Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics.
Autor(a) principal: | |
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Data de Publicação: | 2015 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
Texto Completo: | http://www.alice.cnptia.embrapa.br/alice/handle/doc/1023012 |
Resumo: | DNA methods are useful to identify ingested prey items from the gut of predators, but reliable detection is hampered by low amounts of degraded DNA. PCR-based methods can retrieve minute amounts of starting material but suffer from amplification biases and cross-reactions with the predator and related species genomes. Here, we use PCR-free direct shotgun sequencing of total DNA isolated from the gut of the harlequin ladybird Harmonia axyridis at five time points after feeding on a single pea aphid Acyrthosiphon pisum. Sequence reads were matched to three reference databases: Insecta mitogenomes of 587 species, including H. axyridis sequenced here; A. pisum nuclear genome scaffolds; and scaffolds and complete genomes of 13 potential bacterial symbionts. Immediately after feeding, multicopy mtDNA of A. pisum was detected in tens of reads, while hundreds of matches to nuclear scaffolds were detected. Aphid nuclear DNA and mtDNA decayed at similar rates (0.281 and 0.11 h1 respectively), and the detectability periods were 32.7 and 23.1 h. Metagenomic sequencing also revealed thousands of reads of the obligate Buchnera aphidicola and facultative Regiella insecticola aphid symbionts, which showed exponential decay rates significantly faster than aphid DNA (0.694 and 0.80 h 1, respectively). However, the facultative aphid symbionts Hamiltonella defensa, Arsenophonus spp. and Serratia symbiotica showed an unexpected temporary increase in population size by 1?2 orders of magnitude in the predator guts before declining. Metagenomics is a powerful tool that can reveal complex relationships and the dynamics of interactions among predators, prey and their symbionts. |
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Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics.CoccinellidAnalyte detectability half-lifePulgãoDNA methods are useful to identify ingested prey items from the gut of predators, but reliable detection is hampered by low amounts of degraded DNA. PCR-based methods can retrieve minute amounts of starting material but suffer from amplification biases and cross-reactions with the predator and related species genomes. Here, we use PCR-free direct shotgun sequencing of total DNA isolated from the gut of the harlequin ladybird Harmonia axyridis at five time points after feeding on a single pea aphid Acyrthosiphon pisum. Sequence reads were matched to three reference databases: Insecta mitogenomes of 587 species, including H. axyridis sequenced here; A. pisum nuclear genome scaffolds; and scaffolds and complete genomes of 13 potential bacterial symbionts. Immediately after feeding, multicopy mtDNA of A. pisum was detected in tens of reads, while hundreds of matches to nuclear scaffolds were detected. Aphid nuclear DNA and mtDNA decayed at similar rates (0.281 and 0.11 h1 respectively), and the detectability periods were 32.7 and 23.1 h. Metagenomic sequencing also revealed thousands of reads of the obligate Buchnera aphidicola and facultative Regiella insecticola aphid symbionts, which showed exponential decay rates significantly faster than aphid DNA (0.694 and 0.80 h 1, respectively). However, the facultative aphid symbionts Hamiltonella defensa, Arsenophonus spp. and Serratia symbiotica showed an unexpected temporary increase in population size by 1?2 orders of magnitude in the predator guts before declining. Metagenomics is a powerful tool that can reveal complex relationships and the dynamics of interactions among predators, prey and their symbionts.DEBORA PIRES PAULA, CENARGEN; BENJAMIN LINARD, Department of Life Sciences, Natural History Museum, Cromwell Rd, London; DAVID A. ANDOW, Department of Entomology, University of Minnesota; EDISON RYOITI SUJII, CENARGEN; CARMEN SILVIA SOARES PIRES, CENARGEN; ALFRIED P. VOGLER, Department of Life Sciences, Natural History Museum, Cromwell Rd, London.PAULA, D. P.LINARD, B.ANDOW, D. A.SUJII, E. R.PIRES, C. S. S.VOGLER, A. P.2018-07-17T00:52:22Z2018-07-17T00:52:22Z2015-08-3120152018-07-17T00:52:22Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleMolecular Ecology Resources, v. 15, n. 4, p. 880-892, 2015.http://www.alice.cnptia.embrapa.br/alice/handle/doc/102301210.1111/1755-0998.12364enginfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)instacron:EMBRAPA2018-07-17T00:52:28Zoai:www.alice.cnptia.embrapa.br:doc/1023012Repositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestopendoar:21542018-07-17T00:52:28falseRepositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestcg-riaa@embrapa.bropendoar:21542018-07-17T00:52:28Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa)false |
dc.title.none.fl_str_mv |
Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics. |
title |
Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics. |
spellingShingle |
Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics. PAULA, D. P. Coccinellid Analyte detectability half-life Pulgão |
title_short |
Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics. |
title_full |
Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics. |
title_fullStr |
Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics. |
title_full_unstemmed |
Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics. |
title_sort |
Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics. |
author |
PAULA, D. P. |
author_facet |
PAULA, D. P. LINARD, B. ANDOW, D. A. SUJII, E. R. PIRES, C. S. S. VOGLER, A. P. |
author_role |
author |
author2 |
LINARD, B. ANDOW, D. A. SUJII, E. R. PIRES, C. S. S. VOGLER, A. P. |
author2_role |
author author author author author |
dc.contributor.none.fl_str_mv |
DEBORA PIRES PAULA, CENARGEN; BENJAMIN LINARD, Department of Life Sciences, Natural History Museum, Cromwell Rd, London; DAVID A. ANDOW, Department of Entomology, University of Minnesota; EDISON RYOITI SUJII, CENARGEN; CARMEN SILVIA SOARES PIRES, CENARGEN; ALFRIED P. VOGLER, Department of Life Sciences, Natural History Museum, Cromwell Rd, London. |
dc.contributor.author.fl_str_mv |
PAULA, D. P. LINARD, B. ANDOW, D. A. SUJII, E. R. PIRES, C. S. S. VOGLER, A. P. |
dc.subject.por.fl_str_mv |
Coccinellid Analyte detectability half-life Pulgão |
topic |
Coccinellid Analyte detectability half-life Pulgão |
description |
DNA methods are useful to identify ingested prey items from the gut of predators, but reliable detection is hampered by low amounts of degraded DNA. PCR-based methods can retrieve minute amounts of starting material but suffer from amplification biases and cross-reactions with the predator and related species genomes. Here, we use PCR-free direct shotgun sequencing of total DNA isolated from the gut of the harlequin ladybird Harmonia axyridis at five time points after feeding on a single pea aphid Acyrthosiphon pisum. Sequence reads were matched to three reference databases: Insecta mitogenomes of 587 species, including H. axyridis sequenced here; A. pisum nuclear genome scaffolds; and scaffolds and complete genomes of 13 potential bacterial symbionts. Immediately after feeding, multicopy mtDNA of A. pisum was detected in tens of reads, while hundreds of matches to nuclear scaffolds were detected. Aphid nuclear DNA and mtDNA decayed at similar rates (0.281 and 0.11 h1 respectively), and the detectability periods were 32.7 and 23.1 h. Metagenomic sequencing also revealed thousands of reads of the obligate Buchnera aphidicola and facultative Regiella insecticola aphid symbionts, which showed exponential decay rates significantly faster than aphid DNA (0.694 and 0.80 h 1, respectively). However, the facultative aphid symbionts Hamiltonella defensa, Arsenophonus spp. and Serratia symbiotica showed an unexpected temporary increase in population size by 1?2 orders of magnitude in the predator guts before declining. Metagenomics is a powerful tool that can reveal complex relationships and the dynamics of interactions among predators, prey and their symbionts. |
publishDate |
2015 |
dc.date.none.fl_str_mv |
2015-08-31 2015 2018-07-17T00:52:22Z 2018-07-17T00:52:22Z 2018-07-17T00:52:22Z |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/publishedVersion info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
Molecular Ecology Resources, v. 15, n. 4, p. 880-892, 2015. http://www.alice.cnptia.embrapa.br/alice/handle/doc/1023012 10.1111/1755-0998.12364 |
identifier_str_mv |
Molecular Ecology Resources, v. 15, n. 4, p. 880-892, 2015. 10.1111/1755-0998.12364 |
url |
http://www.alice.cnptia.embrapa.br/alice/handle/doc/1023012 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.source.none.fl_str_mv |
reponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa) instacron:EMBRAPA |
instname_str |
Empresa Brasileira de Pesquisa Agropecuária (Embrapa) |
instacron_str |
EMBRAPA |
institution |
EMBRAPA |
reponame_str |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
collection |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
repository.name.fl_str_mv |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa) |
repository.mail.fl_str_mv |
cg-riaa@embrapa.br |
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1794503458636693504 |