| Registro completo |
| Provedor de dados: |
ArchiMer
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| País: |
France
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| Título: |
Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network
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| Autores: |
Meng, Arnaud
Corre, Erwan
Probert, Ian
Gutierrez-rodriguez, Andres
Siano, Raffaele
Annamale, Anita
Alberti, Adriana
Da Silva, Corinne
Wincker, Patrick
Le Crom, Stephane
Not, Fabrice
Bittner, Lucie
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| Data: |
2018-05
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| Ano: |
2018
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| Palavras-chave: |
Genomics
Proteomics
Microbial biology
Molecular evolution
Protists
Transcriptomics
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| Resumo: |
Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and used a sequence similarity network (SSN) to compare the underlying genomic basis of functional features within the group. This approach constitutes the most comprehensive picture to date of the genomic potential of dinoflagellates. A core-predicted proteome composed of 252 connected components (CCs) of putative conserved protein domains (pCDs) was identified. Of these, 206 were novel and 16 lacked any functional annotation in public databases. Integration of functional information in our network analyses allowed investigation of pCDs specifically associated with functional traits. With respect to toxicity, sequences homologous to those of proteins found in species with toxicity potential (e.g., sxtA4 and sxtG) were not specific to known toxin-producing species. Although not fully specific to symbiosis, the most represented functions associated with proteins involved in the symbiotic trait were related to membrane processes and ion transport. Overall, our SSN approach led to identification of 45,207 and 90,794 specific and constitutive pCDs of, respectively, the toxic and symbiotic species represented in our analyses. Of these, 56% and 57%, respectively (i.e., 25,393 and 52,193 pCDs), completely lacked annotation in public databases. This stresses the extent of our lack of knowledge, while emphasizing the potential of SSNs to identify candidate pCDs for further functional genomic characterization.
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| Tipo: |
Text
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| Idioma: |
Inglês
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| Identificador: |
https://archimer.ifremer.fr/doc/00444/55550/57209.pdf
DOI:10.1111/mec.14579
https://archimer.ifremer.fr/doc/00444/55550/
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| Editor: |
Wiley
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| Formato: |
application/pdf
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| Fonte: |
Molecular Ecology (0962-1083) (Wiley), 2018-05 , Vol. 27 , N. 10 , P. 2365-2380
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| Direitos: |
2018 John Wiley & Sons Ltd
info:eu-repo/semantics/openAccess
restricted use
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