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Peer-reviewed

Research Article

The Plastid Genome of the CryptomonadTeleaulax amphioxeia

The Plastid Genome of the CryptomonadTeleaulax amphioxeia

  • Jong Im Kim, 
  • Hwan Su Yoon, 
  • Gangman Yi, 
  • Hyung Seop Kim, 
  • Wonho Yih, 
  • Woongghi Shin
PLOS
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Figures

Fig 1
Table 1
Table 2
Table 3
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Abstract

Teleaulax amphioxeia is a photosynthetic unicellular cryptophyte alga that is distributed throughout marine habitats worldwide. This alga is an important plastid donor to the dinoflagellateDinophysis caudata through the ciliateMesodinium rubrum in the marine food web. To better understand the genomic characteristics ofT.amphioxeia, we have sequenced and analyzed its plastid genome. The plastid genome sequence ofT.amphioxeia is similar to that ofRhodomonas salina, and they share significant synteny. This sequence exhibits less similarity to that ofGuillardia theta, the representative plastid genome of photosynthetic cryptophytes. The gene content and order of the three photosynthetic cryptomonad plastid genomes studied is highly conserved. The plastid genome ofT.amphioxeia is composed of 129,772 bp and includes 143 protein-coding genes, 2 rRNA operons and 30 tRNA sequences. The DNA polymerase III gene (dnaX) was most likely acquired via lateral gene transfer (LGT) from a firmicute bacterium, identical to what occurred inR.salina. On the other hand, thepsbN gene was independently encoded by the plastid genome without a reverse transcriptase gene as an intron. To clarify the phylogenetic relationships of the algae with red-algal derived plastids, phylogenetic analyses of 32 taxa were performed, including three previously sequenced cryptophyte plastid genomes containing 93 protein-coding genes. The stramenopiles were found to have branched out from the Chromista taxa (cryptophytes, haptophytes, and stramenopiles), while the cryptophytes and haptophytes were consistently grouped into sister relationships with high resolution.

Citation:Kim JI, Yoon HS, Yi G, Kim HS, Yih W, Shin W (2015) The Plastid Genome of the CryptomonadTeleaulax amphioxeia. PLoS ONE 10(6): e0129284. https://doi.org/10.1371/journal.pone.0129284

Academic Editor:Jude Marek Przyborski, Philipps-University Marburg, GERMANY

Received:January 5, 2015;Accepted:May 6, 2015;Published: June 5, 2015

Copyright: © 2015 Kim et al. This is an open access article distributed under the terms of theCreative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Data Availability:The genome sequence is deposited in GenBank with the accession number "KP889713".

Funding:This research was supported by the National Research Foundation (NRF) of Korea funded by the Ministry of Science, ICT & Future Planning, Basic Science Research Program (MSIP; NRF-2013R1A1A3012539) to J.I. Kim; the Ministry of Education (NRF-2013R1A1A2063006) to G. Yi; the Mid-career Researcher Program by MSIP (NRF-C1ABA001-2010-0020700) to W. Yih; NRF (MEST: 2014R1A2A2A01003588), Korean RDA Next-generation BioGreen21 (PJ009525), the Marine Biotechnology Program (PJT200620) funded by Ministry of Oceans and Fisheries, Korea, to H.S. Yoon; and the Korea Polar Research (Grant PE15020) to W. Shin.

Competing interests: The authors have declared that no competing interests exist.

Introduction

The genusTeleaulax belongs to the class Cryptophyceae and is an ecologically important component of marine phytoplankton communities [1–7]. In addition to its importance in the trophic web,Teleaulax is significant in the context of kleptoplasty due to its complex relationship with the grazer ciliateMesodinium rubrum and its indirect relationships with dinoflagellates, such asDinophysis andAmylax [8–12].

Since Charles Darwin described an extensive reddish discoloration in the sea south of Valparaiso near the southern boundary of the Peru coastal current [13], the marine ciliateMesodinium rubrum has been identified worldwide as a bloom-forming ciliate [12,14–21].Mesodinium rubrum contains functional chloroplasts derived from cryptophycean species of the generaTeleaulax andGeminigera [22–26]. In addition, phototrophic dinoflagellate species of the generaDinophysis andAmylax also contain plastids of cryptophyte origin, particularly ofTeleaulax amphioxeia andGeminigera cryophila origin [9,27–34]. Cryptophyte plastids were acquired by the marine ciliateM.rubrum and then transferred to dinoflagellates via feeding. Recently, Kim et al. [9] have revealed thatDinophysis caudata feeds on the mixotrophic ciliateM.rubrum and secondarily retains the plastids ofT.amphioxeia, transforming them into stellate compound chloroplasts. Kleptoplasty is a well-known phenomenon occurring in dinoflagellates [27,29,30], ciliates [24], and sacoglossan sea slugs [35,36], which sequester chloroplasts from algal food resources. However, the longevity of a photosynthetically functional plastid in predator cytoplasm depends on the kleptoplast genome itself [37] and not on the lateral transfer of algal nuclear genes to the predator [38,39]. Therefore, plastid genome analysis ofT.amphioxeia may be important to better understand the kleptoplastic relationship betweenT.amphioxeia andM.rubrum.

Cryptophytes have unique secondary plastids and possess four genomes (host nuclear, mitochondrial, plastid, and nucleomorph genomes). Cryptophyte plastids display four envelope membranes, with a eukaryotic compartment between the outer and inner membrane pairs. Plastid-containing cryptophytes are important models for plastid evolution through secondary endosymbiosis between phagotrophic and photoautotrophic eukaryotes [40,41], a process that has presumably also occurred in several other protist lineages [42,43]. Nucleomorphs derived from red algal nuclei persist in the remnant cytosol of engulfed algal cells, between the inner and outer pairs of plastid membranes [44–46]. To date, nine cryptomonad organelle genomes, including 3 plastid, 2 mitochondrial, 3 nucleomorph and 1 nuclear genome, have been sequenced. For example, the plastid [47] and mitochondrial genomes [48] ofRhodomonas salina have been completely sequenced, and the nucleomorph and mitochondrial genomes ofHemiselmis andersenii have also been published [49,50]. In addition, the nuclear [46], nucleomorph [51] and plastid genomes [52] of the model cryptomonad speciesGuillardia theta have been sequenced, as well as the nucleomorph [53] and plastid genomes [54] of the nonphotosynthetic cryptomonadCryptomonas paramecium. More recently, theChroomonas mesostigmatica nucleomorph genome was also sequenced [55].

Here, we present the complete plastid genome ofTeleaulax amphioxeia together with analyses of its genome structure and gene content. This plastid genome sequence is the first to be reported with the full characterization of the plastid genes in the genusTeleaulax. Comparative analysis was conducted using the genome ofT.amphioxeia and three published plastid genomes of the cryptophytesCryptomonas paramecium,Guillardia theta, andRhodomonas salina. To identify the taxonomic relationships and evolutionary history of algae with red-algal derived plastid, we reconstructed plastid phylogenies based on 93 protein-coding genes from the currently available genomic data, using 28 plastid genomes, including the genomes of 4 cryptophytes, 4 haptophytes, 12 stramenopiles, and 9 red algal species. Additionally, we demonstrate herein the conserved properties and variability of the plastid genomes among the cryptophyte lineages. Our genetic information and plastid genome comparisons among the cryptophytes provide important insights into both the evolution of organelle genomes and the harmful algae-associated trophic web in marine ecosystems.

Materials and Methods

DNA isolation and sequencing

A culture derived from a single-cell isolate ofTeleaulax amphioxeia collected from Gomso Bay, Korea (35° 40’ N, 126° 40’ E), which was established in a previous study [56], was selected for genome sequencing. DNA was extracted from the cultivated sample using a QIAGEN DNEasy Blood Mini Kit (QIAGEN, Valencia, CA, USA), following the manufacturer’s instructions. A sequencing library was prepared using an Ion Xpress Plus gDNA Fragment Library Preparation Kit and an Ion OneTouch 200 Template Kit v2 DL (Life Technologies, San Francisco, CA, USA) according to the manufacturer’s protocol and sequenced with an Ion Torrent Personal Genome Machine (PGM) at the Yoon laboratory at Sungkyunkwan University (Suwon, Korea) using an Ion PGM Sequencing 200 Kit v2 (Life Technologies, San Francisco, CA, USA).

Genome assembly and plastid contig selection

The data were trimmed (i.e., base = 80 bp, error threshold = 0.05, n ambiguities = 2) using CLC Genomics Workbench (CLC Bio, Aarhus, Denmark) prior to producing ade novo assembly with the default options (automatic bubble size, minimum contig length = 1,000 bp). The raw reads were then mapped to the assembled contigs (similarity = 95%, length fraction = 75%), and regions with no evidence of short-read data were removed (up to 1,000 bp). The resulting assembly had an average coverage of ~15x and included one large contig of 191,270 bp that was determined to be the plastid genome based on the following criteria: (1) BLAST searches of commonly known plastid genes against the entire assembly produced hits on this contig with significant e-values (e#10220); and (2) the genome size of 129,772 bp is consistent with the sizes of other photosynthetic cryptophyte plastid genomes, which range from 121 (Guillardia theta NC000926) to 136 kbp (Rhodomonas salina NC009573). Each contig that contained a plastid sequence was then manually aligned with Genetic Data Environment (MacGDE2.5) program [57], and a consensus sequence was produced. The assemblies were further verified by examining the paired-end distance and depth after re-mapping the reads to the assembled sequence.

Genome annotation and sequence analysis

Databases of protein-coding genes and rRNA and tRNA genes were compiled from all previously sequenced cryptophyte plastid genomes. Preliminary annotations for the protein-coding genes were performed using GeneMarkS (http://opal.biology.gatech.edu/genemarks.cgi) to identify coding sequences (CDSs) and generate a basic option. The final annotation file was evaluated with Geneious Pro 5.1.7 (http://www.geneious.com/) using ORF Finder with the standard genetic code. After the alignments for each gene were completed, they were checked manually, and the corresponding open reading frames (ORFs) in the genome sequences were annotated. Annotations of ORFs with putative functional domains were included in the genome.

To identify the tRNA sequences, the plastid genome was submitted to tRNAscan-SE version 1.2.1 server (http://lowelab.ucsc.edu/tRNAscan-SE/). The genome was searched with the default settings, using the “Mito/Chloroplast” model. To determine the rRNA sequences, a set of known plastid rRNA sequences was extracted from the plastid genome ofRhodomonas salina and used as query sequences to search theR.salina genome using BLASTn. The annotated sequence was deposited into NCBI GenBank database as KP899713. The graphical gene map was designed with OrganellarGenomeDRAW program (http://ogdraw.mpimp-golm.mpg.de/).

Gene arrangement comparisons

The three published cryptophyte plastid genomes with annotations were downloaded from GenBank [48,52,54]. For the structure and arrangement comparisons, the genomes were aligned using Mauve Genome Alignment version 2.2.0 [58] with the default settings. To aid in visualization, we designated the beginning of thetrnY andrpl19 markers as position 1 in each genome.

Phylogenetic analysis

Phylogenetic analysis was conducted to determine the taxonomic relationships and evolution of the red algal-derived plastid. A dataset was created, combining 93 homologous protein-coding gene sequences in 29 plastid genomes from red algal plastid-bearing organisms, including 4 cryptophytes, 4 haptophytes, 12 stramenopiles and 9 red algae (S1 Table). The sequences of 2 chlorophytes and 1 glaucophyte were used as outgroup taxa to root the tree. The dataset was concatenated into 18,181 amino acids and a single continuous sequence of 56,565 nucleotides to initiate alignment by eye using MacGDE2.5 program (S2 Table).

Maximum likelihood (ML) phylogenetic analyses were performed using RAxML version 8.0.0 [59] with the Le and Gascuel with gamma (LG+GAMMA) model [60] for the amino acid data selected by ProtTest 3 [61] and with the general time-reversible plus gamma (GTR+GAMMA) model for the nucleotide data [62]. We used 1,000 independent tree inferences and identified the best tree with the-# option within the program. The gamma correction values and the proportion of invariable sites in the combined dataset were obtained automatically by the program (S3 Table). Bootstrap values (MLBS) were calculated using 1,000 replicates with the same substitution model.

Maximum parsimony (MP) and distance (neighbor-joining; NJ) trees were constructed from a combined dataset with PAUP* using a heuristic search algorithm with the following settings: 100 random sequence-addition replicates, tree bisection and reconnection (TBR) branch swapping, MulTrees, all characters unordered and unweighted, and branches with a maximum length of zero collapsed to yield polytomies. The MLBS for the resulting nodes were assessed using bootstrapping with 1,000 iterations on each tree. For NJ analyses, we analyzed the dataset using the Modeltest parameters (S3 Table).

ThednaX protein encoded by theT.amphioxeia plastid was used as a query to identify and retrieve a diverse set ofdnaX, polymerase III gamma/tau and replication factor C proteins from public protein databases. The BLAST search was resulted the conserved protein domain models Cog2812 and TIGR02397. We selected 220 unambiguously aligned amino acid sequences from 90 homologous taxa. Sequences were aligned using MacGDE 2.5 and analyzed using RAxML as described above.

Results and Discussion

The plastid genome ofTeleaulax amphioxeia

The plastid genome ofTeleaulax amphioxeia was found to be 129,772 bp in size and is illustrated inFig 1. TheT.amphioxeia genome size is similar to those ofGuillardia theta andRhodomonas salina. Eighty percent of theT.amphioxeia plastid genome was predicted to consist of coding regions (Table 1), including structural RNA genes, similar to the percentages of coding regions inG.theta (87.7%),Cryptomonas paramecium (87.0%) andR.salina (80.8%). The proportion of intergenic space inT.amphioxeia was 15.5%, which is comparable to those of algae with red-algal derived plastid and other red algal plastid descendants (i.e., haptophytes and stramenopiles). The G+C content was 34.21% forT.amphioxeia, which is similar to those ofC.paramecium (38%),R.salina (34%), andG.theta (32%). The overall G+C content was highly similar to those of other chromists and red algae [52,63–65].

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Fig 1. Circular map of the plastid genome of the cryptophyteTeleaulax amphioxeia.

All of the genes are transcribed in a clockwise direction. Note the dense gene arrangement and the single large intergenic region. The protein-coding genes and ribosomal RNA and transfer RNA genes are labeled inside or outside of the circle. The genes are color coded according to the functional categories listed in the index below the map.

https://doi.org/10.1371/journal.pone.0129284.g001

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Table 1. Characteristics of the cryptophyte plastid genome analyzed in this study.

https://doi.org/10.1371/journal.pone.0129284.t001

TheT.amphioxeia plastid genome was predicted to encode 179 genes, including 2 rRNA operons and 30 tRNA genes (Fig 1 andS4 Table). The ochre termination codon TAA was determined to be used inT.amphioxeia 86.7% of the time, and the amber (TAG) and opal (TGA) codons were found to be used 10.5% and 2.8% of the time, respectively. Seven genes contained a valine (GTG) rather than a methionine start codon (chll,hlpA,rpl23,rps3,rps8,rps13, andpsbC), and a TTG start codon was present in one gene (ycf65). A set of 136 protein-coding genes was shared by all of the plastid genomes evaluated in this study, while 170 genes were unique amongst the three photosynthetic cryptophyte species, except forC.paramecium, which is an osmotrophic, colorless species (S1 Table). An additional 107 genes, including 76 protein-coding genes were shared betweenT.amphioxeia andC.paramecium.

The four cryptomonads shared a similar tRNA gene set, with 30 tRNAs inT.amphioxeia, 29 tRNAs inC.paramecium, 30 tRNAs inG.theta, and 31 tRNAs inR.salina (Table 2), and their tRNAs included redundant isotypes for the amino acids 2 glycine, 2–3 serine, 3 arginine, and 3 leucine and three distinct methionine tRNAs.

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Table 2. tRNA sequences present in the cryptophyte plastid genome.

https://doi.org/10.1371/journal.pone.0129284.t002

Similar to the two photosynthetic cryptophytes,T.amphioxeia contained two small (approximately 4.8 kb) and almost identical repeats of rRNA operons encoding 16S, 23S and 5S rRNAs and the two tRNA genestrnA (GAT) andtrnI (TGC). Inverted repeats (IRs) consisting of rRNA operons (and in some cases, a few additional genes) were generally found in the plastid genomes, which represents an ancestral feature [66–68]. These repeats are present in theG.theta andR.salina genomes [47,52], as well as in the haptophyteEmiliania huxleyi [65] and several diatoms [69].C.paramecium lacks this IR arrangement, and it contains only one rRNA operon in a 16S-trnI-trnA-23S-5S configuration [54].

Four instances of overlapping genes were found inT.amphioxeia, many of which were also identified in the other chromist plastid genomes. ThepsbD-psbC overlap found inT.amphioxeia existed in all of the sequenced chromist genomes, although the amount of overlap varied. Overlaps involvingatpD-atpF andrpl4-rpl23 were common in the stramenopiles and cryptophytes, but not in the haptophytes. Single-nucleotide overlaps betweenrpl16-rpl29 andorf142-orf146 were present inT.amphioxeia, similar to what was previously found inR.salina andG.theta.

Gene content and synteny

TheT.amphioxeia plastid genome was found to contain 143 predicted protein-coding genes (Table 3 andFig 1). Overall, this genome shows a high degree of syntenic conservation with that ofR.salina [47]. The gene order was generally well conserved among the four cryptomonad plastid genomes. Large tracts of complete gene order conservation were observed, such as the highly conserved and co-expressed ribosomal protein genes and theatp gene cluster (Fig 1).

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Table 3. List of genes in theTeleaulax amphioxeia plastid genome (143 total).

https://doi.org/10.1371/journal.pone.0129284.t003

Many proteins associated with cell and organelle division were found to be encoded within theT.amphioxeia plastid genome (Table 3) by genes includinghlpA (encoding a chromatin-associated architectural protein),dnaB (encoding a DNA helicase), andminD andminE (encoding proteins that prevent the creation of DNA-less “minicells” during division [70]). Specifically,hlpA, which encodes a histone-like protein, has been previously identified in the two photosynthetic cryptomonads. This gene is also present in the genomes of the red algaeCyanidioschyzon merolae [64] andGaldieria sulphuraria (NC024665), but it is absent from the haptophyte and stramenopile plastid genomes. The ApicomplexanhlpA gene was present in the nuclear genome [71–73]. Additional chaperone protein-encoding genes, such asgroEL anddnaK (a member of thehsp70 family), were present in theT.amphioxeia plastid genome, and their products presumably participate in protein import and folding [74]. TheftsH gene, which encodes a protease responsible for the removal of damaged D1 protein from the photosystem II (PSII) complex [37], was identified in the photosynthetic speciesT.amphioxeia,R.salina andG.theta but not inC.paramecium.

The components of a protein translocation system, thesec transport system, were maintained (secA,secG, andsecY), and thesufB andsufC genes were also present in theT.amphioxeia plastid genome, the products of which play roles in iron-sulfur cluster assembly [75]. The identification of thechlI gene in theT.amphioxeia plastid genome may provide additional insights into the role of this magnesium chelatase component in plastid-to-nucleus signaling [76]. The gene encoding thesec-independent transport proteintatC was also present, as was the proteolytic degradation pathway geneclpC. The plastid ofT.amphioxeia thus appears to have retained the ability to import necessary proteins from the cytoplasm (e.g., proteins linked to cell division) and can mediate their degradation.

TheT.amphioxeia plastid genome possesses a nearly full complement of the 8atp synthase subunit genes found in the other cryptomonads. These genes showed varying degrees of sequence conservation in the four cryptomonads. A total of 24rpl genes encoding the 50S ribosomal subunit protein and 18rps genes encoding the 30S ribosomal subunit protein were also found inT.amphioxeia. Additional genes (includingcpeB,ilvB,ilvH, andinfB) were present in the plastid genome of the cryptophyte but were absent from those of the stramenopiles and/or haptophytes. The three pseudogenes (chlB,chlN, andchlL) encoding light-independent protochlorophyllide reductase, which is involved in the light-independent synthesis of chlorophyll [77], were identified in theR.salina plastid genome but not in theT.amphioxeia orG.theta genome (Table 3). The reverse transcriptase gene, which is present as an intron within the photosystem genepsbN, was identified inR.salina [47]; however, thepsbN gene in theT.amphioxeia plastid genome lacked the reverse transcriptase gene.

Photosynthetic genes

The gene encoding the β subunit of phycoerythrin (cpeB), which is part of the phycobiliprotein complex in cryptomonads, was present in the plastid genomes ofT.amphioxeia,R.salina andG.theta [47,52] but was missing from that ofC.paramecium [54]. The photosynthetic regulator and electron transfer geneftrB was present in all of the photosynthetic cryptophyte plastids. TherbcL andrbcS genes encoding the large and small subunits of ribulose 1, 5-bisphosphate carboxylase/oxygenase were present in all of the cryptophyte plastids, includingC.paramecium.

Thepsa andpsb gene families encode the protein subunits of photosystem I (PSI) and PSII, respectively. A total of 11psa and 18psb genes were present in the plastid genomes of the three photosynthetic cryptomonads [47,52]. The loss of thepsa andpsb genes from the plastid genome ofC.paramecium accounts for approximately 7.5 kbp of missing plastid DNA [54].

The products of the photosyntheticpet gene family form a complex required for oxygenic photosynthesis, particularly for noncyclic electron flow mediated by the cytochrome b6f complex [78]. The 8pet genes were present in the plastid genomes ofT.amphioxeia,G.theta, andR.salina; however, they were missing from that of inC.paramecium, with the curious exception ofpetF. In other organisms that have secondarily lost their photosynthetic abilities (e.g.,Euglena longa andAneura mirabilis), thepet genes are either missing or have become pseudogenes [79,80].

Lateral gene transfer

The most unexpected finding in theT.amphioxeia andR.salina plastid genomes was the presence of a gene with strong similarity todnaX, which encodes the tau/gamma components of bacterial DNA polymerase [47,81,82]. Phylogenetic analysis revealed that theR.salina andT.amphioxeia dnaX genes were acquired by lateral gene transfer (LGT), with the direct transfer ofT.amphioxeia dnaX from a cryptophyte alga. ThednaX proteins ofR.salina andT.amphioxeia were found to be derived from firmicutes, i.e., parasitic mycoplasmas and related organisms [47] (S1 Fig).

Plastid genome rearrangements

Mauve pairwise alignments of theT.amphioxeia genome with each of the other four plastid genomes used in this study are shown inFig 2. All three of the photosynthetic cryptophytes were found to have highly conserved gene arrangements and contents. All of the cryptophyte plastid genes were located in gene clusters that could be readily reconstructed from theC.paramecium genome via a small number of inversion events (Fig 2). The three photosynthetic cryptophyte plastid genomes were co-linear.C.paramecium had the smallest rearrangement distance, and almost all photosynthetic genes were found to be lost compared with the other plastid genomes; furthermore, it differed from the photosynthetic cryptophyte by only three inversions, suggesting that most of its photosynthetic genes were lost after it acquired phototrophy.

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Fig 2. Overview of the red algal plastid genomes.

Linearized maps of the completeT.amphioxeia plastid genome is compared with those of other cryptophytes. Color-coded syntenic blocks are shown above each genome, and gene maps are shown below each genome. The syntenic blocks above the horizontal line are on the same strand, and those below the line are on the opposite strand. The horizontal bars inside of the syntenic blocks indicate sequence conservation. The block boundaries correspond to sites at which inversion events occurred. On the gene maps, the genes above the horizontal line are transcribed from left to right, and those below the horizontal line are transcribed from right to left. The rRNA operons are shown in red.

https://doi.org/10.1371/journal.pone.0129284.g002

Phylogeny

Phylogenomic analysis was completed using a concatenate of 93 proteins encoded by 29 complete plastid genomes from algae with red-algal derived plastid (including 4 cryptophyte, 4 haptophyte, 12 stramenopile, and 9 rhodophyte genomes) using 3 outgroups (2 chlorophyte and 1 glaucophyte genome). The sequences of chlorophyll c-containing dinoflagellates were not included due to the limited sizes of their plastid genomes. RAxML trees based on 18,180 amino acids (Fig 3A) and 56,569 nucleotides (Fig 3C) differed at the rhodophyte lineages. The cryptophyte clade was strongly supported as a monophyletic clade, which is congruent with gene synteny (Fig 3B). The resulting phylogeny suggested that the cryptophytes had sister relationships with the haptophytes in both trees. In the amino acid-based tree (Fig 3A), the Cyanidiophyceae clade was located at the base of the red-algal derived lineage, but all red algal species in the Florideophyceae and Bangiophyceae clades branched out as sisters of the Cryptophyta/Haptophyta lineage, with the exclusion of the Cyanidiophyceae clade [47,54,83]. In contrast with the protein ML tree, a tree based on a combined dataset of 93 protein-coding gene sequences (Fig 3C) showed that the Rhodophyta was a monophyletic clade sistered with taxa of hacrobian lineages.

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Fig 3. Phylogenetic tree of the cryptophyte plastids.

(A) RAxML phylogeny constructed from a concatenate of 93 proteins (18,180 amino acids). The ML and MP bootstrap values are shown above or below the branches. (B) A simple overview of cryptophyte plastid gene synteny. (C) RAxML phylogeny constructed based on 93 protein-coding genes (56,569 nucleotides). The ML, MP and NJ bootstrap values are shown above or below the branches. The bold branches indicate strongly supported values (ML, MP, and NJ = 100%). The asterisks indicate supported values = 100%, and the dashes indicate values with < 50% support. The scale bar depicts the number of substitutions/site.

https://doi.org/10.1371/journal.pone.0129284.g003

Previous phylogenetic studies have demonstrated that cryptophyte, stramenopile, and haptophyte plastids are derived from a red alga [66,84,85]. Among the three groups (cryptophytes, haptophytes, and stramenopiles), the stramenopiles were branched outside of a cluster of chromist taxa, while the cryptophytes and haptophytes were consistently branched together as the closest relatives. These results differ from those of other analyses of five plastid genes (16S rRNA,psaA,psbA,rbcL, andtufA), which have indicated that the stramenopiles and haptophytes are grouped together [86,87]. The common ancestry of hacrobian (cryptophyte and haptophyte) plastids is also strongly supported ([47,44,83] in this study), consistent with the LGT ofrpl36 in the cryptophyte and haptophyte plastid genomes as evidence of the sisterhood of these 2 groups and the exclusion of stramenopiles [88]. The findings of nuclear gene analyses also support this interpretation [89,90]. However, phylogenomic data reported by other studies strongly suggest that cryptophytes and haptophytes have separate origins [91,92]. These analyses have indicated that the haptophytes are sisters of the SAR (Stramenopile, Alveolate, and Rhizaria) group and that the cryptophytes are grouped together with the katablepharids as a broken “hacrobiana” taxa [92]. According to recent model of serial plastid endosymbioses [93], the cryptophyte plastid is more closely related to the stramenopile plastid than the haptophyte plastid. However, our phylogenies suggest the grouping together of the cryptophytes and haptophytes with moderate to high bootstrap support.

Conclusions

We have determined the plastid genome sequence of the cryptophyteT.amphioxeia, which is the first plastid genome reported for the genusTeleaulax. As increasing numbers of genomes are annotated and published, comparative genomic analyses of secondary plastids will provide new insights into the patterns and processes of endosymbiosis, particularly in lineages with red-algal derived plastids. The genes that are common to all cryptophyte plastids are likely essential for plastid function and represent a useful starting point for the future annotation of plastid genomes. Several previous studies focusing on cryptophyte plastids have shown the potential of plastid genome research for answering unresolved questions about the history of these lineages, increasing our understanding of the evolution of cryptophyte plastids. The addition of theT.amphioxeia plastid genome to the suite of complete plastid genome sequences increases the breadth of plastid genomes that have been sampled to date and will help to identify common trends in organellar genomes. Many studies have shown that theTeleaulax species donated its plastid to the ciliateMesodinium rubrum and then to the dinoflagellatesDinophysis caudata andAmylax triacantha through the trophic web and that these species have retained the acquired plastid and produce water blooms in marine ecosystems. OurT.amphioxeia plastid genome data will provide clues about the complicated plastid relationships between the donor cryptophyteTeleaulax and retainers, such as the ciliateMesodinium and the dinoflagellatesDinophysis andAmylax.

Supporting Information

S1 Fig.The phylogenetic tree constructed from 90dnaX homologs.

RAxML bootstrap values are shown above the branches with > 50% support. The scale bars indicate the number of substitutions/amino acid site.

https://doi.org/10.1371/journal.pone.0129284.s001

(EPS)

S1 Table.Cryptophyte plastid genome alignments.

https://doi.org/10.1371/journal.pone.0129284.s002

(XLSX)

S2 Table.Concatenated data set of protein-coding genes for constructing phylogenetic tree.

https://doi.org/10.1371/journal.pone.0129284.s003

(XLSX)

S3 Table.Evolutionary models, log likelihood values (-lnL), and model parameters proposed by ProtTest3 for amino acids [61] and Modeltest 3.7 for nucleotides [93].

https://doi.org/10.1371/journal.pone.0129284.s004

(DOCX)

S4 Table.The gene contents and arrangement of theTeleaulax amphioxeia plastid genome.

https://doi.org/10.1371/journal.pone.0129284.s005

(DOCX)

Author Contributions

Conceived and designed the experiments: JIK WS. Performed the experiments: JIK. Analyzed the data: JIK GY. Contributed reagents/materials/analysis tools: HSY HSK WY. Wrote the paper: JIK WS.

References

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