ICHA 2018 21-26 OCTOBER NANTES FRANCE Evolution of the Oxidative phosphorylation pathway in Dinoflagellates and sister taxa The importance of the use of metadata and manual curation Jeremy Szymczak *1 , Erwan Corre 2 , Laure Guillou 1, Ehsan Kayal 1 1: UMR-7144, 2: ABiMS-FR2424, Station Biologique de Roscoff, Roscoff, France, *: Presenting author Introduction The organisms The OXPHOS pathway

A B C The mitochondrion is one of the main sites of chemical energy production in the form of adenosine triphosphate (ATP) through the highly conserved oxidative phosphorylation pathway (OXPHOS). In recent years, variations of the OXPHOS pathway has been documented in a variety of organisms. Thanks to recent micro-eukaryotic transcriptomic and genomic projects,

including the Marine Microbial Eukaryote Transcriptome Sequencing D E F Project (MMETSP), a large amount of data is now available for the analysis of various metabolic pathways in marine protists. The alveolates V represent a major group of protists with a great diversity of lifestyles V (phototrophy, mixotrophy, heterotrophy and symbiosis) and include, among others, ciliates, parasitic apicomplexes and dinoflagellates. Recent studies have suggested the modification or even the loss of key complexes of the OXPHOS pathway in Apicomplexa, and more recently, in Dinozoa. Overview of the alveolate. A: Ciliophoran Myrionecta rubra (scale 50 µm, source: https://www.eoas.ubc.ca) B: Apicomplexan Lankesteria abbotti (scale 60 µm, source: Leander et al,. 2006) C: Chromerid Chromera velia (scale 20 µm, Objective: Reconstruction of the OXPHOS source: Miroslav Oborník) D: Perkinsean Parvilucifera infectans (sclale 3 µm, source: Boo Seong et al,. 2018) E: Syndiniales Amoebophrya sp. (green)

pathways from “omics” data through automated infecting a dinoflagellate (blue) (scale 10 µm, source: Aurélie Chambouvet); F : Mitochondrion Alexandrium catenella (scale 25 µm, source: https://www.eoas.ubc.ca) method followed by manual validation. Schematic of the classical oxidative phosphorylation pathway located in + the mitochondria of aerobic eukaryotes. H : proton, O2: dioxygen, CoQ pool: quinones; P : inorganic phosphate; the five complexes are noted Materiel and Methods i from I to V Data source: alveolate transcriptomes from MMETSP; transcriptomes and genomes for four Syndiniales (unpublished) Target subjects: HMM motifs of proteins involved in the electron transport chin (ETC) of OXPHOS from Pfam database

Prediction of peptides Alignment per motif Merge per complex

Transcriptomes Peptidomes Annotations Phylogenies Curated lists of genes OXPHOS pathway

HMM motif search Contaminants filtration (from Pfam) (checked with BLASTp) Manually validated Automatic annotation type

Results Complexes

phylum gender sp complex1 complex2 complex3 complex4 complex5 ETFs AOX Chromerids Chromera velia Summary of key OXPHOS subunits identified in alveolates. Blue: Core subunits Chromerids Vitrella brassicaformis Ciliophora Aristerostoma sp Ciliophora Blepharisma japonicum complex1 complex2 complex3 Complex4 Complex5 Ciliophora Climacostomum virens presence of protein subunit phylum gender sp NDUFA4 NDUFA12 sdhA sdhB cyc UCR14KD CytochromB qcr6 qcr9 COX1 cox3 COX5B cox10 cox11 cox15 sco ATP5A ATP5B ATPc ATPgamma ETFa ETFb ETFQO AOX AOX_putative Chromerids Chromera velia Ciliophora Euplotes crassus Chromerids Vitrella brassicaformis Ciliophora Euplotes focardii Ciliophora Aristerostoma sp Ciliophora Euplotes harpa Ciliophora Blepharisma japonicum Ciliophora Favella taraikaensis Ciliophora Climacostomum virens Motifs representing key subunits of the OXPHOS pathway Ciliophora Litonotus pictus Ciliophora Euplotes crassus Ciliophora Euplotes focardii Ciliophora Mesodinium pulex Ciliophora Euplotes harpa Ciliophora Platyophrya macrostoma

NDUFA4 NDUFA5 NDUFA12 Sdh5 sdhA sdhafs sdhB Sdh_cyt risp cyc Cytochrom_Bqcr6 QCR9 UCR_14kD cob UcrQ cox1 cox2 cox3 COX4 COX5 COX6 cox10 Cox11 COX15 COX16 cox17 cox19 ATP5A ATP5B ATPa ATPb ATPc Mt_ATP-synt_DATPdelta ATPepsilon ATPgamma ATP-synt_10DHODHD-LDH2 ETFa ETF ETFb ETFQO G14LDH L-LDH NDH AOX Ciliophora Favella taraikaensis Chromera_velia Ciliophora Protocruzia adherens Vitrella_brassicaformis Ciliophora Litonotus pictus Anophryoides_haemophila Aristerostoma_sp Ciliophora Pseudokeronopsis sp Blepharisma_japonicum Ciliophora Mesodinium pulex Climacostomum_virens Ciliophora Strombidinopsis acuminatum Condylostoma_magnum Ciliophora Platyophrya macrostoma Euplotes_crassus Euplotes_focardii Ciliophora Protocruzia adherens Ciliophora Strombidinopsis sp Euplotes_harpa Fabrea_salina Favella_taraikaensis Ciliophora Pseudokeronopsis sp Ciliophora Strombidium inclinatum Litonotus_pictus Mesodinium_pulex Ciliophora Strombidinopsis acuminatum Myrionecta_rubra Ciliophora Strombidium rassoulzadegani Platyophrya_macrostoma Protocruzia_adherens Ciliophora Strombidinopsis sp Pseudokeronopsis_sp Dinophyceae Alexandrium andersonii Strombidinopsis_acuminatum Ciliophora Strombidium inclinatum Strombidinopsis_sp Strombidium_inclinatum Ciliophora Strombidium rassoulzadegani Dinophyceae Alexandrium catenella Strombidium_rassoulzadegani Tiarina_fusus Uronema_sp Dinophyceae Alexandrium andersonii Dinophyceae Alexandrium margalefi Akashiwo_sanguinea Alexandrium_andersonii Dinophyceae Alexandrium catenella Alexandrium_catenella Dinophyceae Alexandrium minutum Alexandrium_fundyense Alexandrium_margalefi Dinophyceae Alexandrium fundyense Alexandrium_minutum Dinophyceae Alexandrium monilatum Alexandrium_monilatum Dinophyceae Alexandrium margalefi Alexandrium_temarense Amphidinium_carterae Dinophyceae Alexandrium minutum Dinophyceae Alexandrium temarense Amphidinium_massartii Azadinium_spinosum Brandtodinium_nutriculum Dinophyceae Alexandrium monilatum Dinophyceae Amphidinium massartii Ceratium_fusus Crypthecodinium_cohnii Dinophyceae Alexandrium temarense Dinophysis_acuminata Dinophyceae Azadinium spinosum Durinskia_baltica Gambierdiscus_australes Dinophyceae Amphidinium carterae Gonyaulax_spinifera Dinophyceae Brandtodinium nutriculum Gymnodinium_catenatum Dinophyceae Amphidinium massartii Gyrodinium_dominans Heterocapsa_arctica Dinophyceae Azadinium spinosum Dinophyceae Crypthecodinium cohnii Heterocapsa_rotundata Heterocapsa_triquetra Karenia_brevis Dinophyceae Brandtodinium nutriculum Dinophyceae Dinophysis acuminata Karlodinium_micrum Kryptoperidinium_foliaceum Dinophyceae Ceratium fusus Lessardia_elongata Dinophyceae Durinskia baltica Lingulodinium_polyedra Dinophyceae Crypthecodinium cohnii Noctiluca_scintillans Oxyrrhis_marina Dinophyceae Gambierdiscus australes Pelagodinium_beii Dinophyceae Dinophysis acuminata Peridinium_aciculiferum

Organisms Dinophyceae Heterocapsa arctica Polarella_glacialis Dinophyceae Durinskia baltica Prorocentrum_lima Prorocentrum_micans Dinophyceae Heterocapsa rotundata Prorocentrum_minimum Dinophyceae Gambierdiscus australes Prorocentrum_reticulatum Pyrocystis_lunula Dinophyceae Gonyaulax spinifera Dinophyceae Heterocapsa triquetra Pyrodinium_bahamense Scrippsiella_acuminata Dinophyceae Gymnodinium catenatum Scrippsiella_hangoei-like Dinophyceae Karenia brevis Scrippsiella_hangoei Scrippsiella_trochoidea Dinophyceae Heterocapsa arctica Symbiodinium_kawagutii Dinophyceae Karlodinium micrum Symbiodinium_sp Dinophyceae Heterocapsa rotundata Thoracosphaera_heimii Togula_jolla Dinophyceae Kryptoperidinium foliaceum Parvilucifera_infectans Dinophyceae Heterocapsa triquetra Parvilucifera_rostrata Perkinsus_chesapeaki Dinophyceae Karenia brevis Dinophyceae Lingulodinium polyedra Perkinsus_marinus GSA120 Dinophyceae Karlodinium micrum GSA25 Dinophyceae Noctiluca scintillans Amoebophrya_sp Dinophyceae Kryptoperidinium foliaceum Dinophyceae Oxyrrhis marina Dinophyceae Lingulodinium polyedra Dinophyceae Noctiluca scintillans Dinophyceae Pelagodinium beii Dinophyceae Oxyrrhis marina Dinophyceae Peridinium aciculiferum At this point, the results contain “false positives” which render interpretation difficult Dinophyceae Pelagodinium beii Dinophyceae Polarella glacialis Dinophyceae Peridinium aciculiferum Dinophyceae Prorocentrum minimum Dinophyceae Polarella glacialis Dinophyceae Prorocentrum minimum Dinophyceae Scrippsiella hangoei-like Dinophyceae Scrippsiella hangoei-like Dinophyceae Scrippsiella hangoei Dinophyceae Scrippsiella hangoei Dinophyceae Scrippsiella trochoidea Dinophyceae Scrippsiella trochoidea Dinophyceae Symbiodinium sp Dinophyceae Symbiodinium sp Dinophyceae Togula jolla Dinophyceae Togula jolla Perkinsea Perkinsus chesapeaki Perkinsea Perkinsus chesapeaki Perkinsea Perkinsus marinus Perkinsea Perkinsus marinus Discussion Syndiniales Amoebophrya 120 Syndiniales Amoebophrya 120 Syndiniales Amoebophrya 25 Syndiniales Amoebophrya 25 Syndiniales Amoebophrya sp Our results confirm and extend the diversity of the OXPHOS pathway in Strengths: Alveolata, including a novel organization in Syndiniales. The loss of the • A strong phylogeny-based filtration method to validate “true positives” complex I is likely a synapomorphy of MYzozoa (apicomplexans, • A quick and adaptable approach for the identification of metabolic pathways dinoflagellates and related taxa). Secondary and independent loss of Weaknesses: the complex III in syndiniales and the chromerid Chomeara velia. • Absence of genes does not necessarily mean absence of pathway due to the incomplete nature of transcriptomes Ciliophora Alveolata • Difficulties in separating sequences from closely-related co-occurring organisms (meta-”omics” data)

Apicomplexa Perspectives: Loss of complex I • Need to complement with genome data in order to resolve false negatives Chromerida • Multivariate analysis aiming to highlight correlations between the composition of the OXPHOS Perkinsea Complex III lost in Chromera pathway and life history traits Dinophyceae

Syndiniales Loss of complex III Heterotroph

Alert False positives! Free living Use of metadata: Example 1/ Symbiodinium sp. harbours many cnidarian genes:

 This data set is contaminated by its host due to the difficulty to extract from the host tissue Parasite

Example 2/ Strombidinopsis acuminata harbours an Alternative Oxidase (AOX): Photosynthesis  This sequence falls within the dinoflagellates clade, on which this ciliate prey.

Use of manual curation: High likelihood of contamination in motif search results, particularly for highly conserved motifs  A phylogenetic approach allows to filtrate for alveolate genes Example of life history trait correlations, under MNDS visualisation

Keeling, P.J., Burki, F., Wilcox, H.M., Allam, B., Allen, E.E., Amaral-Zettler, L.A., Armbrust, E.V., Archibald, J.M., Bharti, A.K., Bell, C.J., Beszteri, B., Bidle, K.D., Cameron, C.T., Campbell, L., Caron, D.A., Cattolico, R.A., Collier, J.L., Coyne, K., Davy, S.K., Deschamps, P., Dyhrman, S.T., Edvardsen, B., Gates, R.D., Gobler, C.J., Greenwood, S.J., Guida, S.M., Jacobi, J.L., Jakobsen, K.S., James, E.R., Jenkins, B., John, U., Johnson, M.D., Juhl, A.R., Kamp, A., Katz, L.A., Kiene, R., Kudryavtsev, A., Leander, B.S., Lin, S., Lovejoy, C., Lynn, D., Marchetti, A., McManus, G., Nedelcu, A.M., Menden-Deuer, S., Miceli, C., Mock, T., Montresor, M., Moran, M.A., Murray, S., Nadathur, G., Nagai, S., Ngam, P.B., Palenik, B., Pawlowski, J., Petroni, G., Piganeau, G., Posewitz, M.C., Rengefors, K., Romano, G., Rumpho, M.E., Rynearson, T., Schilling, K.B., Schroeder, D.C., Simpson, A.G.B., Slamovits, C.H., Smith, D.R., Smith, G.J., Smith, S.R., Sosik, H.M., Stief, P., Theriot, E., Twary, S.N., Umale, P.E., Vaulot, D., Wawrik, B., Wheeler, G.L., Wilson, W.H., Xu, Y., Zingone, A., Worden, A.Z., 2014. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing. PLOS Biology 12, e1001889. https://doi.org/10.1371/journal.pbio.1001889 Nash, E.A., Nisbet, R.E.R., Barbrook, A.C., Howe, C.J., 2008. Dinoflagellates: a mitochondrial genome all at sea. Trends Genet. 24, 328–335. https://doi.org/10.1016/j.tig.2008.04.001 Oborník, M., Lukeš, J., 2015. The Organellar Genomes of Chromera and Vitrella, the Phototrophic Relatives of Apicomplexan Parasites. Annu. Rev. Microbiol. 69, 129–144. https://doi.org/10.1146/annurev-micro-091014-104449 Flegontov, P., Michálek, J., Janouškovec, J., Lai, D.-H., Jirků, M., Hajdušková, E., Tomčala, A., Otto, T.D., Keeling, P.J., Pain, A., Oborník, M., Lukeš, J., 2015. Divergent mitochondrial respiratory chains in phototrophic relatives of apicomplexan parasites. Mol. Biol. Evol. 32, 1115–1131. https://doi.org/10.1093/molbev/msv021