A Hypothesis for the Evolution of Nuclear-Encoded, Plastid-Targeted Glyceraldehyde-3-Phosphate Dehydrogenase Genes in “Chromalveolate” Members

Abstract

Eukaryotes bearing red alga-derived plastids — photosynthetic alveolates (dinoflagellates plus the apicomplexan Toxoplasma gondii plus the chromerid Chromera velia), photosynthetic stramenopiles, haptophytes, and cryptophytes — possess unique plastid-targeted glyceraldehyde-3-phosphate dehydrogenases (henceforth designated as “GapC1”). Pioneering phylogenetic studies have indicated a single origin of the GapC1 enzymes in eukaryotic evolution, but there are two potential idiosyncrasies in the GapC1 phylogeny: Firstly, the GapC1 tree topology is apparently inconsistent with the organismal relationship among the “GapC1-containing” groups. Secondly, four stramenopile GapC1 homologues are consistently paraphyletic in previously published studies, although these organisms have been widely accepted as monophyletic. For a closer examination of the above issues, in this study GapC1 gene sampling was improved by determining/identifying nine stramenopile and two cryptophyte genes. Phylogenetic analyses of our GapC1 dataset, which is particularly rich in the stramenopile homologues, prompt us to propose a new scenario that assumes multiple, lateral GapC1 gene transfer events to explain the incongruity between the GapC1 phylogeny and the organismal relationships amongst the “GapC1-containing” groups. Under our new scenario, GapC1 genes uniquely found in photosynthetic alveolates, photosynthetic stramenopiles, haptophytes, and cryptopyhytes are not necessarily a character vertically inherited from a common ancestor.

About the Authors:

Kiyotaka Takishita

* E-mail: [email protected]

Affiliation: Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan

Haruyo Yamaguchi

Affiliation: Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan

Tadashi Maruyama

Affiliation: Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan

Yuji Inagaki

Affiliation: Center for Computational Sciences and Institute of Biological Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan

Introduction

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an ubiquitous enzyme catalyzing the reversible interconversion between glyceraldehyde-3-phosphate and 1,3-diphosphoglycerate. GAPDH gene sequences are available for diverged eukaryotes, and intensive phylogenetic investigations have revealed a complex evolution of GAPDH genes in photosynthetic eukaryotes. Photosynthetic eukaryotes generally possess two different types of GAPDH genes in their nuclear genomes. One of the two GAPDH enzymes works in the cytosol and is involved in glycolysis/gluconeogenesis, while the other is targeted to plastids and catalyzes Calvin cycle reactions. In land plants, green algae, red algae, glaucophytes, and euglenids, plastid-targeted GAPDH enzymes bear a clear evolutionary affinity to cyanobacterial homologues (so-called GapA/B), and are distantly related to cytosolic enzymes (so-called GapC). These findings suggest that an ancestral GapA/B gene was acquired from an endosymbiotic cyanobacterium that gave rise to plastids, being phylogenetically distinctive from the cytosolic counterpart [1]–[5]. In sharp contrast, all known photosynthetic eukaryotes with red alga-derived plastids (Chromera, the vast majority of photosynthetic dinoflagellates, photosynthetic stramenopiles, cryptophytes, and haptophytes) as well as the apicomplexan parasite Toxoplasma utilize GapC-related enzymes for plastids instead of GapA/B [6]–[12]. Henceforth, we designate nucleus-encoded, plastid-targeted GapC genes/enzymes as “GapC1” genes/enzymes according to Liaud et al. (1997) [6]. All GapC1 genes form a robust monophyletic clade in global GAPDH phylogeny including GapC1, GapC, and closely related bacterial homologues [13]. The interpretation of this tree topology was that the GapC1 gene was produced by a single duplication of the gene encoding the cytosolic enzyme followed by changing sub-cellular localization from the cytosol to plastids [9], [10].

Cavalier-Smith (1999, 2002) [14], [15] has proposed that (i) alveolates (including dinoflagellates, ciliates, and apicomplexans), stramenopiles, haptophytes, and cryptophytes — collectively called “chromalveolates” — are monophyletic, (ii) their common ancestor acquired plastids through a single endosymbiosis associated with a red alga, and (iii) multiple lineages in the four groups became secondarily non-photosynthetic (e.g. ciliates). Importantly, it has been widely accepted that the single origin of GapC1 genes is compatible with the monophyly of chromalveolates (e.g. [9], [10]). It is believed that the original GapC1 gene was established in the ancestral chromalveolate cells and was vertically inherited by the extant photosynthetic chromalveolate lineages. However, this simple scenario assuming vertical transfer of the GapC1 genes inevitably confronts serious contradictions. In GapC1 phylogenies, the homologue of the apicomplexan Toxoplasma robustly branches with the haptophyte homologues, challenging both host affinity between apicomplexans and dinoflagellates (e.g. [16]), and that between cryptophytes and haptophytes [17]–[19]. In addition, there is a peculiarity regarding GapC1 sequences from stramenopiles. Previously published phylogenies have failed to recover the monophyly of the GapC1 homologues of four stramenopile species, the raphidophycean alga Heterosigma akashiwo, the synurophycean alga Mallomonas rasilis, and two bacillariophycean algae (diatoms) Phaeodactylum tricornutum and Odontella senensis, not as would be anticipated from a well established host monophyly of stramenopiles. In order to examine the stramenopile “paraphyly” in GapC1 phylogenies, an improved sampling of stramenopile GapC1 genes is needed. These idiosyncratic aspects in GapC1 phylogeny have implied that the evolution of these unique genes may be more complex than previously thought, but this has not been deeply investigated to date.

In the present study, we determined and identified GapC1 genes from nine stramenopiles and two cryptophytes. By analyzing our GapC1 dataset including 14 homologues from nine stramenopile classes, we have addressed the two issues in the current GapC1 evolution scenario (see above); the incongruity between the gene and host phylogenies, and the stramenopile paraphyly. Based on the results from phylogenetic analyses of the updated GapC1 dataset, we propose a new evolutionary scenario that can explain the idiosyncratic aspects of GapC1 evolution. In contrast to the widely accepted scenario which assumes vertical transfer of GapC1 genes throughout chromalveolate evolution, we speculate that (i) there was a common ancestor of stramenopiles and alveolates as the “innovator” of the original GapC1 gene, and (ii) multiple lateral transfer events have taken place in GapC1 evolution. We also discuss the validity of evaluating the host and plastid evolution in the chromalveolate members by using the GapC1 phylogeny.

Results and Discussion

Incongruity between the GapC1 phylogeny and the phylogeny amongst the host lineages bearing GapC1 genes

Previously published GapC1 phylogenies (e.g. [12]) considered only four homologues from three classes of stramenopiles, such as Synurophyceae, Bacillariophyceae, and Raphidophyceae. It may be inadequate to make the four homologues from the three classes represent the diversity of stramenopiles. Aiming for a better coverage of the stramenopile diversity, we experimentally determined new GapC1 genes from four stramenopile species (Nannochloropsis oculata, Haramons dimorpha, Olisthodiscus luteus, and Vaucheria litorea) as well as two cryptophytes (Chroomonas nordstedtii and Cryptomonas ovata) in this study. In addition, six stramenopile GapC1 sequences, which have not been considered in the previously published GapC1 phylogenies, were identified from public sequence databases. Here, we re-examined GapC1 evolution by analyzing a new data set including homologues from nine classes in stramenopiles.

In the GapC1 phylogeny shown in Figure 1, all GapC1 homologues considered in this study were separated into two Clades; “A” and “B”: In Clade A, the homologues of photosynthetic stramenopiles, cryptophytes, and “phylogenetically-diverged” dinoflagellates were grouped with 99–100% ML bootstrap values (BP) and 1.00 posterior probabilities (PP). The dinoflagellate homologues and the cryptophyte homologues formed respective monophyletic clades with 98–100% BP and 1.00 PP, and these two clades were separately placed within the radiation of the stramenopile homologues.

[Figure omitted. See PDF.]

Figure 1. Nuclear-encoded plastid-targeted GAPDH (GapC1) phylogeny.

The maximum-likelihood tree was inferred from a GapC1 dataset (38-OTU, 312 amino acid positions) by using RAxML. The tree was rooted by cytosolic GAPDH sequences of two ciliates. The GapC1 tree was divided into two major clades, Clades A and B, highlighted by green and orange shades, respectively. The stramenopile homologues are written with bold letters. ML bootstrap probabilities (RAxML/PhyML) over 50% are shown at the branches. The thick branches represent Bayesian posterior probability over 0.95. Major taxonomic groups are labeled on the right.

https://doi.org/10.1371/journal.pone.0004737.g001

The GapC1 homologues from haptophytes, dinoflagellates belonging to the genera Karenia, Karlodinium, and Lepidodinium, the apicomplexan Toxoplasma, and the chromerid Chromera formed Clade B with 91–95% BP and 1.00 PP. In Clade B, the Karenia, Karlodinium, and Lepidodinium homologues grouped with the homologues of prymnesiphycean haptophytes with 98–100% BP and 1.00 PP. Since the plastids present in Karenia and Karlodinium are the remnants of an endosymbiotic haptophyte, GapC1 genes from the two dinoflagellate genera are most likely from an endosymbiont (haptophyte) transferred to the host (dinoflagellate) nuclear genome. It has been proposed that Lepidodinium with green alga-derived plastids acquired GapC1 gene from a haptophyte in a non-endosymbiotic context [20]. Consequently, the GapC1 homologues from Karenia, Karlodinium, and Lepidodinium can be considered as haptophyte homologues.

The overall GapC1 tree topology shown in Figure 1 agreed with those recovered in previously published studies (e.g. [9]–[12], [20], [21]). However, it has been pointed out that the GapC1 phylogeny is significantly incongruent with the organismal (host) relationships among apicomplexans plus the chromerid Chromera (henceforth designated as apicomplexans+), dinoflagellates, haptophytes, and cryptophytes widely accepted to date (e.g. [20]). Apicomplexans and dinoflagellates are two out of the three major sub-groups of a large protist assemblage, Alveolata [22]. In “phylogenomic” analyses, the sister relationship between cryptophytes and haptophytes has been consistently recovered [17]–[19]. Nevertheless, the GapC1 phylogeny here recovered neither the host affinity between apicomplexans+ and dinoflagellates nor that between cryptophytes and haptophytes (Figure 1). The dinoflagellate homologues were nested in Clade A, while the homologues from apicomplexans+ formed Clade B with the haptophyte homologues. Likewise, the cryptophyte and haptophyte homologues were separately included in Clades A and B, respectively. The approximately unbiased (AU) test successfully complemented the ML phylogenetic analysis shown in Figure 1. Alternative tree topologies bearing the monophyly of dinoflagellate and apicomplexan+ homologues and the monophyly of the cryptophyte and haptophyte homologues were rejected at the 1% level (P = 2×10−6 and 0.003, respectively; the details of the alternative trees are shown in Figure S1).

A new hypothesis for GapC1 gene evolution

The results from our analyses (see above) strongly suggest that GapC1 evolution cannot be explained by any scenarios only invoking vertical transfer of GapC1 genes from the common ancestor of cryptophytes, haptophytes, stramenopiles, dinoflagellates, and apicomplexans+. There is extensive literature on lateral transfer of cytosolic GAPDH genes [11], [13], [23], [24], and, intriguingly, GapC1 evolution appears not to be immune from lateral gene transfer (LGT) [20]. Combining the idiosyncratic aspects in the GapC1 phylogeny with “lateral mobility” of GAPDH genes in general, we propose a new hypothesis for GapC1 evolution.

If the dinoflagellate and cryptophyte homologues are excluded, Clade A in Figure 1 agrees well with the general view of the stramenopile (host) phylogeny. In Figure 1, monophylies of three classes, Bacillariophyceae (diatoms), Raphidophyceae, and Phaeophyceae, were robustly recovered. In addition, the intimate affinity between Chrysophyceae and Synurophyceae and that between Phaeophyceae and Xanthophyceae were successfully reconstructed as anticipated from phylogenies based on other molecular markers (e.g. [25]). The tree topology of Clade A leads us to a scenario assuming that (i) the homologues of this clade are essentially from stramenopiles, and (ii) the ancestral cells of extant dinoflagellate species and of the extant cryptophytes separately acquired GapC1 genes from two distinctive stramenopile species (schematically shown in Figure 2). The dinoflagellate and cryptophyte clades branched with the Aureococcus homologue and the diatom homologue, respectively, although the support for these relationships was inconclusive in ML bootstrap analyses (Figure 1).

[Figure omitted. See PDF.]

Figure 2. New proposed scheme for GapC1 evolution.

A. The original GapC1 gene was established in a common ancestor of stramenopiles and alveolates [including dinoflagellates and aplicomplexans plus Chromera (designated as apicomplexans+); ciliates are excluded in this figure] shown by an arrowhead. Photosynthetic stramenopiles and apicomplexans+ possessed the vertically transferred GapC1 genes. The ancestral dinoflagellates replaced the “vertical” GapC1 gene by a laterally acquired homologue from an unknown stramenopile species. We also assume two lateral GapC1 gene transfer events — one between an unknown stramenopile species and the ancestral cryptophyte cells, and the other between an unknown member of apicomplexan+ and the ancestral haptophyte cells. The three LGT events were highlighted by red arrows. Putative replacements of plastid-targeted GAPDH took place after the lateral gene transfers (black arrows). The original type of plastid-targeted GAPDH enzymes in a common ancestor of cryptophytes and haptophytes remains uncertain. The homologues belonging to Clade A in the GapC1 phylogeny (Figure 1) are shown in green, while those belonging to Clade B are shown in orange. The host (or organismal) phylogeny is shown grey shading. In this figure, the host monophyly of haptophytes, cryptophytes, stramenopiles, and alveolates are not assumed. B. The same scheme as shown in A but assuming a host monophyly of haptophytes, cryptophytes, stramenopiles, and alveolates. The original GapC1 gene was established in a common ancestor of the four groups (arrowhead). Under this assumption, a common ancestor of cryptophytes and haptophytes originally utilized the “vertical” GapC1 genes.

https://doi.org/10.1371/journal.pone.0004737.g002

Next, we hypothesize the evolutionary process of Clade B in Figure 1 composed of the Toxoplasma, Chromera, and haptophyte homologues (Figure 1). This unexpected grouping has been suspected to have been produced through LGT (e.g. [10]). In respect of the close (host) relationship between Toxoplasma and Chromera [26], these homologues should have been robustly grouped, excluding the haptophyte homologues. In reality, in Clade B, the haptophyte clade as a whole was nested within the homologues from Toxoplasma and Chromera (Figure 1). Thus, the tree topology of Clade B can be reconciled by assuming GapC1 transfer from an unknown member of apicomplexans+ to the ancestral haptophyte cells (schematically shown in Figure 2). In this scenario, GapC1 homologues of the extant haptophytes are fundamentally from apicomplexans+.

The host sisterhood between stramenopiles and alveolates (including apicomplexans+) and the life style of their ancestral cells may hold the key to exploring deeper GapC1 evolution. Firstly, a robust host monophyly of stramenopiles and alveolates has been constantly recovered [16]–[19], [27], [28]. Secondly, many of non-photosynthetic members of stramenopiles and alveolates — oomycetes, Perkinsus, Oxyrrhis, apicomplexans, and ciliates — still retain relic plastids and/or plastid-derived genes in their nuclear genomes [29]–[36]. These findings suggest that stramenopiles and alveolates evolved from a single, photosynthetic ancestor, and secondary loss of photosynthetic ability (or plastid as a whole) took place in multiple, independent lineages in the two groups. If the origins of the Clade A and Clade B homologues are from stramenopiles and apicomplexans+, respectively, the first GapC1 genes may have been established in a common ancestor of stramenopiles and alveolates (arrowhead in Figure 2A). In the subsequent evolution of stramenopiles/alveolates, GapC1 genes may have been lost in secondarily non-photosynthetic lineages.

Implication for the host and plastid relationships amongst the “chromalveolate” lineages

Photosynthetic stramenopiles, photosynthetic alveolates (including Toxoplasma), haptophytes, and cryptophytes utilize GapC1 enzymes for their red alga-derived plastids. This unique molecular “synapomorphy” in the four photosynthetic eukaryotic lineages has prompted a scenario assuming that GapC1 genes were vertically inherited from a common ancestor of these chromalveolate lineages. While this scenario has won popularity, significant incongruity between the GapC1 and host phylogenies has been noticed [20]. Rather, our new hypothesis, in which the incongruity is resolved by invoking LGT, is more favorable than the “standard” hypothesis assuming vertical GapC1 gene transfer in the chromalveolate host evolution. Noteworthy, our hypothesis invoking LGT lends no support to either monophyly or paraphyly of the chromalveolate host lineages, due to no information regarding the original plastid-targeted GAPDH enzymes for cryptophyte and haptophyte plastids. For instance, the putative GapC1 evolution proposed here and the monophyly of chromalveolate host lineages can fit with each other by assuming that cryptophytes and haptophytes originally utilized the GapC1 genes vertically inherited from the ancestral chromalveolates before the putative LGT events (Figure 2B). We consider such “GapC1-to-GapC1” replacements are not unlikely, since a similar event has been already introduced to explain the origin of GapC1 genes in extant dinoflagellates (Figure 2). The uncertainties in the hypothesis for GapC1 evolution discussed above need to be thoroughly re-examined when deeper insights regarding the host and plastid evolution in the chromalveolate lineages are available in the future. At any rate, we recommend splitting the GapC1 evolution and the host evolution of GapC1-containing lineages.

Plastid-encoded gene phylogenies generally support the monophyly of plastids in chromalveolate cells (chromalveolate plastids) (e.g. [37]). On the other hand, the host monophyly of the chromalveolate members has not been validated by any nucleus-encoded gene phylogenies (e.g. [17]–[19]). To reconcile the discrepancy between the chromalveolate host and plastid phylogenies, theories regarding (i) the paraphyly of the chromalveolate host lineages, and (ii) the spread of plastids amongst the chromalveolate lineages via tertiary endosymbioses, have been recently proposed [38]–[40]. However, the GapC1 phylogeny is fundamentally neutral in regard to the theories described above. There is no strong reason to believe that during plastid replacement via tertiary endosymbiosis nucleus-encoded genes for the pre-existing plastids were always replaced by orthologous genes brought by an endosymbiont cell. In fact, the dinoflagellate Karenia brevis bearing haptophyte tertiary plastids possesses plastid-targeted genes with phylogenetically diverged origins [41]. A similar phylogenetically chimeric proteome is known from the chlorarachniophyte alga Bigelowiella natans [42]. More specifically, the dinoflagellate Lepidodinium, which most likely acquired its current plastids from an endosymbiotic green alga, utilizes plastid-targeted GAPDH gene of haptophyte origin [20]. Considering multiple origins of plastid-targeted genes in the nuclear genomes in photosynthetic eukaryotes, we should be aware of the potential “gap” between the evolution of GapC1 genes and that of chromalveolate plastids.

Materials and Methods

Algal strains

Two stramenopile species (Haramonas dimorpha NIES716 and Olisthodiscus luteus NIES15) and two cryptophytes (Chroomonas nordstedtii NIES706 and Cryptomonas ovata NIES275) were purchased from the Microbial Culture Collection at the National Institute for Environmental Studies (NIES, 16-2 Onogawwa, Tsukuba, Ibaraki 305-8506, Japan). Other stramenopile species, Vaucheria litorea CCMP2940 and Nannochloropsis oculata CCMP525, were purchased from the Provasoli-Guillard National Center for Culture of Marine Phytoplankton (CCMP: 180 McKown Point Road, West Boothbay Harbor, Maine 04575, USA). These algal cells were grown according to the instructions from CCMP and NIES.

New plastid-targeted GAPDH sequences

Genomic DNA samples from Haramonas and Olisthodiscus were prepared by using a SepaGene kit (Sanko Junyaku Co. Ltd., Tokyo, Japan). Total RNA samples from other strains were prepared by using the Absolutely RNA RT-PCR Miniprep Kit (Stratagene, La Jolla, CA, USA) after homogenizing the cell pellets with glass beads in lysis buffer in this kit. Synthesis of cDNA from total RNA was performed using SuperScript III RNase H− reverse transcriptase (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. PCR amplification using genomic DNA or cDNA as a template was conducted using HotStarTaq DNA polymerase (QIAGEN, Tokyo, Japan). GapC1 genes were amplified using one set of primers (forward: 5′-CCAAGGTCGGNATHAAYGGNTTYGG-3′ and reverse: 5′-CGAGTAGCCCCAYTCRTTRTCRTACCA-3′) [9]. Thermal cycling was comprised of 35 cycles of 0.5–1 min at 94°C, 1 min at 45–50°C, and 2 min at 72°C. The PCR-amplified DNA fragments were cloned into the pCR2.1 vector of the TOPO TA Cloning Kit (Invitrogen). The DNA sequence of each amplified fragment was confirmed with multiple clones. The cytosolic GapC genes were identified from the three species (Haramons, Olisthodiscus, and Vaucheria) (data not shown). The gene sequences determined in the present study have been deposited in the DNA Data Bank of Japan (DDBJ) under accession numbers AB459521–AB459529.

We also identified GapC1 sequences in ongoing-genome and expressed sequence tag (EST) data of four stramenopile species. The GapC1 genes were retrieved from the genome sequence data of the pelagophycean alga Aureococcus anophagefferens and the diatom Thalassiosira pseudonana (DOE Joint Genome Institue; www.jgi.doe.org). We also identified GapC1 transcripts in the EST data of the phaeophycean alga Sargassum binderi and the diatom Flagilariopsis cylindrus. The transcripts were assembled into contigs, and the corresponding amino acid sequences were then deduced from the contig sequences.

Phylogenetic analyses

We manually aligned GapC1 amino acid (aa) sequences from 14 stramenopile species, 11 dinoflagellates, four cryptophytes, four haptophytes, the apicomplexan Toxoplasma, and the chromelid Chromera, and two cytosolic GAPDH sequences from ciliates (Parameciuim tetraurelia and Tetrahymena thermophila) as the outgroup. Unambiguously aligned 312 aa positions were retained in the final alignment. This GapC1 dataset was firstly subjected to ProtTest [43] to find the best fit model for ML phylogenetic analyses described below. The “WAG+I+Γ+F” model, in which among-site rate variation was approximated by a discrete gamma distribution plus the proportion of invariant positions, and aa frequencies were estimated from the data, was selected for the GapC1 analyses according to Akaike Information Criterion.

The GapC1 data set was subjected to ML phylogenetic analyses by using RAxML 7.0.4 [44] under the WAG+I+Γ+F model [45]. In the RAxML analyses, the tree search was started from 10 distinct parsimony starting trees. Bootstrap analyses (100 replicates) were conducted as described above except the tree search initiated from a single parsimony tree per replicate. We repeated the ML analysis using PhyML [46] under the WAG+I+Γ+F model. The tree search in the PhyML analysis was started from a BIONJ tree.

The GapC1 data set was analyzed by the Bayesian method by using MrBayes 3.0 [47] under the WAG+I+Γ model, which was the best model selected by ProtTest according to Bayesian Information Criterion. One cold and three heated Markov chain Monte Carlo (MCMC) chains with default-chain temperatures were run for 106 generations, sampling log-likelihoods (InLs), and trees at 100-generation intervals (104 InLs and trees were saved during MCMC). The first 105 generations were discarded as “burn-in”, and Bayesian posterior probabilities and branch-lengths were estimated from the remaining 9×105 generations.

Approximately unbiased (AU) test

We heuristically searched for (i) the optimal tree with the monophyly of the dinoflagellate and apicomplexan+ homologues, (ii) that with the monophyly of the cryptophyte and haptophyte homologues, and (iii) that with both dinoflagellates–apicomplexans+ and cryptophytes–haptophytes monophylies, by using RAxML. The details of RAxML tree searches were same as described above. The three alternative trees and the ML tree were subjected to AU test. For each test trees, site-wise log likelihoods (site-lnLs) were calculated by Tree-Puzzle v.7.2 [48]. The resultant site-lnLs data were then input to CONSEL [49].

Supporting Information

[Figure omitted. See PDF.]

Figure S1.

Alternative trees subjected to the AU test. The optimal trees bearing the monophyly of cryptophyte and haptophyte homologues (left) and that bearing the monophyly of the dinoflagellate and apicomplexan+ GapC1 homologues (right) were compared to the ML tree shown in Figure 1 by using the AU test. Branch lengths are ignored in these figures. On the left, the clade of the haptphyte homologues (“H”) and cryptophyte homologues (“C”) is shaded. On the right, the clade of the dinoflagellate homologues (“D”) and apicomplexan+ homologues (“A”) is shaded. The stramenopile homologues are indicated as “S”.

https://doi.org/10.1371/journal.pone.0004737.s001

(6.53 MB TIF)

Acknowledgments

We thank Dr. J. D. Reimer (Rising Star Program, University of the Ryukyus) for critical reading of this manuscript.

Author Contributions

Conceived and designed the experiments: KT YI. Performed the experiments: KT YI. Analyzed the data: KT YI. Contributed reagents/materials/analysis tools: KT HY TM YI. Wrote the paper: KT YI.

Citation: Takishita K, Yamaguchi H, Maruyama T, Inagaki Y (2009) A Hypothesis for the Evolution of Nuclear-Encoded, Plastid-Targeted Glyceraldehyde-3-Phosphate Dehydrogenase Genes in “Chromalveolate” Members. PLoS ONE4(3): e4737. https://doi.org/10.1371/journal.pone.0004737

References

1. Brinkmann H, Cerff R, Salomon M, Soll J (1989) Cloning and sequence analysis of cDNAs encoding the cytosolic precursors of subunits GapA and GapB of chloroplast glyceraldehyde-3-phosphate dehydrogenase from pea and spinach. Plant Mol Biol 13: 81–94.H. BrinkmannR. CerffM. SalomonJ. Soll1989Cloning and sequence analysis of cDNAs encoding the cytosolic precursors of subunits GapA and GapB of chloroplast glyceraldehyde-3-phosphate dehydrogenase from pea and spinach.Plant Mol Biol138194

2. Martin W, Brinkmann H, Savonna C, Cerff R (1993) Evidence for a chimeric nature of nuclear genomes: eubacterial origin of eukaryotic glyceraldehyde-3-phosphate dehydrogenase genes. Proc Natl Acad Sci U S A 90: 8692–8696.W. MartinH. BrinkmannC. SavonnaR. Cerff1993Evidence for a chimeric nature of nuclear genomes: eubacterial origin of eukaryotic glyceraldehyde-3-phosphate dehydrogenase genes.Proc Natl Acad Sci U S A9086928696

3. Liaud MF, Valentin C, Martin W, Bouget FY, Kloareg B, et al. (1994) The evolutionary origin of red algae as deduced from the nuclear genes encoding cytosolic and chloroplast glyceraldehyde-3-phosphate dehydrogenases from Chondrus crispus. J Mol Evol 38: 319–327.MF LiaudC. ValentinW. MartinFY BougetB. Kloareg1994The evolutionary origin of red algae as deduced from the nuclear genes encoding cytosolic and chloroplast glyceraldehyde-3-phosphate dehydrogenases from Chondrus crispus.J Mol Evol38319327

4. Henze K, Badr A, Wettern M, Cerff R, Martin W (1995) A nuclear gene of eubacterial origin in Euglena gracilis reflects cryptic endosymbioses during protist evolution. Proc Natl Acad Sci U S A 92: 9122–9126.K. HenzeA. BadrM. WetternR. CerffW. Martin1995A nuclear gene of eubacterial origin in Euglena gracilis reflects cryptic endosymbioses during protist evolution.Proc Natl Acad Sci U S A9291229126

5. Petersen J, Teich R, Becker B, Cerff R, Brinkmann H (2006) The GapA/B gene duplication marks the origin of Streptophyta (charophytes and land plants). Mol Biol Evol 23: 1109–1118.J. PetersenR. TeichB. BeckerR. CerffH. Brinkmann2006The GapA/B gene duplication marks the origin of Streptophyta (charophytes and land plants).Mol Biol Evol2311091118

6. Liaud MF, Brandt U, Scherzinger M, Cerff R (1997) Evolutionary origin of cryptomonad microalgae: two novel chloroplast/cytosol-specific GAPDH genes as potential markers of ancestral endosymbiont and host cell components. J Mol Evol 44: Suppl 1S28–37.MF LiaudU. BrandtM. ScherzingerR. Cerff1997Evolutionary origin of cryptomonad microalgae: two novel chloroplast/cytosol-specific GAPDH genes as potential markers of ancestral endosymbiont and host cell components.J Mol Evol44Suppl 1S2837

7. Liaud MF, Lichtle C, Apt K, Martin W, Cerff R (2000) Compartment-specific isoforms of TPI and GAPDH are imported into diatom mitochondria as a fusion protein: evidence in favor of a mitochondrial origin of the eukaryotic glycolytic pathway. Mol Biol Evol 17: 213–223.MF LiaudC. LichtleK. AptW. MartinR. Cerff2000Compartment-specific isoforms of TPI and GAPDH are imported into diatom mitochondria as a fusion protein: evidence in favor of a mitochondrial origin of the eukaryotic glycolytic pathway.Mol Biol Evol17213223

8. Fagan T, Hastings JW, Morse D (1998) The phylogeny of glyceraldehyde-3-phosphate dehydrogenase indicates lateral gene transfer from cryptomonads to dinoflagellates. J Mol Evol 47: 633–639.T. FaganJW HastingsD. Morse1998The phylogeny of glyceraldehyde-3-phosphate dehydrogenase indicates lateral gene transfer from cryptomonads to dinoflagellates.J Mol Evol47633639

9. Fast NM, Kissinger JC, Roos DS, Keeling PJ (2001) Nuclear-encoded, plastid-targeted genes suggest a single common origin for apicomplexan and dinoflagellate plastids. Mol Biol Evol 18: 418–426.NM FastJC KissingerDS RoosPJ Keeling2001Nuclear-encoded, plastid-targeted genes suggest a single common origin for apicomplexan and dinoflagellate plastids.Mol Biol Evol18418426

10. Harper JT, Keeling PJ (2003) Nucleus-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase (GAPDH) indicates a single origin for chromalveolate plastids. Mol Biol Evol 20: 1730–1735.JT HarperPJ Keeling2003Nucleus-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase (GAPDH) indicates a single origin for chromalveolate plastids.Mol Biol Evol2017301735

11. Takishita K, Ishida K, Maruyama T (2003) An enigmatic GAPDH gene in the symbiotic dinoflagellate genus Symbiodinium and its related species (the order Suessiales): possible lateral gene transfer between two eukaryotic algae, dinoflagellate and euglenophyte. Protist 154: 443–454.K. TakishitaK. IshidaT. Maruyama2003An enigmatic GAPDH gene in the symbiotic dinoflagellate genus Symbiodinium and its related species (the order Suessiales): possible lateral gene transfer between two eukaryotic algae, dinoflagellate and euglenophyte.Protist154443454

12. Oborník M, Janouskovec J, Chrudimsky T, Lukes J (2009) Evolution of the apicoplast and its hosts: From heterotrophy to autotrophy and back again. Int J Parasitol 39: 1–12.M. OborníkJ. JanouskovecT. ChrudimskyJ. Lukes2009Evolution of the apicoplast and its hosts: From heterotrophy to autotrophy and back again.Int J Parasitol39112

13. Takishita K, Inagaki Y (2009) Eukaryotic origin of glyceraldehyde-3-phosphate dehydrogenase genes in Clostridium thermocellum and Clostridium cellulolyticum genomes and putative fates of the exogenous gene in the subsequent genome evolution. Gene. K. TakishitaY. Inagaki2009Eukaryotic origin of glyceraldehyde-3-phosphate dehydrogenase genes in Clostridium thermocellum and Clostridium cellulolyticum genomes and putative fates of the exogenous gene in the subsequent genome evolution.Gene(in press) doi:10.1016/j.gene.2008.03.001. (in press) doi:10.1016/j.gene.2008.03.001.

14. Cavalier-Smith T (1999) Principles of protein and lipid targeting in secondary symbiogenesis: euglenoid, dinoflagellate, and sporozoan plastid origins and the eukaryote family tree. J Eukaryot Microbiol 46: 347–366.T. Cavalier-Smith1999Principles of protein and lipid targeting in secondary symbiogenesis: euglenoid, dinoflagellate, and sporozoan plastid origins and the eukaryote family tree.J Eukaryot Microbiol46347366

15. Cavalier-Smith T (2002) Chloroplast evolution: secondary symbiogenesis and multiple losses. Curr Biol 12: R62–64.T. Cavalier-Smith2002Chloroplast evolution: secondary symbiogenesis and multiple losses.Curr Biol12R6264

16. Fast NM, Xue L, Bingham S, Keeling PJ (2002) Re-examining alveolate evolution using multiple protein molecular phylogenies. J Eukaryot Microbiol 49: 30–37.NM FastL. XueS. BinghamPJ Keeling2002Re-examining alveolate evolution using multiple protein molecular phylogenies.J Eukaryot Microbiol493037

17. Burki F, Shalchian-Tabrizi K, Minge M, Skjaeveland A, Nikolaev SI, et al. (2007) Phylogenomics reshuffles the eukaryotic supergroups. PLoS ONE 2: e790.F. BurkiK. Shalchian-TabriziM. MingeA. SkjaevelandSI Nikolaev2007Phylogenomics reshuffles the eukaryotic supergroups.PLoS ONE2e790

18. Hackett JD, Yoon HS, Li S, Reyes-Prieto A, Rummele SE, et al. (2007) Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates. Mol Biol Evol 24: 1702–1713.JD HackettHS YoonS. LiA. Reyes-PrietoSE Rummele2007Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates.Mol Biol Evol2417021713

19. Patron NJ, Inagaki Y, Keeling PJ (2007) Multiple gene phylogenies support the monophyly of cryptomonad and haptophyte host lineages. Curr Biol 17: 887–891.NJ PatronY. InagakiPJ Keeling2007Multiple gene phylogenies support the monophyly of cryptomonad and haptophyte host lineages.Curr Biol17887891

20. Takishita K, Kawachi M, Noel MH, Matsumoto T, Kakizoe N, et al. (2008) Origins of plastids and glyceraldehyde-3-phosphate dehydrogenase genes in the green-colored dinoflagellate Lepidodinium chlorophorum. Gene 410: 26–36.K. TakishitaM. KawachiMH NoelT. MatsumotoN. Kakizoe2008Origins of plastids and glyceraldehyde-3-phosphate dehydrogenase genes in the green-colored dinoflagellate Lepidodinium chlorophorum.Gene4102636

21. Takishita K, Ishida K, Maruyama T (2004) Phylogeny of nuclear-encoded plastid-targeted GAPDH gene supports separate origins for the peridinin- and the fucoxanthin derivative-containing plastids of dinoflagellates. Protist 155: 447–458.K. TakishitaK. IshidaT. Maruyama2004Phylogeny of nuclear-encoded plastid-targeted GAPDH gene supports separate origins for the peridinin- and the fucoxanthin derivative-containing plastids of dinoflagellates.Protist155447458

22. Cavalier-Smith T (1993) Kingdom protozoa and its 18 phyla. Microbiol Rev 57: 953–994.T. Cavalier-Smith1993Kingdom protozoa and its 18 phyla.Microbiol Rev57953994

23. Figge RM, Schubert M, Brinkmann H, Cerff R (1999) Glyceraldehyde-3-phosphate dehydrogenase gene diversity in eubacteria and eukaryotes: evidence for intra- and inter-kingdom gene transfer. Mol Biol Evol 16: 429–440.RM FiggeM. SchubertH. BrinkmannR. Cerff1999Glyceraldehyde-3-phosphate dehydrogenase gene diversity in eubacteria and eukaryotes: evidence for intra- and inter-kingdom gene transfer.Mol Biol Evol16429440

24. Figge RM, Cerff R (2001) GAPDH gene diversity in spirochetes: a paradigm for genetic promiscuity. Mol Biol Evol 18: 2240–2249.RM FiggeR. Cerff2001GAPDH gene diversity in spirochetes: a paradigm for genetic promiscuity.Mol Biol Evol1822402249

25. Ben Ali A, De Baere R, De Wachter R, Van de Peer Y (2002) Evolutionary relationships among heterokont algae (the autotrophic stramenopiles) based on combined analyses of small and large subunit ribosomal RNA. Protist 153: 123–132.A. Ben AliR. De BaereR. De WachterY. Van de Peer2002Evolutionary relationships among heterokont algae (the autotrophic stramenopiles) based on combined analyses of small and large subunit ribosomal RNA.Protist153123132

26. Moore RB, Oborník M, Janouskovec J, Chrudimsky T, Vancova M, et al. (2008) A photosynthetic alveolate closely related to apicomplexan parasites. Nature 451: 959–963.RB MooreM. OborníkJ. JanouskovecT. ChrudimskyM. Vancova2008A photosynthetic alveolate closely related to apicomplexan parasites.Nature451959963

27. Van de Peer Y, De Wachter R (1997) Evolutionary relationships among the eukaryotic crown taxa taking into account site-to-site rate variation in 18S rRNA. J Mol Evol 45: 619–630.Y. Van de PeerR. De Wachter1997Evolutionary relationships among the eukaryotic crown taxa taking into account site-to-site rate variation in 18S rRNA.J Mol Evol45619630

28. Harper JT, Waanders E, Keeling PJ (2005) On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes. Int J Syst Evol Microbiol 55: 487–496.JT HarperE. WaandersPJ Keeling2005On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes.Int J Syst Evol Microbiol55487496

29. McFadden GI, Reith ME, Munholland J, Lang-Unnasch N (1996) Plastid in human parasites. Nature 381: 482.GI McFaddenME ReithJ. MunhollandN. Lang-Unnasch1996Plastid in human parasites.Nature381482

30. Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RH, et al. (2006) Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science 313: 1261–1266.BM TylerS. TripathyX. ZhangP. DehalRH Jiang2006Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis.Science31312611266

31. Grauvogel C, Reece KS, Brinkmann H, Petersen J (2007) Plastid isoprenoid metabolism in the oyster parasite Perkinsus marinus connects dinoflagellates and malaria pathogens–new impetus for studying alveolates. J Mol Evol 65: 725–729.C. GrauvogelKS ReeceH. BrinkmannJ. Petersen2007Plastid isoprenoid metabolism in the oyster parasite Perkinsus marinus connects dinoflagellates and malaria pathogens–new impetus for studying alveolates.J Mol Evol65725729

32. Stelter K, El-Sayed NM, Seeber F (2007) The expression of a plant-type ferredoxin redox system provides molecular evidence for a plastid in the early dinoflagellate Perkinsus marinus. Protist 158: 119–130.K. StelterNM El-SayedF. Seeber2007The expression of a plant-type ferredoxin redox system provides molecular evidence for a plastid in the early dinoflagellate Perkinsus marinus.Protist158119130

33. Teles-Grilo ML, Tato-Costa J, Duarte SM, Maia A, Casal G, et al. (2007) Is there a plastid in Perkinsus atlanticus (Phylum Perkinsozoa)? Eur J Protistol 43: 163–167.ML Teles-GriloJ. Tato-CostaSM DuarteA. MaiaG. Casal2007Is there a plastid in Perkinsus atlanticus (Phylum Perkinsozoa)?Eur J Protistol43163167

34. Matsuzaki M, Kuroiwa H, Kuroiwa T, Kita K, Nozaki H (2008) A cryptic algal group unveiled: a plastid biosynthesis pathway in the oyster parasite Perkinsus marinus. Mol Biol Evol 25: 1167–1179.M. MatsuzakiH. KuroiwaT. KuroiwaK. KitaH. Nozaki2008A cryptic algal group unveiled: a plastid biosynthesis pathway in the oyster parasite Perkinsus marinus.Mol Biol Evol2511671179

35. Reyes-Prieto A, Moustafa A, Bhattacharya D (2008) Multiple genes of apparent algal origin suggest ciliates may once have been photosynthetic. Curr Biol 18: 956–962.A. Reyes-PrietoA. MoustafaD. Bhattacharya2008Multiple genes of apparent algal origin suggest ciliates may once have been photosynthetic.Curr Biol18956962

36. Slamovits CH, Keeling PJ (2008) Plastid-derived genes in the nonphotosynthetic alveolate Oxyrrhis marina. Mol Biol Evol 25: 1297–1306.CH SlamovitsPJ Keeling2008Plastid-derived genes in the nonphotosynthetic alveolate Oxyrrhis marina.Mol Biol Evol2512971306

37. Iida K, Takishita K, Ohshima K, Inagaki Y (2007) Assessing the monophyly of chlorophyll-c containing plastids by multi-gene phylogenies under the unlinked model conditions. Mol Phylogenet Evol 45: 227–238.K. IidaK. TakishitaK. OhshimaY. Inagaki2007Assessing the monophyly of chlorophyll-c containing plastids by multi-gene phylogenies under the unlinked model conditions.Mol Phylogenet Evol45227238

38. Bodyl A (2005) Do plastid-related characters support the chromalveolate hypothesis? J Phycol 41: 712–719.A. Bodyl2005Do plastid-related characters support the chromalveolate hypothesis?J Phycol41712719

39. Bodyl A, Moszczynski K (2006) Did the peridinin plastid evolve through tertiary endosymbiosis? A hypothesis. Eur J Phycol 41: 435–448.A. BodylK. Moszczynski2006Did the peridinin plastid evolve through tertiary endosymbiosis? A hypothesis.Eur J Phycol41435448

40. Sanchez-Puerta MV, Delwiche CF (2008) A hypothesis for plastid evolution in chromalveolates. J Phycol 44: 1097–1107.MV Sanchez-PuertaCF Delwiche2008A hypothesis for plastid evolution in chromalveolates.J Phycol4410971107

41. Nosenko T, Lidie KL, Van Dolah FM, Lindquist E, Cheng JF, et al. (2006) Chimeric plastid proteome in the Florida “red tide” dinoflagellate Karenia brevis. Mol Biol Evol 23: 2026–2038.T. NosenkoKL LidieFM Van DolahE. LindquistJF Cheng2006Chimeric plastid proteome in the Florida “red tide” dinoflagellate Karenia brevis.Mol Biol Evol2320262038

42. Archibald JM, Rogers MB, Toop M, Ishida K, Keeling PJ (2003) Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natans. Proc Natl Acad Sci U S A 100: 7678–7683.JM ArchibaldMB RogersM. ToopK. IshidaPJ Keeling2003Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natans.Proc Natl Acad Sci U S A10076787683

43. Abascal F, Zardoya R, Posada D (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21: 2104–2105.F. AbascalR. ZardoyaD. Posada2005ProtTest: selection of best-fit models of protein evolution.Bioinformatics2121042105

44. Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688–2690.A. Stamatakis2006RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.Bioinformatics2226882690

45. Whelan S, Goldman N (2001) A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 18: 691–699.S. WhelanN. Goldman2001A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach.Mol Biol Evol18691699

46. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696–704.S. GuindonO. Gascuel2003A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.Syst Biol52696704

47. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572–1574.F. RonquistJP Huelsenbeck2003MrBayes 3: Bayesian phylogenetic inference under mixed models.Bioinformatics1915721574

48. Schmidt HA, Strimmer K, Vingron M, von Haeseler A (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18: 502–504.HA SchmidtK. StrimmerM. VingronA. von Haeseler2002TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing.Bioinformatics18502504

49. Shimodaira H, Hasegawa M (2001) CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17: 1246–1247.H. ShimodairaM. Hasegawa2001CONSEL: for assessing the confidence of phylogenetic tree selection.Bioinformatics1712461247