Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network

Type Article
Date 2018-05
Language English
Author(s) Meng ArnaudORCID1, Corre Erwan2, Probert Ian3, Gutierrez-Rodriguez Andres4, Siano Raffaele5, Annamale Anita6, 7, 8, Alberti Adriana6, 7, 8, Da Silva Corinne6, 7, 8, Wincker Patrick6, 7, 8, Le Crom Stephane1, Not Fabrice9, Bittner LucieORCID1
Affiliation(s) 1 : Sorbonne Univ, UPMC Univ Paris 06, Univ Antilles Guyane, Univ Nice Sophia Antipolis,CNRS,EPS IBPS, Paris, France.
2 : UPMC, CNRS, FR2424, ABiMS,Stn Biol, Roscoff, France.
3 : UPMC, CNRS, FR2424, Roscoff Culture Collect,Stn Biol Roscoff, Pl Georges Teissier, Roscoff, France.
4 : Natl Inst Water & Atmospher Res NIWA Ltd, Wellington, New Zealand.
5 : IFREMER, Ctr Brest, DYNECO PELAGOS, Plouzane, France.
6 : CEA, Inst Genom, GENOSCOPE, Evry, France.
7 : CNRS, UMR8030, Evry, France.
8 : Univ Evry Val dEssonne, Evry, France.
9 : CNRS, UMR 7144, Stn Biol Roscoff, Pl Georges Teissier, Roscoff, France.
Source Molecular Ecology (0962-1083) (Wiley), 2018-05 , Vol. 27 , N. 10 , P. 2365-2380
DOI 10.1111/mec.14579
WOS© Times Cited 5
Keyword(s) genomics, proteomics, microbial biology, molecular evolution, protists, transcriptomics
Abstract 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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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 (2018). Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network. Molecular Ecology, 27(10), 2365-2380. Publisher's official version : https://doi.org/10.1111/mec.14579 , Open Access version : https://archimer.ifremer.fr/doc/00444/55550/