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Complete Plastid Genome of the Recent Holoparasite Lathraea squamaria Reveals Earliest Stages of Plastome Reduction in Orobanchaceae

  • Tahir H. Samigullin ,

    samigullin.t.h@gmail.com

    Affiliation A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia

  • Maria D. Logacheva,

    Affiliations A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, Pirogov Russian National Research Medical University, Moscow, Russia

  • Aleksey A. Penin,

    Affiliations A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia

  • Carmen M. Vallejo-Roman

    Affiliation A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia

Complete Plastid Genome of the Recent Holoparasite Lathraea squamaria Reveals Earliest Stages of Plastome Reduction in Orobanchaceae

  • Tahir H. Samigullin, 
  • Maria D. Logacheva, 
  • Aleksey A. Penin, 
  • Carmen M. Vallejo-Roman
PLOS
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Abstract

Plants from the family Orobanchaceae are widely used as a model to study different aspects of parasitic lifestyle including host–parasite interactions and physiological and genomic adaptations. Among the latter, the most prominent are those that occurred due to the loss of photosynthesis; they include the reduction of the photosynthesis-related gene set in both nuclear and plastid genomes. In Orobanchaceae, the transition to non-photosynthetic lifestyle occurred several times independently, but only one lineage has been in the focus of evolutionary studies. These studies included analysis of plastid genomes and transcriptomes and allowed the inference of patterns and mechanisms of genome reduction that are thought to be general for parasitic plants. Here we report the plastid genome of Lathraea squamaria, a holoparasitic plant from Orobanchaceae, clade Rhinantheae. We found that in this plant the degree of plastome reduction is the least among non-photosynthetic plants. Like other parasites, Lathraea possess a plastome with elevated absolute rate of nucleotide substitution. The only gene lost is petL, all other genes typical for the plastid genome are present, but some of them–those encoding photosystem components (22 genes), cytochrome b6/f complex proteins (4 genes), plastid-encoded RNA polymerase subunits (2 genes), ribosomal proteins (2 genes), ccsA and cemA–are pseudogenized. Genes for cytochrome b6/f complex and photosystems I and II that do not carry nonsense or frameshift mutations have an increased ratio of non-synonymous to synonymous substitution rates, indicating the relaxation of purifying selection. Our divergence time estimates showed that transition to holoparasitism in Lathraea lineage occurred relatively recently, whereas the holoparasitic lineage Orobancheae is about two times older.

Introduction

Photosynthesis has been lost independently numerous times in flowering plant lineages during the transition to a parasitic lifestyle. By recent estimates, approximately 4500 species (~1%) of flowering plants are parasitic [1]. About 80% of these are hemiparasites, i.e. photosynthetically competent plants with various efficiencies of photosynthesis; some parasites can even survive without a host (facultative hemiparasites), though usually they are associated with the host. The largest parasitic family is Orobanchaceae; it consists of ca. 2047 species of 89 genera [2] and includes both a single autotrophic lineage, the genus Lindenbergia Lehm., and all types of parasitism: facultative, obligate hemiparasites, and holoparasites (plants that completely lack photosynthetic activity) [3]. The results of phylogenetic studies indicate that there are at least three (up to five) origins of holoparasitism in Orobanchaceae, one on the branch to Orobancheae (~180 species), another on the branch to Lathraea (5–7 species), the third on the branch to Hyobanche (Harveya) (~70 species) [4, 5, 6, 7].

There are sixteen Orobanchaceae parasitic species for which complete sequences of the plastid genome are now available, including Epifagus virginiana (L.) W.P.C.Barton, the first parasitic plant with a fully sequenced plastome [8], the hemiparasite Schwalbea americana L., and holoparasites Boulardia latisquama F.W.Schultz, Cistanche phelypaea Cout., Conopholis americana (L.) Wallr., Myzorrhiza californica (Cham. & Schltdl.) Rydb., Orobanche crenata Forssk., Orobanche gracilis Sm., Phelipanche purpurea (Jacq.) Soják, Phelipanche ramosa (L.) Pomel [9], Cistanche deserticola Ma [10], Orobanche austrohispanica M.J.Y.Foley, Orobanche densiflora Salzm. Ex. Reut., Orobanche rapum-genistae Thuill., Orobanche cumana Wallr., Orobanche pancicii Beck [11]. All of the holoparasites represent the Orobancheae branch of loss of photosynthesis, thus processes of plastome modification in this clade are well characterized. The plastomes of holoparasites exhibit various degrees of reduction of both gene content and size due to the release of selective constraints after the switchover to parasitic lifestyle [9]. The reduction appears to be a common feature of plastid genome evolution of heterotrophic plants (obtaining nutrients from other plants or from fungi) and to follow a certain path generalized in a model of plastid genome degradation proposed by Barrett and Davis [12, 13]. Increased rate of nucleotide substitution seems to be another general feature that characterizes the nuclear, mitochondrial, and plastid genomes of parasitic plants [14, 15]. Faster rate of plastome nucleotide substitutions was also reported in another group of heterotrophic plants, mycoheterotrophs [16, 17] (but see [18]), and in some photosynthetic plants; in this latter case it is usually correlated with highly rearranged plastid genome [19, 20].

In this study, we report the complete plastid genome of Lathraea squamaria L. (common toothwort)—a non-photosynthetic plant widespread in Europe; it parasitizes on the roots of hazel, alder and other trees. L. squamaria represents the second branch within the Orobanchaceae family where loss of photosynthesis occurred—the Rhinantheae clade (sensu McNeal et al. [5]). In contrast to the Orobancheae clade, where most representatives are non-photosynthetic, the genus Lathraea is the only holoparasitic one in this clade. The plastomes of the Orobancheae clade have been extensively studied, allowing inference of patterns and mechanisms of genome reduction that are thought to be general for parasitic plants [9, 11]. Characterization of the L. squamaria plastome will reveal if these patterns are conserved in other clades. A partial sequence of the plastid genome of its close relative, the facultative hemiparasite Bartsia inaequalis Benth., was recently published [21], and thus provides a basis for comparative analysis.

Materials and Methods

Genome sequencing, assembly, and annotation

Total DNA was extracted using the CTAB method [22] from a single plant growing in the wild in Vorobyevy Gory Park (Moscow, Russia). L. squamaria is not an endangered or protected species and no specific permissions were required for collection. A voucher specimen was deposited at the Herbarium of Moscow State University, Russia (MW, M.D.Logacheva 16). One microgram of DNA was sheared by sonication using a Covaris S220 instrument (Covaris Inc., USA). Further steps of library preparation were performed using a TruSeq DNA Sample Prep Kit (Illumina, USA) according to the manufacturer’s instructions. The library was sequenced using an Illumina HiSeq 2000 instrument with read length 101 bp from each end of the fragment. Resulting reads were processed using the CLC Genomics Workbench v. 5.5 software. The processing included trimming of low quality (q<30) nucleotides and adapters and assembly with the following parameters: bubble size 50 nt, word size 21 nt (automatic choice), minimal contig length 1000 nt, no scaffolding. Among the resulting contigs, we selected those that have high similarity to plastid genomes but do not contain any sequences with similarity to mitochondrial genomes. These contigs were aligned to the Lindenbergia plastome; since no rearrangements relative to Lindenbergia were found within contigs, we assumed that gene order in Lathraea is not changed in general. Based on this assumption, we ordered the contigs and designed primers that match the ends of the contigs for joining them using PCR (the list of primers is available in S1 Table). PCR products were sequenced using Sanger technology (short amplicons, less than 1000 bp) or using Illumina sequencing (longer amplicons). The boundaries of the inverted repeats and single copy regions as well as the lack of petL in the psbE-petG region were verified with PCR followed by Sanger sequencing and by mapping of trimmed read pairs to the assembly and to Lindenbergia petL sequence using the Novoalign V.3.02.10 software (www.novocraft.com). The assembled plastid genome sequence was annotated using the online tool CpGAVAS [23] with default options and checked manually.

Gene expression and editing

To check the presence of spliced transcripts and/or stop-codon RNA editing of several plastid genes (rpoC1, rpoC2, rbcL), we extracted RNA and obtained cDNA of Lathraea. RNA was extracted from two parts–immature fruits and perianth. The cDNA was synthesized with a ThermoScript RT-PCR System for first-strand cDNA synthesis (Invitrogen, USA) with random hexamers used as primers. Then partial cDNA was amplified using gene-specific primers (S1 Table), and the PCR products were cleaned and sequenced using the same primers.

Genome analyses

Phylogenetic analysis was performed using a set of sequences of two rRNA and 35 protein-coding genes from 14 Orobanchaceae plastid genomes (Lindenbergia, NC_022859; Schwalbea, NC_023115; Boulardia, NC_025641; Cistanche phelypaea, NC_025642; Cistanche deserticola, NC_021111; Conopholis, NC_023131; Epifagus, NC_001568; Myzorrhiza, NC_025651; Orobanche crenata, NC_024845; Orobanche gracilis, NC_023464; Phelipanche purpurea, NC_023132; Phelipanche ramosa, NC_023465; Bartsia, KF922718 and Lathraea, NC_027838) and three genomes as an outgroup (Tectona, NC_020098; Salvia, NC_020431; and Solanum lycopesicum, NC_007898). We considered only plastid genes present both in Lathraea and in other plants. Nucleotide sequences were aligned according to the corresponding amino acid alignment produced by MUSCLE [24], and frameshift mutations were corrected manually. The most variable and gap-rich positions were excluded from the alignment using the GBLOCKS program [25], the “softest” settings being used. We tested for saturation of substitutions using DAMBE [26], and the analysis showed no substantial saturation (Iss<Iss.c; P<0.0001) [27]. Phylogenetic trees were reconstructed using the maximum likelihood approach as implemented in RAxML [28]. The GTR+Γ model was used, and the best partition scheme was selected in the PartitionFinder program [29]. ML branch support was assessed via 100 nonparametric bootstrap pseudoreplicates using the “rapid” bootstrap approach. The obtained topology was used in the divergence time estimation with the Bayesian approach as implemented in MCMCtree of PAML 4.8 [30]. We used the GTR+Γ model for nucleotide substitution and the independent rates model for the relaxed molecular clock, which was selected after comparison of marginal likelihoods estimated with the stepping stone sampling (-log likelihoods were 197,259, 198,531, and 202,465 for independent rates, correlated rates, and strict clock, respectively). Three time calibration points obtained by Wikström et al. [31] − the Lamiales–Solanales split at 95–109 million years ago (MYA), the Lamiaceae–Orobanchaceae split at 44–60 MYA, and the Orobanchaceae crown group age at 13–38 million years (MY) − were applied to corresponding nodes as age constraints. To ascertain whether convergence was achieved, three independent MCMC analyses were performed, each with 2×106 steps, the first 2×105 steps being discarded as burn-in. Absolute substitution rate was calculated by dividing the ML tree branch length by the age of the branch.

The codon-based Z-test of neutrality [32] and Tajima’s relative rate test [33] were performed in the MEGA 6 program [34] using a reduced five-species set (Lathraea, Bartsia, Lindenbergia, Tectona, Salvia). Relative rates in Lathraea and Bartsia versus Lindenbergia with Tectona as an outgroup were compared, as well as Lathraea versus Bartsia with Lindenbergia as an outgroup. Comparisons were performed using all concatenated data, as well as separately in groups of genes combined according to their function (ribosomal RNA genes, psa+psb+pet genes, rpo genes, atp genes, rpl+rps genes), and genes accD, clpP, matK, ycf1, and ycf2 were analyzed individually.

The proportion of synonymous and nonsynonymous substitutions per synonymous and nonsynonymous site (dS and dN, respectively) and the ratio ω = dN /dS were assessed with the maximum likelihood approach as implemented in the CODEML program of the PAML package, “branch” models with the F3x4 codon frequency model being used. Evaluation of ω difference in parasitic and photosynthetic plant lineages was performed using the five-species set because of reduction of gene content in Orobancheae plastid genomes. Four hypotheses of different dN /dS ratios for Lathraea versus photosynthetic plants + Bartsia and Bartsia versus photosynthetic plants + Lathraea were tested. Branch models corresponding to the hypotheses were a “one-ratio” model that assumes that all the branches have the same ω-values (model M1), a “three-ratio” model that assumes different ω-values for photosynthetic, hemiparasitic, and holoparasitic branches (model M3), a “two-ratio” model in which the hemiparasitic branch (Bartsia) is allowed to have a separate ω-value (model M2B), and another “two-ratio” model in which the same is allowed in the holoparasitic branch (Lathraea, model M2L). Likelihood ratio tests (LRT) M1 versus M2B and M2L versus M3 examined whether the ω-ratio for the Bartsia branch is different from the background ratio, and LRT M1 versus M2L and M2B versus M3 examined the Lathraea branch. Twice log-likelihood difference between models was tested against the χ2 distribution with one degree of freedom, and P values for multiple comparisons were Bonferroni corrected: the corrected significance level was calculated as α divided by the number of hypotheses being tested.

Evidence for positive selection acting on the accD, clpP, matK, ycf1, ycf2 and atp genes was tested using the full set of taxa (except for those that were lacking the corresponding gene) with the CODEML program in the PAML package using “branch-site” models, which allow ω to vary both among sites in the sequence and across pre-specified branches or clades on the tree. We used a model A and performed test 2 as described in Zhang et al. [35]. When atp genes were used, both terminal and internal branches within the parasitic subtree of Orobanchaceae were tested with Bonferroni correction for multiple comparisons. The same test was applied solely to the Lathraea branch using accD, clpP, matK, ycf1, and ycf2 sequences.

Results

As a result of sequencing, 7,079,624 paired end reads were obtained and assembled into 293 contigs. Among them, we revealed eight contigs of length more than 5,000 nucleotides with high similarity to the plastid genome of Lindenbergia. The coverage of two of them, 251X and 293X, suggesting that they correspond to repeat region, and the coverage of the remaining six was 130X to 143X. The complete plastid genome of L. squamaria is a circular molecule 150,504 bp in length and possesses a typical architecture with a large single-copy (LSC) region of 81,981 bp separated from the 16,061 bp small single-copy (SSC) region by two inverted repeats (IRs), each of 26,231 bp. The GC content is heavily biased (38.13%) (Table 1).

The annotated plastome was deposited in GenBank (accession number NC_027838). The gene map for the plastome of L. squamaria is shown in Fig 1.

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Fig 1. Gene map of the plastid chromosome of Lathraea squamaria.

Genes shown inside the circle are transcribed clockwise; those outside the circle are transcribed counterclockwise. The large single copy region (LSC) and the small single copy region (SSC) are separated by two inverted repeats (IRa and IRb). Pseudogenes are marked by Ψ.

http://dx.doi.org/10.1371/journal.pone.0150718.g001

Among the 78 unique genes present in L. squamaria, a set of 46 protein-coding genes, 30 tRNA genes, and four rRNA genes were identified (S2 Table). No major rearrangements were observed based on alignment to the autotrophic Lindenbergia plastome. The petL gene was completely lost (no reads were mapped to petL of Lindenbergia), and 32 putative pseudogenes (reading frame interrupted by internal stop codons or insertion/deletion events) were detected among the protein coding genes in the Lathraea plastome. Nine plastid genes encoding subunits of the NAD(P)H dehydrogenase complex (ndh genes) became pseudogenes, and ndhC and ndhE ORF persisted. Three genes of photosystem I (psaA, psaB, psaJ), eight of the photosystem II subunit (psbA, psbB, psbC, psbD, psbH, psbJ, psbK, psbT), four members of the cytochrome b6/f complex (petA, petB, petD, petG), and two genes for ribosomal proteins (rps19, rpl23) were detected as pseudogenes. Two of four genes of the plastid-encoded RNA polymerase (PEP), rpoA and rpoC2, were also found to be pseudogenes due to multiple frameshifts in the former and an internal stop codon in the latter. The sequence of the RUBISCO large subunit gene rbcL contains an internal stop codon. Lathraea also has pseudogenes for cytochrome C biogenesis protein ccsA, envelope membrane protein cemA, and the putative photosystem I protein ycf4. No pseudogenes were detected in encoding subunits of the ATP synthase complex (atp genes).

Visual inspection of the mapped reads recovered multiple single nucleotide polymorphisms and indels, which were unevenly scattered over the plastome with rpoC1, rpoB, psaA, psaB, cemA, ycf2, ndhB, and ndhG being the most abundant. Interestingly, within the rbcL sequence one of three single nucleotide variants affected the premature stop codon so that a CGA triplet was restored whereas others did not change amino acids but always restored conserved codons (S1 Appendix), thus at least two different rbcL copies coexist in Lathraea. A second copy location is currently unknown: it may either be transferred to the mitochondrial genome or represent plastid heteroplasmy. Sequencing of the rbcL cDNA showed that both the pseudogene (major variant) and the putatively functional (minor) sequence were transcribed in a proportion similar to a major-to-minor DNA variants ratio suggesting no RNA editing in the Lathraea rbcL sequence (S1 Fig). rpoC2 cDNA sequencing also showed no stop codon editing and confirmed rpoC2 pseudogenization. It should be noted also, that the rpoC1 spliced intron was found in fruits, but no intron processing was detectable in perianth.

Phylogenetic analyses of the coding genes yielded a completely resolved Orobanchaceae tree (Fig 2) with the autotrophic genus Lindenbergia as a basal branch with bootstrap support (BS) 100%.

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Fig 2. Phylogenetic tree of the 17 taxa inferred by the maximum likelihood approach.

Bootstrap support values are provided at the nodes. The scale bar corresponds to 0.1 substitution per site.

http://dx.doi.org/10.1371/journal.pone.0150718.g002

Hemiparasitic Schwalbea is a sister to the remaining broomrape clades (BS 100%). The next split within the plastid tree occurs between the Bartsia and Lathraea clades on one hand and the clade including the other holoparasitic genera (BS 100%) on the other. The latter clade groups Cistanche species with Conopholis and Epifagus, as well as Phelipanche species and Myzorrhiza with Orobanche species and Boulardia (BS 97%-100%). The estimated time of split of Bartsia and Lathraea lineages was 13.88 MYA (95% HPD 8.17–21.59 MY, S2 Fig), which gives absolute substitution rates 1×10−9 and 1.3×10−9 substitutions per site per year in Bartsia and Lathraea lineages, respectively, whereas in sampled autotrophic lineages the substitution rate does not exceed 0.76×10−9 (Fig 3).

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Fig 3. Estimates of divergence time of 17 taxa on the ML tree.

The values at the nodes represent mean ages in million years, and the 95% highest posterior density (HPD) interval is indicated by a blue bar. At terminal branches, substitution rates (per site per year) are provided. Nodes where parasitism and holoparasitism evolved are indicated by blue and yellow arrows, respectively. Age constraints were applied to nodes marked by red dots.

http://dx.doi.org/10.1371/journal.pone.0150718.g003

The length of a Lathraea branch on the phylogram is comparable with the branches of Bartsia, Tectona, or Lindenbergia. The fact that Lindenbergia is at least two times older than Lathraea and Bartsia implies considerable difference in their sequence evolution rates. The genome-wide relative rate test confirms that the rate difference is statistically significant (at α = 0.05) in all comparisons. However, the substitution rate acceleration is not uniform across compared genomes and functional groups of genes. Thus, there is no significant rate difference in rRNA sequences, but other groups of genes in Lathraea and Bartsia evolve faster than in photosynthetic plants. Relative rate tests show also insignificant rate difference in rpo, atp, and rpl/rps sequences between Bartsia and Lathraea, while psa/psb/pet genes and a group of miscellaneous genes (accD/clpP/matK/ycf1/ycf2) in Lathraea evolve faster than in Bartsia. In the latter case the difference is due to the matK gene, because in accD, ycf1, and ycf2 the rate difference is not significant (clpP from Bartsia is not available) when the genes are tested separately.

Ratio ω (dN /dS) can be considered uniform for all groups of genes when hemiparasitic Bartsia is pre-specified as a foreground branch: ω-value differences are not significant, and the null hypotheses (neither “one-ratio” nor “two-ratio” models) cannot be rejected at 1.25% level. The same is true for the rpo, atp, and rpl/rps genes when Lathraea is a branch of interest. However, for photosynthesis-related genes psa/psb/pet, models M2L and M3 fit the data significantly better than M1 and M2B (P<0.0001), suggesting individual ω-value for a holoparasitic lineage (Lathraea) being more than 7× that of other taxa (0.286 and 0.04, respectively). The LRT also indicates a better fit of a “two-ratio” model (models M3 and M2B were not tested) for the clpP gene (P<0.0001) with the ω estimate for Lathraea being equal to 1, i.e. reaching neutrality (ω = 0.05 for background branches). For accD, matK, ycf1, or ycf2, none of the tested branch models has a significantly better fit.

Ratios ω (dN /dS) estimated using the “three-ratio” model M3 did not exceed 1 and exceeded 0.5 (close to neutral evolution) for a few fast evolving genes (clpP, matK, ycf1, ycf2). The codon-based Z-test rejected the null hypothesis of neutrality in favor of negative selection in pairwise comparisons for individually analyzed genes and all groups except for the clpP gene. The branch-site test for evidence of positive selection acting on atp genes was applied to all eleven branches of the parasitic subtree of Orobanchaceae. The likelihood ratio statistic was non-zero for the Lathraea (1.126) and Myzorrhiza (3.99) branches, but in no case was the LRT statistic significant after Bonferroni correction (P = 0.144 and P = 0.023 for Lathraea and Myzorrhiza, respectively) at α = 0.0045. Among other genes (accD, clpP, matK, ycf1, ycf2) tested with Lathraea lineage specified as a foreground branch, only clpP displayed statistically significant positive selection (P = 0.001) at α = 0.05, but no particular codons with high posterior probability (higher than 0.95) of being under positive selection were identified.

Discussion

The newly determined sequence for the L. squamaria plastid genome displays a typical quadripartite architecture with the large single-copy and small single-copy regions separated by two inverted repeats. The plastome is the longest one among known holoparasites of the Orobanchaceae family [9, 11], and it has not suffered structural rearrangements. However, relaxed selective constraint for the function of photosynthesis resulted in extensive pseudogenization of the plastome.

The result of the phylogenetic analysis (Fig 2) is consistent with results of phylogenetic analyses of all plastid ribosomal protein genes [9] and with previous studies with multilocus data sets based on the three nuclear (ITS, PHYA, PHYB) and two plastid (matK, rps2) markers [5] except for the placement of Cistanche: in McNeal et al. [5] Cistanche species are closer to the Orobanche/Phelipanche clade than to Conopholis/Epifagus. In our tree parasitic species form a monophyletic group whereas holoparasites do not, and it is very unlikely that hemiparasitic Bartsia and holoparasitic Lathraea lineages could have a holoparasite as a common ancestor. Therefore, the topology obtained does not contradict a single transition to a parasitic lifestyle and independent transitions to obligate parasitism in Orobanchaceae as it was stated earlier in [6, 36, 4].

Our divergence time estimates (Fig 3, S2 Fig) show that this transition in Lathraea lineage occurred relatively recently, whereas the holoparasitic lineage Orobancheae is about two times older, and support recent findings that parasitism in Orobanchaceae originated within 5 MY [11]. Age estimates for some nodes are compared to those reported earlier in other studies in Fig 4.

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Fig 4. Comparison of estimated here divergence ages for four nodes and the Orobanchaceae crown group age (CGA) with reported ages from other studies and with the Orobanchaceae stem group age (SGA).

Mean and 95% HPD interval of each estimation (when provided) is shown with a reference given in brackets. Asterisks mean this study.

http://dx.doi.org/10.1371/journal.pone.0150718.g004

The age estimates of nodes MyzorrhizaPhelipanche (32.78 MY, 95% HPD 29.33–36.84 MY), BoulardiaOrobanche (30.59 MY, 95% HPD 26.45–34.90 MY) and MyzorrhizaOrobanche (35.85 MY, 95% HPD 32.85–39.90 MY) are close to those calculated with a clock calibrated with an ITS substitution rate taken from Gentianella (Gentianaceae) [37] and with the results of recent age-constrained dating analyses of Orobanchaceae plastid genomes [11], while ages of some other nodes differ substantially from those obtained earlier. Thus, based on nuclear ITS molecular clock, estimate of the absolute timing of the diversification of lineages within Orobanchaceae resulted in divergence time of a LathraeaBartsia split at 21 MYA (no HPD interval provided) [7], which is marginal in our HPD interval of 8.17–21.59 MY (mean 13.88 MY). Recently, Uribe-Convers and Tank used geological data in addition to secondary calibration points from Wolfe et al. [7] and deduced the age of the same point at 27.38 MY (95% HPD 20.87–33.57 MY) from plastid trnT–trnL intergenic spacer and the nuclear ITS region [38]. Focusing on basal eudicots and using 79 chloroplast protein-coding genes Wu et al. [39] revealed the EpifagusCistanche split age of 42 MY, the same node was calculated at 39.4 MY by Wolfe et al. [7], while a younger age of 36.35 MY (95% HPD 33.29–40.43 MY) is obtained here. For the split of Conopholis and Epifagus, an age of 7.8 MY was estimated by Wolfe et al [7] which is here estimated at 22.46 MY (95% HPD 17–28 MY). We deduced the Orobanchaceae crown group age of 40.47 MY (95% HPD 37.67–44.8 MY), which is consistent with analyses using similar age-constraints [11], but it corresponds rather to recent estimates of the Orobanchaceae stem group age (40 MY, 95% HPD 28–51 MY in Wikström et al. [31]; 35.91 MY, 95% HPD 25.38–55.01 MY in Magallón et al. [40]; 38 MY, 95% HPD 28–47 MY in Bell et al. [41], 32 MY, 95% HPD 13–52 MY in Naumann et al. [42]; but the crown group age of 57 MY was provided in Wu et al. [39], 52 MY in Wolfe et al. [7], 48 MY and the stem group age of 64 MY in Bremer et al. [43]), thus ages obtained here may be overestimated to some extent. Limited with available broomrape plastid genomes, our dating approach suffers from undersampling of Orobanchaceae; nevertheless, even being only rough approximations, our results reveal relative ages of broomrape holoparasites and clearly demonstrate absolute rate difference in Lathraea and photosynthetic lineages, the genome-wide rate of nucleotide substitution in plastid genome of Lathraea being elevated as in other parasitic plants.

Surprisingly, the overall genomic structure of the L. squamaria plastome is more similar to the plastid genome of autotrophic Lindenbergia than to that of the closely related holoparasite Lathraea clandestina. Hybridization experiments demonstrated that the plastome of L. clandestina was approximately 110-kb long and has a drastically reduced SSC region (which in land plants contains most of the ndh genes for subunits of a plastid NAD(P)H dehydrogenase), in addition to pseudogenization of atpB and atpE genes [44]. In the L. squamaria plastome, atpB and atpE were maintained as functional genes and none of the ndh genes was lost, but nine out of the eleven ndh genes were pseudogenized. Degradation of the ndh complex is not attributed solely to heterotrophs and occurred independently in many angiosperm lineages, including bryophytes [45], gymnosperms [46], orchids [47, 48, 49], Lentibulariaceae [50], Alismatales [51, 52], Santalales [53], Cactaceae [54], and Geraniaceae [55]. The lack of functional ndh genes is typical for parasitic Orobanchaceae ([9, 11], this study). Wicke et al. [9] proposed that four ndh genes (ndhA, ndhD, ndhG, ndhF) were pseudogenized after the transition to obligate parasitism and mapped this event to a common ancestor of Schwalbea and other parasites [9, 11]. However, a functional ndhA gene is present in facultative hemiparasite Bartsia [21], while ndhD, ndhG and ndhF are not pseudogenized in another hemiparasite Castilleja miniata (Pedicularideae clade, sensu McNeal et al. [5]) [38], what suggests that the ndh loss-of-function in Schwalbea, Lathraea, and Orobancheae lineages occurred convergently. Within mycoheterotrophic Orchidaceae, ndh losses have been frequent and have occured in both photosynthetic and nonphotosynthetic lineages [49], in parallel with that, one may also expect a complex pattern of independent gene loss and pseudogenization across both holo- and hemiparasites in Orobanchaceae.

The majority of subunit genes of photosystem I and II (psa, psb), as well as many members of the cytochrome b6/f complex (pet) of the Lathraea plastome, have been turned into pseudogenes. The remaining psa/psb/pet genes retained intact open-reading frames but clearly displayed signature of relaxed selective constraint: the estimated ω-ratio (dN /dS) is approximately seven times higher than that of non-holoparasite lineages (0.286 and 0.040, respectively), and this difference is statistically significant (P<0.0001). Contrary to Lathraea, the psa/psb/pet genes in Bartsia evolved under the same negative selection constraints as in the photosynthetic Lindenbergia and outgroups.

Since in the Lathraea plastid genome only two of four plastid-encoded RNA-polymerase (PEP) genes (rpoB and rpoC1) have intact reading frames, the PEP seems to be nonfunctional, similarly to L. clandestina [56]. It is believed that the PEP transcribed by the nuclear-encoded RNA-polymerase (NEP) is responsible for transcription of photosynthesis-related genes, so this function in Lathraea may be rendered redundant. The rpo genes themselves are transcribed, and at least two of them, rpoC1 and rpoC2, were amplified by RT-PCR and did not contain detectable RNA-editing sites. It is interesting to note a tissue-specificity of processing of the rpoC1 intron: spliced intron was found in fruits, but no intron processing was detectable in perianth (S1 Fig), it still being not quite clear why such specificity exists. In Arabidopsis rpoC1 intron is spliced by the nuclear encoded CRS2–CAF1 complex [57], so the cause will be found most probably outside of the plastid genome.

As neither ribosomal RNA genes nor transfer RNAs are lost or pseudogenized in the Lathraea plastome, all basic housekeeping functions seem to be preserved despite pseudogenization of two ribosomal protein genes, rps19 and rpl23. In the plastomes of eudicots, rpl23, as well as some other ribosomal protein genes, have been independently lost in several lineages [58] with no harm to the translation apparatus due to import of missing elements [59].

Not being associated with housekeeping processes, a set of ATP synthase complex genes (atp) is also putatively functional. A similar situation has been reported for other non-photosynthetic plants–holoparasites [60, 9] and mycoheterotrophs [45, 13, 18]. Recently, an ATP hydrolysis function in assistance to the Twin-arginine translocator (Tat) system was suggested for non-photosynthetic plastid ATP synthase genes [61]. The Tat-related role may explain the retention of the intact atp complex genes in the Lathraea plastome after the loss of photosynthesis.

In non-green mycoheterotrophic Corallorhiza species the atp complex displayed evidence for positive selection [13], but our test showed no signature of divergent selection acting on atp genes in any of branches of the parasitic subtree of Orobanchaceae. Our inference of positive selection in fast-evolving gene clpP needs to be confirmed by further investigation with broader sampling of Orobanchaceae representatives. In the last decade, many studies of DNA variation patterns have inferred positive selection at different plastid sequences, including photosynthesis related, PEP, matK, clpP, ycf1, and ycf2 genes (reviewed in Bock et al. [62]). However, without experimental evidence, drivers and evolutionary significance of the revealed examples of adaptive organelle evolution remain obscure.

Lastly, our mapping of the paired reads to the plastome assembly revealed the high level of nucleotide polymorphism, and polymorphic sites were recovered both in pseudogenes and coding sequences. Definitely, some of single nucleotide variants and indels are of mitochondrial origin, since the transfer of plastid DNA into the mitochondrial genome is a well-known phenomenon [63] and almost all of plastid genes have been shown in various plants transferred to the mitochondria (e.g., [64, 65]. Most of the transferred protein-coding sequences have no intact gene structure or have frameshifts/indels but still may be transcribed: transcription of non-plastid ndh sequences (including pseudogenes) was recently shown in Orchidaceae [66]. On the other hand, we cannot exclude presence of plastid heteroplasmy in Lathraea. In mycoheterotrophic Neottia nidus-avis at least three distinct rbcL sequences were found as pseudogenes and were likely located in the plastid genome [67]. Among broomrape species, Hyobanche glabrata was shown to have five different rbcL transcripts and all also encoded pseudogenes [68]. In recent years, growing data on plant mitochondrial genomes have made possible more thorough evaluation of plastome heteroplasmy which appeared to be more common than thought previously (discussed in Sabir et al. [69]). We expect that the characterization of the Lathraea complete mitochondrial genome sequence will help to distinguish between the possible causes of the observed polymorphism.

Supporting Information

S1 Appendix. Alignments of Lathraea squamaria minor sequences and pseudogenes to orthologs of photosynthetic plants.

doi:10.1371/journal.pone.0150718.s001

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S1 Fig. Analysis of rpoC1, rpoC2, and rbcL cDNAs.

doi:10.1371/journal.pone.0150718.s002

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S2 Fig. Estimated mean ages and 95% highest posterior density intervals.

doi:10.1371/journal.pone.0150718.s003

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S1 Table. Primers used for plastome assembly, verification, and cDNA amplification.

doi:10.1371/journal.pone.0150718.s004

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S2 Table. List of genes present in the plastid genome of Lathraea squamaria and Lindenbergia philippensis.

doi:10.1371/journal.pone.0150718.s005

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Acknowledgments

We thank Richard H. Lozier for editing and Claude W. dePamphilis for his useful suggestions and comments on the initial version on the manuscript.

Author Contributions

Conceived and designed the experiments: MDL THS. Performed the experiments: MDL CMV AAP. Analyzed the data: THS. Contributed reagents/materials/analysis tools: MDL CMV AAP. Wrote the paper: THS.

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