One’s trash is someone else’s treasure: sequence read archives from Lepidoptera genomes provide material for genome reconstruction of their endosymbionts
Abstract Background Maternally inherited bacterial symbionts are extremely widespread in insects. They owe their success to their ability to promote their own transmission through various manipulations of their hosts’ life-histories. Many symbionts however very often go undetected. Consequently, we...
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| Format: | Article |
| Language: | English |
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BMC
2022-08-01
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| Series: | BMC Microbiology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12866-022-02602-1 |
| _version_ | 1798032402346409984 |
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| author | Victoria G. Twort Daniel Blande Anne Duplouy |
| author_facet | Victoria G. Twort Daniel Blande Anne Duplouy |
| author_sort | Victoria G. Twort |
| collection | DOAJ |
| description | Abstract Background Maternally inherited bacterial symbionts are extremely widespread in insects. They owe their success to their ability to promote their own transmission through various manipulations of their hosts’ life-histories. Many symbionts however very often go undetected. Consequently, we have only a restricted idea of the true symbiont diversity in insects, which may hinder our understanding of even bigger questions in the field such as the evolution or establishment of symbiosis. Results In this study, we screened publicly available Lepidoptera genomic material for two of the most common insect endosymbionts, namely Wolbachia and Spiroplasma, in 1904 entries, encompassing 106 distinct species. We compared the performance of two screening software, Kraken2 and MetaPhlAn2, to identify the bacterial infections and using a baiting approach we reconstruct endosymbiont genome assemblies. Of the 106 species screened, 20 (19%) and nine (8.5%) were found to be infected with either Wolbachia or Spiroplasma, respectively. Construction of partial symbiotic genomes and phylogenetic analyses suggested the Wolbachia strains from the supergroup B were the most prevalent type of symbionts, while Spiroplasma infections were scarce in the Lepidoptera species screened here. Conclusions Our results indicate that many of the host-symbiont associations remain largely unexplored, with the majority of associations we identify never being recorded before. This highlights the usefulness of public databases to explore the hidden diversity of symbiotic entities, allowing the development of hypotheses regarding host-symbiont associations. The ever-expanding genomic databases provide a diverse databank from which one can characterize and explore the true diversity of symbiotic entities. |
| first_indexed | 2024-04-11T20:13:29Z |
| format | Article |
| id | doaj.art-2e77509dfda34c9c925834d7fcca75f6 |
| institution | Directory Open Access Journal |
| issn | 1471-2180 |
| language | English |
| last_indexed | 2024-04-11T20:13:29Z |
| publishDate | 2022-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Microbiology |
| spelling | doaj.art-2e77509dfda34c9c925834d7fcca75f62022-12-22T04:05:03ZengBMCBMC Microbiology1471-21802022-08-0122111610.1186/s12866-022-02602-1One’s trash is someone else’s treasure: sequence read archives from Lepidoptera genomes provide material for genome reconstruction of their endosymbiontsVictoria G. Twort0Daniel Blande1Anne Duplouy2Finnish Natural History Museum, LUOMUS, The University of HelsinkiOrganismal and Evolutionary Biology, The University of HelsinkiOrganismal and Evolutionary Biology, The University of HelsinkiAbstract Background Maternally inherited bacterial symbionts are extremely widespread in insects. They owe their success to their ability to promote their own transmission through various manipulations of their hosts’ life-histories. Many symbionts however very often go undetected. Consequently, we have only a restricted idea of the true symbiont diversity in insects, which may hinder our understanding of even bigger questions in the field such as the evolution or establishment of symbiosis. Results In this study, we screened publicly available Lepidoptera genomic material for two of the most common insect endosymbionts, namely Wolbachia and Spiroplasma, in 1904 entries, encompassing 106 distinct species. We compared the performance of two screening software, Kraken2 and MetaPhlAn2, to identify the bacterial infections and using a baiting approach we reconstruct endosymbiont genome assemblies. Of the 106 species screened, 20 (19%) and nine (8.5%) were found to be infected with either Wolbachia or Spiroplasma, respectively. Construction of partial symbiotic genomes and phylogenetic analyses suggested the Wolbachia strains from the supergroup B were the most prevalent type of symbionts, while Spiroplasma infections were scarce in the Lepidoptera species screened here. Conclusions Our results indicate that many of the host-symbiont associations remain largely unexplored, with the majority of associations we identify never being recorded before. This highlights the usefulness of public databases to explore the hidden diversity of symbiotic entities, allowing the development of hypotheses regarding host-symbiont associations. The ever-expanding genomic databases provide a diverse databank from which one can characterize and explore the true diversity of symbiotic entities.https://doi.org/10.1186/s12866-022-02602-1LepidopteraSymbiontsTrace archivesMetagenomesWolbachiaSpiroplasma |
| spellingShingle | Victoria G. Twort Daniel Blande Anne Duplouy One’s trash is someone else’s treasure: sequence read archives from Lepidoptera genomes provide material for genome reconstruction of their endosymbionts BMC Microbiology Lepidoptera Symbionts Trace archives Metagenomes Wolbachia Spiroplasma |
| title | One’s trash is someone else’s treasure: sequence read archives from Lepidoptera genomes provide material for genome reconstruction of their endosymbionts |
| title_full | One’s trash is someone else’s treasure: sequence read archives from Lepidoptera genomes provide material for genome reconstruction of their endosymbionts |
| title_fullStr | One’s trash is someone else’s treasure: sequence read archives from Lepidoptera genomes provide material for genome reconstruction of their endosymbionts |
| title_full_unstemmed | One’s trash is someone else’s treasure: sequence read archives from Lepidoptera genomes provide material for genome reconstruction of their endosymbionts |
| title_short | One’s trash is someone else’s treasure: sequence read archives from Lepidoptera genomes provide material for genome reconstruction of their endosymbionts |
| title_sort | one s trash is someone else s treasure sequence read archives from lepidoptera genomes provide material for genome reconstruction of their endosymbionts |
| topic | Lepidoptera Symbionts Trace archives Metagenomes Wolbachia Spiroplasma |
| url | https://doi.org/10.1186/s12866-022-02602-1 |
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