Ribosomal RNA (rRNA) sequences from 33 globally distributed mosquito species for improved metagenomics and species identification
Total RNA sequencing (RNA-seq) is an important tool in the study of mosquitoes and the RNA viruses they vector as it allows assessment of both host and viral RNA in specimens. However, there are two main constraints. First, as with many other species, abundant mosquito ribosomal RNA (rRNA) serves as...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
eLife Sciences Publications Ltd
2023-01-01
|
| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/82762 |
| _version_ | 1797870929366220800 |
|---|---|
| author | Cassandra Koh Lionel Frangeul Hervé Blanc Carine Ngoagouni Sébastien Boyer Philippe Dussart Nina Grau Romain Girod Jean-Bernard Duchemin Maria-Carla Saleh |
| author_facet | Cassandra Koh Lionel Frangeul Hervé Blanc Carine Ngoagouni Sébastien Boyer Philippe Dussart Nina Grau Romain Girod Jean-Bernard Duchemin Maria-Carla Saleh |
| author_sort | Cassandra Koh |
| collection | DOAJ |
| description | Total RNA sequencing (RNA-seq) is an important tool in the study of mosquitoes and the RNA viruses they vector as it allows assessment of both host and viral RNA in specimens. However, there are two main constraints. First, as with many other species, abundant mosquito ribosomal RNA (rRNA) serves as the predominant template from which sequences are generated, meaning that the desired host and viral templates are sequenced far less. Second, mosquito specimens captured in the field must be correctly identified, in some cases to the sub-species level. Here, we generate mosquito rRNA datasets which will substantially mitigate both of these problems. We describe a strategy to assemble novel rRNA sequences from mosquito specimens and produce an unprecedented dataset of 234 full-length 28S and 18S rRNA sequences of 33 medically important species from countries with known histories of mosquito-borne virus circulation (Cambodia, the Central African Republic, Madagascar, and French Guiana). These sequences will allow both physical and computational removal of rRNA from specimens during RNA-seq protocols. We also assess the utility of rRNA sequences for molecular taxonomy and compare phylogenies constructed using rRNA sequences versus those created using the gold standard for molecular species identification of specimens—the mitochondrial cytochrome c oxidase I (COI) gene. We find that rRNA- and COI-derived phylogenetic trees are incongruent and that 28S and concatenated 28S+18S rRNA phylogenies reflect evolutionary relationships that are more aligned with contemporary mosquito systematics. This significant expansion to the current rRNA reference library for mosquitoes will improve mosquito RNA-seq metagenomics by permitting the optimization of species-specific rRNA depletion protocols for a broader range of species and streamlining species identification by rRNA sequence and phylogenetics. |
| first_indexed | 2024-04-10T00:36:15Z |
| format | Article |
| id | doaj.art-4db68f1e4faf48839fc08149771dbb3d |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-10T00:36:15Z |
| publishDate | 2023-01-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-4db68f1e4faf48839fc08149771dbb3d2023-03-14T15:23:15ZengeLife Sciences Publications LtdeLife2050-084X2023-01-011210.7554/eLife.82762Ribosomal RNA (rRNA) sequences from 33 globally distributed mosquito species for improved metagenomics and species identificationCassandra Koh0https://orcid.org/0000-0003-2466-6731Lionel Frangeul1Hervé Blanc2Carine Ngoagouni3Sébastien Boyer4Philippe Dussart5https://orcid.org/0000-0002-1931-3037Nina Grau6Romain Girod7Jean-Bernard Duchemin8Maria-Carla Saleh9https://orcid.org/0000-0001-8593-4117Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, F-75015, Paris, FranceInstitut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, F-75015, Paris, FranceInstitut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, F-75015, Paris, FranceInstitut Pasteur de Bangui, Medical Entomology Laboratory, Bangui, Central African RepublicInstitut Pasteur du Cambodge, Medical and Veterinary Entomology Unit, Phnom Penh, CambodiaInstitut Pasteur du Cambodge, Virology Unit, Phnom Penh, CambodiaInstitut Pasteur de Madagascar, Medical Entomology Unit, Antananarivo, MadagascarInstitut Pasteur de Madagascar, Medical Entomology Unit, Antananarivo, MadagascarInstitut Pasteur de la Guyane, Vectopôle Amazonien Emile Abonnenc, Cayenne, French GuianaInstitut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, F-75015, Paris, FranceTotal RNA sequencing (RNA-seq) is an important tool in the study of mosquitoes and the RNA viruses they vector as it allows assessment of both host and viral RNA in specimens. However, there are two main constraints. First, as with many other species, abundant mosquito ribosomal RNA (rRNA) serves as the predominant template from which sequences are generated, meaning that the desired host and viral templates are sequenced far less. Second, mosquito specimens captured in the field must be correctly identified, in some cases to the sub-species level. Here, we generate mosquito rRNA datasets which will substantially mitigate both of these problems. We describe a strategy to assemble novel rRNA sequences from mosquito specimens and produce an unprecedented dataset of 234 full-length 28S and 18S rRNA sequences of 33 medically important species from countries with known histories of mosquito-borne virus circulation (Cambodia, the Central African Republic, Madagascar, and French Guiana). These sequences will allow both physical and computational removal of rRNA from specimens during RNA-seq protocols. We also assess the utility of rRNA sequences for molecular taxonomy and compare phylogenies constructed using rRNA sequences versus those created using the gold standard for molecular species identification of specimens—the mitochondrial cytochrome c oxidase I (COI) gene. We find that rRNA- and COI-derived phylogenetic trees are incongruent and that 28S and concatenated 28S+18S rRNA phylogenies reflect evolutionary relationships that are more aligned with contemporary mosquito systematics. This significant expansion to the current rRNA reference library for mosquitoes will improve mosquito RNA-seq metagenomics by permitting the optimization of species-specific rRNA depletion protocols for a broader range of species and streamlining species identification by rRNA sequence and phylogenetics.https://elifesciences.org/articles/82762mosquitometagenomicssurveillanceribosomal RNAmolecular taxonomyRNA-seq |
| spellingShingle | Cassandra Koh Lionel Frangeul Hervé Blanc Carine Ngoagouni Sébastien Boyer Philippe Dussart Nina Grau Romain Girod Jean-Bernard Duchemin Maria-Carla Saleh Ribosomal RNA (rRNA) sequences from 33 globally distributed mosquito species for improved metagenomics and species identification eLife mosquito metagenomics surveillance ribosomal RNA molecular taxonomy RNA-seq |
| title | Ribosomal RNA (rRNA) sequences from 33 globally distributed mosquito species for improved metagenomics and species identification |
| title_full | Ribosomal RNA (rRNA) sequences from 33 globally distributed mosquito species for improved metagenomics and species identification |
| title_fullStr | Ribosomal RNA (rRNA) sequences from 33 globally distributed mosquito species for improved metagenomics and species identification |
| title_full_unstemmed | Ribosomal RNA (rRNA) sequences from 33 globally distributed mosquito species for improved metagenomics and species identification |
| title_short | Ribosomal RNA (rRNA) sequences from 33 globally distributed mosquito species for improved metagenomics and species identification |
| title_sort | ribosomal rna rrna sequences from 33 globally distributed mosquito species for improved metagenomics and species identification |
| topic | mosquito metagenomics surveillance ribosomal RNA molecular taxonomy RNA-seq |
| url | https://elifesciences.org/articles/82762 |
| work_keys_str_mv | AT cassandrakoh ribosomalrnarrnasequencesfrom33globallydistributedmosquitospeciesforimprovedmetagenomicsandspeciesidentification AT lionelfrangeul ribosomalrnarrnasequencesfrom33globallydistributedmosquitospeciesforimprovedmetagenomicsandspeciesidentification AT herveblanc ribosomalrnarrnasequencesfrom33globallydistributedmosquitospeciesforimprovedmetagenomicsandspeciesidentification AT carinengoagouni ribosomalrnarrnasequencesfrom33globallydistributedmosquitospeciesforimprovedmetagenomicsandspeciesidentification AT sebastienboyer ribosomalrnarrnasequencesfrom33globallydistributedmosquitospeciesforimprovedmetagenomicsandspeciesidentification AT philippedussart ribosomalrnarrnasequencesfrom33globallydistributedmosquitospeciesforimprovedmetagenomicsandspeciesidentification AT ninagrau ribosomalrnarrnasequencesfrom33globallydistributedmosquitospeciesforimprovedmetagenomicsandspeciesidentification AT romaingirod ribosomalrnarrnasequencesfrom33globallydistributedmosquitospeciesforimprovedmetagenomicsandspeciesidentification AT jeanbernardduchemin ribosomalrnarrnasequencesfrom33globallydistributedmosquitospeciesforimprovedmetagenomicsandspeciesidentification AT mariacarlasaleh ribosomalrnarrnasequencesfrom33globallydistributedmosquitospeciesforimprovedmetagenomicsandspeciesidentification |