| Registro completo |
| Provedor de dados: |
ArchiMer
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| País: |
France
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| Título: |
Transcription factors in microalgae: genome-wide prediction and comparative analysis
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| Autores: |
Thiriet-rupert, Stanislas
Carrier, Gregory
Chenais, Benoit
Trottier, Camille
Bougaran, Gael
Cadoret, Jean-paul
Schoefs, Benoit
Saint-jean, Bruno
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| Data: |
2016-04
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| Ano: |
2016
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| Palavras-chave: |
Algae
Endosymbiotic gene transfer
Haptophytes
Prediction pipeline
Stramenopiles
Tisochrysis lutea
Transcription factors
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| Resumo: |
Background: Studying transcription factors, which are some of the key players in gene expression, is of outstanding interest for the investigation of the evolutionary history of organisms through lineage-specific features. In this study we performed the first genome-wide TF identification and comparison between haptophytes and other algal lineages. Results: For TF identification and classification, we created a comprehensive pipeline using a combination of BLAST, HMMER and InterProScan software. The accuracy evaluation of the pipeline shows its applicability for every alga, plant and cyanobacterium, with very good PPV and sensitivity. This pipeline allowed us to identify and classified the transcription factor complement of the three haptophytes Tisochrysis lutea, Emiliania huxleyi and Pavlova sp.; the two stramenopiles Phaeodactylum tricornutum and Nannochloropsis gaditana; the chlorophyte Chlamydomonas reinhardtii and the rhodophyte Porphyridium purpureum. By using T. lutea and Porphyridium purpureum, this work extends the variety of species included in such comparative studies, allowing the detection and detailed study of lineage-specific features, such as the presence of TF families specific to the green lineage in Porphyridium purpureum, haptophytes and stramenopiles. Our comprehensive pipeline also allowed us to identify fungal and cyanobacterial TF families in the algal nuclear genomes. Conclusions: This study provides examples illustrating the complex evolutionary history of algae, some of which support the involvement of a green alga in haptophyte and stramenopile evolution.
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| Tipo: |
Text
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| Idioma: |
Inglês
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| Identificador: |
https://archimer.ifremer.fr/doc/00333/44403/44072.pdf
DOI:10.1186/s12864-016-2610-9
https://archimer.ifremer.fr/doc/00333/44403/
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| Editor: |
Biomed Central Ltd
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| Formato: |
application/pdf
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| Fonte: |
Bmc Genomics (1471-2164) (Biomed Central Ltd), 2016-04 , Vol. 17 , N. 282 , P. 1-16
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| Direitos: |
2016 Thiriet-Rupert et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativ
info:eu-repo/semantics/openAccess
restricted use
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