Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches
Abstract Background Most metazoans are involved in durable relationships with microbes which can take several forms, from mutualism to parasitism. The advances of NGS technologies and bioinformatics tools have opened opportunities to shed light on the diversity of microbial communities and to give s...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2018-10-01
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| Series: | Microbiome |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s40168-018-0562-9 |
| _version_ | 1817997657687195648 |
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| author | Cervin Guyomar Fabrice Legeai Emmanuelle Jousselin Christophe Mougel Claire Lemaitre Jean-Christophe Simon |
| author_facet | Cervin Guyomar Fabrice Legeai Emmanuelle Jousselin Christophe Mougel Claire Lemaitre Jean-Christophe Simon |
| author_sort | Cervin Guyomar |
| collection | DOAJ |
| description | Abstract Background Most metazoans are involved in durable relationships with microbes which can take several forms, from mutualism to parasitism. The advances of NGS technologies and bioinformatics tools have opened opportunities to shed light on the diversity of microbial communities and to give some insights into the functions they perform in a broad array of hosts. The pea aphid is a model system for the study of insect-bacteria symbiosis. It is organized in a complex of biotypes, each adapted to specific host plants. It harbors both an obligatory symbiont supplying key nutrients and several facultative symbionts bringing additional functions to the host, such as protection against biotic and abiotic stresses. However, little is known on how the symbiont genomic diversity is structured at different scales: across host biotypes, among individuals of the same biotype, or within individual aphids, which limits our understanding on how these multi-partner symbioses evolve and interact. Results We present a framework well adapted to the study of genomic diversity and evolutionary dynamics of the pea aphid holobiont from metagenomic read sets, based on mapping to reference genomes and whole genome variant calling. Our results revealed that the pea aphid microbiota is dominated by a few heritable bacterial symbionts reported in earlier works, with no discovery of new microbial associates. However, we detected a large and heterogeneous genotypic diversity associated with the different symbionts of the pea aphid. Partitioning analysis showed that this fine resolution diversity is distributed across the three considered scales. Phylogenetic analyses highlighted frequent horizontal transfers of facultative symbionts between host lineages, indicative of flexible associations between the pea aphid and its microbiota. However, the evolutionary dynamics of symbiotic associations strongly varied depending on the symbiont, reflecting different histories and possible constraints. In addition, at the intra-host scale, we showed that different symbiont strains may coexist inside the same aphid host. Conclusions We present a methodological framework for the detailed analysis of NGS data from microbial communities of moderate complexity and gave major insights into the extent of diversity in pea aphid-symbiont associations and the range of evolutionary trajectories they could take. |
| first_indexed | 2024-04-14T02:40:21Z |
| format | Article |
| id | doaj.art-b071c8b260df4ac696c8765068f4d305 |
| institution | Directory Open Access Journal |
| issn | 2049-2618 |
| language | English |
| last_indexed | 2024-04-14T02:40:21Z |
| publishDate | 2018-10-01 |
| publisher | BMC |
| record_format | Article |
| series | Microbiome |
| spelling | doaj.art-b071c8b260df4ac696c8765068f4d3052022-12-22T02:17:08ZengBMCMicrobiome2049-26182018-10-016112110.1186/s40168-018-0562-9Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approachesCervin Guyomar0Fabrice Legeai1Emmanuelle Jousselin2Christophe Mougel3Claire Lemaitre4Jean-Christophe Simon5INRA, UMR 1349 INRA/Agrocampus Ouest/Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes (IGEPP)INRA, UMR 1349 INRA/Agrocampus Ouest/Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes (IGEPP)INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de BaillarguetINRA, UMR 1349 INRA/Agrocampus Ouest/Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes (IGEPP)Université Rennes 1, Inria, CNRS, IRISAINRA, UMR 1349 INRA/Agrocampus Ouest/Université Rennes 1, Institut de Génétique, Environnement et Protection des Plantes (IGEPP)Abstract Background Most metazoans are involved in durable relationships with microbes which can take several forms, from mutualism to parasitism. The advances of NGS technologies and bioinformatics tools have opened opportunities to shed light on the diversity of microbial communities and to give some insights into the functions they perform in a broad array of hosts. The pea aphid is a model system for the study of insect-bacteria symbiosis. It is organized in a complex of biotypes, each adapted to specific host plants. It harbors both an obligatory symbiont supplying key nutrients and several facultative symbionts bringing additional functions to the host, such as protection against biotic and abiotic stresses. However, little is known on how the symbiont genomic diversity is structured at different scales: across host biotypes, among individuals of the same biotype, or within individual aphids, which limits our understanding on how these multi-partner symbioses evolve and interact. Results We present a framework well adapted to the study of genomic diversity and evolutionary dynamics of the pea aphid holobiont from metagenomic read sets, based on mapping to reference genomes and whole genome variant calling. Our results revealed that the pea aphid microbiota is dominated by a few heritable bacterial symbionts reported in earlier works, with no discovery of new microbial associates. However, we detected a large and heterogeneous genotypic diversity associated with the different symbionts of the pea aphid. Partitioning analysis showed that this fine resolution diversity is distributed across the three considered scales. Phylogenetic analyses highlighted frequent horizontal transfers of facultative symbionts between host lineages, indicative of flexible associations between the pea aphid and its microbiota. However, the evolutionary dynamics of symbiotic associations strongly varied depending on the symbiont, reflecting different histories and possible constraints. In addition, at the intra-host scale, we showed that different symbiont strains may coexist inside the same aphid host. Conclusions We present a methodological framework for the detailed analysis of NGS data from microbial communities of moderate complexity and gave major insights into the extent of diversity in pea aphid-symbiont associations and the range of evolutionary trajectories they could take.http://link.springer.com/article/10.1186/s40168-018-0562-9Host-microbiota interactionsAphidsMetagenomicsSymbiosisPhylogeny |
| spellingShingle | Cervin Guyomar Fabrice Legeai Emmanuelle Jousselin Christophe Mougel Claire Lemaitre Jean-Christophe Simon Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches Microbiome Host-microbiota interactions Aphids Metagenomics Symbiosis Phylogeny |
| title | Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches |
| title_full | Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches |
| title_fullStr | Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches |
| title_full_unstemmed | Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches |
| title_short | Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches |
| title_sort | multi scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches |
| topic | Host-microbiota interactions Aphids Metagenomics Symbiosis Phylogeny |
| url | http://link.springer.com/article/10.1186/s40168-018-0562-9 |
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