Photosynthetic evolution in parasitic plants: insight from the chloroplast genome

Comparative and evolutionary analysis of chloroplast genomes from five rare Styrax species

BACKGROUND

Styrax, a vital raw material for shipbuilding, construction, perfumes, and drugs, represents the largest and most diverse genus in the Styracaceae. However, there is a relative scarcity of research on Styrax, particularly in evolution and genetics. Therefore, this study conducted comparative and evolutionary analyses of the chloroplast genomes of five rare Styrax species (S. argentifolius, S. buchananii, S. chrysocarpus, S. finlaysonianus, and S. rhytidocarpus).

RESULTS

The results indicated that, despite high levels of conservation in chloroplast genome structure among these species, specific mutation hotspot regions exist, particularly involving the expansion and contraction of the IR region. Additionally, evidence of positive selection was detected in eight genes (atpB, ccsA, ndhD, petA, rbcL, rpoC1, ycf1, and ycf2), which may be associated with adaptive evolution in response to environmental changes. Phylogenetic analysis revealed conflicts between trees constructed based on coding sequences and complete chloroplast genomes for several species, which were similar to previous phylogenetic studies.

CONCLUSION

This study underscores the importance of increasing sample sizes to enhance the accuracy of phylogenetic analyses and provides a new perspective on understanding the adaptive evolution of Styrax species. These findings are not only important for the conservation and sustainable use of Styrax, but also provide valuable insights for research in plant evolution and ecology within the genus.

Is There a Key Primer for Amplification of Core Land Plant DNA Barcode Regions (rbcL and matK)?

The DNA barcode is a technique for molecular identification of species. Two core genes, matK and rbcL, are widely used for land plants. In this technique, the selection of primers is a fundamental step for the success of amplification. Then, we aim to evaluate the primer amplification capability for the DNA barcode regions rbcL and matK. We extracted primer sequences from DNA barcode studies in the Web of Science and used chloroplast genome sequences from NCBI for in silico PCR tests using OpenprimeR. Physicochemical properties of in silico PCR were evaluated using OpenprimeR. Our literature review resulted in 366 and 489 different rbcL and matK primers. These were tested in 8665 sequences, 8463 species from 98 orders. Evaluating only the primer and sequence match, the primers with the highest number of sequences covered were 96.39% and 93.81% forward and reverse for rbcL, and 91.56% and 61.62% forward and reverse for matK. No universal primer for all land plants was found, but two rbcL primer pairs could amplify > 99% of the sequences. In contrast to the results obtained for the matK region, the 10 pairs optimized for the greatest coverage of sequences were not covered by > 85% of the sequences. Therefore, it is advisable to pay attention when selecting primers for the matK region and the need to develop new primers. Here, we recommend a set of primers to cover the largest number of sequences and orders.

Revealing the Dynamic History of Parasitic Plant Plastomes via Structural Characterization, Comparative Analysis, and Phylogenomics

Background: The shift to a parasitic lifestyle in plants often leaves distinct marks on their plastid genomes, given the central role plastids play in photosynthesis. Studying these unique adaptations in parasitic plants is essential for understanding the mechanisms and evolutionary patterns driving plastome reduction in angiosperms. By exploring these changes, we can gain deeper insights into how parasitism reshapes the genomic architecture of plants. Method: This study analyzed and compared the plastomes of 113 parasitic plants from different families. Results: The Orobanchaceae family (hemiparasitic plants) displayed the largest plastome size, while Apodanthaceae exhibited the shortest. Additionally, Orobanchaceae showcased little to no gene loss in their plastomes. However, holoparasitic species typically had reduced plastome sizes. Convolvulaceae exhibited significantly reduced plastome sizes due to high gene loss, and Apodanthaceae retained only a few genes. Gene divergence among different families was also investigated, and rps15, rps18, and rpl33 in Orobanchaceae; accD and ycf1 in Convolvulaceae; atpF and ccsA in Loranthaceae; and rpl32 in Santalaceae showed greater divergence. Additionally, Orobanchaceae had the highest numbers of all repeat types, whereas Loranthaceae and Convolvulaceae exhibited the lowest repeat numbers. Similarly, more simple sequence repeats were reported in Loranthaceae and Santalaceae. Our phylogenetic analysis also uncovered a distinct clade comprising Loranthaceae, with a single Schoepfiaceae species clustering nearby. Contrary to expectations, parasitic and hemiparasitic plants formed mixed groupings instead of segregating into separate clades. Conclusions: These findings offer insights into parasitic plants' evolutionary relationships, revealing shared and divergent genomic features across diverse lineages.

Comparative plastome analyses and evolutionary relationships of 25 East Asian species within the medicinal plant genus Scrophularia (Scrophulariaceae)

Backgroud

Scrophularia L., a genus of the Scrophulariaceae, is a group of important medicinal plants used for eliminating heat and detoxifying. East Asia has an abundance of potentially medicinal Scrophularia species, and it serves as a secondary diversity center of the genus. However, the genomic resources available for germplasm identification and pharmaceutical exploration of East Asian Scrophularia are insufficient, hindering its commercial and industrial development. Additionally, the interspecific relationships of most East Asian Scrophularia species remain unclear.

Methods

In this study, we sequenced the leaves of 25 East Asian species of the genus Scrophularia, assembled and annotated the complete chloroplast genomes, and subsequently performed comparative and phylogenetic analyses on these genomes.

Results and discussion

The conserved plastome length of these 25 species ranged from 151,582 bp to 153,239 bp, containing a total of 132 coding genes, including 18 duplicated genes and 114 unique genes. Through genome alignment of these 25 species, 38-53 repeated sequences and 7 shared SSRs were identified, along with regions with high nucleotide polymorphism (Pi), which could potentially serve as molecular markers for species identification. The genome structure, gene content, and arrangement showed conservation, while variations were observed in the IR boundary regions and IGS. Phylogenetic inferences based on whole plastomes or on coding sequences (CDS) only yielded congruent results. We categorized the 25 East Asian Scrophularia species into six distinct clades and further explored their interspecies relationships using morphological characteristics, such as flower color, the relative position of stamens and corolla, and plant height. This could lay a genetic basis for future resource development of Scrophularia in East Asia.

Intraspecific Differentiation of Styrax japonicus (Styracaceae) as Revealed by Comparative Chloroplast and Evolutionary Analyses

Styrax japonicus is a medicinal and ornamental shrub belonging to the Styracaceae family. To explore the diversity and characteristics of the chloroplast genome of S. japonicus, we conducted sequencing and comparison of the chloroplast genomes of four naturally distributed S. japonicus. The results demonstrated that the four chloroplast genomes (157,914-157,962 bp) exhibited a typical quadripartite structure consisting of a large single copy (LSC) region, a small single copy (SSC) region, and a pair of reverse repeats (IRa and IRb), and the structure was highly conserved. DNA polymorphism analysis revealed that three coding genes (infA, psbK, and rpl33) and five intergene regions (petA-psbJ, trnC-petN, trnD-trnY, trnE-trnT, and trnY-trnE) were identified as mutation hotspots. These genetic fragments have the potential to be utilized as DNA barcodes for future identification purposes. When comparing the boundary genes, a small contraction was observed in the IR region of four S. japonicus. Selection pressure analysis indicated positive selection for ycf1 and ndhD. These findings collectively suggest the adaptive evolution of S. japonicus. The phylogenetic structure revealed conflicting relationships among several S. japonicus, indicating divergent evolutionary paths within this species. Our study concludes by uncovering the genetic traits of the chloroplast genome in the differentiation of S. japonicus variety, offering fresh perspectives on the evolutionary lineage of this species.

Comparative and phylogenetic analyses of Loranthaceae plastomes provide insights into the evolutionary trajectories of plastome degradation in hemiparasitic plants

BACKGROUND

The lifestyle transition from autotrophy to heterotrophy often leads to extensive degradation of plastomes in parasitic plants, while the evolutionary trajectories of plastome degradation associated with parasitism in hemiparasitic plants remain poorly understood. In this study, phylogeny-oriented comparative analyses were conducted to investigate whether obligate Loranthaceae stem-parasites experienced higher degrees of plastome degradation than closely related facultative root-parasites and to explore the potential evolutionary events that triggered the 'domino effect' in plastome degradation of hemiparasitic plants.

RESULTS

Through phylogeny-oriented comparative analyses, the results indicate that Loranthaceae hemiparasites have undergone varying degrees of plastome degradation as they evolved towards a heterotrophic lifestyle. Compared to closely related facultative root-parasites, all obligate stem-parasites exhibited an elevated degree plastome degradation, characterized by increased downsizing, gene loss, and pseudogenization, thereby providing empirical evidence supporting the theoretical expectation that evolution from facultative parasitism to obligate parasitism may result in a higher degree of plastome degradation in hemiparasites. Along with infra-familial divergence in Loranthaceae, several lineage-specific gene loss/pseudogenization events occurred at deep nodes, whereas further independent gene loss/pseudogenization events were observed in shallow branches.

CONCLUSIONS

The findings suggest that in addition to the increasing levels of nutritional reliance on host plants, cladogenesis can be considered as another pivotal evolutionary event triggering the 'domino effect' in plastome degradation of hemiparasitic plants. These findings provide new insights into the evolutionary trajectory of plastome degradation in hemiparasitic plants.

The size diversity of the Pteridaceae family chloroplast genome is caused by overlong intergenic spacers

BACKGROUND

While the size of chloroplast genomes (cpDNAs) is often influenced by the expansion and contraction of inverted repeat regions and the enrichment of repeats, it is the intergenic spacers (IGSs) that appear to play a pivotal role in determining the size of Pteridaceae cpDNAs. This provides an opportunity to delve into the evolution of chloroplast genomic structures of the Pteridaceae family. This study added five Pteridaceae species, comparing them with 36 published counterparts.

RESULTS

Poor alignment in the non-coding regions of the Pteridaceae family was observed, and this was attributed to the widespread presence of overlong IGSs in Pteridaceae cpDNAs. These overlong IGSs were identified as a major factor influencing variations in cpDNA size. In comparison to non-expanded IGSs, overlong IGSs exhibited significantly higher GC content and were rich in repetitive sequences. Species divergence time estimations suggest that these overlong IGSs may have already existed during the early radiation of the Pteridaceae family.

CONCLUSIONS

This study reveals new insights into the genetic variation, evolutionary history, and dynamic changes in the cpDNA structure of the Pteridaceae family, providing a fundamental resource for further exploring its evolutionary research.

Distinctive plastome evolution in carnivorous angiosperms

BACKGROUND

Independent origins of carnivory in multiple angiosperm families are fabulous examples of convergent evolution using a diverse array of life forms and habitats. Previous studies have indicated that carnivorous plants have distinct evolutionary trajectories of plastid genome (plastome) compared to their non-carnivorous relatives, yet the extent and general characteristics remain elusive.

RESULTS

We compared plastomes from 9 out of 13 carnivorous families and their non-carnivorous relatives to assess carnivory-associated evolutionary patterns. We identified inversions in all sampled Droseraceae species and four species of Utricularia, Pinguicula, Darlingtonia and Triphyophyllum. A few carnivores showed distinct shifts in inverted repeat boundaries and the overall repeat contents. Many ndh genes, along with some other genes, were independently lost in several carnivorous lineages. We detected significant substitution rate variations in most sampled carnivorous lineages. A significant overall substitution rate acceleration characterizes the two largest carnivorous lineages of Droseraceae and Lentibulariaceae. We also observe moderate substitution rates acceleration in many genes of Cephalotus follicularis, Roridula gorgonias, and Drosophyllum lusitanicum. However, only a few genes exhibit significant relaxed selection.

CONCLUSION

Our results indicate that the carnivory of plants have different effects on plastome evolution across carnivorous lineages. The complex mechanism under carnivorous habitats may have resulted in distinctive plastome evolution with conserved plastome in the Brocchinia hechtioides to strongly reconfigured plastomes structures in Droseraceae. Organic carbon obtained from prey and the efficiency of utilizing prey-derived nutrients might constitute possible explanation.

Cellular roadmaps of viroid infection

Viroids are single-stranded circular noncoding RNAs that infect plants. According to the International Committee on Taxonomy of Viruses, there are 44 viroids known to date. Notably, more than 20 000 distinct viroid-like RNA sequences have recently been identified in existing sequencing datasets, suggesting an unprecedented complexity in biological roles of viroids and viroid-like RNAs. Interestingly, a human pathogen, hepatitis delta virus (HDV), also replicates via a rolling circle mechanism like viroids. Therefore, knowledge of viroid infection is informative for research on HDV and other viroid-like RNAs reported from various organisms. Here, we summarize recent advancements in understanding viroid shuttling among subcellular compartments for completing replication cycles, emphasizing regulatory roles of RNA motifs and structural dynamics in diverse biological processes. We also compare the knowledge of viroid intracellular trafficking with known pathways governing cellular RNA movement in cells. Future investigations on regulatory RNA structures and cognate factors in regulating viroid subcellular trafficking and replication will likely provide new insights into RNA structure-function relationships and facilitate the development of strategies controlling RNA localization and function in cells.

Adaptive evolution and co-evolution of chloroplast genomes in Pteridaceae species occupying different habitats: overlapping residues are always highly mutated

BACKGROUND

The evolution of protein residues depends on the mutation rates of their encoding nucleotides, but it may also be affected by co-evolution with other residues. Chloroplasts function as environmental sensors, transforming fluctuating environmental signals into different physiological responses. We reasoned that habitat diversity may affect their rate and mode of evolution, which might be evidenced in the chloroplast genome. The Pteridaceae family of ferns occupy an unusually broad range of ecological niches, which provides an ideal system for analysis.

RESULTS

We conducted adaptive evolution and intra-molecular co-evolution analyses of Pteridaceae chloroplast DNAs (cpDNAs). The results indicate that the residues undergoing adaptive evolution and co-evolution were mostly independent, with only a few residues being simultaneously involved in both processes, and these overlapping residues tend to exhibit high mutations. Additionally, our data showed that Pteridaceae chloroplast genes are under purifying selection. Regardless of whether we grouped species by lineage (which corresponded with ecological niches), we determined that positively selected residues mainly target photosynthetic genes.

CONCLUSIONS

Our work provides evidence for the adaptive evolution of Pteridaceae cpDNAs, especially photosynthetic genes, to different habitats and sheds light on the adaptive evolution and co-evolution of proteins.

Comparative and phylogenetic analyses of the chloroplast genomes of Filipendula species (Rosoideae, Rosaceae)

Genus Filipendula (Rosoideae, Rosaceae) comprises about 15 species and mainly distributed in Northern Hemisphere. The phylogenetic relationships based on the nrITS marker are not consistent with the traditional taxonomic systems of the genus. Here, we first analysed the complete chloroplast (cp) genomes of seven Filipendula species (including two varieties of F. palmate). Our results indicated that the cp genomes of Filipendula species had few changes in size, ranging from 154,205 bp to 154,633 bp and the average of 36.63% GC content. A total of 126 annotated genes had the identical order and orientation, implying that the cp genome structure of Filipendula species was rather conserved. However, the cp genomes of Filipendula species exhibited structural differences, including gene loss, transposition and inversion when compared to those of other genera of Rosoideae. Moreover, SSRs with the different number were observed in the cp genome of each Filipendula species and sequence divergence mainly occurred in noncoding regions, in which four mutational hotspots were identified. In contrast, only two positive selection genes (matK and rps8) were found. Phylogenetic and molecular-dating analysis indicated that Filipendula species were divergent from other genera of Rosoideae at about 82.88 Ma. Additionally, Filipendula species from East Asia were split at about 9.64 Ma into two major clades. These results provide a basis for further studying the infrageneric classification of Filipendula.

Comparative Analyses of Chloroplast Genomes for Parasitic Species of Santalales in the Light of Two Newly Sequenced Species, Taxillus nigrans and Scurrula parasitica

When a flowering plant species changes its life history from self-supply to parasite, its chloroplast genomes may have experienced functional physical reduction, and gene loss. Most species of Santalales are hemiparasitic and few studies focus on comparing the chloroplast genomes of the species from this order. In this study, we collected and compared chloroplast genomes of 12 species of Santalales and sequenced the chloroplast genomes of Taxillus nigrans and Scurrula parasitica for the first time. The chloroplast genomes for these species showed typical quadripartite structural organization. Phylogenetic analysis suggested that these 12 species of Santalales clustered into three clades: Viscum (4 spp.) and Osyris (1 sp.) in the Santalaceae and Champereia (1 sp.) in the Opiliaceae formed one clade, while Taxillus (3 spp.) and Scurrula (1 sp.) in the Loranthaceae and Schoepfia (1 sp.) in the Schoepfiaceae formed another clade. Erythropalum (1 sp.), in the Erythropalaceae, appeared as a third, most distant, clade within the Santalales. In addition, both Viscum and Taxillus are monophyletic, and Scurrula is sister to Taxillus. A comparative analysis of the chloroplast genome showed differences in genome size and the loss of genes, such as the ndh genes, infA genes, partial ribosomal genes, and tRNA genes. The 12 species were classified into six categories by the loss, order, and structure of genes in the chloroplast genome. Each of the five genera (Viscum, Osyris, Champereia, Schoepfia, and Erythropalum) represented an independent category, while the three Taxillus species and Scurrula were classified into a sixth category. Although we found that different genes were lost in various categories, most genes related to photosynthesis were retained in the 12 species. Hence, the genetic information accorded with observations that they are hemiparasitic species. Our comparative genomic analyses can provide a new case for the chloroplast genome evolution of parasitic species.

Infrageneric Plastid Genomes of Cotoneaster (Rosaceae): Implications for the Plastome Evolution and Origin of C. wilsonii on Ulleung Island

Cotoneaster is a taxonomically and ornamentally important genus in the family Rosaceae; however, phylogenetic relationships among its species are complicated owing to insufficient morphological diagnostic characteristics and hybridization associated with polyploidy and apomixis. In this study, we sequenced the complete plastomes of seven Cotoneaster species (C. dielsianus, C. hebephyllus, C. integerrimus, C. mongolicus, C. multiflorus, C. submultiflorus, and C. tenuipes) and included the available complete plastomes in a phylogenetic analysis to determine the origin of C. wilsonii, which is endemic to Ulleung Island, Korea. Furthermore, based on 15 representative lineages within the genus, we carried out the first comparative analysis of Cotoneaster plastid genomes to gain an insight into their molecular evolution. The plastomes were highly conserved, with sizes ranging from 159,595 bp (C. tenuipes) to 160,016 bp (C. hebephyllus), and had a GC content of 36.6%. The frequency of codon usage showed similar patterns among the 15 Cotoneaster species, and 24 of the 35 protein-coding genes were predicted to undergo RNA editing. Eight of the 76 common protein-coding genes, including ccsA, matK, ndhD, ndhF, ndhK, petA, rbcL, and rpl16, were positively selected, implying their potential roles in adaptation and speciation. Of the 35 protein-coding genes, 24 genes (15 photosynthesis-related, seven self-replications, and three others) were found to harbor RNA editing sites. Furthermore, several mutation hotspots were identified, including trnG-UCC/trnR-UCU/atpA and trnT-UGU/trnL-UAA. Maximum likelihood analysis based on 57 representative plastomes of Cotoneaster and two Heteromeles plastomes as outgroups revealed two major lineages within the genus, which roughly correspond to two subgenera, Chaenopetalum and Cotoneaster. The Ulleung Island endemic, C. wilsonii, shared its most recent common ancestor with two species, C. schantungensis and C. zabelii, suggesting its potential origin from geographically close members of the subgenus Cotoneaster, section Integerrimi.

Recent Advances in Understanding the Structural and Functional Evolution of FtsH Proteases

The FtsH family of proteases are membrane-anchored, ATP-dependent, zinc metalloproteases. They are universally present in prokaryotes and the mitochondria and chloroplasts of eukaryotic cells. Most bacteria bear a single ftsH gene that produces hexameric homocomplexes with diverse house-keeping roles. However, in mitochondria, chloroplasts and cyanobacteria, multiple FtsH homologs form homo- and heterocomplexes with specialized functions in maintaining photosynthesis and respiration. The diversification of FtsH homologs combined with selective pairing of FtsH isomers is a versatile strategy to enable functional adaptation. In this article we summarize recent progress in understanding the evolution, structure and function of FtsH proteases with a focus on the role of FtsH in photosynthesis and respiration.

Plant Parasites under Pressure: Effects of Abiotic Stress on the Interactions between Parasitic Plants and Their Hosts

Parasitic angiosperms, comprising a diverse group of flowering plants, are partially or fully dependent on their hosts to acquire water, mineral nutrients and organic compounds. Some have detrimental effects on agriculturally important crop plants. They are also intriguing model systems to study adaptive mechanisms required for the transition from an autotrophic to a heterotrophic metabolism. No less than any other plant, parasitic plants are affected by abiotic stress factors such as drought and changes in temperature, saline soils or contamination with metals or herbicides. These effects may be attributed to the direct influence of the stress, but also to diminished host availability and suitability. Although several studies on abiotic stress response of parasitic plants are available, still little is known about how abiotic factors affect host preferences, defense mechanisms of both hosts and parasites and the effects of combinations of abiotic and biotic stress experienced by the host plants. The latter effects are of specific interest as parasitic plants pose additional pressure on contemporary agriculture in times of climate change. This review summarizes the existing literature on abiotic stress response of parasitic plants, highlighting knowledge gaps and discussing perspectives for future research and potential agricultural applications.

Relaxed selection underlies genome erosion in socially parasitic ant species

Inquiline ants are highly specialized and obligate social parasites that infiltrate and exploit colonies of closely related species. They have evolved many times convergently, are often evolutionarily young lineages, and are almost invariably rare. Focusing on the leaf-cutting ant genus Acromyrmex, we compared genomes of three inquiline social parasites with their free-living, closely-related hosts. The social parasite genomes show distinct signatures of erosion compared to the host lineages, as a consequence of relaxed selective constraints on traits associated with cooperative ant colony life and of inquilines having very small effective population sizes. We find parallel gene losses, particularly in olfactory receptors, consistent with inquiline species having highly reduced social behavioral repertoires. Many of the genomic changes that we uncover resemble those observed in the genomes of obligate non-social parasites and intracellular endosymbionts that branched off into highly specialized, host-dependent niches.

Holoparasitic plant-host interactions and their impact on Mediterranean ecosystems

Although photosynthesis is essential to sustain life on Earth, not all plants use sunlight to synthesize nutrients from carbon dioxide and water. Holoparasitic plants, which are important in agricultural and natural ecosystems, are dependent on other plants for nutrients. Phytohormones are crucial in holoparasitic plant-host interactions, from seed germination to senescence, not only because they act as growth and developmental regulators, but also because of their central role in the regulation of host photosynthesis and source-sink relations between the host and the holoparasitic plant. Here, we compile and discuss current knowledge on the impact and ecophysiology of holoparasitic plants (such as the broomrapes Orobanche sp. and Phelipanche sp.) that infest economically important dicotyledonous crops in Mediterranean agroecosystems (legumes [Fabaceae], sunflowers [Helianthus sp.], or tomato [Solanum lycopersicum] plants). We also highlight the role of holoparasitic plant-host interactions (such as those between Cytinus hypocistis and various shrubs of the genus Cistus) in shaping natural Mediterranean ecosystems. The roles of phytohormones in controlling plant-host interactions, abiotic factors in parasitism, and the biological significance of natural seed banks and how dormancy and germination are regulated, will all be discussed. Holoparasitic plants are unique organisms; improving our understanding of their interaction with hosts as study models will help us to better manage parasitic plants, both in agricultural and natural ecosystems.

Analysis of codon usage bias of chloroplast genes in Oryza species : Codon usage of chloroplast genes in Oryza species

The codon usage bias in chloroplast genes of Oryza species was low and AT rich. The pattern of codon usage was different among Oryza species and mainly influenced by mutation pressure and natural selection. Codon usage bias (CUB) is the unequal usage of synonymous codons in which some codons are more preferred to others in the coding sequences of genes. It shows a species-specific property. We studied the patterns of codon usage and the factors that influenced the CUB of protein-coding chloroplast (cp) genes in 18 Oryza species as no work was yet reported. The nucleotide composition analysis revealed that the overall GC content of cp genes in different species of Oryza was lower than 50%, i.e., Oryza cp genes were AT rich. Synonymous codon usage order (SCUO) suggested that CUB was weak in the cp genes of different Oryza species. A highly significant correlation was observed between overall nucleotides and its constituents at the third codon position suggesting that both, mutation pressure and natural selection, might influence the CUB. Correspondence analysis (COA) revealed that codon usage pattern differed across Oryza species. In the neutrality plot, a narrow range of GC3 distribution was recorded and some points were diagonally distributed in all the plots, suggesting that natural selection and mutation pressure might have influenced the CUB. The slope of the regression line was < 0.5, augmenting our inference that natural selection might have played a major role, while mutation pressure had a minor role in shaping the CUB of cp genes. The magnitudes of mutation pressure and natural selection on cp genes varied across Oryza species.

The Organelle Genomes in the Photosynthetic Red Algal Parasite Pterocladiophila hemisphaerica (Florideophyceae, Rhodophyta) Have Elevated Substitution Rates and Extreme Gene Loss in the Plastid Genome

Comparative organelle genome studies of parasites can highlight genetic changes that occur during the transition from a free-living to a parasitic state. Our study focuses on a poorly studied group of red algal parasites, which are often closely related to their red algal hosts and from which they presumably evolved. Most of these parasites are pigmented and some show photosynthetic capacity. Here, we assembled and annotated the complete organelle genomes of the photosynthetic red algal parasite, Pterocladiophila hemisphaerica. The plastid genome is the smallest known red algal plastid genome at 68,701 bp. The plastid genome has many genes missing, including all photosynthesis-related genes. In contrast, the mitochondrial genome is similar in architecture to that of other free-living red algae. Both organelle genomes show elevated mutation rates and significant changes in patterns of selection, measured as dN/dS ratios. This caused phylogenetic analyses, even of multiple aligned proteins, to be unresolved or give contradictory relationships. Full plastid datasets interfered by selected best gene evolution models showed the supported relationship of P. hemisphaerica within the Ceramiales, but the parasite was grouped with support as sister to the Gracilariales when interfered under the GHOST model. Nuclear rDNA showed a supported grouping of the parasite within a clade containing several red algal orders including the Gelidiales. This photosynthetic parasite, which is unable to photosynthesize with its own plastid due to the total loss of all photosynthesis genes, raises intriguing questions on parasite-host organelle genome capabilities and interactions.

The Complete Plastomes of Five Hemiparasitic Plants (Osyris wightiana, Pyrularia edulis, Santalum album, Viscum liquidambaricolum, and V. ovalifolium): Comparative and Evolutionary Analyses Within Santalales

Most species of Santalales (the sandalwood order) are hemiparasites, including both facultative and obligate hemiparasites. Despite its rich diversity, only a small fraction of the species in the sandalwood order have sequenced plastomes. The evolution of parasitism-associated plastome reduction in Santalales remains under-studied. Here, we report the complete plastomes of three facultative hemiparasites (Pyrularia edulis, Cervantesiaceae; Osyris wightiana, and Santalum album, Santalaceae), and two obligate hemiparasites (Viscum liquidambaricolum and Viscum ovalifolium, Viscaceae). Coupled with publicly available data, we investigated the dynamics of plastome degradation in Santalales hemiparasites. Our results indicate that these hemiparasites can be characterized by various degrees of plastome downsizing, structural rearrangement, and gene loss. The loss or pseudogenization of ndh genes was commonly observed in Santalales hemiparasites, which may be correlated to the lifestyle shift from photoautotroph to hemiparasitism. However, the obligate hemiparasites did not exhibit a consistently higher level of gene loss or pseudogenization compared to facultative hemiparasites, which suggests that the degree of plastome reduction is not correlated with the trophic level facultative or obligate hemiparasitism. Instead, closely related taxa tend to possess highly similar plastome size, structure, and gene content. This implies the parasitism-associated plastome degradation in Santalales may evolve in a lineage-specific manner.

Convergent Plastome Evolution and Gene Loss in Holoparasitic Lennoaceae

The Lennoaceae, a small monophyletic plant family of root parasites endemic to the Americas, are one of the last remaining independently evolved lineages of parasitic angiosperms lacking a published plastome. In this study, we present the assembled and annotated plastomes of two species spanning the crown node of Lennoaceae, Lennoa madreporoides and Pholisma arenarium, as well as their close autotrophic relative from the sister family Ehretiaceae, Tiquilia plicata. We find that the plastomes of L. madreporoides and P. arenarium are similar in size and gene content, and substantially reduced compared to T. plicata, consistent with trends seen in other holoparasitic lineages. In particular, most plastid genes involved in photosynthesis function have been lost, whereas housekeeping genes (ribosomal protein-coding genes, rRNAs, and tRNAs) are retained. One notable exception is the persistence of a rbcL open reading frame in P. arenarium but not L. madreporoides suggesting a nonphotosynthetic function for this gene. Of the retained coding genes, d_N/d_S ratios indicate that some remain under purifying selection, whereas others show relaxed selection. Overall, this study supports the mounting evidence for convergent plastome evolution in flowering plants following the shift to heterotrophy.

Mobile Elements Shape Plastome Evolution in Ferns

Plastid genomes display remarkable organizational stability over evolutionary time. From green algae to angiosperms, most plastid genomes are largely collinear, with only a few cases of inversion, gene loss, or, in extremely rare cases, gene addition. These plastome insertions are mostly clade-specific and are typically of nuclear or mitochondrial origin. Here, we expand on these findings and present the first family-level survey of plastome evolution in ferns, revealing a novel suite of dynamic mobile elements. Comparative plastome analyses of the Pteridaceae expose several mobile open reading frames that vary in sequence length, insertion site, and configuration among sampled taxa. Even between close relatives, the presence and location of these elements is widely variable when viewed in a phylogenetic context. We characterize these elements and refer to them collectively as Mobile Open Reading Frames in Fern Organelles (MORFFO). We further note that the presence of MORFFO is not restricted to Pteridaceae, but is found across ferns and other plant clades. MORFFO elements are regularly associated with inversions, intergenic expansions, and changes to the inverted repeats. They likewise appear to be present in mitochondrial and nuclear genomes of ferns, indicating that they can move between genomic compartments with relative ease. The origins and functions of these mobile elements are unknown, but MORFFO appears to be a major driver of structural genome evolution in the plastomes of ferns, and possibly other groups of plants.

Similarities in the evolution of plants and cars

While one system is animate and the other inanimate, both plants and cars are powered by a highly successful process which has evolved in a changing environment. Each process (the photosynthetic pathway and the car engine, respectively) originated from a basic scheme and evolved greater efficiency by adding components to the existing structure, which has remained largely unchanged. Here we present a comparative analysis of two variants on the original C3 photosynthetic pathway (C4 and CAM) and two variants on the internal combustion engine (the turbocharger and the hybrid electric vehicle). We compare the timeline of evolution, the interaction between system components, and the effects of environmental conditions on both systems. This analysis reveals striking similarities in the development of these processes, providing insight as to how complex systems—both natural and built—evolve and adapt to changing environmental conditions in a modular fashion.

Enhancing (crop) plant photosynthesis by introducing novel genetic diversity

Although some elements of the photosynthetic light reactions might appear to be ideal, the overall efficiency of light conversion to biomass has not been optimized during evolution. Because crop plants are depleted of genetic diversity for photosynthesis, efforts to enhance its efficiency with respect to light conversion to yield must generate new variation. In principle, three sources of natural variation are available: (i) rare diversity within extant higher plant species, (ii) photosynthetic variants from algae, and (iii) reconstruction of no longer extant types of plant photosynthesis. Here, we argue for a novel approach that outsources crop photosynthesis to a cyanobacterium that is amenable to adaptive evolution. This system offers numerous advantages, including a short generation time, virtually unlimited population sizes and high mutation rates, together with a versatile toolbox for genetic manipulation. On such a synthetic bacterial platform, 10 000 years of (crop) plant evolution can be recapitulated within weeks. Limitations of this system arise from its unicellular nature, which cannot reproduce all aspects of crop photosynthesis. But successful establishment of such a bacterial host for crop photosynthesis promises not only to enhance the performance of eukaryotic photosynthesis but will also reveal novel facets of the molecular basis of photosynthetic flexibility.This article is part of the themed issue 'Enhancing photosynthesis in crop plants: targets for improvement'.

Comparative genomic analysis of Genlisea (corkscrew plants-Lentibulariaceae) chloroplast genomes reveals an increasing loss of the ndh genes

In the carnivorous plant family Lentibulariaceae, all three genome compartments (nuclear, chloroplast, and mitochondria) have some of the highest rates of nucleotide substitutions across angiosperms. While the genera Genlisea and Utricularia have the smallest known flowering plant nuclear genomes, the chloroplast genomes (cpDNA) are mostly structurally conserved except for deletion and/or pseudogenization of the NAD(P)H-dehydrogenase complex (ndh) genes known to be involved in stress conditions of low light or CO2 concentrations. In order to determine how the cpDNA are changing, and to better understand the evolutionary history within the Genlisea genus, we sequenced, assembled and analyzed complete cpDNA from six species (G. aurea, G. filiformis, G. pygmaea, G. repens, G. tuberosa and G. violacea) together with the publicly available G. margaretae cpDNA. In general, the cpDNA structure among the analyzed Genlisea species is highly similar. However, we found that the plastidial ndh genes underwent a progressive process of degradation similar to the other terrestrial Lentibulariaceae cpDNA analyzed to date, but in contrast to the aquatic species. Contrary to current thinking that the terrestrial environment is a more stressful environment and thus requiring the ndh genes, we provide evidence that in the Lentibulariaceae the terrestrial forms have progressive loss while the aquatic forms have the eleven plastidial ndh genes intact. Therefore, the Lentibulariaceae system provides an important opportunity to understand the evolutionary forces that govern the transition to an aquatic environment and may provide insight into how plants manage water stress at a genome scale.

The complete chloroplast genome sequence of the CAM epiphyte Spanish moss (Tillandsia usneoides, Bromeliaceae) and its comparative analysis

Spanish moss (Tillandsia usneoides) is an epiphytic bromeliad widely distributed throughout tropical and warm temperate America. This plant is highly adapted to extreme environmental conditions. Striking features of this species include specialized trichomes (scales) covering the surface of its shoots aiding the absorption of water and nutrients directly from the atmosphere and a specific photosynthesis using crassulacean acid metabolism (CAM). Here we report the plastid genome of Spanish moss and present the comparison of genome organization and sequence evolution within Poales. The plastome of Spanish moss has a quadripartite structure consisting of a large single copy (LSC, 87,439 bp), two inverted regions (IRa and IRb, 26,803 bp) and short single copy (SSC, 18,612 bp) region. The plastid genome had 37.2% GC content and 134 genes with 88 being unique protein-coding genes and 20 of these are duplicated in the IR, similar to other reported bromeliads. Our study shows that early diverging lineages of Poales do not have high substitution rates as compared to grasses, and plastid genomes of bromeliads show structural features considered to be ancestral in graminids. These include the loss of the introns in the clpP and rpoC1 genes and the complete loss or partial degradation of accD and ycf genes in the Graminid clade. Further structural rearrangements appeared in the graminids lacking in Spanish moss, which include a 28-kb inversion between the trnG-UCC-rps14 region and 6-kb in the trnG-UCC-psbD, followed by a third <1kb inversion in the trnT sequence.

On the brink: the highly reduced plastomes of nonphotosynthetic Ericaceae

Ericaceae (the heather family) is a large and diverse group of plants that forms elaborate symbiotic relationships with mycorrhizal fungi, and includes several nonphotosynthetic lineages. Using an extensive sample of fully mycoheterotrophic (MH) species, we explored inter- and intraspecific variation as well as selective constraints acting on the plastomes of these unusual plants. The plastomes of seven MH genera were analysed in a phylogenetic context with two geographically disparate individuals sequenced for Allotropa, Monotropa, and Pityopus. The plastomes of nonphotosynthetic Ericaceae are highly reduced in size (c. 33-41 kbp) and content, having lost all photosynthesis-related genes, and are reduced to encoding housekeeping genes as well as a protease subunit (clpP)-like and acetyl-CoA carboxylase subunit D (accD)-like open reading frames. Despite an increase in the rate of their nucleotide substitutions, the remaining protein-coding genes are typically under purifying selection in full MHs. We also identified ribosomal proteins under relaxed or neutral selection. These plastomes also exhibit striking structural rearrangements. Intraspecific variation within MH Ericaceae ranges from a few differences (Allotropa) to extensive population divergences (Monotropa, Hypopitys), which indicates that cryptic speciation may be occurring in several lineages. The pattern of gene loss within fully MH Ericaceae plastomes suggests an advanced state of degradation.

The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae

A reference genome sequence for Pseudotsuga menziesii var. menziesii (Mirb.) Franco (Coastal Douglas-fir) is reported, thus providing a reference sequence for a third genus of the family Pinaceae. The contiguity and quality of the genome assembly far exceeds that of other conifer reference genome sequences (contig N50 = 44,136 bp and scaffold N50 = 340,704 bp). Incremental improvements in sequencing and assembly technologies are in part responsible for the higher quality reference genome, but it may also be due to a slightly lower exact repeat content in Douglas-fir vs. pine and spruce. Comparative genome annotation with angiosperm species reveals gene-family expansion and contraction in Douglas-fir and other conifers which may account for some of the major morphological and physiological differences between the two major plant groups. Notable differences in the size of the NDH-complex gene family and genes underlying the functional basis of shade tolerance/intolerance were observed. This reference genome sequence not only provides an important resource for Douglas-fir breeders and geneticists but also sheds additional light on the evolutionary processes that have led to the divergence of modern angiosperms from the more ancient gymnosperms.

Inferring the evolutionary mechanism of the chloroplast genome size by comparing whole-chloroplast genome sequences in seed plants

The chloroplast genome originated from photosynthetic organisms and has retained the core genes that mainly encode components of photosynthesis. However, the causes of variations in chloroplast genome size in seed plants have only been thoroughly analyzed within small subsets of spermatophytes. In this study, we conducted the first comparative analysis on a large scale to examine the relationship between sequence characteristics and genome size in 272 seed plants based on cross-species and phylogenetic signal analysis. Our results showed that inverted repeat regions, large or small single copies, intergenic regions, and gene number can be attributed to the variations in chloroplast genome size among closely related species. However, chloroplast gene length underwent evolution affecting chloroplast genome size in seed plants irrespective of whether phylogenetic information was incorporated. Among chloroplast genes, atpA, accD and ycf1 account for 13% of the variation in genome size, and the average Ka/Ks values of homologous pairs of the three genes are larger than 1. The relationship between chloroplast genome size and gene length might be affected by selection during the evolution of spermatophytes. The variation in chloroplast genome size may influence energy generation and ecological strategy in seed plants.

Degeneration of photosynthetic capacity in mixotrophic plants, Chimaphila japonica and Pyrola decorata (Ericaceae)

The evolution of photosynthesis is an important feature of mixotrophic plants. Previous inferences proposed that mixotrophic taxa tend to retain most genes relating to photosynthetic functions but vary in plastid gene content. However, no sequence data are available to test this hypothesis in Ericaceae. To investigate changes in plastid genomes that may result from a transition from autotrophy to mixotrophy, the plastomes of two mixotrophic plants, Pyrola decorata and Chimaphila japonica, were sequenced at Illumina's Genome Analyzer and compared to the published plastome of the autotrophic plant Rhododendron simsii, which also belongs to Ericaceae. The greatest discrepancy between mixotrophic and autotrophic plants was that ndh genes for both P. decorata and C. japonica plastomes have nearly all become pseudogenes. P. decorata and C. japonica also retained all genes directly involved in photosynthesis under strong selection. The calculated rate of nonsynonymous nucleotide substitutions and synonymous substitutions of protein-coding genes (dN/dS) showed that substitution rates in shade plants were apparently higher than those in sunlight plants. The two mixotrophic plastomes were generally very similar to that of non-parasitic plants, although ndh genes were largely pseudogenized. Photosynthesis genes under strong selection were retained in the two mixotrophs, however, with greatly increased substitution rates. Further research is needed to gain a clearer understanding of the evolution of autotrophy and mixotrophy in Ericaceae.

Dynamic Interplay between Nucleoid Segregation and Genome Integrity in Chlamydomonas Chloroplasts

The chloroplast (cp) genome is organized as nucleoids that are dispersed throughout the cp stroma. Previously, a cp homolog of bacterial recombinase RecA (cpRECA) was shown to be involved in the maintenance of cp genome integrity by repairing damaged chloroplast DNA and by suppressing aberrant recombination between short dispersed repeats in the moss Physcomitrella patens Here, overexpression and knockdown analysis of cpRECA in the green alga Chlamydomonas reinhardtii revealed that cpRECA was involved in cp nucleoid dynamics as well as having a role in maintaining cp genome integrity. Overexpression of cpRECA tagged with yellow fluorescent protein or hemagglutinin resulted in the formation of giant filamentous structures that colocalized exclusively to chloroplast DNA and cpRECA localized to cp nucleoids in a heterogenous manner. Knockdown of cpRECA led to a significant reduction in cp nucleoid number that was accompanied by nucleoid enlargement. This phenotype resembled those of gyrase inhibitor-treated cells and monokaryotic chloroplast mutant cells and suggested that cpRECA was involved in organizing cp nucleoid dynamics. The cp genome also was destabilized by induced recombination between short dispersed repeats in cpRECA-knockdown cells and gyrase inhibitor-treated cells. Taken together, these results suggest that cpRECA and gyrase are both involved in nucleoid dynamics and the maintenance of genome integrity and that the mechanisms underlying these processes may be intimately related in C. reinhardtii cps.

A few-gene plastid phylogenetic framework for mycoheterotrophic monocots

PREMISE OF THE STUDY

Few-gene studies with broad taxon sampling have provided major insights into phylogeny and underpin plant classification. However, they have typically excluded heterotrophic plants because of loss, pseudogenization, or rapid evolution of plastid genes. Here we performed a phylogenetic survey of three commonly retained plastid genes to assess their utility in placing mycoheterotrophs.

METHODS

We surveyed accD, clpP, and matK for 34 taxa from seven monocot families that include full mycoheterotrophs and a broad sampling of photosynthetic taxa. After screening for weak contaminants, we conducted phylogenetic analyses and characterized among-lineage rate variation.

KEY RESULTS

Likelihood analyses strongly supported local placements of fully mycoheterotrophic taxa for Corsiaceae, Iridaceae, Orchidaceae, and Petrosaviaceae, in positions consistent with other studies. Depression of likelihood bootstrap support values near mycoheterotrophic clades was alleviated when each mycoheterotrophic family was considered separately. Triuridaceae (Sciaphila) monophyly was recovered in a partitioned likelihood analysis, and the family then placed as sister to Cyclanthaceae-Pandanaceae. Burmanniaceae placed in Dioscoreales with weak to strong support depending on analysis details, and we inferred a plastid-based phylogeny for the family. Thismiaceae species may retain a plastid genome, based on accD retention. The inferred position of Thismiaceae is unstable, but was close to Taccaceae (Dioscoreales) in some analyses.

CONCLUSIONS

Long branches/elevated substitution rates, missing genes, and occasional contaminants are challenges for plastid-based phylogenetic inference with full mycoheterotrophs. However, most mycoheterotrophs can be readily integrated into the broad picture of plant phylogeny using several plastid genes and broad taxonomic sampling.

Detecting and Characterizing the Highly Divergent Plastid Genome of the Nonphotosynthetic Parasitic Plant Hydnora visseri (Hydnoraceae)

Plastid genomes of photosynthetic flowering plants are usually highly conserved in both structure and gene content. However, the plastomes of parasitic and mycoheterotrophic plants may be released from selective constraint due to the reduction or loss of photosynthetic ability. Here we present the greatly reduced and highly divergent, yet functional, plastome of the nonphotosynthetic holoparasite Hydnora visseri (Hydnoraceae, Piperales). The plastome is 27 kb in length, with 24 genes encoding ribosomal proteins, ribosomal RNAs, tRNAs, and a few nonbioenergetic genes, but no genes related to photosynthesis. The inverted repeat and the small single copy region are only approximately 1.5 kb, and intergenic regions have been drastically reduced. Despite extreme reduction, gene order and orientation are highly similar to the plastome of Piper cenocladum, a related photosynthetic plant in Piperales. Gene sequences in Hydnora are highly divergent and several complementary approaches using the highest possible sensitivity were required for identification and annotation of this plastome. Active transcription is detected for all of the protein-coding genes in the plastid genome, and one of two introns is appropriately spliced out of rps12 transcripts. The whole-genome shotgun read depth is 1,400× coverage for the plastome, whereas the mitochondrial genome is covered at 40× and the nuclear genome at 2×. Despite the extreme reduction of the genome and high sequence divergence, the presence of syntenic, long transcriptionally active open-reading frames with distant similarity to other plastid genomes and a high plastome stoichiometry relative to the mitochondrial and nuclear genomes suggests that the plastome remains functional in H. visseri. A four-stage model of gene reduction, including the potential for complete plastome loss, is proposed to account for the range of plastid genomes in nonphotosynthetic plants.

Non-functional plastid ndh gene fragments are present in the nuclear genome of Norway spruce (Picea abies L. Karsch): insights from in silico analysis of nuclear and organellar genomes

Many genes have been lost from the prokaryote plastidial genome during the early events of endosymbiosis in eukaryotes. Some of them were definitively lost, but others were relocated and functionally integrated to the host nuclear genomes through serial events of gene transfer during plant evolution. In gymnosperms, plastid genome sequencing has revealed the loss of ndh genes from several species of Gnetales and Pinaceae, including Norway spruce (Picea abies). This study aims to trace the ndh genes in the nuclear and organellar Norway spruce genomes. The plastid genomes of higher plants contain 11 ndh genes which are homologues of mitochondrial genes encoding subunits of the proton-pumping NADH-dehydrogenase (nicotinamide adenine dinucleotide dehydrogenase) or complex I (electron transport chain). Ndh genes encode 11 NDH polypeptides forming the Ndh complex (analogous to complex I) which seems to be primarily involved in chloro-respiration processes. We considered ndh genes from the plastidial genome of four gymnosperms (Cryptomeria japonica, Cycas revoluta, Ginkgo biloba, Podocarpus totara) and a single angiosperm species (Arabidopsis thaliana) to trace putative homologs in the nuclear and organellar Norway spruce genomes using tBLASTn to assess the evolutionary fate of ndh genes in Norway spruce and to address their genomic location(s), structure, integrity and functionality. The results obtained from tBLASTn were subsequently analyzed by performing homology search for finding ndh specific conserved domains using conserved domain search. We report the presence of non-functional plastid ndh gene fragments, excepting ndhE and ndhG genes, in the nuclear genome of Norway spruce. Regulatory transcriptional elements like promoters, TATA boxes and enhancers were detected in the upstream regions of some ndh fragments. We also found transposable elements in the flanking regions of few ndh fragments suggesting nuclear rearrangements in those regions. These evidences support the hypothesis that, at least in Picea, ndh translocations from the plastid to the nuclear genome have occurred, and that there might have been a functional machinery at some time during evolution to accommodate them within a nuclear-encoded environment, or attempts to form it.

RECA plays a dual role in the maintenance of chloroplast genome stability in Physcomitrella patens

Chloroplast DNA (cpDNA) encodes essential genes for chloroplast functions, including photosynthesis. Homologous recombination occurs frequently in cpDNA; however, its significance and underlying mechanism remain poorly understood. In this study, we analyzed the role of a nuclear-encoded chloroplast-localized homolog of RecA recombinase, which is a key factor in homologous recombination in bacteria, in the moss Physcomitrella patens. Complete knockout (KO) of the P. patens chloroplast RecA homolog RECA2 caused a modest growth defect and conferred sensitivity to methyl methanesulfonate and UV. The KO mutant exhibited low recovery of cpDNA from methyl methanesulfonate damage, suggesting that RECA2 knockout impairs repair of damaged cpDNA. The RECA2 KO mutant also exhibited reduced cpDNA copy number and an elevated level of cpDNA molecule resulting from aberrant recombination between short dispersed repeats (13-63 bp), indicating that the RECA2 KO chloroplast genome was destabilized. Taken together, these data suggest a dual role for RECA2 in the maintenance of chloroplast genome stability: RECA2 suppresses aberrant recombination between short dispersed repeats and promotes repair of damaged DNA.

The Highly Reduced Plastome of Mycoheterotrophic Sciaphila (Triuridaceae) Is Colinear with Its Green Relatives and Is under Strong Purifying Selection

The enigmatic monocot family Triuridaceae provides a potentially useful model system for studying the effects of an ancient loss of photosynthesis on the plant plastid genome, as all of its members are mycoheterotrophic and achlorophyllous. However, few studies have placed the family in a comparative context, and its phylogenetic placement is only partly resolved. It was also unclear whether any taxa in this family have retained a plastid genome. Here, we used genome survey sequencing to retrieve plastid genome data for Sciaphila densiflora (Triuridaceae) and ten autotrophic relatives in the orders Dioscoreales and Pandanales. We recovered a highly reduced plastome for Sciaphila that is nearly colinear with Carludovica palmata, a photosynthetic relative that belongs to its sister group in Pandanales, Cyclanthaceae-Pandanaceae. This phylogenetic placement is well supported and robust to a broad range of analytical assumptions in maximum-likelihood inference, and is congruent with recent findings based on nuclear and mitochondrial evidence. The 28 genes retained in the S. densiflora plastid genome are involved in translation and other nonphotosynthetic functions, and we demonstrate that nearly all of the 18 protein-coding genes are under strong purifying selection. Our study confirms the utility of whole plastid genome data in phylogenetic studies of highly modified heterotrophic plants, even when they have substantially elevated rates of substitution.

Why chloroplasts and mitochondria retain their own genomes and genetic systems: Colocation for redox regulation of gene expression

Chloroplasts and mitochondria are subcellular bioenergetic organelles with their own genomes and genetic systems. DNA replication and transmission to daughter organelles produces cytoplasmic inheritance of characters associated with primary events in photosynthesis and respiration. The prokaryotic ancestors of chloroplasts and mitochondria were endosymbionts whose genes became copied to the genomes of their cellular hosts. These copies gave rise to nuclear chromosomal genes that encode cytosolic proteins and precursor proteins that are synthesized in the cytosol for import into the organelle into which the endosymbiont evolved. What accounts for the retention of genes for the complete synthesis within chloroplasts and mitochondria of a tiny minority of their protein subunits? One hypothesis is that expression of genes for protein subunits of energy-transducing enzymes must respond to physical environmental change by means of a direct and unconditional regulatory control--control exerted by change in the redox state of the corresponding gene product. This hypothesis proposes that, to preserve function, an entire redox regulatory system has to be retained within its original membrane-bound compartment. Colocation of gene and gene product for redox regulation of gene expression (CoRR) is a hypothesis in agreement with the results of a variety of experiments designed to test it and which seem to have no other satisfactory explanation. Here, I review evidence relating to CoRR and discuss its development, conclusions, and implications. This overview also identifies predictions concerning the results of experiments that may yet prove the hypothesis to be incorrect.

Comparative genomics of ten solanaceous plastomes

Availability of complete plastid genomes of ten solanaceous species, Atropa belladonna, Capsicum annuum, Datura stramonium, Nicotiana sylvestris, Nicotiana tabacum, Nicotiana tomentosiformis, Nicotiana undulata, Solanum bulbocastanum, Solanum lycopersicum, and Solanum tuberosum provided us with an opportunity to conduct their in silico comparative analysis in depth. The size of complete chloroplast genomes and LSC and SSC regions of three species of Solanum is comparatively smaller than that of any other species studied till date (exception: SSC region of A. belladonna). AT content of coding regions was found to be less than noncoding regions. A duplicate copy of trnH gene in C. annuum and two alternative tRNA genes for proline in D. stramonium were observed for the first time in this analysis. Further, homology search revealed the presence of rps19 pseudogene and infA genes in A. belladonna and D. stramonium, a region identical to rps19 pseudogene in C. annum and orthologues of sprA gene in another six species. Among the eighteen intron-containing genes, 3 genes have two introns and 15 genes have one intron. The longest insertion was found in accD gene in C. annuum. Phylogenetic analysis using concatenated protein coding sequences gave two clades, one for Nicotiana species and another for Solanum, Capsicum, Atropa, and Datura.

Analyses of charophyte chloroplast genomes help characterize the ancestral chloroplast genome of land plants

Despite the significance of the relationships between embryophytes and their charophyte algal ancestors in deciphering the origin and evolutionary success of land plants, few chloroplast genomes of the charophyte algae have been reconstructed to date. Here, we present new data for three chloroplast genomes of the freshwater charophytes Klebsormidium flaccidum (Klebsormidiophyceae), Mesotaenium endlicherianum (Zygnematophyceae), and Roya anglica (Zygnematophyceae). The chloroplast genome of Klebsormidium has a quadripartite organization with exceptionally large inverted repeat (IR) regions and, uniquely among streptophytes, has lost the rrn5 and rrn4.5 genes from the ribosomal RNA (rRNA) gene cluster operon. The chloroplast genome of Roya differs from other zygnematophycean chloroplasts, including the newly sequenced Mesotaenium, by having a quadripartite structure that is typical of other streptophytes. On the basis of the improbability of the novel gain of IR regions, we infer that the quadripartite structure has likely been lost independently in at least three zygnematophycean lineages, although the absence of the usual rRNA operonic synteny in the IR regions of Roya may indicate their de novo origin. Significantly, all zygnematophycean chloroplast genomes have undergone substantial genomic rearrangement, which may be the result of ancient retroelement activity evidenced by the presence of integrase-like and reverse transcriptase-like elements in the Roya chloroplast genome. Our results corroborate the close phylogenetic relationship between Zygnematophyceae and land plants and identify 89 protein-coding genes and 22 introns present in the chloroplast genome at the time of the evolutionary transition of plants to land, all of which can be found in the chloroplast genomes of extant charophytes.

Possible loss of the chloroplast genome in the parasitic flowering plant Rafflesia lagascae (Rafflesiaceae)

Rafflesia is a genus of holoparasitic plants endemic to Southeast Asia that has lost the ability to undertake photosynthesis. With short-read sequencing technology, we assembled a draft sequence of the mitochondrial genome of Rafflesia lagascae Blanco, a species endemic to the Philippine island of Luzon, with ∼350× sequencing depth coverage. Using multiple approaches, however, we were only able to identify small fragments of plastid sequences at low coverage depth (<2×) and could not recover any substantial portion of a chloroplast genome. The gene fragments we identified included photosynthesis and energy production genes (atp, ndh, pet, psa, psb, rbcL), ribosomal RNA genes (rrn16, rrn23), ribosomal protein genes (rps7, rps11, rps16), transfer RNA genes, as well as matK, accD, ycf2, and multiple nongenic regions from the inverted repeats. None of the identified plastid gene sequences had intact reading frames. Phylogenetic analysis suggests that ∼33% of these remnant plastid genes may have been horizontally transferred from the host plant genus Tetrastigma with the rest having ambiguous phylogenetic positions (<50% bootstrap support), except for psaB that was strongly allied with the plastid homolog in Nicotiana. Our inability to identify substantial plastid genome sequences from R. lagascae using multiple approaches—despite success in identifying and developing a draft assembly of the much larger mitochondrial genome—suggests that the parasitic plant genus Rafflesia may be the first plant group for which there is no recognizable plastid genome, or if present is found in cryptic form at very low levels.

Insights from the complete chloroplast genome into the evolution of Sesamum indicum L

Sesame (Sesamum indicum L.) is one of the oldest oilseed crops. In order to investigate the evolutionary characters according to the Sesame Genome Project, apart from sequencing its nuclear genome, we sequenced the complete chloroplast genome of S. indicum cv. Yuzhi 11 (white seeded) using Illumina and 454 sequencing. Comparisons of chloroplast genomes between S. indicum and the 18 other higher plants were then analyzed. The chloroplast genome of cv. Yuzhi 11 contains 153,338 bp and a total of 114 unique genes (KC569603). The number of chloroplast genes in sesame is the same as that in Nicotiana tabacum, Vitis vinifera and Platanus occidentalis. The variation in the length of the large single-copy (LSC) regions and inverted repeats (IR) in sesame compared to 18 other higher plant species was the main contributor to size variation in the cp genome in these species. The 77 functional chloroplast genes, except for ycf1 and ycf2, were highly conserved. The deletion of the cp ycf1 gene sequence in cp genomes may be due either to its transfer to the nuclear genome, as has occurred in sesame, or direct deletion, as has occurred in Panax ginseng and Cucumis sativus. The sesame ycf2 gene is only 5,721 bp in length and has lost about 1,179 bp. Nucleotides 1–585 of ycf2 when queried in BLAST had hits in the sesame draft genome. Five repeats (R10, R12, R13, R14 and R17) were unique to the sesame chloroplast genome. We also found that IR contraction/expansion in the cp genome alters its rate of evolution. Chloroplast genes and repeats display the signature of convergent evolution in sesame and other species. These findings provide a foundation for further investigation of cp genome evolution in Sesamum and other higher plants.

Establishing genomic tools and resources for Guizotia abyssinica (L.f.) Cass.-the development of a library of expressed sequence tags, microsatellite loci, and the sequencing of its chloroplast genome

We present an EST library, chloroplast genome sequence, and nuclear microsatellite markers that were developed for the semi-domesticated oilseed crop noug (Guizotia abyssinica) from Ethiopia. The EST library consists of 25 711 Sanger reads, assembled into 17 538 contigs and singletons, of which 4781 were functionally annotated using the Arabidopsis Information Resource (TAIR). The age distribution of duplicated genes in the EST library shows evidence of two paleopolyploidizations-a pattern that noug shares with several other species in the Heliantheae tribe (Compositae family). From the EST library, we selected 43 microsatellites and then designed and tested primers for their amplification. The number of microsatellite alleles varied between 2 and 10 (average 4.67), and the average observed and expected heterozygosities were 0.49 and 0.54, respectively. The chloroplast genome was sequenced de novo using Illumina's sequencing technology and completed with traditional Sanger sequencing. No large re-arrangements were found between the noug and sunflower chloroplast genomes, but 1.4% of sites have indels and 1.8% show sequence divergence between the two species. We identified 34 tRNAs, 4 rRNA sequences, and 80 coding sequences, including one region (trnH-psbA) with 15% sequence divergence between noug and sunflower that may be particularly useful for phylogeographic studies in noug and its wild relatives.

Potential functional replacement of the plastidic acetyl-CoA carboxylase subunit (accD) gene by recent transfers to the nucleus in some angiosperm lineages

Eukaryotic cells originated when an ancestor of the nucleated cell engulfed bacterial endosymbionts that gradually evolved into the mitochondrion and the chloroplast. Soon after these endosymbiotic events, thousands of ancestral prokaryotic genes were functionally transferred from the endosymbionts to the nucleus. This process of functional gene relocation, now rare in eukaryotes, continues in angiosperms. In this article, we show that the chloroplastic acetyl-CoA carboxylase subunit (accD) gene that is present in the plastome of most angiosperms has been functionally relocated to the nucleus in the Campanulaceae. Surprisingly, the nucleus-encoded accD transcript is considerably smaller than the plastidic version, consisting of little more than the carboxylase domain of the plastidic accD gene fused to a coding region encoding a plastid targeting peptide. We verified experimentally the presence of a chloroplastic transit peptide by showing that the product of the nuclear accD fused to green fluorescent protein was imported in the chloroplasts. The nuclear gene regulatory elements that enabled the erstwhile plastidic gene to become functional in the nuclear genome were identified, and the evolution of the intronic and exonic sequences in the nucleus is described. Relocation and truncation of the accD gene is a remarkable example of the processes underpinning endosymbiotic evolution.

The contributions of wobbling and superwobbling to the reading of the genetic code

Reduced bacterial genomes and most genomes of cell organelles (chloroplasts and mitochondria) do not encode the full set of 32 tRNA species required to read all triplets of the genetic code according to the conventional wobble rules. Superwobbling, in which a single tRNA species that contains a uridine in the wobble position of the anticodon reads an entire four-fold degenerate codon box, has been suggested as a possible mechanism for how tRNA sets can be reduced. However, the general feasibility of superwobbling and its efficiency in the various codon boxes have remained unknown. Here we report a complete experimental assessment of the decoding rules in a typical prokaryotic genetic system, the plastid genome. By constructing a large set of transplastomic knock-out mutants for pairs of isoaccepting tRNA species, we show that superwobbling occurs in all codon boxes where it is theoretically possible. Phenotypic characterization of the transplastomic mutant plants revealed that the efficiency of superwobbling varies in a codon box-dependent manner, but--contrary to previous suggestions--it is independent of the number of hydrogen bonds engaged in codon-anticodon interaction. Finally, our data provide experimental evidence of the minimum tRNA set comprising 25 tRNA species, a number lower than previously suggested. Our results demonstrate that all triplets with pyrimidines in third codon position are dually decoded: by a tRNA species utilizing standard base pairing or wobbling and by a second tRNA species employing superwobbling. This has important implications for the interpretation of the genetic code and will aid the construction of synthetic genomes with a minimum-size translational apparatus.

Multiple and different genomic rearrangements of the rbcL gene are present in the parasitic orchid Neottia nidus-avis

In parasitic plants that have lost most, if not all, of their photosynthetic genes, the genome of their plastids has also undergone a dramatic reduction. For example, photosynthetic genes, such as rbcL, frequently become pseudogenes, in which large portions of the gene have been found to be deleted. Orchids are flowering plants with several parasitic lineages. This is consistent with the observation that parasitic orchids can invade pre-existing mutualistic associations between ectomycorrhizal trees and fungi to obtain fixed carbon and nutrients. In addition, some parasitic species are devoid of chlorophyll, and consequently, have lost their photosynthetic capacity. Here, the organization of the plastid genome of the parasitic orchid Neottia nidus-avis (L.) Rich. was investigated using sequencing and hybridization experiments. In particular, genomic rearrangements in the rbcL region of this parasitic orchid were analyzed. At least three distinct rbcL sequences were found to be present as pseudogenes and were likely located in the plastid genome. Based on these results, it is hypothesized that N. nidus-avis contains different plastomes, each with a different pseudogene, and these can exist within the same individual plant.

The plastid genome of the mycoheterotrophic Corallorhiza striata (Orchidaceae) is in the relatively early stages of degradation

PREMISE OF THE STUDY

Plastid genomes of nonphotosynthetic, mycoheterotrophic plants represent apt systems in which to study effects of relaxed evolutionary constraints. The few mycoheterotrophic angiosperm plastomes sequenced to date display drastic patterns of degradation/reduction relative to those of photosynthetic relatives. The goal of this study was to focus on a mycoheterotrophic orchid hypothesized to be in the "early" stages of plastome degradation, to provide perspective on this process.

METHODS

Short-read sequencing was used to generate a complete plastome sequence for Corallorhiza striata var. vreelandii, a mycoheterotrophic orchid, to investigate the extent of plastome degradation. Patterns of nonsynonymous/synonymous mutations were also assessed, and comparisons were made between Corallorhiza and other heterotrophic plant lineages.

KEY RESULTS

Corallorhiza yielded a plastome of 137505 bp, with several photosynthesis-related genes either lost or pseudogenized. Members of all major photosynthesis complexes, except ATP-synthase genes, were affected. "Housekeeping" genes were intact, despite the loss of a single tRNA. Intact photosynthesis genes (excluding atp genes) together displayed elevated nonsynonymous changes, while housekeeping genes did not.

CONCLUSIONS

The Corallorhiza plastome is not drastically reduced in overall size (∼6% reduction relative to that of photosynthetic Oncidium), but displays a pattern congruent with a loss of photosynthetic function. Comparing Corallorhiza with other heterotrophs allows some emergent evolutionary patterns to be inferred, but these remain as hypotheses to be tested, especially at lower taxonomic levels, and in lineages illustrating transitions from autotrophy to heterotrophy. The independent, unique processes of plastome modification among mycoheterotrophic lineages illustrate the urgency of their conservation.