism interactions.
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Viljakainen L, Holmberg I, Abril S, Jurvansuu J. Viruses of invasive Argentine ants from the European Main supercolony: characterization, interactions and evolution. J Gen Virol 2018; 99:1129-1140. [DOI: 10.1099/jgv.0.001104] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Lumi Viljakainen
- 1Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Ida Holmberg
- 1Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Sílvia Abril
- 2Department of Environmental Sciences, University of Girona, Girona, Spain
| | - Jaana Jurvansuu
- 1Department of Ecology and Genetics, University of Oulu, Oulu, Finland
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Cooling MD, Hoffmann BD, Gruber MAM, Lester PJ. Indirect evidence of pathogen-associated altered oocyte production in queens of the invasive yellow crazy ant, Anoplolepis gracilipes, in Arnhem Land, Australia. BULLETIN OF ENTOMOLOGICAL RESEARCH 2018; 108:451-460. [PMID: 28920560 DOI: 10.1017/s0007485317000967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Anoplolepis gracilipes is one of the six most widespread and pestiferous invasive ant species. Populations of this invader in Arnhem Land, Australia have been observed to decline, but the reasons behind these declines are not known. We investigated if there is evidence of a pathogen that could be responsible for killing ant queens or affecting their reproductive output. We measured queen number per nest, fecundity and fat content of queens from A. gracilipes populations in various stages of decline or expansion. We found no significant difference in any of these variables among populations. However, 23% of queens were found to have melanized nodules, a cellular immune response, in their ovaries and fat bodies. The melanized nodules found in dissected queens are highly likely to indicate the presence of pathogens or parasites capable of infecting A. gracilipes. Queens with nodules had significantly fewer oocytes in their ovaries, but nodule presence was not associated with low ant population abundances. Although the microorganism responsible for the nodules is as yet unidentified, this is the first evidence of the presence of a pathogenic microorganism in the invasive ant A. gracilipes that may be affecting reproduction.
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Affiliation(s)
- M D Cooling
- School of Biological Sciences,Victoria University of Wellington,PO Box 600,Wellington 6140,New Zealand
| | - B D Hoffmann
- CSIRO,Tropical Ecosystems Research Centre,PMB 44,Winnellie,NT 0822,Australia
| | - M A M Gruber
- School of Biological Sciences,Victoria University of Wellington,PO Box 600,Wellington 6140,New Zealand
| | - P J Lester
- School of Biological Sciences,Victoria University of Wellington,PO Box 600,Wellington 6140,New Zealand
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Valles SM, Porter SD, Calcaterra LA. Prospecting for viral natural enemies of the fire ant Solenopsis invicta in Argentina. PLoS One 2018; 13:e0192377. [PMID: 29466388 PMCID: PMC5821328 DOI: 10.1371/journal.pone.0192377] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 01/20/2018] [Indexed: 11/18/2022] Open
Abstract
Metagenomics and next generation sequencing were employed to discover new virus natural enemies of the fire ant, Solenopsis invicta Buren in its native range (i.e., Formosa, Argentina) with the ultimate goal of testing and releasing new viral pathogens into U.S. S. invicta populations to provide natural, sustainable control of this ant. RNA was purified from worker ants from 182 S. invicta colonies, which was pooled into 4 groups according to location. A library was created from each group and sequenced using Illumina Miseq technology. After a series of winnowing methods to remove S. invicta genes, known S. invicta virus genes, and all other non-virus gene sequences, 61,944 unique singletons were identified with virus identity. These were assembled de novo yielding 171 contiguous sequences with significant identity to non-plant virus genes. Fifteen contiguous sequences exhibited very high expression rates and were detected in all four gene libraries. One contig (Contig_29) exhibited the highest expression level overall and across all four gene libraries. Random amplification of cDNA ends analyses expanded this contiguous sequence yielding a complete virus genome, which we have provisionally named Solenopsis invicta virus 5 (SINV-5). SINV-5 is a positive-sense, single-stranded RNA virus with genome characteristics consistent with insect-infecting viruses from the family Dicistroviridae. Moreover, the replicative genome strand of SINV-5 was detected in worker ants indicating that S. invicta serves as host for the virus. Many additional sequences were identified that are likely of viral origin. These sequences await further investigation to determine their origins and relationship with S. invicta. This study expands knowledge of the RNA virome diversity found within S. invicta populations.
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Affiliation(s)
- Steven M. Valles
- Center for Medical, Agricultural and Veterinary Entomology, USDA-ARS, Gainesville, Florida, United States of America
- * E-mail:
| | - Sanford D. Porter
- Center for Medical, Agricultural and Veterinary Entomology, USDA-ARS, Gainesville, Florida, United States of America
| | - Luis A. Calcaterra
- Fundación para el Estudio de Especies Invasivas, Bolívar, B1686EFA Hurlingham, Buenos Aires, Argentina
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Favreau E, Martínez-Ruiz C, Rodrigues Santiago L, Hammond RL, Wurm Y. Genes and genomic processes underpinning the social lives of ants. CURRENT OPINION IN INSECT SCIENCE 2018; 25:83-90. [PMID: 29602366 DOI: 10.1016/j.cois.2017.12.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 12/05/2017] [Indexed: 05/06/2023]
Abstract
The >15000 ant species are all highly social and show great variation in colony organization, complexity and behavior. The mechanisms by which such sociality evolved, as well as those underpinning the elaboration of ant societies since their ∼140 million year old common ancestor, have long been pondered. Here, we review recent insights generated using various genomic approaches. This includes understanding the molecular mechanisms underlying caste differentiation and the diversity of social structures, studying the impact of eusociality on genomic evolutionary rates, and investigating gene expression changes associated with differences in lifespan between castes. Furthermore, functional studies involving RNAi and CRISPR have recently been successfully applied to ants, opening the door to exciting research that promises to revolutionize the understanding of the evolution and diversification of social living.
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Affiliation(s)
- Emeline Favreau
- Organismal Biology Department, School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Carlos Martínez-Ruiz
- Organismal Biology Department, School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Leandro Rodrigues Santiago
- Organismal Biology Department, School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Robert L Hammond
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, United Kingdom.
| | - Yannick Wurm
- Organismal Biology Department, School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom.
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Gruber MAM, Cooling M, Baty JW, Buckley K, Friedlander A, Quinn O, Russell JFEJ, Sébastien A, Lester PJ. Single-stranded RNA viruses infecting the invasive Argentine ant, Linepithema humile. Sci Rep 2017; 7:3304. [PMID: 28607437 PMCID: PMC5468335 DOI: 10.1038/s41598-017-03508-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 04/28/2017] [Indexed: 11/17/2022] Open
Abstract
Social insects host a diversity of viruses. We examined New Zealand populations of the globally widely distributed invasive Argentine ant (Linepithema humile) for RNA viruses. We used metatranscriptomic analysis, which identified six potential novel viruses in the Dicistroviridae family. Of these, three contigs were confirmed by Sanger sequencing as Linepithema humile virus-1 (LHUV-1), a novel strain of Kashmir bee virus (KBV) and Black queen cell virus (BQCV), while the others were chimeric or misassembled sequences. We extended the known sequence of LHUV-1 to confirm its placement in the Dicistroviridae and categorised its relationship to closest relatives, which were all viruses infecting Hymenoptera. We examined further for known viruses by mapping our metatranscriptomic sequences to all viral genomes, and confirmed KBV, BQCV, LHUV-1 and Deformed wing virus (DWV) presence using qRT-PCR. Viral replication was confirmed for DWV, KBV and LHUV-1. Viral titers in ants were higher in the presence of honey bee hives. Argentine ants appear to host a range of' honey bee' pathogens in addition to a virus currently described only from this invasive ant. The role of these viruses in the population dynamics of the ant remain to be determined, but offer potential targets for biocontrol approaches.
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Affiliation(s)
- Monica A M Gruber
- Centre for Biodiversity and Restoration Ecology, School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand.
- Pacific Biosecurity, Victoria Link Limited, Victoria University of Wellington, PO Box 1762, Wellington, New Zealand.
| | - Meghan Cooling
- Centre for Biodiversity and Restoration Ecology, School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
- Pacific Biosecurity, Victoria Link Limited, Victoria University of Wellington, PO Box 1762, Wellington, New Zealand
| | - James W Baty
- Centre for Biodiversity and Restoration Ecology, School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
- Malaghan Institute of Medical Research, PO Box 7060, Wellington, New Zealand
| | - Kevin Buckley
- School of Engineering and Computer Science, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Anna Friedlander
- School of Engineering and Computer Science, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Oliver Quinn
- Centre for Biodiversity and Restoration Ecology, School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Jessica F E J Russell
- Centre for Biodiversity and Restoration Ecology, School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Alexandra Sébastien
- Centre for Biodiversity and Restoration Ecology, School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Philip J Lester
- Centre for Biodiversity and Restoration Ecology, School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
- Pacific Biosecurity, Victoria Link Limited, Victoria University of Wellington, PO Box 1762, Wellington, New Zealand
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Kamenova S, Bartley T, Bohan D, Boutain J, Colautti R, Domaizon I, Fontaine C, Lemainque A, Le Viol I, Mollot G, Perga ME, Ravigné V, Massol F. Invasions Toolkit. ADV ECOL RES 2017. [DOI: 10.1016/bs.aecr.2016.10.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Valles SM, Oi DH, Becnel JJ, Wetterer JK, LaPolla JS, Firth AE. Isolation and characterization of Nylanderia fulva virus 1, a positive-sense, single-stranded RNA virus infecting the tawny crazy ant, Nylanderia fulva. Virology 2016; 496:244-254. [PMID: 27372180 PMCID: PMC4980443 DOI: 10.1016/j.virol.2016.06.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 06/15/2016] [Accepted: 06/16/2016] [Indexed: 12/18/2022]
Abstract
We report the discovery of Nylanderia fulva virus 1 (NfV-1), the first virus identified and characterized from the ant, Nylanderia fulva. The NfV-1 genome (GenBank accession KX024775) is 10,881 nucleotides in length, encoding one large open reading frame (ORF). Helicase, protease, RNA-dependent RNA polymerase, and jelly-roll capsid protein domains were recognized within the polyprotein. Phylogenetic analysis placed NfV-1 in an unclassified clade of viruses. Electron microscopic examination of negatively stained samples revealed particles with icosahedral symmetry with a diameter of 28.7±1.1nm. The virus was detected by RT-PCR in larval, pupal, worker and queen developmental stages. However, the replicative strand of NfV-1 was only detected in larvae. Vertical transmission did not appear to occur, but horizontal transmission was facile. The inter-colonial field prevalence of NfV-1 was 52±35% with some local infections reaching 100%. NfV-1 was not detected in limited samples of other Nylanderia species or closely related ant species.
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Affiliation(s)
- Steven M Valles
- Center for Medical, Agricultural and Veterinary Entomology, USDA-ARS, 1600 SW 23rd Drive, Gainesville, FL 32608, USA.
| | - David H Oi
- Center for Medical, Agricultural and Veterinary Entomology, USDA-ARS, 1600 SW 23rd Drive, Gainesville, FL 32608, USA
| | - James J Becnel
- Center for Medical, Agricultural and Veterinary Entomology, USDA-ARS, 1600 SW 23rd Drive, Gainesville, FL 32608, USA
| | - James K Wetterer
- Wilkes Honors College, Florida Atlantic University, 5353 Parkside Drive, Jupiter, FL 33458, USA
| | - John S LaPolla
- Department of Biological Sciences, Towson University, 8000 York Road, Towson, MD 21252, USA
| | - Andrew E Firth
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
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Cooling M, Hoffmann BD. Here today, gone tomorrow: declines and local extinctions of invasive ant populations in the absence of intervention. Biol Invasions 2015. [DOI: 10.1007/s10530-015-0963-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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17
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Palomeque T, Sanllorente O, Maside X, Vela J, Mora P, Torres MI, Periquet G, Lorite P. Evolutionary history of the Azteca-like mariner transposons and their host ants. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2015. [PMID: 26195134 DOI: 10.1007/s00114-015-1294-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Three different complete mariner elements were found in the genome of the ant Tapinoma nigerrimum. One (Tnigmar-Mr) was interrupted by a 900-bp insertion that corresponded to an incomplete member of a fourth mariner element, called Azteca. In this work, we isolate and characterize full-length Tnigmar-Az elements in T. nigerrimum. The purpose of this study is to clarify the evolutionary history of Azteca elements and their hosts as well as the possible existence of horizontal transfer processes. For this, Azteca-like elements were also retrieved from the available sequences of various ant genomes, representing four different ant subfamilies: Dolichoderinae, Formicinae, Myrmicinae, and Ponerinae. The tree topology resulting for the Azteca-like elements bore very little resemblance to that of their respective hosts. The pervasive presence of Azteca-like elements in all ant genomes, together with the observation that extant copies are usually younger than the genomes that host them, could be explained either by lineage sorting or by recent horizontal transfer of active elements. However, the finding of closer genetic relationships between elements than between the ants that host them is consistent with the latter scenario. This is clearly observed in Sinvmar-Az, Tnigmar-Az, Acepmar-Az, and Cflomar-Az elements, suggesting the existence of horizontal transfer processes. On the contrary, some elements displayed more divergence than did the hosts harboring them. This may reflect either further horizontal transfer events or random lineage sorting.
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Affiliation(s)
- Teresa Palomeque
- Departamento de Biología Experimental, Universidad de Jaén, 23071, Jaén, Spain
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18
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Plowes RM, Becnel JJ, LeBrun EG, Oi DH, Valles SM, Jones NT, Gilbert LE. Myrmecomorba nylanderiae gen. et sp. nov., a microsporidian parasite of the tawny crazy ant Nylanderia fulva. J Invertebr Pathol 2015; 129:45-56. [PMID: 26031565 DOI: 10.1016/j.jip.2015.05.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Revised: 05/19/2015] [Accepted: 05/21/2015] [Indexed: 10/23/2022]
Abstract
A new microsporidian genus and species, Myrmecomorba nylanderiae, is described from North American populations of the tawny crazy ant, Nylanderia fulva. This new species was found to be heterosporous producing several types of binucleate spores in both larval and adult stages and an abortive octosporoblastic sporogony in adult ants. While microsporidia are widespread arthropod parasites, this description represents only the fifth species described from an ant host. Molecular analysis indicated that this new taxon is phylogenetically closely allied to the microsporidian family Caudosporidae, a group known to parasitize aquatic black fly larvae. We report the presence of 3 spore types (Type 1 DK, Type 2 DK, and octospores) with infections found in all stages of host development and reproductive castes. This report documents the first pathogen infecting N. fulva, an invasive ant of considerable economic and ecological consequence.
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Affiliation(s)
- Robert M Plowes
- Brackenridge Field Laboratory, University of Texas at Austin, 2907 Lake Austin Blvd, Austin, TX 78703, United States.
| | - James J Becnel
- USDA, ARS, Center for Medical, Agricultural and Veterinary Entomology, 1600 SW 23rd Drive, Gainesville, FL 32608, United States
| | - Edward G LeBrun
- Brackenridge Field Laboratory, University of Texas at Austin, 2907 Lake Austin Blvd, Austin, TX 78703, United States
| | - David H Oi
- USDA, ARS, Center for Medical, Agricultural and Veterinary Entomology, 1600 SW 23rd Drive, Gainesville, FL 32608, United States
| | - Steven M Valles
- USDA, ARS, Center for Medical, Agricultural and Veterinary Entomology, 1600 SW 23rd Drive, Gainesville, FL 32608, United States
| | - Nathan T Jones
- Brackenridge Field Laboratory, University of Texas at Austin, 2907 Lake Austin Blvd, Austin, TX 78703, United States
| | - Lawrence E Gilbert
- Brackenridge Field Laboratory, University of Texas at Austin, 2907 Lake Austin Blvd, Austin, TX 78703, United States
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Johansson H, Dhaygude K, Lindström S, Helanterä H, Sundström L, Trontti K. A metatranscriptomic approach to the identification of microbiota associated with the ant Formica exsecta. PLoS One 2013; 8:e79777. [PMID: 24260298 PMCID: PMC3832538 DOI: 10.1371/journal.pone.0079777] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 09/25/2013] [Indexed: 11/19/2022] Open
Abstract
Social insects live in cooperative colonies, often in high densities and with closely related individuals, and interact using social contact behaviours. Compared to solitary insects, social insects have evolved multi-level immunity that includes immune responses common to holometabolous insects, and social immunity, which is exclusive to social taxa. This suggests that social insects may be subject to high pathogen pressure, yet relatively little is known about the range of symbiotic and pathogenic microbial communities that associate with social insects. In this study we examined transcriptome data generated from the ant Formica exsecta for sequences identifying as microbes (or other organisms potentially of non-ant origin). Sequences showing homology to two viruses and several other potentially or obligate intracellular organisms, such as Wolbachia, Arsenophonus, Entomoplasmatales and Microsporidia, were present in the transcriptome data. These homologous sequence matches correspond to genera/species that have previously been associated with a variety of insects, including social insects. There were also sequences with identity to several other microbes such as common moulds and soil bacteria. We conclude that this sequence data provides a starting point for a deeper understanding of the biological interactions between a species of ant and the micro- and macrobiotic communities that it potentially encounters.
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Affiliation(s)
- Helena Johansson
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
- * E-mail:
| | - Kishor Dhaygude
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Stafva Lindström
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Heikki Helanterä
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Liselotte Sundström
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Kalevi Trontti
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
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Bonfert T, Csaba G, Zimmer R, Friedel CC. Mining RNA-seq data for infections and contaminations. PLoS One 2013; 8:e73071. [PMID: 24019895 PMCID: PMC3760913 DOI: 10.1371/journal.pone.0073071] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 07/16/2013] [Indexed: 02/06/2023] Open
Abstract
RNA sequencing (RNA-seq) provides novel opportunities for transcriptomic studies at nucleotide resolution, including transcriptomics of viruses or microbes infecting a cell. However, standard approaches for mapping the resulting sequencing reads generally ignore alternative sources of expression other than the host cell and are little equipped to address the problems arising from redundancies and gaps among sequenced microbe and virus genomes. We show that screening of sequencing reads for contaminations and infections can be performed easily using ContextMap, our recently developed mapping software. Based on mapping-derived statistics, mapping confidence, similarities and misidentifications (e.g. due to missing genome sequences) of species/strains can be assessed. Performance of our approach is evaluated on three real-life sequencing data sets and compared to state-of-the-art metagenomics tools. In particular, ContextMap vastly outperformed GASiC and GRAMMy in terms of runtime. In contrast to MEGAN4, it was capable of providing individual read mappings to species and resolving non-unique mappings, thus allowing the identification of misalignments caused by sequence similarities between genomes and missing genome sequences. Our study illustrates the importance and potentials of routinely mining RNA-seq experiments for infections or contaminations by microbes and viruses. By using ContextMap, gene expression of infecting agents can be analyzed and novel insights in infection processes and tumorigenesis can be obtained.
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Affiliation(s)
- Thomas Bonfert
- Institute for Informatics, Ludwig–Maximilians–Universität München, Munich, Germany
| | - Gergely Csaba
- Institute for Informatics, Ludwig–Maximilians–Universität München, Munich, Germany
| | - Ralf Zimmer
- Institute for Informatics, Ludwig–Maximilians–Universität München, Munich, Germany
| | - Caroline C. Friedel
- Institute for Informatics, Ludwig–Maximilians–Universität München, Munich, Germany
- * E-mail:
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21
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Imported crazy ant displaces imported fire ant, reduces and homogenizes grassland ant and arthropod assemblages. Biol Invasions 2013. [DOI: 10.1007/s10530-013-0463-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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22
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Evidence for negative-strand RNA virus infection in fungi. Virology 2013; 435:201-9. [DOI: 10.1016/j.virol.2012.10.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Revised: 09/27/2012] [Accepted: 10/02/2012] [Indexed: 11/22/2022]
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23
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Jang HB, Kim YK, del Castillo CS, Nho SW, Cha IS, Park SB, Ha MA, Hikima JI, Hong SJ, Aoki T, Jung TS. RNA-seq-based metatranscriptomic and microscopic investigation reveals novel metalloproteases of Neobodo sp. as potential virulence factors for soft tunic syndrome in Halocynthia roretzi. PLoS One 2012; 7:e52379. [PMID: 23300657 PMCID: PMC3531462 DOI: 10.1371/journal.pone.0052379] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 11/12/2012] [Indexed: 12/14/2022] Open
Abstract
Bodonids and trypanosomatids are derived from a common ancestor with the bodonids being a more primitive lineage. The Neobodonida, one of the three clades of bodonids, can be free-living, commensal or parasitic. Despite the ecological and evolutionary significance of these organisms, however, many of their biological and pathological features are currently unknown. Here, we employed metatranscriptomics using RNA-seq technology combined with field-emission microscopy to reveal the virulence factors of a recently described genus of Neobodonida that is considered to be responsible for ascidian soft tunic syndrome (AsSTS), but whose pathogenesis is unclear. Our microscopic observation of infected tunic tissues suggested putative virulence factors, enabling us to extract novel candidate transcripts; these included cysteine proteases of the families C1 and C2, serine proteases of S51 and S9 families, and metalloproteases grouped into families M1, M3, M8, M14, M16, M17, M24, M41, and M49. Protease activity/inhibition assays and the estimation of expression levels within gene clusters allowed us to identify metalloprotease-like enzymes as potential virulence attributes for AsSTS. Furthermore, a multimarker-based phylogenetic analysis using 1,184 concatenated amino acid sequences clarified the order Neobodo sp. In sum, we herein used metatranscriptomics to elucidate the in situ expression profiles of uncharacterized putative transcripts of Neobodo sp., combined these results with microscopic observation to select candidate genes relevant to pathogenesis, and used empirical screening to define important virulence factors.
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Affiliation(s)
- Ho Bin Jang
- Aquatic Biotechnology Center of WCU Project, College of Veterinary Medicine, Gyeongsang National University, Jinju, South Korea
| | - Young Kyu Kim
- Aquatic Biotechnology Center of WCU Project, College of Veterinary Medicine, Gyeongsang National University, Jinju, South Korea
| | - Carmelo S. del Castillo
- Aquatic Biotechnology Center of WCU Project, College of Veterinary Medicine, Gyeongsang National University, Jinju, South Korea
| | - Seong Won Nho
- Aquatic Biotechnology Center of WCU Project, College of Veterinary Medicine, Gyeongsang National University, Jinju, South Korea
| | - In Seok Cha
- Aquatic Biotechnology Center of WCU Project, College of Veterinary Medicine, Gyeongsang National University, Jinju, South Korea
| | - Seong Bin Park
- Aquatic Biotechnology Center of WCU Project, College of Veterinary Medicine, Gyeongsang National University, Jinju, South Korea
| | - Mi Ae Ha
- Aquatic Biotechnology Center of WCU Project, College of Veterinary Medicine, Gyeongsang National University, Jinju, South Korea
| | - Jun-ichi Hikima
- Aquatic Biotechnology Center of WCU Project, College of Veterinary Medicine, Gyeongsang National University, Jinju, South Korea
| | - Sung Jong Hong
- Department of Medical Environmental Biology, College of Medicine, Chung-Ang University, DongJak-Gu, Seoul, South Korea
| | - Takashi Aoki
- Aquatic Biotechnology Center of WCU Project, College of Veterinary Medicine, Gyeongsang National University, Jinju, South Korea
- Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Tae Sung Jung
- Aquatic Biotechnology Center of WCU Project, College of Veterinary Medicine, Gyeongsang National University, Jinju, South Korea
- * E-mail:
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25
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Ant Interactions with Soil Organisms and Associated Semiochemicals. J Chem Ecol 2012; 38:728-45. [DOI: 10.1007/s10886-012-0140-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 05/03/2012] [Accepted: 05/11/2012] [Indexed: 12/17/2022]
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26
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Xiong X, Frank DN, Robertson CE, Hung SS, Markle J, Canty AJ, McCoy KD, Macpherson AJ, Poussier P, Danska JS, Parkinson J. Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing. PLoS One 2012; 7:e36009. [PMID: 22558305 PMCID: PMC3338770 DOI: 10.1371/journal.pone.0036009] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Accepted: 03/29/2012] [Indexed: 01/19/2023] Open
Abstract
With the advent of high through-put sequencing (HTS), the emerging science of metagenomics is transforming our understanding of the relationships of microbial communities with their environments. While metagenomics aims to catalogue the genes present in a sample through assessing which genes are actively expressed, metatranscriptomics can provide a mechanistic understanding of community inter-relationships. To achieve these goals, several challenges need to be addressed from sample preparation to sequence processing, statistical analysis and functional annotation. Here we use an inbred non-obese diabetic (NOD) mouse model in which germ-free animals were colonized with a defined mixture of eight commensal bacteria, to explore methods of RNA extraction and to develop a pipeline for the generation and analysis of metatranscriptomic data. Applying the Illumina HTS platform, we sequenced 12 NOD cecal samples prepared using multiple RNA-extraction protocols. The absence of a complete set of reference genomes necessitated a peptide-based search strategy. Up to 16% of sequence reads could be matched to a known bacterial gene. Phylogenetic analysis of the mapped ORFs revealed a distribution consistent with ribosomal RNA, the majority from Bacteroides or Clostridium species. To place these HTS data within a systems context, we mapped the relative abundance of corresponding Escherichia coli homologs onto metabolic and protein-protein interaction networks. These maps identified bacterial processes with components that were well-represented in the datasets. In summary this study highlights the potential of exploiting the economy of HTS platforms for metatranscriptomics.
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Affiliation(s)
- Xuejian Xiong
- Program in Molecular Structure and Function, The Hospital for Sick Children, Toronto, Canada
| | - Daniel N. Frank
- Division of Infectious Diseases, University of Colorado, Aurora, Colorado, United States of America
| | - Charles E. Robertson
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Stacy S. Hung
- Program in Molecular Structure and Function, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Janet Markle
- Department of Immunology, University of Toronto, Toronto, Canada
- Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Angelo J. Canty
- Department of Mathematics and Statistics, McMaster University, Hamilton, Canada
| | - Kathy D. McCoy
- Department Klinische Forschung, University of Bern, Bern, Switzerland
| | | | - Philippe Poussier
- Department of Immunology, University of Toronto, Toronto, Canada
- Sunnybrook Health Sciences Centre Research Institute, University of Toronto, Toronto, Canada
| | - Jayne S. Danska
- Department of Immunology, University of Toronto, Toronto, Canada
- Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - John Parkinson
- Program in Molecular Structure and Function, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
- * E-mail:
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