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Citation for Study 19079

Citation title: "Transcription factors in microalgae: Genome-wide prediction and comparative analysis".

Study name: "Transcription factors in microalgae: Genome-wide prediction and comparative analysis".

This study is part of submission 19079 (Status: Published).

Citation

Thiriet-rupert S., Carrier G., Chenais B., Trottier C., Bougaran G., Cadoret J., Schoefs B., & Saint-jean B. 2016. Transcription factors in microalgae: Genome-wide prediction and comparative analysis. BMC Genomics, .

Authors

• Thiriet-rupert S. (submitter)
• Carrier G.
• Chenais B.
• Trottier C.
• Bougaran G.
• Cadoret J.
• Schoefs B.
• Saint-jean B.

Abstract

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

Keywords

algae, endosymbiotic gene transfer, haptophytes, prediction pipeline, stramenopiles, Tisochrysis lutea, transcription factors

External links

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S19079
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref25711,
  	 author = {Stanislas  THIRIET-RUPERT and Gregory  CARRIER and Beno?  CHENAIS and Camille  TROTTIER and Gael  BOUGARAN and Jean-Paul  CADORET and Beno?  SCHOEFS and Bruno  SAINT-JEAN},
  	 title = {Transcription factors in microalgae: Genome-wide prediction and comparative analysis},
  	 year = {2016},
  	 keywords = {algae, endosymbiotic gene transfer, haptophytes, prediction pipeline, stramenopiles, Tisochrysis lutea, transcription factors},
  	 doi = {},
  	 url = {http://},
  	 pmid = {},
  	 journal = {BMC Genomics},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {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
  }
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 25711
  AU  - THIRIET-RUPERT,Stanislas 
  AU  - CARRIER,Gregory 
  AU  - CHENAIS,Beno? 
  AU  - TROTTIER,Camille 
  AU  - BOUGARAN,Gael 
  AU  - CADORET,Jean-Paul 
  AU  - SCHOEFS,Beno? 
  AU  - SAINT-JEAN,Bruno 
  T1  - Transcription factors in microalgae: Genome-wide prediction and comparative analysis
  PY  - 2016
  KW  - algae
  KW  - endosymbiotic gene transfer
  KW  - haptophytes
  KW  - prediction pipeline
  KW  - stramenopiles
  KW  - Tisochrysis lutea
  KW  - transcription factors
  UR  - http://dx.doi.org/
  N2  - 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
  
  L3  - 
  JF  - BMC Genomics
  VL  - 
  IS  - 
  ER  -