Conservation and diversification of small RNA pathways within flatworms
Abstract Background Small non-coding RNAs, including miRNAs, and gene silencing mediated by RNA interference have been described in free-living and parasitic lineages of flatworms, but only few key factors of the small RNA pathways have been exhaustively investigated in a limited number of species....
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| Format: | Article |
| Language: | English |
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BMC
2017-09-01
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| Series: | BMC Evolutionary Biology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12862-017-1061-5 |
| _version_ | 1830448292982423552 |
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| author | Santiago Fontenla Gabriel Rinaldi Pablo Smircich Jose F. Tort |
| author_facet | Santiago Fontenla Gabriel Rinaldi Pablo Smircich Jose F. Tort |
| author_sort | Santiago Fontenla |
| collection | DOAJ |
| description | Abstract Background Small non-coding RNAs, including miRNAs, and gene silencing mediated by RNA interference have been described in free-living and parasitic lineages of flatworms, but only few key factors of the small RNA pathways have been exhaustively investigated in a limited number of species. The availability of flatworm draft genomes and predicted proteomes allowed us to perform an extended survey of the genes involved in small non-coding RNA pathways in this phylum. Results Overall, findings show that the small non-coding RNA pathways are conserved in all the analyzed flatworm linages; however notable peculiarities were identified. While Piwi genes are amplified in free-living worms they are completely absent in all parasitic species. Remarkably all flatworms share a specific Argonaute family (FL-Ago) that has been independently amplified in different lineages. Other key factors such as Dicer are also duplicated, with Dicer-2 showing structural differences between trematodes, cestodes and free-living flatworms. Similarly, a very divergent GW182 Argonaute interacting protein was identified in all flatworm linages. Contrasting to this, genes involved in the amplification of the RNAi interfering signal were detected only in the ancestral free living species Macrostomum lignano. We here described all the putative small RNA pathways present in both free living and parasitic flatworm lineages. Conclusion These findings highlight innovations specifically evolved in platyhelminths presumably associated with novel mechanisms of gene expression regulation mediated by small RNA pathways that differ to what has been classically described in model organisms. Understanding these phylum-specific innovations and the differences between free living and parasitic species might provide clues to adaptations to parasitism, and would be relevant for gene-silencing technology development for parasitic flatworms that infect hundreds of million people worldwide. |
| first_indexed | 2024-12-21T07:36:26Z |
| format | Article |
| id | doaj.art-80afd1ba185749b3ad312d8584d51185 |
| institution | Directory Open Access Journal |
| issn | 1471-2148 |
| language | English |
| last_indexed | 2024-12-21T07:36:26Z |
| publishDate | 2017-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Evolutionary Biology |
| spelling | doaj.art-80afd1ba185749b3ad312d8584d511852022-12-21T19:11:26ZengBMCBMC Evolutionary Biology1471-21482017-09-0117111610.1186/s12862-017-1061-5Conservation and diversification of small RNA pathways within flatwormsSantiago Fontenla0Gabriel Rinaldi1Pablo Smircich2Jose F. Tort3Departamento de Genética, Facultad de Medicina, Universidad de la República (UDELAR)Parasite Genomics, Wellcome Trust Sanger InstituteDepartamento de Genética, Facultad de Medicina, Universidad de la República (UDELAR)Departamento de Genética, Facultad de Medicina, Universidad de la República (UDELAR)Abstract Background Small non-coding RNAs, including miRNAs, and gene silencing mediated by RNA interference have been described in free-living and parasitic lineages of flatworms, but only few key factors of the small RNA pathways have been exhaustively investigated in a limited number of species. The availability of flatworm draft genomes and predicted proteomes allowed us to perform an extended survey of the genes involved in small non-coding RNA pathways in this phylum. Results Overall, findings show that the small non-coding RNA pathways are conserved in all the analyzed flatworm linages; however notable peculiarities were identified. While Piwi genes are amplified in free-living worms they are completely absent in all parasitic species. Remarkably all flatworms share a specific Argonaute family (FL-Ago) that has been independently amplified in different lineages. Other key factors such as Dicer are also duplicated, with Dicer-2 showing structural differences between trematodes, cestodes and free-living flatworms. Similarly, a very divergent GW182 Argonaute interacting protein was identified in all flatworm linages. Contrasting to this, genes involved in the amplification of the RNAi interfering signal were detected only in the ancestral free living species Macrostomum lignano. We here described all the putative small RNA pathways present in both free living and parasitic flatworm lineages. Conclusion These findings highlight innovations specifically evolved in platyhelminths presumably associated with novel mechanisms of gene expression regulation mediated by small RNA pathways that differ to what has been classically described in model organisms. Understanding these phylum-specific innovations and the differences between free living and parasitic species might provide clues to adaptations to parasitism, and would be relevant for gene-silencing technology development for parasitic flatworms that infect hundreds of million people worldwide.http://link.springer.com/article/10.1186/s12862-017-1061-5FlatwormsSmall RNA pathwaysmiRNARNAiDicerArgonaute |
| spellingShingle | Santiago Fontenla Gabriel Rinaldi Pablo Smircich Jose F. Tort Conservation and diversification of small RNA pathways within flatworms BMC Evolutionary Biology Flatworms Small RNA pathways miRNA RNAi Dicer Argonaute |
| title | Conservation and diversification of small RNA pathways within flatworms |
| title_full | Conservation and diversification of small RNA pathways within flatworms |
| title_fullStr | Conservation and diversification of small RNA pathways within flatworms |
| title_full_unstemmed | Conservation and diversification of small RNA pathways within flatworms |
| title_short | Conservation and diversification of small RNA pathways within flatworms |
| title_sort | conservation and diversification of small rna pathways within flatworms |
| topic | Flatworms Small RNA pathways miRNA RNAi Dicer Argonaute |
| url | http://link.springer.com/article/10.1186/s12862-017-1061-5 |
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