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Parallel re-modeling of EF-1α function: divergent EF-1α genes co-occur with EFL genes in diverse distantly… Kamikawa, Ryoma; Brown, Matthew W; Nishimura, Yuki; Sako, Yoshihiko; Heiss, Aaron A; Yubuki, Naoji; Gawryluk, Ryan; Simpson, Alastair G; Roger, Andrew J; Hashimoto, Tetsuo; Inagaki, Yuji Jun 26, 2013

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RESEARCH ARTICLE Open AccessParallel re-modeling of EF-1α function: divergentEF-1α genes co-occur with EFL genes in diversedistantly related eukaryotesRyoma Kamikawa1,2*, Matthew W Brown3, Yuki Nishimura4, Yoshihiko Sako5, Aaron A Heiss6, Naoji Yubuki7,Ryan Gawryluk3, Alastair GB Simpson6, Andrew J Roger3, Tetsuo Hashimoto4,8 and Yuji Inagaki4,8AbstractBackground: Elongation factor-1α (EF-1α) and elongation factor-like (EFL) proteins are functionally homologous toone another, and are core components of the eukaryotic translation machinery. The patchy distribution of the twoelongation factor types across global eukaryotic phylogeny is suggestive of a ‘differential loss’ hypothesis thatassumes that EF-1α and EFL were present in the most recent common ancestor of eukaryotes followed byindependent differential losses of one of the two factors in the descendant lineages. To date, however, just onediatom and one fungus have been found to have both EF-1α and EFL (dual-EF-containing species).Results: In this study, we characterized 35 new EF-1α/EFL sequences from phylogenetically diverse eukaryotes. Inso doing we identified 11 previously unreported dual-EF-containing species from diverse eukaryote groupsincluding the Stramenopiles, Apusomonadida, Goniomonadida, and Fungi. Phylogenetic analyses suggested verticalinheritance of both genes in each of the dual-EF lineages. In the dual-EF-containing species we identified, the EF-1αgenes appeared to be highly divergent in sequence and suppressed at the transcriptional level compared to theco-occurring EFL genes.Conclusions: According to the known EF-1α/EFL distribution, the differential loss process should have occurredindependently in diverse eukaryotic lineages, and more dual-EF-containing species remain unidentified. We predictthat dual-EF-containing species retain the divergent EF-1α homologues only for a sub-set of the original functions.As the dual-EF-containing species are distantly related to each other, we propose that independent re-modelling ofEF-1α function took place in multiple branches in the tree of eukaryotes.Keywords: Diatoms, Differential Gene Loss, EF-1α, EFL, Functional Remodeling, Goniomonas, Pythium, Spizellomyces,ThecamonasBackgroundElongation factor 1α (EF-1α) proteins in eukaryotes andarchaebacteria, and their orthologues in bacteria (elong-ation factor Tu), are GTPases required for the centralprocess of translation [1,2]. The primary sequence of EF-1α is highly conserved across the tree of life, suggestingthat this protein was established in the last universalcommon ancestor, and inherited by extant organisms[3]. However, genomic and transcriptomic data fromdiverse organisms have shown that some eukaryotic line-ages lack EF-1α, and these lineages instead were foundto possess a putative EF-1α-related GTPase [4]. Theseelongation factor-like (EFL) proteins are believed toperform the same function in translation as EF-1α, asthere is no significant functional divergence in theregions that are critical for EF-1α function [4]. The func-tional equivalence of EFL and EF-1α would explain themutually exclusive distributions of EFL and EF-1α genesamongst eukaryotes since EF-1α would be functionally* Correspondence: kamikawa.ryoma.7v@kyoto-u.ac.jp1Graduate School of Global Environmental Studies, Kyoto University, Kyoto606-8501, Japan2Graduate School of Human and Environmental Studies, Kyoto University,Kyoto 606-8501, JapanFull list of author information is available at the end of the article© 2013 Kamikawa et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the CreativeCommons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, andreproduction in any medium, provided the original work is properly cited.Kamikawa et al. BMC Evolutionary Biology 2013, 13:131http://www.biomedcentral.com/1471-2148/13/131redundant in eukaryotes with EFL-mediated translationelongation, and vice versa.Intensive surveys for EFL genes in phylogeneticallydiverse eukaryotes revealed a number of groups thathave both ‘EF-1α-containing’ and ‘EFL-containing’species [5-10]. The co-existence of EF-1α-containingand EFL-containing species in a monophyletic groupcan be explained by the ancestral co-occurrence of EF-1α and EFL, and subsequent losses of either of the twoelongation factors in the descendants. Henceforth, wedesignate the above scenario simply as the ‘differentialloss’ hypothesis [8]. Many aspects of this hypothesisare difficult to test experimentally. Nonetheless, dualexpression of EF-1α and EFL proteins in Trypanosomabrucei cells, which corresponds to the ancestral stateassumed in the differential loss hypothesis, had no ap-parent impact on cell viability [11].It was previously found that examined diatom specieswere either EF-1α-containing or EFL-containing, exceptfor a single species, Thalassiosira pseudonana, whosegenome encodes both EF-1α and EFL genes [7].According to the differential loss hypothesis describedabove, the EF-1α/EFL gene data from diatoms can beexplained as follows: (1) the ancestral diatom genomewas ‘dual-EF-containing,’ (2) the T. pseudonana genomeretains the ancestral state, and (3) the EF-1α (or EFL) genewas lost in the extant EFL-containing (or EF-1α-containing) descendants [7]. A similar situation has beenproposed for Fungi; although the vast majority of fungalspecies are either EF-1α-containing or EFL-containing, asingle species, Basidiobolus ranarum, was found to bedual-EF-containing [12]. Under the differential loss hy-pothesis, T. pseudonana and B. ranarum retain the ances-tral state of diatom and fungal genomes, respectively.The differential loss hypothesis is an increasinglypopular explanation of the current EF-1α/EFL genedistribution in the tree of eukaryotes. Nevertheless,dual-EF-containing species, which are believed to re-flect the ancestral state of their phylogenetic relativescontaining either EF-1α or EFL, have, to date, onlybeen described in diatoms and Fungi. In this study, byexperimental surveys and data mining in publiclyavailable genome and/or transcriptomic data, four in-dependent lineages—Stramenopiles, Apusomonadida,Goniomonadida, and Fungi—were found to contain atleast one dual EF-containing species (11 species werenewly identified in total). All EF-1α genes in the dualEF-containing species examined here appear to be di-vergent, and are transcribed at a much lower level thanthe co-occurring EFL genes, suggesting that EF-1α hasfunctionally diverged in these species. We propose thatthe re-modeling of the original EF-1α functions seem-ingly occurred in several independent branches of the treeof eukaryotes.ResultsWe successfully isolated/identified 20 and 15 previ-ously unidentified EF-1α and EFL sequences, respect-ively, by a PCR survey or mining publicly available andin-house genomic/transcriptomic databases (Table 1).Five diatoms, three oomycetes, one goniomonad, oneapusomonad, and a chytridiomycete fungus were foundto be dual-EF-containing in this study, in addition tothe two previously reported dual-EF-containing species,the diatom T. pseudonana [7] and a fungus of uncertaintaxonomic affiliation, B. ranarum [12]. We updated EF-1αand EFL alignments by adding the new sequences listedin Table 1, and both alignments were analyzed withmaximum-likelihood (ML) and Bayesian phylogeneticmethods (Figures 1 and 2).Dual-EF-containing species in diatomsThe majority of diatom species, in which EF-1α/EFL se-quences have been characterized to date, appear to possessEFL genes, except for the genomes of Phaeodactylumtricornutum [13], which encodes only an EF-1α gene, andT. pseudonana, which encodes both EF-1α and EFLgenes [7]. In this study, we surveyed EF-1α/EFL genesin diatoms further, and identified five more dual-EF-containing species, indicating that dual-EF-containingspecies are quite prevalent amongst diatoms. EF-1α tran-scripts were detected in Detonula confervacea, Achnantheskuwaitensis, Fragilariopsis cylindrus, Thalassionema nitz-schioides, and Asterionella glacialis, all of which were previ-ously considered to be ‘EFL-containing’. In the EF-1α MLtree, all diatom homologues grouped together with anML bootstrap value (MLBP) of 57% (node A in Figure 1),and this group branches with the EF-1α homologues ofthe bolidophyte Bolidomonas pacifica. Although the statis-tical support for the diatom-Bolidomonas affiliation wasmoderate (MLBP = 75%; node B in Figure 1), this particu-lar affiliation found in the EF-1α phylogeny is consistentwith their close (organismal) relationships [14]. Thus weconcluded that there had been vertical descent of EF-1αgenes in the diatom-Bolidomonas clade. As shown inprevious studies e.g., [7], the updated EFL phylogeny alsoincludes a diatom clade, indicating the vertical descent ofEFL genes in this lineage (Figure 2).Quantitative reverse transcriptase PCR (qRT-PCR) as-says revealed that the expression level of the EFL gene ismuch greater than that of the EF-1α gene in each of thedual EF-containing diatom species identified in this study(Table 2), except for F. cylindrus, for which these assayswere not performed. However, EF-1α transcripts are likelymuch less abundant than EFL transcripts in F. cylindrusas well, since only EFL transcripts were detected in theF. cylindrus transcriptomic data publicly available fromthe Joint Genome Institute (http://genome.jgi.doe.gov/).Kamikawa et al. BMC Evolutionary Biology 2013, 13:131 Page 2 of 12http://www.biomedcentral.com/1471-2148/13/131Table 1 EF-1α and EFL homologues isolated/identified in this studyGene Taxon name Classification Survey Accession nos.EF-1α* Detonula confervcace CCMP353 Diatoms PCR AB766031EF-1α* Achnanthes kuwaitensis NIES1349 Diatoms PCR AB775895EF-1α* Fragilariopsis cylindrus Diatoms Genome, public See Additional file 3EF-1α* Thalassionema nitzschioides NIES534 Diatoms PCR AB766032EF-1α* Asterionella glacialis NIES417 Diatoms PCR AB766030EF-1α Bolidomonas pacifica CCMP1866 Bolidophyceae PCR AB766033EF-1α* Pythium intermedium MAFF306022 Oomycetes PCR AB766039EF-1α* Pythium ultimum DAOM BR144 Oomycetes Genome, public See Additional file 3EST, publicEF-1α* Pythium apleroticum MAFF425515 Oomycetes PCR AB766038EF-1α Goniomonas sp. ATCC PRA68 Goniomonadida PCR AB766034EF-1α* Goniomonas sp. ATCC 50180 Goniomonadida PCR AB766037EF-1α Goniomonas truncata NIES 1373 Goniomonadida PCR AB766036EF-1α Goniomonas sp. CCAP 980_1 Goniomonadida PCR AB766035EF-1α* Spizellomyces punctatus DAOM BR117 Chytridiomycota Genome, public See Additional file 3EST, publicEF-1α Subulatomonas sp. strain PCMinv5 Breviata EST, in-house AB766043EF-1α Breviata-like biflagellate strain PCbi66 Breviata EST, in-house AB766042EF-1α Roombia sp. NY0200 Katablepharida PCR AB766040EF-1α Mantamonas plastica Bass1 (CCAP 1946/1) Mantamonadida EST, in-house AB766041EF-1α* Thecamonas trahens ATCC50062 Apusomonadida EST, public See Additional file 3Genome, publicEF-1α microaerophilic cercozoan strain DMV Filosa EST, in-house AB824019EFL¶ Goniomonas sp. ATCC 50180 Goniomonadida PCR AB766045EFL Goniomonas sp. NIES 1374 Goniomonadida PCR AB766044EFL Pythium spinosum MAFF425453 Oomycetes PCR AB766051EFL¶ Pythium intermedium MAFF306022 Oomycetes PCR AB766049EFL Pythium uncinulatum MAFF240295 Oomycetes PCR AB766052EFL Pythium conidiophorum MAFF245320 Oomycetes PCR AB766047EFL Pythium porphyrae MAFF239483 Oomycetes PCR AB766050EFL¶ Pythium apleroticum MAFF425515 Oomycetes PCR AB766046EFL Pythium echinulatum MAFF425510 Oomycetes PCR AB766048EFL Pythium insidiosum CBS119452 Oomycetes EST, public See Additional file 3EFL¶ Spizellomyces punctatus DAOM BR117 Chytridiomycota Genome, public See Additional file 3EST, publicEFL¶ Thecamonas trahens ATCC50062 Apusomonadida Genome, public See Additional file 3EST, publicEFL Capromyxa protea CF08-5 (ATCC PRA-324) Tubulinida EST, in-house AB766053EFL Fabomonas tropica strain NYK3C Ancyromonadida EST, in-house AB766055EFL Ancyromonas sigmides strain B70 (CCAP 1958/3) Ancyromonadida EST, in-house AB766054*co-occurred with EFL, ¶co-occurred with EF-1α. Accession numbers for the sequences obtained by public database search are not described, but their proteinsequences were shown in Additional file 3.Kamikawa et al. BMC Evolutionary Biology 2013, 13:131 Page 3 of 12http://www.biomedcentral.com/1471-2148/13/131Dual-EF-containing species in oomycetesOnly EF-1α homologues were identified in well-studiedmembers of the Oomycetes (e.g., Phytophthora infestans,for which a complete genome is available [15]), but someof us have recently reported EFL genes in Pythiumoligandrum and Pythium ultimum [16]. In this study, weresurveyed EF-1α/EFL sequences in 8 members of thegenus Pythium, and identified Pythium intermedium, Py.ultimum, and Py. apleroticum as dual-EF-containing. TheEF-1α phylogenetic analysis successfully recovered themonophyly of all of oomycetes, suggesting that Py. inter-medium, Py. ultimum, and Py. apleroticum verticallyinherited their EF-1α genes from a common oomycete an-cestor. We suspect that the ML bootstrap support for theoomycete clade in the EF-1α analysis was lowered due tothe divergent nature of the Py. intermedium, Py. ultimum,and Py. apleroticum homologues (MLBP = 22%; node C inFigure 1). The EFL phylogeny also robustly unites alloomycete EFL sequences, including those of the threedual-EF-containing Pythium spp. (Figure 2).The EF-1α gene of Py. ultimum is seemingly much lesstranscribed than its EFL gene. In Illumina transcriptomicdata, the k-mer frequency for EFL contig was significantlyhigher than that for a cytoskeletal protein, α-tubulinJakobidaGlaucophytaGoniomonadidaRhodophytaFilosaDiplomonadidaParabasaliaMantamonadidaPreaxostylaKatablepharidaAmoebozoaMalawimonadidaTelonemaHeteroloboseaCiliophoraEuglenozoaViridiplantaeApicomplexaApusomonadidaCiliophoraAmoebozoaBreviataFonticulaFungiChoanoflagellataIchthyosporeaCapsasporaCorallochytriumAncyromonadidaEndomyxaStramenopilesoomycetesdiatoms0.2 substitutions/siteMicroaerophilic cercozoan DMVMantamonas plasticaReclinomonas americanaPythium apleroticumGiardia intestinalisMastigamoeba balamuthiAcanthamoeba castellaniiRoombia sp.Capsaspora owczarzakiPythium ultimumPlanomonas micraTrimastix pyriformisMonosiga ovataArabidopsis thalianaPythium vexansPorphyra haitanensisPythium intermediumPaulinella chromatophoraDictyostelium discoideumPhaeodactylum tricornutumCandida tropicalisLaminaria digitataThecamonas trahensThalassionema nitzschioidesEuplotes crassusFiloreta japonicaMalawimonas jakobiformisChytriomyces confervaeGoniomonas sp. NIES 1373Trypanosoma bruceiThalassiosira pseudonanaGoniomonas sp. CCAP 980_1Albugo laibachiiGoniomonas pacificaBasidiobolus ramorumGoniomonas sp. ATCC50108Nicotiana tabacumHeterosigma akashiwoAphanomyces cochlioidesGaldieria sulphurariaTrichomonas vaginalisPlasmodium knowlesiApusomonas proboscideaPhytophthora parasiticaBiflagellate BreviateAcetabularia acetabulumStylonychia lemnaeBolidomonas pacificaPhytophthora infestansIchthyophonus irregularisCryptosporidium parvumGoniomonas sp. ATCC PRA68Pyropia yezoensisApodachlya brachynemaSubulatomonas sp. Spizellomyces punctatusStreblomastix strixSalpingoeca amphoridiumCyanidioschyzon merolaePlectospira myriandraAcrasis roseaCorallochytrium limacisporumAstonella glacialisParacercomonas marinaTelonema sp.Jakoba liberaHistomonas meleagridisDetonula confervaceaEchinostelium arboreumMallomonas racilisEntamoeba histolyticaNaegleria gruberiTetrahymena pyriformisAchnanthes kuwaitensisCyanophora paradoxaHexamita inflataFonticula albaEuglena gracilisFragilariopsis cylindrus83999285100100879910070100789789100989110058/0.9722/0.9457/0.99A75/1.00BC37/0.99E41/0.94FDFigure 1 EF-1α phylogeny. The unrooted maximum-likelihood tree was inferred from 79 EF-1α sequences with 400 unambiguously alignedamino acid positions. Bootstrap values less than 70% are not shown except at nodes that are relevant to EF-1α gene evolution in Fungi, diatoms,oomycetes, and Apusomonadida (nodes A to F). The nodes supported by Bayesian posterior probabilities ≥ 0.95 are highlighted by thick lines.Branches leading to the taxa containing both EFL and EF-1α genes are highlighted in red. The lineages comprising both EF-1α-containing andEFL-containing species are highlighted in magenta. The new sequences isolated/identified in this study are indicated by stars.Kamikawa et al. BMC Evolutionary Biology 2013, 13:131 Page 4 of 12http://www.biomedcentral.com/1471-2148/13/131(Table 3). In sharp contrast, no contig for EF-1α wasobtained in the transcriptomic data (Table 3), even thoughour RT-PCR successfully detected EF-1α transcripts in Py.ultimum (data not shown).Dual-EF-containing species in goniomonadsPrior to this study, EF-1α/EFL data were available foronly two goniomonad species: EF-1α transcripts weredetected in Goniomonas pacifica [17], while an EFL genewas isolated from Goniomonas amphinema [18]. In thisstudy, we experimentally surveyed EF-1α/EFL sequencesin five Goniomonas strains (ATCC 50108, ATCC PRA68,NIES-1373, NIES-1374, and CCAP 980_1). Of these,strain ATCC 50108 appeared to be dual-EF-containing(Table 1). A qRT-PCR assay revealed that EFL tran-scripts were more abundant than EF-1α transcripts instrain ATCC 50108 (Table 2).The EF-1α sequences amplified from strains ATCC50108, ATCC PRA68, NIES-1373, and CCAP 980_1,together with that of G. pacifica, formed a clade in theEF-1α phylogeny (MLBP = 58%; node D in Figure 1).The new EFL homologues from strains NIES 1374 andATCC 50108 showed a close relationship to the G.amphinema homologue (Figure 2). Both EF-1α and EFLphylogenies suggest vertical inheritance of the genesencoding the two elongation factors in this lineage.0.3 substitutions/siteRhodophytaFilosaFilosa (Chlorarachniophyta)EuglenozoaEuglenozoaIchtyosporeaViridiplantaeCryptomonadidaViridiplantaeHaptophytaCentrohelidaDinoflagellataFilosa (Chlorarachniophyta,periplastid-targeting)AmoebozoaEuglenozoaKatablepharidaRadiolariaForaminiferaRadiolariaEndomyxaPalpitomonasAncyromonadidaViridiplantaePlanomonadidaViridiplantaeViridiplantaeChoanozoaGoniomonadidaApusomonadidaFungioomycetesdiatoms StramenopilesAncyromonas sigmoides'Fabomonas tropica'Capromyxa proteaRaphidiophrys contractilisPavlova lutheriPalpitomonas bilixPythium ultimumNephroselmis olivaceaPythium insidiosumSalpingoeca sp. ATCC 50818Helicosporidium sp.Chlorococcum sp.Cryptomonas ovataSpizellomyces punctatusThecamonas trahensDiplonema ambulatorEmiliania huxleyiPythium intermediumMicromonas pusilaHeterocapsa triquetraGoniomonas sp. NIES 1374Sphaeroforma arcticaRozella allomycesScenedesmus obliquusThalassiosira pseudonanaThaumatomastix sp.Pythium echinulatumDetonula confervaceaMonosiga brevicollisOlpidium brassicaePrototheca wickerhamiiConidiobolus coronatusThalassionema nitzschioidesChlamydomonas reinhardtiiLotharella vacuolataOstreococcus tauliKappaphycus alvareziiPythium apleroticumAchnanthes kuwaitensisAstrolonche sp.Pythium spinosumMataza hastiferaRhynchopus euleeidesAcrochaete repensMesostigma virideFragiopsis cylindrusLeucocryptos japonicaGoniomonas amphinemaTetraselmis tetrathelePhyllostaurus sp.Pythium porphyraeAsterionella glacialisEucheuma denticulatumPlanoglabratella opecularisChondrus crispusLotharella vacuolataGoniomonas sp. ATCC50108Oxyrrhis marinaEucyrtidium acuminatumReticulomyxa filosaGracilaria changiiGromia sphaericaBlastocladiella emersoniiAllomyces macrogynusNeobodo saliensPseudoperkinsus tapetisPythium uncinulatumBigelowiella natansPerkinsus marinusCreolimax fragrantissimaTrypanoplasma borreliPetalomonas cantuscygniCollozoum amoeboidesGuillardia thetaPythium conidiophorumCoelomomyces stegomyiaBasidiobolus ranarumPythium oligandrumPorphyridium cruentumBigelowiella natans1008170100818010074947072719010094961009710093781007998941001009098739985100Figure 2 EFL phylogeny. The unrooted maximum-likelihood tree was inferred from 80 EFL sequences with 407 amino acid positions. Onlybootstrap values ≥ 70% are shown. The nodes supported by Bayesian posterior probabilities ≥ 0.95 are highlighted by thick lines. All other detailsof the figure are as described in the legend to Figure 1.Kamikawa et al. BMC Evolutionary Biology 2013, 13:131 Page 5 of 12http://www.biomedcentral.com/1471-2148/13/131Other dual-EF-containing species in Apusomonadida andFungiWe detected both EFL and EF-1α sequences in bothwhole-genome shotgun and transcriptomic data fromthe apusomonad Thecamonas trahens (http://www.broadinstitute.org/). The EF-1α sequences of twoapusomonads, T. trahens and Apusomonas proboscidea,grouped together in the ML tree topology (MLBP =37%; node E in Figure 1), consistent with their organis-mal relationship. The large discrepancy in branch lengthbetween the two apusomonad sequences is likely re-sponsible for the low ML bootstrap support. In the EFLphylogeny, the T. trahens sequence branched at the baseof the diatom-oomycete clade (Figure 2). Unfortunately,the current analysis does not allow us to determine ifEFL genes were the result of descent through vertical in-heritance in apusomonads, because: (i) only one EFL se-quence is known for apusomonads, and (ii) T. trahens andopisthokonts were distant from each other in the EFLphylogeny, in contrast to the close organismal relationshipbetween apusomonads and opisthokonts e.g., [19].Our EF-1α/EFL gene survey also identified the genomeof the chytridiomycote fungus Spizellomyces punctatusas encoding both kinds of elongation factors. The EF-1αsequences of S. punctatus and B. ranarum bore the well-known Opisthokonta-specific insertion (Additional file 1),and formed a clade with other fungal sequences in thephylogenetic analyses (MLBP = 41%; node F in Figure 1),suggesting that the EF-1α genes of S. punctatus and B.ranarum and those of other fungal species share an exclu-sive ancestry. Again, the grouping of the two long-branched sequences of S. punctatus and B. ranarum withother fungal sequences did not receive high ML bootstrapsupport. We are currently unsure whether the extant EFLgenes in fungi are the descendents of a single gene in theancestral fungal species: The monophyly of fungi was notrecovered in the ML tree inferred from the EFL alignment(Figure 2), but the approximately unbiased test [20] failedto reject the alternative hypothesis, in which all fungalEFL sequences were enforced to be monophyletic, at the5% level (data not shown).In both T. trahens and S. punctatus there is a large dif-ference in transcriptional levels between EF-1α and EFLgenes. In the transcriptomic data of the two species, thek-mer frequency for EFL was much greater than that forEF-1α (Table 3), as seen in other dual-EF-containingspecies (see above).New EF-1α/EFL data from other eukaryotesOur EF-1α/EFL survey successfully revealed that thetaxa Katablepharida, Amoebozoa (or a subgroup ofAmoebozoa), and Ancyromonadida contain both EFL-containing and EF-1α-containing species. For amoebozoansand ancyromonads, only EF-1α-containing species wereknown prior to this study (see Figure 1), however, wedetected EFL sequences in the amoebozoan Copromyxaprotea and the ancyromonad Fabomonas tropica (Table 1).Likewise, the first-surveyed katablepharid Leucocryptosmarina was EFL-containing [16], but a RT-PCR survey of asecondly-surveyed katablepharid, Roombia sp., identifiedEF-1α transcripts (Table 1).DiscussionSeveral eukaryote lineages include multiple dual-EF-containing speciesAncestral co-occurrence of EF-1α and EFL followed bydifferential loss of one of the two elongation factors mostlikely shaped the current EF-1α/EFL distribution withineukaryotes. In this scenario, the extant dual-EF-containingspecies retain the ancestral state and thus are analogousto the inferred intermediates that led to descendant lin-eages that contain either EF-1α or EFL (Figure 3). In thisstudy, we found 11 new dual-EF-containing species infour distantly related lineages: (1) Goniomonadida, (2)Apusomonadida, (3) Stramenopiles (including diatomsand oomycetes), and (4) Fungi (including S. punctatusand B. ranarum). In light of the differential loss processproposed for EF-1α/EFL evolution, we speculate thatmore dual-EF-containing species remain undetected inother lineages that contain both EF-1α-containing andEFL-containing species, including: Viridiplantae [6],Euglenozoa [8], Choanoflagellata [5], Endomyxa [10],Filosa [9], Rhodophyta [18], Katablepharida (this study),Amoebozoa (this study), and Ancyromonadida (this study)(highlighted in pink in Figures 1 and 2). Considering therevised distribution of EF-1α/EFL genes, we cannot ex-clude the possibility that the last eukaryotic commonancestor was dual-EF-containing.Table 3 k-mer frequencies for EF-1α, EFL, and α-tubulin intranscriptomic datak-mer frequencyOrganisms Data sources EFL EF-1α α-tubulinThecamonas trahens SRR343042 1540 21 530Spizellomyces punctatus SRR343043 4797 7 805Pythium ultimum SRR059026 556 Not detected 31Table 2 Relative copy numbers of EF-1α and EFLtranscripts by qRT PCROrganism EFL (sd) EF-1α (sd)Goniomonas sp. ATCC 50108 1.50 (0.28) 4.10 × 10-4 (7.63 × 10-5)Asterionella glacialis 38.77 (6.29) 0.09 (0.04)Achnanthes kuwaitensis 23.22 (1.52) 0.01 (0.002)Detonula confervacea 0.08 (0.03) 4.88 × 10-4 (0.11 × 10-4)Thalassionema nitzschiodes 0.33 (0.10) 6.36 × 10-4 (9.55 × 10-4)Notes—normalized by the copy number of α-tubulin transcripts.Kamikawa et al. BMC Evolutionary Biology 2013, 13:131 Page 6 of 12http://www.biomedcentral.com/1471-2148/13/131Finally, it will be of interest to continue surveying dual-EF-containing species, especially within Stramenopilesand Fungi. Kamikawa et al. [16] postulated that thedual-EF status can be traced back to the ancestralstramenopile species, based on the monophyly ofstramenopiles in EF-1α phylogenies (Figure 1), and ofdiatoms and oomycetes in EFL phylogenies (Figure 2:Note that no EFL homologue has been identified to datein any stramenopile subgroups except diatoms andoomycetes). Thus, we predict that dual-EF-containing spe-cies should be found in so-far unsampled stramenopiles.Similarly, S. punctatus and B. ranarum are unlikely to bethe sole fungal species with a dual-EF status, given thatthe most recent common ancestral fungus was proposedto be dual-EF-containing [12].Parallel re-modeling of EF-1α function in eukaryoticevolutionIn the dual EF-containing diatom T. pseudonana, someof us [7] proposed that the EF-1α homolog performsonly a subset of its original functions, and does not par-ticipate in protein synthesis as an elongation factor, forthe following reasons. Firstly, in an EF-1α phylogeny, theT. pseudonana homologue was much more divergentthan that of a closely related EF-1α-containing species,P. tricornutum, suggesting that the former is under fewerfunctional constraints than the latter. Secondly, EF-1αtranscripts were much less abundant in T. pseudonanathan the transcripts of EFL or of an α-tubulin gene. Asobserved in T. pseudonana, the five dual EF-containingdiatoms identified in this study (i.e. A. kuwaitensis, A.glacialis, D. confervacea, F. cylindrus, and T. nitzschioides)appeared to possess divergent EF-1α genes (Figure 1). Ineach of the five diatoms, the transcriptional level of theEF-1α gene was heavily suppressed compared to that ofthe co-occurring EFL gene (Table 2). Thus, the five dual-EF-containing diatoms most likely use EFL as the principalelongation factor, while a sub-set of the original EF-1αfunctions is assigned to the divergent EF-1α. These dual-EF-containing diatoms have most likely re-modeled theirEF-1α functions, such that they carry out only the auxil-iary roles that the proteins originally performed, such asinteractions with cytoskeletal proteins and ubiquitin-dependent protein degradation [1,21,22].It is likely that similar re-modeling of EF-1α functionhas also occurred in other dual-EF-containing lineages.In the non-diatom dual-EF-containing species, the EF-1α sequences were also divergent (Figure 1), and weretranscribed at a low level compared to the co-occurringEFL genes (Tables 2 and 3). These results strongly sug-gest that dual-EF-containing species in general utilizeEF-1α for subsets of the original functions, while EFLparticipates in translation as a core factor. Significantly,the re-modeling of EF-1α function probably took placeseparately in Stramenopiles (including diatoms andoomycetes), Goniomonadida, Apusomonadida, and Fungi,as these lineages are distantly related to one another inthe organismal phylogeny. Moreover, diatoms (photo-synthetic heterokont algae) and oomycetes (non-photo-synthetic stramenopiles) may have also re-modeled theirEF-1α functions in parallel as they are relatively dis-tantly related within stramenopiles. We also suspectHypothetical ancestorEFLEF-1αDual-EF-containingintermediate stateEFLEF-1αHypotheticalHypotheticalEFLEF-1αintermediatestateEFL-containingEFLEF-1α-containingEF-1αDual-EF-containingEFLEF-1αDual-EF-containing,yet-to-be foundEFLEF-1αFigure 3 Scheme for EF-1α/EFL evolution in eukaryotes. A differential loss process from the hypothetical dual-EF-containing ancestor (center;open) produced four descendent types (shaded): (i) EFL-containing descendent (lower left), (ii) EF-1α-containing descendent (upper right),(iii) dual-EF-containing descendent with a transcriptionally suppressed EF-1α (lower right), and (iv) dual-EF-containing descendent with atranscriptionally suppressed EFL gene (upper left). The EF-1α gene is blackened in the descendent shown in lower right, as this gene isfunctionally reduced and transcriptionally suppressed, which is likely analogous to the hypothetical intermediate that leads to the EFL-containingtype that lacks EF-1α. Likewise, the other type of dual-EF-containing descendent (upper left), if exist, bears the re-modeled EFL gene (blackened),and is analogous to the hypothetical intermediate that led to the EF-1α-containing descendants that lack EFL.Kamikawa et al. BMC Evolutionary Biology 2013, 13:131 Page 7 of 12http://www.biomedcentral.com/1471-2148/13/131that parallel re-modeling of EF-1α function occurredwithin Fungi, as S. punctatus and B. ranarum are notparticularly close relatives [12].We are currently unsure about the precise functionsof the divergent EF-1α in the dual-EF-containing species.Under the parallel re-modeling scenario proposed above,the suite of retained EF-1α functions could vary betweenany of two dual-EF-containing lineages. However, theoverall substitution patterns in divergent EF-1α se-quences in distantly related dual-EF-containing speciesare found to be similar to each other (Additional file 2).This observation hints at parallel loss of the same as-pects of EF-1α function and retention of a subset of ori-ginal functions in multiple dual-EF-containing lineagesscattered over the tree of eukaryotes. These speculationscould be tested more directly by biochemical studies ofEF-1α function in selected representatives of theselineages.ConclusionsAccording to the differential loss hypothesis for EF-1α/EFL evolution, a dual-EF-containing ancestor likely gaverise to two types of descendants—one containing onlyEFL and the other containing only EF-1α. Nevertheless,EF-1α/EFL surveys, including this study, have identifiedan additional type of descendent retaining the ancestralarrangement (i.e. dual-EF-containing) in multiple branchesof the tree of eukaryotes. If EF-1α/EFL sequences are sur-veyed in a broader spectrum of eukaryotes, it is highlylikely that the number and diversity of known dual-EF-containing species will grow further.Curiously, all dual-EF-containing species identified sofar appear to retain divergent, low-expressed EF-1αgenes (see above), which are analogous to the hypothet-ical intermediate leading to EFL-containing descendants(Figure 3). We suspect that the multiple functions of thecanonical EF-1α may have prevented the dual-EF-containing cells from losing this protein immediatelyafter EFL took over from EF-1α as the core translationfactor. The presence of dual-EF-containing species indi-cates that the adoption of EFL as the dominant core factorin translation does not necessarily lead to the eliminationof EF-1α from the entire cellular system.Curiously, we found little evidence for living analoguesof the hypothetical intermediate that led to EF-1α-containing descendants, which would possess a diver-gent, low-transcribed EFL gene. The presence or absenceof dual-EF-containing species, in which a divergent EFLgene is transcribed at lower levels than the co-occurringEF-1α gene, would be crucial to understanding the evo-lutionary processes that shaped the current EF-1α/EFLgene distribution across the tree of eukaryotes. We needto re-examine EFL sequences in the species currentlyrecognized as ‘EF-1α-containing’ since low-expressedEFL genes might be overlooked in these taxa, especially ifgenomic or high-coverage transcriptomic data is lacking.MethodsStrainsAchnanthes kuwaitensis (NIES-1349), Asterionella glacialis(NIES-417), Thalassionema nitzschioides (NIES-534),Goniomonas amphinema (NIES1371), Goniomonas trun-cata (NIES-1373), and Goniomonas sp. (NIES-1374) werepurchased from the Microbial Culture Collection at theNational Institute for Environmental Study in Japan.Detonula confervacea (CCMP353) and Bolidomonas pacif-ica (CCMP1866) were purchased from the Provasoli-Guillard National Center for Marine Algae and Microbiota.Goniomonas sp. (CCAP 980/1) was purchased from theCulture Collection of Algae and Protozoa. Goniomonas sp.(ATCC PRA-68) and Goniomonas sp. (ATCC 50108) werepurchased from American Type Culture Collection.Pythium apleroticum (MAFF425515), Py. conidiophorum(MAFF245320), Py. echinulatum (MAFF425510), Py. inter-medium (MAFF306022), Py. porphyrae (MAFF239483), Py.spinosum (MAFF425453), Py. ultimum (MAFF425505),and Py. uncinulatum (MAFF240295) were purchasedfrom the GeneBank (Microorganism Section) at theNational Institute of Agrobiological Sciences in Japan.Roombia sp. strain NY0200 was cultivated with bacterialprey in URO-YT medium (Moriya et al. 2000). RNA wasextracted from the harvested cells by using an RNeasyPlant Mini kit (QIAGEN), and then subjected to oligo(dT)-primed reverse transcriptase (RT) reactions by usingthe 3’ rapid amplification of cDNA ends kit (Invitrogen).Each of the two procedures described above wasconducted following the corresponding manufacturers’instructions.PCR-based survey of EF-1α and EFL transcriptsWe amplified EF-1α and/or EFL sequences of Roombiasp., diatoms, Bolidomonas pacifica, and goniomonads (seethe previous section) by a two-step procedure: For the firstRT-PCR, the combination of one of three forward primers(5′-GGCCACGTGGAYTCNGGNAARTCNAC, 5′-GGCCACGTGGAYAGYGGNAARTCNAC, or 5′-GGCCACGTGGAYGCNGGNAARTCNAC) and a reverse primer(5′-ACGAAATCTCTCTTRTGNCCNGGNGCRTC) wereused. These primer sets can amplify the 5′ portions of thetranscripts (~250 bp in length) for EF-1α and EFL, as wellas other EF-1α-related proteins in a single reaction. Foreach reaction, amplicons were cloned into pGEMTEasyvector (Promega), and sequenced ≥12 clones to surveyEF-1α/EFL sequences. Secondly, the 3′ portions ofRoombia, diatom, and goniomonad EF-1α/EFL tran-scripts were amplified by the 3′ rapid amplification ofcDNA ends (RACE) kit (Invitrogen) with exact-matchprimers based on the nucleotide sequences of the initialKamikawa et al. BMC Evolutionary Biology 2013, 13:131 Page 8 of 12http://www.biomedcentral.com/1471-2148/13/131amplicons. We amplified the 3′ portion of the EF-1αtranscript of B. pacifica by the combination of an exact-match primer (see above) and a degenerate primer,which can anneal to the 3′ portion of EF-1α open read-ing frame (5′-CAGAATTGCGACAGCNACNGTYTG).Amplicons were cloned and sequenced completely asdescribed above.From all of the seven species belonging to the oomycetegenus Pythium examined in this study, we obtained theamplicons covering most of the EFL-coding region by RT-PCR with a set of primers 5′-AGCCGAGAAGGGTGGTTTCG and 5′-ACAGATAATCTGACCAACACC. Thedetails of cloning and sequencing of the EFL ampliconswere same as described above.We then screened the 5′ portion of EF-1α sequencesin the seven Pythium spp. in two separate trials. Firstly,we applied the combinations of primers for EF-1α se-quences in phylogenetically diverse eukaryotes; twoforward primers (5′-GTGGACGCCGGNAARTCNACNACNAC and 5′-GTGGACGCCGGNAARAGYACNACNAC) and two reverse primers (5′-TCGGCCTGGGANGTNCCNGTNATCAT and 5′-TCGGCCTGGGTNGTNCCNGTNATCAT). The RT-PCR with these ‘universal’primers succeeded in amplifying the partial EF-1α tran-scripts in Py. apleroticum. For the second trial, we pre-pared new degenerate primers, which were more specificto oomycete EF-1α sequences than those used in the firsttrial: PytEF1aFA, PytEF1aFB, and PytEF1aR (5′-TCGGCAAGACGTCGTWCAAGTAC, 5′-GGTCACCGCGATTTCATCAAGAAC, and 5′-GACNGGNACCGTGCCAATACC, respectively). EF-1α transcripts in the Pythiumspp. were surveyed by the hemi-nested RT-PCR, in whichthe combination of PytEF1aFA and PytEF1aR, and that ofPytEF1aFB and PytEF1aR were used for the first and sec-ond reactions, respectively. The partial EF-1α transcript inPy. intermedium was amplified in the second trial withthe ‘oomycete-oriented’ primers. We could not detectany EF-1α transcripts in the Pythium species examined inthis study, other than Py. apleroticum and Py. intermedium.The 3′ portions of Py. apleroticum and Py. intermediumEF-1α transcripts were amplified by the 3′ RACE,followed by cloning and sequencing. The details of the 3′RACE, and cloning and sequencing of the amplicons weresame as described above.Illumina transcriptomic analysesWe obtained transcriptomic data from the followingorganisms; two ancyromonads, Ancyromonas sigmidesB70 (CCAP 1958/3) and Fabomonas tropica NYK3C,the breviates, Breviata-like biflagellate PCbi66 andSubulatomonas sp. PCMinv5, the mantamonad Manta-monas plastica Bass1 (CCAP 1946/1), the tubulinidamoebozoan Capromyxa protea CF08-5 (ATCC PRA-324), and the microaerophilic cercozoan strain DMV.A. sigmoides and ‘F. tropica’ were cultivated with bacter-ial prey (Enterobacter aerogenes) in a mixture of 50%ATCC 802 medium and 50% filtered sterile seawater, andin a mixture of 50% seawater and 50% ddH2O, respect-ively. Strain PCbi66 was grown in ATCC 1525 mediumwith bacterial prey (Klebsiella pneumoniae ATCC 23432).Subulatomonas sp. was cultivated with bacterial preyin ATCC 1773 medium made with 50% seawater and50% ddH2O. M. plastica was grown with bacterial prey(K. pneumoniae ATCC 23432) in a mixture of 50% sea-water and 50% ddH2O. C. protea was grown on weakmalt yeast agar plates (0.02 g Yeast extract, 0.02 g Maltextract, 0.75 g K2HPO4, 1 L ddH2O, 15 g Agar) withstreaks of Escherichia coli as food. Stain DMV was grownin ATCC 802 medium, with bacterial prey (K. pneumoniaeATCC 23432) killed at 65°C for 1 hour.Total RNA was isolated using Trizol (Tri-reagent)following the protocol supplied by the manufacturer(Sigma). Construction of cDNA libraries and illuminaRNAseq was performed by Macrogen (South Korea) forstrain PCbi66 and A. sigmoides, by GeneWiz (USA) for‘F. tropica’, Subulatomonas sp., and M. plastica, and bythe Institut de Recherche en Immunologie et Cancérologie(IRIC) of Universite de Montreal (Canada) for C. proteaand strain DMV.Raw sequence read data were filtered based on qual-ity scores with the fastq_quality_filter program ofFASTXTOOLS (http://hannonlab.cshl.edu/fastx_toolkit/),using a cutoff filter (a minimum 70% of bases must havequality of 20 or greater). Filtered sequences were thenassembled into clusters using the Inchworm assembler ofthe TRINITY r2001-5-13 package [23]. EF-1α/EFL se-quences were identified using basic local alignment searchtool (tblastn).Database search of EFL and EF-1α genesBy using T. pseudonana EFL and EF-1α amino acid se-quences as the queries, we performed tblastn searcheswith E-value cutoff < 10-100. Putative EF-1α/EFL se-quences identified by the initial tblastn search were thenconfirmed by blastp searches with E-value cutoff < 10-100.The reciprocal similarity searches identified both EFL andEF-1α genes in the genomes of T. trahens and S. punctatusfrom the whole genome shotgun database in NCBI(http://www.ncbi.nlm.nih.gov/). Likewise, both EF-1αand EFL genes were detected in the genome databasesof the diatom F. cylindrus (http://genome.jgi-psf.org/Fracy1/Fracy1.home.html) and the oomycete Py. ultimum(http://pythium.plantbiology.msu.edu/). For the IlluminaRNAseq data of T. trahens, S. punctatus, and Py. ultimumwe collected raw sequence data from the NCBI’s ShortReads Archive (SRA), accessions SRR343042, SRR343043,and SRR059026, respectively. These raw data were as-sembled into clusters using the Inchworm assembler ofKamikawa et al. BMC Evolutionary Biology 2013, 13:131 Page 9 of 12http://www.biomedcentral.com/1471-2148/13/131the TRINITY r2001-5-13 package, as above. We thenidentified the contigs pertaining to EFL, EF-1α, and α-tubulin through tblastn, and compared the k-mer fre-quency of each respective contig to compare the rela-tive transcriptional level between the co-occurring EFLand EF-1α genes (Table 3). We provide the amino acidsequences mentioned here as Additional file 3.Phylogenetic analysisEFL and EF-1α amino acid sequences were sampledfrom the broad spectrum of eukaryotes. Datasets of thetwo elongation factor families were separately aligned,and then ambiguously aligned positions were excludedbefore phylogenetic analyses. The final EFL and EF-1αdatasets contained 80 sequences with 407 amino acid po-sitions and 79 sequences with 400 amino acid positions,respectively. The two datasets were analyzed using bothML and Bayesian phylogenetic methods. ML analyseswere performed using RAxML 7.2.1 [24] under the LGmodel [25] incorporating empirical amino acid frequenciesand among-site rate variation approximated by a discretegamma distribution with four categories (LG + Γ + Fmodel). The ML tree was estimated by heuristic searchesbased on 300 distinct parsimony starting trees. In RAxMLbootstrap analyses (1000 replicates), the heuristic treesearch was performed from a single parsimony tree perreplicate.The EFL and EF-1α datasets were also subjected toBayesian analysis using PhyloBayes v.3.3 [26] with theLG + Γ + F model. For the EF-1α analysis, two parallelMarkov Chain Monte Carlo (MCMC) runs were run for63,799 and 63,885 generations, sampling log-likelihoodsand every 10 trees (maxdiff = 0.16254; ‘burn-in’ was setas 100 based on the log-likelihood plots). The EFLdataset was analyzed as described above, except twoMCMC runs were run for 12,520 and 12,511 generations(maxdiff = 0.113078).Quantitative reverse transcriptase (qRT) PCRTo normalize the copy numbers of EFL and EF-1αtranscripts, we amplified the α-tubulin sequence ofGoniomonas sp. ATCC 50108 by RT-PCR with the follow-ing degenerate primers: 5′-RGTNGGNAAYGCNTGYTGGGA and 5′-CCATNCCYTCNCCNACRTACCA. Toamplify the α-tubulin sequences of diatoms A. kuwaitensis,A. glacialis, and T. nitzschioides, we used a second set ofdegenerate primers: 5′-GARCTNTAYTGYCTNGARCAYGG and 5′-CGCGCCATNCCYTCNCCNACRTACCA.The α-tubulin sequence of the diatom D. confervacea wasamplified by using the following primers: 5′-CGCGCCATNCCYTCNCCNACRTACCA and 5′-CGTAGANAGCCTCGTTGTC. The cloning and sequencing of the α-tubulin amplicons were carried out as described above.Accession nos. for the sequences are AB766056 –AB766059.In Table 4 we list the exact-match primers used forqRT-PCR assays designed based on the EF-1α, EFL,and α-tubulin sequences in the four diatoms andGoniomonas sp. ATCC 50108. The plasmids carryingthe EFL, EF-1α, and α-tubulin amplicons (see above)were used as the standards for qRT-PCR. A mixture forqRT-PCR contained SYBR Green I (TaKaRa), PremixExTaq (TaKaRa), a set of exact-match primers (finalconcentration of 0.3 μM each), and template solution:Table 4 Primers and annealing temperatures for qRT PCROrganisms Genes (°C)* PrimersAchnentheskuwaitensisEFL (57) 5'-GTCACTTGATCTTCAAGCAG5'-TGTCGGTGAAGAACTCCTTGEF-1α (60) 5'-GAGGAGTTGACGAGAACACG5'-TTGGAGACTCGAACTTCCAGα-tubulin (60) 5'-TGGAGCCCTACAACTCCATC5'-CACCAGGTTGGTCTGGAACTCAsterionellaglacialisEFL (58) 5'-TATCTCTGAGCGTGAGATGAAG5'-CTTGGTGTTGCACTGAATGGEF-1α (54) 5'-TGAAGAACGAACTATGGAAG5'-CCAAAGTGAAATATCGATTGα-tubulin (58) 5'-ACATGGCATGCTGCCTCATG5'-ATCCTCGAAAGAGCTTCTGCDetonulaconfervaceaEFL (58) 5'-AGGAATCTCTGCTCGTGAG5'-GAACTCCTTGGTGTTACACTGEF-1α (58) 5'-GAAACCATCGACAAGTACG5'-GAAACTTCCACAACGTGATATCGα-tubulin (58) 5'-CAAATGCGCAGCGACAAGAC5'-TTCCAGAACGGACCTCGTCThalassionemanitzschioidesEFL (56) 5'-AATCTCTGCTCGAGAGATGG5'-TGTAGTGGTACTTGCCAGTGEF-1α (56) 5'-CGTAGCCGAAAGCATAATAG5'-CCAGACACTGATATCAATAGα-tubulin (56) 5'-TTGTATGATGTCTGCCGTGG5'-AAGCCTTCTCACGCGAAATAGoniomonas sp. EFL (60) 5’-CATCAAGGGTCTCAAGAAGGACAAC5’-CAGTTGATGGCGGTCATCTTCATGEF-1α (60) 5’-GTTCTCTGCTGGATACACTCCAGTG5’-ACGCTATTCATGGAAGGCCTCAACα-tubulin (55) 5’-CATGTACCGTGGTGATGTCG5’-CTGGACCTTGGCAAGATCAC*Numbers in parentheses show primer set-specific annealing temperaturesused in qRT PCR.Kamikawa et al. BMC Evolutionary Biology 2013, 13:131 Page 10 of 12http://www.biomedcentral.com/1471-2148/13/131either cDNA, the corresponding RNA sample (the nega-tive control), or five differently diluted plasmid solutionsincluding 10 to 107 copies of the target gene fragments(the standards). The qRT-PCR thermal cycling conditionswere 95°C for 30 sec followed by 50 cycles comprised of95°C for 5 sec, a gene-specific temperature for 10 sec(Table 4), and 72°C for 10 sec. We confirmed that a singletarget product was amplified by real-time PCR, based onmelting curves (data not shown). In each assay, the targetamplification from the RNA sample was out of the quanti-fiable range. Smart Cycler II (Cepheid) and ThermalCycler Dice (TaKaRa) were used for the assays on the fourdiatoms and that of Goniomonas sp., respectively.Accession numbersAB766030-AB766059, AB775895, and AB824019.Additional filesAdditional file 1: Partial alignment of EF-1α sequences. TheOpisthokonta-specific insertion is highlighted in grey. Numbers above thealignment are the amino acid positions in Thalassiosira pseudonanaEF-1α. The divergent EF-1α homologues in the two dual-EF-containingfungi are highlighted by stars.Additional file 2: Substitution patterns in the divergent EF-1αsequences. The amino acid sequences of the divergent EF-1αhomologues (marked by stars) were compared to those ofphylogenetically related, canonical EF-1α proteins. Amino acids aregrouped into four Dayhoff categories—(i) acidic residues (D and E), (ii)basic residues (H, K, and R), (iii) polar-uncharged residues (C, N, Q, S, T, W,and Y), and (iv) hydrophobic non-polar residues (A, F, G, I, L, M, P, and V).Substitutions across two out of the four Dayhoff categories between thedivergent and canonical EF-1α sequences are highlighted in red.Additional file 3: EF-1α/EFL sequences identified in publiclyavailable databases. The amino acid sequences of EF-1α/EFLhomologues identified in publicly available databases are listed here.Competing interestsNon-financial competing interests.Authors’ contributionsRK, MWB, and YN determined sequences. RK, MWB, and YI performedphylogenetic analyses. NY, YS, AH, and RG provided research materials. RKand YI designed the study and wrote the manuscript. MWB, NY, AGBS, AJR,and TH helped to draft the manuscript. All authors read and approved thefinal manuscript.AcknowledgementsRK was a research fellow supported by the Japan Society for Promotion ofSciences (JSPS; no. 210528). NY was supported by grants from the TulaFoundation (Centre for Microbial Diversity and Evolution at the University ofBritish Columbia) and the Canadian Institute for Advanced Research,Program in Integrated Microbial Biodiversity (CIfAR IMB program). This workwas supported in part by grants from JSPS awarded to RK (no. 24870004), YI(no. 21370031, 23117006) and TH (no. 23405013, 23247038), and by CIfARIMB program support to AGBS. Work carried out in AJR’s laboratory wassupported by grant MOP-62809 from the Canadian Institutes of HealthResearch. AJR acknowledges support from the Canada Research ChairsProgram and the CIfAR IMB program.Author details1Graduate School of Global Environmental Studies, Kyoto University, Kyoto606-8501, Japan. 2Graduate School of Human and Environmental Studies,Kyoto University, Kyoto 606-8501, Japan. 3Centre for Comparative Genomicsand Evolutionary Bioinformatics, Department of Biochemistry and MolecularBiology, Dalhousie University, Halifax, NS, Canada. 4Graduate School of Lifeand Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai,Tsukuba, Ibaraki 305-8572, Japan. 5Graduate School of Agriculture, KyotoUniversity, Kitashirakawa Oiwake-cho, Kyoto 606-8502, Japan. 6Department ofBiology, Dalhousie University, Halifax NS, Canada. 7Department of Botany,University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4,Canada. 8Center for Computational Sciences, University of Tsukuba, 1-1-1Tennoudai, Tsukuba, Ibaraki 305-8577, Japan.Received: 26 April 2013 Accepted: 21 June 2013Published: 26 June 2013References1. 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BMC Evolutionary Biology 2013, 13:131 Page 12 of 12http://www.biomedcentral.com/1471-2148/13/131

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