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Supporting Information Speijer et al. 10.1073/pnas.1501725112 SI Text gion corresponding to the conserved domain defined by Ning Previously Published Evidence for Sex in Major Eukaryotic Lineages. et al. (10) was used as the query. Different inclusion threshold Here we briefly present information used for drawing Fig. 2, E-values were tested in the psi-blast searches, and convergence with specifically the quality of evidence for sex in major eukaryotic lineages the same set of significant hits was achieved using more permissive showninthetree(seethecolumnSexknown?). For several lineages, (the default value of 0.005) and more stringent (1e−15) thresholds. including Metazoa, Fungi, Rhodophyta, Chloroplastida, Strameno- To survey organisms not represented by predicted proteomes, piles, and Alveolata, the presence of sex is textbook knowledge and expressed sequence tags (ESTs) and transcript shotgun assem- no special references need to be cited here. For other lineages, in- blies (TSAs) were searched by tblastn (which allowed the iden- cluding Choanoflagellata, Euglenozoa, and Haptophyta, cases of tification of a HAP2 homolog in Trimastix pyriformis,arepre- sexual behavior of their members are discussed in the main text (see sentative of Preaxostyla). To further improve the taxonomic thecaseofSalpingoeca rosetta, Trypanosoma brucei, and prymne- coverage of our analysis, we used HMMER (hmmer.janelia.org/) siophytes). The presence of sex in Amoebozoa and Rhizaria is dis- to search for HAP2 and GEX1 homologs in the protein sequence cussed in length in ref. 1 and can be considered well documented. set deduced from assembled deeply sequenced transcriptomes of For several other groups, only limited evidence for sex (in- several hundred protist species obtained in the MMETSP project cluding rare direct observations or indirect inference from ge- (marinemicroeukaryotes.org/) (11). For HAP2, we used the pro- nomic data) is available. For a discussion on the occurrence of file HMM model available in the Pfam database (pfam.xfam.org/ sexual cycles in Microsporidia (a subgroup of the recently pro- family/PF10699). For GEX1, a HMM model was built anew using posed more inclusive taxon Opisthosporidia) see refs. 2 and 3. a multiple sequence alignment (created using MAFFT; mafft. Evidence for sex in Fornicata is thus far restricted to the some- cbrc.jp/alignment/server/) of the conserved domain (see above) what problematic case of a single species, Giardia intestinalis from phylogenetically diverse GEX1 homologs identified by by (4, 5). Malik et al. (6) discussed evidence for the presence of psi-blast searches in the protein sequence database at NCBI. meiosis and recombination in Trichomonas vaginalis and pro- We used HMMER and the same HMM models to search vided references to older works suggesting the presence of sex- additional protein sequence datasets thus far missing from the ual cycles in some other parabasalids. Putative atypical sex in NCBI protein database, specifically the predicted proteomes some oxymonads, representing Preaxostyla, was documented by from Sphaerophorma arctica (Ichthyosporea), Fonticula alba Cleveland (7) in 1956, but no modern account seems to exist. (Cristidiscoidea), and Thecamonas trahens (Apusomonadida), Circumstantial evidence for sex in Heterolobosea is discussed by downloaded from the Origins of Multicellularity Database Pánek and Cepiˇcka (8). The rare reports of signs of sex in two (Broad Institute; (www.broadinstitute.org/annotation/genome/ cryptomonad species and indirect hints for the presence of sex in cryptomonads in general are mentioned in the main text. multicellularity_project/MultiHome.html), and the predicted For the remaining lineages in the schematic eukaryote phy- proteome generated by the genome sequencing project for the logeny in Fig. 2, no published evidence for signs of sex is known glaucophyte Cyanophora paradoxa (cyanophora.rutgers.edu/ to us. Many of these lineages are species poor (Mantamonadida, cyanophora/). Finally, we also searched predicted proteomes Tsukubamonadida, Palpitomonadida, and Picozoa each currently derived from our draft genome assemblies for the jakobid Anda- comprise only a single formally described species), and their lucia godoyi and the malawimonad Malawimonas californiana ˇ biology has been poorly explored in general. (M. Eliás, V. Klimes, C. Vlcek, B. F. Lang, deposited NCBI GenBank sequences). The identity of candidate homologs iden- Searching for Homologs of HAP2 (GCS1) and GEX1 (KAR5). The tified by HMMER was checked by blastp against the NCBI pro- nonredundant protein sequence database at the National Center tein database. for Biotechnology Information (NCBI; www.ncbi.nlm.nih.gov/) Table S1 provides accession numbers or sequence IDs of was searched by blastp and psi-blast (9) using known HAP2 and HAP2andGEX1homologsidentifiedinselectedrepresenta- GEX1 sequences as queries. In the case of GEX1, only the re- tivesofthemajoreukaryoticlineagesshowninFig.2. 1. Lahr DJ, Parfrey LW, Mitchell EA, Katz LA, Lara E (2011) The chastity of amoebae: Re- 7. Cleveland LR (1956) Brief accounts of the sexual cycles of the flagellates of crypto- evaluating evidence for sex in amoeboid organisms. Proc Biol Sci 278(1715):2081–2090. cercus. J Protozool 3(4):161–180. 2. Karpov SA, et al. (2014) Morphology, phylogeny, and ecology of the aphelids (Ap- 8. Pánek T, Cepi ckaˇ I (2012) Diversity of Heterolobosea. Genetic Diversity in Microor- helidea, Opisthokonta) and proposal for the new superphylum Opisthosporidia. Front ganisms, ed Caliskan M (InTech, Rijeka, Croatia), pp 3–26. Microbiol 5:112. 9. Altschul SF, et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein 3. Cuomo CA, et al. (2012) Microsporidian genome analysis reveals evolutionary strat- database search programs. Nucleic Acids Res 25(17):3389–3402. egies for obligate intracellular growth. Genome Res 22(12):2478–2488. 10. Ning J, et al. (2013) Comparative genomics in Chlamydomonas and Plasmodium 4. Andersson JO (2012) Double peaks reveal rare diplomonad sex. Trends Parasitol 28(2): identifies an ancient nuclear envelope protein family essential for sexual re- 46–52. production in protists, fungi, plants, and vertebrates. Genes Dev 27(10):1198–1215. 5. Birky CW, Jr (2010) Giardia sex? Yes, but how and how much? Trends Parasitol 26(2): 11. Keeling PJ, et al. (2014) The Marine Microbial Eukaryote Transcriptome Sequencing 70–74. Project (MMETSP): Illuminating the functional diversity of eukaryotic life in the 6. Malik SB, Pightling AW, Stefaniak LM, Schurko AM, Logsdon JM, Jr (2008) An ex- oceans through transcriptome sequencing. PLoS Biol 12(6):e1001889. panded inventory of conserved meiotic genes provides evidence for sex in Tricho- monas vaginalis. PLoS ONE 3(8):e2879. Speijer et al. www.pnas.org/cgi/content/short/1501725112 1of3 Speijer et al. Table S1. HAP2 (GCS1) and GEX1 (KAR5) homologs in eukaryotes Eukaryotic lineage Species (strain) HAP2 (GCS1) GEX1 (KAR5) Sequence database Metazoa Homo sapiens ——NCBI www.pnas.org/cgi/content/short/1501725112 Some other vertebrates — + NCBI Nematostella vectensis XP_001628495.1 XP_001637213.1 NCBI Some other metazoans ++NCBI Choanoflagellata Salpingoeca rosetta XP_004989263.1 XP_004993341.1 NCBI Filasterea Capsaspora owczarzaki XP_004343268.1 EFW42133.2 NCBI Ichtyosporea Sphaeroforma arctica ——NCBI Fungi Saccharomyces cerevisiae — NP_013781.1 NCBI Various other fungi — + NCBI Opisthosporidia Several Microsporidia ——NCBI (a number of complete genome sequences) Rozella allomycis ——NCBI Cristidiscoidea Fonticula alba ——Broad Institute Origins of Multicellularity Database www.broadinstitute.org/ annotation/genome/multicellularity_project/MultiHome.html Apusomonadida Thecamonas trahens ——Broad Institute Origins of Multicellularity Database www.broadinstitute.org/ annotation/genome/multicellularity_project/MultiHome.html Breviatea ? ? No genome or comprehensive transcriptome sequence data available Amoebozoa Dictyostelium discoideum XP_643321.1 XP_637084.1 NCBI Various other ++NCBI amoebozoans Collodictyonida ? ? No genome or comprehensive transcriptome sequence data available Rigifilida ? ? No genome or comprehensive transcriptome sequence data available Mantamonadida ? ? No genome or comprehensive transcriptome sequence data available Ancyromonadida ? ? No genome or comprehensive transcriptome sequence data available Malawimonadida Malawimonas KR230050 KR230051 NCBI californiana Fornicata Giardia intestinalis — ESU39074.1 NCBI Parabasalia Trichomonas vaginalis — XP_001583192.1 NCBI Preaxostyla Trimastix pyriformis GAFH01001525.1 ? NCBI (TSA) Heterolobosea Naegleria gruberi XP_002674350.1 XP_002683391.1 NCBI Euglenozoa Trypanosoma brucei XP_823296.1 XP_827062.1 NCBI Various other ++NCBI, MMETSP euglenozoans Tsukubamonadida ? ? No genome or comprehensive transcriptome sequence data available Jakobida Andalucia godoyi KR230048 KR230049 NCBI Rhodophyta Cyanidioschyzon merolae XP_005536505.1 — NCBI Erythrolobus ? CAMPEP_0185858126 MMETSP (transcriptome sequence assembly) madagascarensis, Strain CCMP3276 Chloroplastida Arabidopsis thaliana NP_192909.2 NP_200360.2 NCBI Various other ++NCBI chloroplastids Glaucophyta Cyanophora paradoxa — ConsensusfromContig9288- Cyanophora genome project cyanophora.rutgers.edu/cyanophora/ snap_masked- ConsensusfromContig9288- abinit-gene-0.0-mRNA-1: 2of3 cds:2442/11–143:0:- Speijer et al. Table S1. Cont. Eukaryotic lineage Species (strain) HAP2 (GCS1) GEX1 (KAR5) Sequence database Alveolata Tetrahymena XP_001030543.1 XP_001470809.1 NCBI
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    A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators David M. Needhama,1, Susumu Yoshizawab,1, Toshiaki Hosakac,1, Camille Poiriera,d, Chang Jae Choia,d, Elisabeth Hehenbergera,d, Nicholas A. T. Irwine, Susanne Wilkena,2, Cheuk-Man Yunga,d, Charles Bachya,3, Rika Kuriharaf, Yu Nakajimab, Keiichi Kojimaf, Tomomi Kimura-Someyac, Guy Leonardg, Rex R. Malmstromh, Daniel R. Mendei, Daniel K. Olsoni, Yuki Sudof, Sebastian Sudeka, Thomas A. Richardsg, Edward F. DeLongi, Patrick J. Keelinge, Alyson E. Santoroj, Mikako Shirouzuc, Wataru Iwasakib,k,4, and Alexandra Z. Wordena,d,4 aMonterey Bay Aquarium Research Institute, Moss Landing, CA 95039; bAtmosphere & Ocean Research Institute, University of Tokyo, Chiba 277-8564, Japan; cLaboratory for Protein Functional & Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan; dOcean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research, 24105 Kiel, Germany; eDepartment of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; fGraduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan; gLiving Systems Institute, School of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4SB, United Kingdom; hDepartment of Energy Joint Genome Institute, Walnut Creek, CA 94598; iDaniel K. Inouye Center for Microbial Oceanography, University of Hawaii, Manoa, Honolulu, HI 96822; jDepartment of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106; and kDepartment of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0032, Japan Edited by W. Ford Doolittle, Dalhousie University, Halifax, Canada, and approved August 8, 2019 (received for review May 27, 2019) Giant viruses are remarkable for their large genomes, often rivaling genomes that range up to 2.4 Mb (Fig.
  • New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life

    New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life

    bioRxiv preprint doi: https://doi.org/10.1101/403329; this version posted August 30, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. New phylogenomic analysis of the enigmatic phylum Telonemia further resolves the eukaryote tree of life Jürgen F. H. Strassert1, Mahwash Jamy1, Alexander P. Mylnikov2, Denis V. Tikhonenkov2, Fabien Burki1,* 1Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden 2Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Yaroslavl Region, Russia *Corresponding author: E-mail: [email protected] Keywords: TSAR, Telonemia, phylogenomics, eukaryotes, tree of life, protists bioRxiv preprint doi: https://doi.org/10.1101/403329; this version posted August 30, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract The broad-scale tree of eukaryotes is constantly improving, but the evolutionary origin of several major groups remains unknown. Resolving the phylogenetic position of these ‘orphan’ groups is important, especially those that originated early in evolution, because they represent missing evolutionary links between established groups. Telonemia is one such orphan taxon for which little is known. The group is composed of molecularly diverse biflagellated protists, often prevalent although not abundant in aquatic environments.