FN Archimer Export Format PT J TI Transcription factors in microalgae: genome-wide prediction and comparative analysis BT AF THIRIET-RUPERT, Stanislas CARRIER, Gregory CHENAIS, Benoit TROTTIER, Camille BOUGARAN, Gael CADORET, Jean-Paul SCHOEFS, Benoit SAINT-JEAN, Bruno AS 1:1;2:1;3:2;4:1;5:1;6:1;7:2;8:1; FF 1:PDG-RBE-BRM-PBA;2:PDG-RBE-BRM-PBA;3:;4:PDG-RBE-BRM-PBA;5:PDG-RBE-BRM-PBA;6:PDG-RBE-BRM;7:;8:PDG-RBE-BRM-PBA; C1 IFREMER, Physiol & Biotechnol Algae Lab, Rue Ile Yeu, F-44311 Nantes, France. Univ Le Mans, CNRS, IUML FR 3473, MicroMar,Mer Mol Sante, Le Mans, France. C2 IFREMER, FRANCE UNIV LE MANS, FRANCE SI NANTES SE PDG-RBE-BRM-PBA PDG-RBE-BRM IN WOS Ifremer jusqu'en 2018 DOAJ copubli-france copubli-univ-france IF 3.729 TC 41 UR https://archimer.ifremer.fr/doc/00333/44403/44072.pdf LA English DT Article DE ;Algae;Endosymbiotic gene transfer;Haptophytes;Prediction pipeline;Stramenopiles;Tisochrysis lutea;Transcription factors AB 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. PY 2016 PD APR SO Bmc Genomics SN 1471-2164 PU Biomed Central Ltd VL 17 IS 282 UT 000373985200001 BP 1 EP 16 DI 10.1186/s12864-016-2610-9 ID 44403 ER EF