Eukaryotic genome evolution: rearrangement and coevolution of compartmentalized genetic information

Genetic and Molecular Genetic Basis of Nuclear-Plastid Incompatibilities

Genetic analysis of nuclear-cytoplasm incompatibilities is not straightforward and requires an elaborated experimental design. A number of species have been genetically studied, but notable advances in genetic mapping of nuclear loci involved in nuclear-plastid incompatibility have been achieved only in wheat and pea. This review focuses on the study of the genetic background underlying nuclear-plastid incompatibilities, including cases where the molecular genetic basis of such incompatibility has been unveiled, such as in tobacco, Oenothera, pea, and wheat.

Novel Plastid-Nuclear Genome Combinations Enhance Resistance to Citrus Canker in Cybrid Grapefruit

Host disease resistance is the most desirable strategy for control of citrus canker, a disease caused by a gram-negative bacterium Xanthomonas citri subsp. citri. However, no resistant commercial citrus cultivar has been identified. Cybridization, a somatic hybridization approach that combines the organelle and nuclear genomes from different species, was used to create cybrids between citrus canker resistant 'Meiwa' kumquat (Fortunella crassifolia Swingle snym. Citrus japonica Thunb.) and susceptible grapefruit (Citrus paradisi Macfad) cultivars. From these fusions, cybrids with grapefruit nucleus, kumquat mitochondria and kumquat chloroplasts and cybrids with grapefruit nucleus, kumquat mitochondria and grapefruit chloroplasts were generated. These cybrids showed a range of citrus canker response, but all cybrids with kumquat chloroplasts had a significantly lower number of lesions and lower Xanthomonas citri subsp. citri populations than the grapefruit controls. Cybrids with grapefruit chloroplasts had a significantly higher number of lesions than those with kumquat chloroplasts. To understand the role of chloroplasts in the cybrid disease defense, quantitative PCR was performed on both cybrid types and their parents to examine changes in gene expression during Xanthomonas citri subsp. citri infection. The results revealed chloroplast influences on nuclear gene expression, since isonuclear cybrids and 'Marsh' grapefruit had different gene expression profiles. In addition, only genotypes with kumquat chloroplasts showed an early up-regulation of reactive oxygen species genes upon Xanthomonas citri subsp. citri infection. These cybrids have the potential to enhance citrus canker resistance in commercial grapefruit orchards. They also serve as models for understanding the contribution of chloroplasts to plant disease response and raise the question of whether other alien chloroplast genotypes would condition similar results.

Microorganism and filamentous fungi drive evolution of plant synapses

In the course of plant evolution, there is an obvious trend toward an increased complexity of plant bodies, as well as an increased sophistication of plant behavior and communication. Phenotypic plasticity of plants is based on the polar auxin transport machinery that is directly linked with plant sensory systems impinging on plant behavior and adaptive responses. Similar to the emergence and evolution of eukaryotic cells, evolution of land plants was also shaped and driven by infective and symbiotic microorganisms. These microorganisms are the driving force behind the evolution of plant synapses and other neuronal aspects of higher plants; this is especially pronounced in the root apices. Plant synapses allow synaptic cell–cell communication and coordination in plants, as well as sensory-motor integration in root apices searching for water and mineral nutrition. These neuronal aspects of higher plants are closely linked with their unique ability to adapt to environmental changes.

Essential nucleoid proteins in early chloroplast development

The plastid transcription machinery can be biochemically purified at different organisational levels as soluble RNA polymerase, transcriptionally active chromosome, or nucleoid. Recent proteomic studies have uncovered several novel proteins in these structures and functional genomic studies have indicated that a lack of many of these proteins results in chlorotic phenotypes of varying degree. The most severe cases exhibit complete albino phenotypes, which led to the conclusion that the proteins that were lacking had important regulatory roles in plastid gene expression and chloroplast development. In this opinion article, we propose an alternative model in which the structural establishment of a transcriptional subdomain within the nucleoid represents an early developmental bottleneck that leads to abortion of proper chloroplast biogenesis if disturbed.

Rates of molecular evolution and diversification in plants: chloroplast substitution rates correlate with species-richness in the Proteaceae

BACKGROUND

Many factors have been identified as correlates of the rate of molecular evolution, such as body size and generation length. Analysis of many molecular phylogenies has also revealed correlations between substitution rates and clade size, suggesting a link between rates of molecular evolution and the process of diversification. However, it is not known whether this relationship applies to all lineages and all sequences. Here, in order to investigate how widespread this phenomenon is, we investigate patterns of substitution in chloroplast genomes of the diverse angiosperm family Proteaceae. We used DNA sequences from six chloroplast genes (6278bp alignment with 62 taxa) to test for a correlation between diversification and the rate of substitutions.

RESULTS

Using phylogenetically-independent sister pairs, we show that species-rich lineages of Proteaceae tend to have significantly higher chloroplast substitution rates, for both synonymous and non-synonymous substitutions.

CONCLUSIONS

We show that the rate of molecular evolution in chloroplast genomes is correlated with net diversification rates in this large plant family. We discuss the possible causes of this relationship, including molecular evolution driving diversification, speciation increasing the rate of substitutions, or a third factor causing an indirect link between molecular and diversification rates. The link between the synonymous substitution rate and clade size is consistent with a role for the mutation rate of chloroplasts driving the speed of reproductive isolation. We find no significant differences in the ratio of non-synonymous to synonymous substitutions between lineages differing in net diversification rate, therefore we detect no signal of population size changes or alteration in selection pressures that might be causing this relationship.

The core of chloroplast nucleoids contains architectural SWIB domain proteins

A highly enriched fraction of the transcriptionally active chromosome from chloroplasts of spinach (Spinacia oleracea) was analyzed by two-dimensional gel electrophoresis and mass spectrometry to identify proteins involved in structuring of the nucleoid core. Among such plastid nucleoid-associated candidate proteins a 12-kD SWIB (SWI/SNF complex B) domain-containing protein was identified. It belongs to a subgroup of low molecular mass SWIB domain proteins, which in Arabidopsis thaliana has six members (SWIB-1 to SWIB-6) with predictions for localization in the two DNA-containing organelles. Green/red fluorescent protein fusions of four of them were shown to be targeted to chloroplasts, where they colocalize with each other as well as with the plastid envelope DNA binding protein in structures corresponding to plastid nucleoids. For SWIB-6 and SWIB-4, a second localization in mitochondria and nucleus, respectively, could be observed. SWIB-4 has a histone H1 motif next to the SWIB domain and was shown to bind to DNA. Moreover, the recombinant SWIB-4 protein was shown to induce compaction and condensation of nucleoids and to functionally complement a mutant of Escherichia coli lacking the histone-like nucleoid structuring protein H-NS.

The hidden function of photosynthesis: a sensing system for environmental conditions that regulates plant acclimation responses

Plants convert light energy from the sun into chemical energy by photosynthesis. Since they are sessile, they have to deal with a wide range of conditions in their immediate environment. Many abiotic and biotic parameters exhibit considerable fluctuations which can have detrimental effects especially on the efficiency of photosynthetic light harvesting. During evolution, plants, therefore, evolved a number of acclimation processes which help them to adapt photosynthesis to such environmental changes. This includes protective mechanisms such as excess energy dissipation and processes supporting energy redistribution, e.g. state transitions or photosystem stoichiometry adjustment. Intriguingly, all these responses are triggered by photosynthesis itself via the interplay of its light reaction and the Calvin-Benson cycle with the residing environmental condition. Thus, besides its primary function in harnessing and converting light energy, photosynthesis acts as a sensing system for environmental changes that controls molecular acclimation responses which adapt the photosynthetic function to the environmental change. Important signalling parameters directly or indirectly affected by the environment are the pH gradient across the thylakoid membrane and the redox states of components of the photosynthetic electron transport chain and/or electron end acceptors coupled to it. Recent advances demonstrate that these signals control post-translational modifications of the photosynthetic protein complexes and also affect plastid and nuclear gene expression machineries as well as metabolic pathways providing a regulatory framework for an integrated response of the plant to the environment at all cellular levels.

A structural phylogenetic map for chloroplast photosynthesis

Chloroplasts are cytoplasmic organelles and the sites of photosynthesis in eukaryotic cells. Advances in structural biology and comparative genomics allow us to identify individual components of the photosynthetic apparatus precisely with respect to the subcellular location of their genes. Here we present outline maps of four energy-transducing thylakoid membranes. The maps for land plants and red and green algae distinguish protein subunits encoded in the nucleus from those encoded in the chloroplast. We find no defining structural feature that is common to all chloroplast gene products. Instead, conserved patterns of gene location are consistent with photosynthetic redox chemistry exerting gene regulatory control over its own rate-limiting steps. Chloroplast DNA carries genes whose expression is placed under this control.

Identification of essential subunits in the plastid-encoded RNA polymerase complex reveals building blocks for proper plastid development

The major RNA polymerase activity in mature chloroplasts is a multisubunit, Escherichia coli-like protein complex called PEP (for plastid-encoded RNA polymerase). Its subunit structure has been extensively investigated by biochemical means. Beside the "prokaryotic" subunits encoded by the plastome-located RNA polymerase genes, a number of additional nucleus-encoded subunits of eukaryotic origin have been identified in the PEP complex. These subunits appear to provide additional functions and regulation modes necessary to adapt transcription to the varying functional situations in chloroplasts. However, despite the enormous progress in genomic data and mass spectrometry techniques, it is still under debate which of these subunits belong to the core complex of PEP and which ones represent rather transient or peripheral components. Here, we present a catalog of true PEP subunits that is based on comparative analyses from biochemical purifications, protein mass spectrometry, and phenotypic analyses. We regard reproducibly identified protein subunits of the basic PEP complex as essential when the corresponding knockout mutants reveal an albino or pale-green phenotype. Our study provides a clearly defined subunit catalog of the basic PEP complex, generating the basis for a better understanding of chloroplast transcription regulation. In addition, the data support a model that links PEP complex assembly and chloroplast buildup during early seedling development in vascular plants.

The transcription machineries of plant mitochondria and chloroplasts: Composition, function, and regulation

Although genomes of mitochondria and plastids are very small compared to those of their bacterial ancestors, the transcription machineries of these organelles are of surprising complexity. With respect to the number of different RNA polymerases per organelle, the extremes are represented on one hand by chloroplasts of eudicots which use one bacterial-type RNA polymerase and two phage-type RNA polymerases to transcribe their genes, and on the other hand by Physcomitrella possessing three mitochondrial RNA polymerases of the phage type. Transcription of genes/operons is often driven by multiple promoters in both organelles. This review describes the principle components of the transcription machineries (RNA polymerases, transcription factors, promoters) and the division of labor between the different RNA polymerases. While regulation of transcription in mitochondria seems to be only of limited importance, the plastid genes of higher plants respond to exogenous and endogenous cues rather individually by altering their transcriptional activities.

Cytoplasmic phylogeny and evidence of cyto-nuclear co-adaptation in Arabidopsis thaliana

In recent years Arabidopsis thaliana has become a model species for genomic variability and adaptation studies. Although impressive quantities of data have been gathered on the nuclear genomic diversity of this species, little has been published regarding its cytoplasmic diversity. We analyzed the diversity of plastid (pt) and mitochondrial (mt) genomes among 95 accessions, covering most Arabidopsis geographic origins. Four intergenic regions of the pt genome were sequenced, and a total of 68 polymorphisms and 65 pt haplotypes were identified. Several strategies were developed to identify mt polymorphisms among a subset of 14 accessions. Fifteen polymorphisms were further developed as PCR-based markers and used to analyze the whole set of 95 accessions. Using statistical parsimony, we built pt and mt phylogenetic networks of haplotype groups. To root the pt network, the pt intergenic regions of two related Arabidopsis species, Arabidopsis lyrata and Arabidopsis arenosa, were also sequenced. The mt and pt phylogenies are highly congruent and could be combined into a single cytoplasmic phylogeny. To estimate whether co-adaptation between nuclear and cytoplasmic genomes exists in A. thaliana, we tested the germination capacity in challenging conditions of 27 pairs of reciprocal F(2) families. We found that the cytoplasm donor had a significant effect on the germination capacity of some F(2) families.

Molecular marker systems for Oenothera genetics

The genus Oenothera has an outstanding scientific tradition. It has been a model for studying aspects of chromosome evolution and speciation, including the impact of plastid nuclear co-evolution. A large collection of strains analyzed during a century of experimental work and unique genetic possibilities allow the exchange of genetically definable plastids, individual or multiple chromosomes, and/or entire haploid genomes (Renner complexes) between species. However, molecular genetic approaches for the genus are largely lacking. In this study, we describe the development of efficient PCR-based marker systems for both the nuclear genome and the plastome. They allow distinguishing individual chromosomes, Renner complexes, plastomes, and subplastomes. We demonstrate their application by monitoring interspecific exchanges of genomes, chromosome pairs, and/or plastids during crossing programs, e.g., to produce plastome-genome incompatible hybrids. Using an appropriate partial permanent translocation heterozygous hybrid, linkage group 7 of the molecular map could be assigned to chromosome 9.8 of the classical Oenothera map. Finally, we provide the first direct molecular evidence that homologous recombination and free segregation of chromosomes in permanent translocation heterozygous strains is suppressed.

Interspecies nuclear transfer: implications for embryonic stem cell biology

Accessibility of human oocytes for research poses a serious ethical challenge to society. This fact categorically holds true when pursuing some of the most promising areas of research, such as somatic cell nuclear transfer and embryonic stem cell studies. One approach to overcoming this limitation is to use an oocyte from one species and a somatic cell from another. Recently, several attempts to capture the promises of this approach have met with varying success, ranging from establishing human embryonic stem cells to obtaining live offspring in animals. This review focuses on the challenges and opportunities presented by the formidable task of overcoming biological differences among species.

The complete nucleotide sequences of the 5 genetically distinct plastid genomes of Oenothera, subsection Oenothera: II. A microevolutionary view using bioinformatics and formal genetic data

A unique combination of genetic features and a rich stock of information make the flowering plant genus Oenothera an appealing model to explore the molecular basis of speciation processes including nucleus–organelle coevolution. From representative species, we have recently reported complete nucleotide sequences of the 5 basic and genetically distinguishable plastid chromosomes of subsection Oenothera (I–V). In nature, Oenothera plastid genomes are associated with 6 distinct, either homozygous or heterozygous, diploid nuclear genotypes of the 3 basic genomes A, B, or C. Artificially produced plastome–genome combinations that do not occur naturally often display interspecific plastome–genome incompatibility (PGI). In this study, we compare formal genetic data available from all 30 plastome–genome combinations with sequence differences between the plastomes to uncover potential determinants for interspecific PGI. Consistent with an active role in speciation, a remarkable number of genes have high Ka/Ks ratios. Different from the Solanacean cybrid model Atropa/tobacco, RNA editing seems not to be relevant for PGIs in Oenothera. However, predominantly sequence polymorphisms in intergenic segments are proposed as possible sources for PGI. A single locus, the bidirectional promoter region between psbB and clpP, is suggested to contribute to compartmental PGI in the interspecific AB hybrid containing plastome I (AB-I), consistent with its perturbed photosystem II activity.

The complete nucleotide sequences of the five genetically distinct plastid genomes of Oenothera, subsection Oenothera: I. sequence evaluation and plastome evolution

The flowering plant genus Oenothera is uniquely suited for studying molecular mechanisms of speciation. It assembles an intriguing combination of genetic features, including permanent translocation heterozygosity, biparental transmission of plastids, and a general interfertility of well-defined species. This allows an exchange of plastids and nuclei between species often resulting in plastome-genome incompatibility. For evaluation of its molecular determinants we present the complete nucleotide sequences of the five basic, genetically distinguishable plastid chromosomes of subsection Oenothera (=Euoenothera) of the genus, which are associated in distinct combinations with six basic genomes. Sizes of the chromosomes range from 163 365 bp (plastome IV) to 165 728 bp (plastome I), display between 96.3% and 98.6% sequence similarity and encode a total of 113 unique genes. Plastome diversification is caused by an abundance of nucleotide substitutions, small insertions, deletions and repetitions. The five plastomes deviate from the general ancestral design of plastid chromosomes of vascular plants by a subsection-specific 56 kb inversion within the large single-copy segment. This inversion disrupted operon structures and predates the divergence of the subsection presumably 1 My ago. Phylogenetic relationships suggest plastomes I-III in one clade, while plastome IV appears to be closest to the common ancestor.

Gene rearrangement analysis and ancestral order inference from chloroplast genomes with inverted repeat

BACKGROUND

Genome evolution is shaped not only by nucleotide substitutions, but also by structural changes including gene and genome duplications, insertions, deletions and gene order rearrangements. The most popular methods for reconstructing phylogeny from genome rearrangements include GRAPPA and MGR. However these methods are limited to cases where equal gene content or few deletions can be assumed. Since conserved duplicated regions are present in many chloroplast genomes, the inference of inverted repeats is needed in chloroplast phylogeny analysis and ancestral genome reconstruction.

RESULTS

We extend GRAPPA and develop a new method GRAPPA-IR to handle chloroplast genomes. A test of GRAPPA-IR using divergent chloroplast genomes from land plants and green algae recovers the phylogeny congruent with prior studies, while analysis that do not consider IR structure fail to obtain the accepted topology. Our extensive simulation study also confirms that GRAPPA has better accuracy then the existing methods.

CONCLUSIONS

Tests on a biological and simulated dataset show GRAPPA-IR can accurately recover the genome phylogeny as well as ancestral gene orders. Close analysis of the ancestral genome structure suggests that genome rearrangement in chloroplasts is probably limited by inverted repeats with a conserved core region. In addition, the boundaries of inverted repeats are hot spots for gene duplications or deletions. The new GRAPPA-IR is available from http://phylo.cse.sc.edu.

Epistatic and cytonuclear interactions govern outbreeding depression in the autotetraploid Campanulastrum americanum

The consequences of combining divergent genomes among populations of a diploid species often involve F1 hybrid vigor followed by hybrid breakdown in later recombinant generations. As many as 70% of plant species are thought to have polyploid origins; yet little is known about the genetic architecture of divergence in polyploids and how it may differ from diploid species. We investigated the genetic architecture of population divergence using controlled crosses among five populations of the autotetraploid herb, Campanulastrum americanum. Plants were reciprocally hybridized to produce F1, F2, and F1-backcross generations that were grown with parental types in a greenhouse and measured for performance. In contrast to diploid expectations, most F1 hybrids lacked heterosis and instead showed strong outbreeding depression for early life traits. Recombinant hybrid generations often showed a recovery of performance to levels approximating, or at times even exceeding, the parental values. This pattern was also evident for an index of cumulative fitness. Analyses of line means indicated nonadditive gene action, especially forms of digenic epistasis, often influenced hybrid performance. However, standard diploid genetic models were not adequate for describing the underlying genetic architecture in a number of cases. Differences between reciprocal hybrids indicated that cytoplasmic and/or cytonuclear interactions also contributed to divergence. An enhanced role of epistasis in population differentiation may be the norm in polyploids, which have more gene copies. This study, the first of its kind on a natural autotetraploid, suggests that gene duplication may cause polyploid populations to diverge in a fundamentally different way than diploids.

Cybrid models of mtDNA disease and transmission, from cells to mice

Oxidative phosphorylation (OXPHOS) is the only mammalian biochemical pathway dependent on the coordinated assembly of protein subunits encoded by both nuclear and mitochondrial DNA (mtDNA) genes. Cytoplasmic hybrid cells, cybrids, are created by introducing mtDNAs of interest into cells depleted of endogenous mtDNAs, and have been a central tool in unraveling effects of disease-linked mtDNA mutations. In this way, the nuclear genetic complement is held constant so that observed effects on OXPHOS can be linked to the introduced mtDNA. Cybrid studies have confirmed such linkage for many defined, disease-associated mutations. In general, a threshold principle is evident where OXPHOS defects are expressed when the proportion of mutant mtDNA in a heteroplasmic cell is high. Cybrids have also been used where mtDNA mutations are not known, but are suspected, and have produced some support for mtDNA involvement in more common neurodegenerative diseases. Mouse modeling of mtDNA transmission and disease has recently taken advantage of cybrid approaches. By using cultured cells as intermediate carriers of mtDNAs, ES cell cybrids have been produced in several laboratories by pretreatment of the cells with rhodamine 6G before cytoplast fusion. Both homoplasmic and heteroplasmic mice have been produced, allowing modeling of mtDNA transmission through the mouse germ line. We also briefly review and compare other transgenic approaches to modeling mtDNA dynamics, including mitochondrial injection into oocytes or zygotes, and embryonic karyoplast transfer. When breakthrough technology for mtDNA transformation arrives, cybrids will remain valuable for allowing exchange of engineered mtDNAs between cells.

Eukaryotic transcription factors in plastids--Bioinformatic assessment and implications for the evolution of gene expression machineries in plants

The expression of genes in higher plant chloroplasts includes a complex transcriptional regulation which can be explained only in part with the action of the actually known components of the transcriptional machinery. This suggests the existence of still unknown important regulatory factors which influence chloroplast transcription. In order to test if such factors could exist we performed in silico analyses of Arabidopsis genes encoding putative transcription factors looking for putative N-terminal chloroplast transit peptides in the amino acid sequences. Our results suggest that 48 (and maybe up to 100) transcription factors of eukaryotic origin are likely to be imported into plastids. None of them has been described yet. This set of transcription factors highly expands the actually known regulation capacity of the chloroplast transcription machinery and provides a possible explanation for the complex initiation patterns of chloroplast transcripts. As consequence of a massive import of eukaryotic transcription factors a comprehensive reconstruction of the ancient prokaryotic gene expression machinery must be assumed resulting in a novel compatible combination of eukaryotic and prokaryotic protein components. In turn, the opposite process has been induced in the nucleus by the integration of prokaryotic components of the plastid ancestor via its loss of genes during endosymbiosis. Thus, a mutual exchange of regulatory factors, i.e. transcription factors occurred which resulted in the unique signalling network of today's plants. An evolutionary model of how this could have emerged during endosymbiosis in a timely coordinated manner is proposed.

Mono- and dicotyledonous plant-specific RNA editing sites are correctly edited in both in organello systems

We set out to analyse the phylogenetic distribution of cox2 RNA editing sites. Database searches have revealed the presence of mono- and dicotyledonous-specific RNA editing sites. Therefore, to better understand tRNA editing system in plants, we developed a new dicotyledonous in organello RNA editing system using cauliflower mitochondria and analysed the transcription of the cox2 gene for both maize and Arabidopsis. These results were compared with those obtained from a maize mitochondrial in organello system. Surprisingly, both the mono- and dicotyledonous cox2 transcripts were efficiently edited in the mitochondrial cauliflower and maize in organello systems, respectively, even for RNA editing sites not present in the endogenous cox2 sequences. Taken together, our observations support a self-guiding-transcript model for RNA editing in higher plants.

Construction, database integration, and application of an Oenothera EST library

Coevolution of cellular genetic compartments is a fundamental aspect in eukaryotic genome evolution that becomes apparent in serious developmental disturbances after interspecific organelle exchanges. The genus Oenothera represents a unique, at present the only available, resource to study the role of the compartmentalized plant genome in diversification of populations and speciation processes. An integrated approach involving cDNA cloning, EST sequencing, and bioinformatic data mining was chosen using Oenothera elata with the genetic constitution nuclear genome AA with plastome type I. The Gene Ontology system grouped 1621 unique gene products into 17 different functional categories. Application of arrays generated from a selected fraction of ESTs revealed significantly differing expression profiles among closely related Oenothera species possessing the potential to generate fertile and incompatible plastid/nuclear hybrids (hybrid bleaching). Furthermore, the EST library provides a valuable source of PCR-based polymorphic molecular markers that are instrumental for genotyping and molecular mapping approaches.

Energy transduction anchors genes in organelles

The work of mitochondria and chloroplasts is energy transduction in respiration and photosynthesis. The physico-chemical mechanisms of bioenergetics do not directly involve genes and heredity, and furthermore, redox chemistry is intrinsically mutagenic. Thus the small, functional genomes of mitochondria and chloroplasts are an oddity. Although extensively sequenced and catalogued, cytoplasmic genomes are still not explained. Genomic lethargy is not the answer. Some genes linger from the bacterial ancestors of these organelles, true, but most have left, and new ones arrive. There is a mounting case for a massive and indiscriminate intracellular gene transfer between organelles and the cell nucleus, with the frequency of relocation being comparable to that of mutation. Nevertheless, a few organellar proteins, all working at the core of bioenergetics, always seem to keep the genes encoding them close at hand. Stability amid flux suggests the invisible hand of selection. Selection for what? There are clues, and the beginnings of experimental support, for the theory that expression of mitochondrial and chloroplast genes is regulated by the function of their gene products. For safe and efficient energy transduction, genes in organelles are in the right place at the right time.

Pigment deficiency in nightshade/tobacco cybrids is caused by the failure to edit the plastid ATPase alpha-subunit mRNA

The subgenomes of the plant cell, the nuclear genome, the plastome, and the chondriome are known to interact through various types of coevolving macromolecules. The combination of the organellar genome from one species with the nuclear genome of another species often leads to plants with deleterious phenotypes, demonstrating that plant subgenomes coevolve. The molecular mechanisms behind this nuclear-organellar incompatibility have been elusive, even though the phenomenon is widespread and has been known for >70 years. Here, we show by direct and reverse genetic approaches that the albino phenotype of a flowering plant with the nuclear genome of Atropa belladonna (deadly nightshade) and the plastome of Nicotiana tabacum (tobacco) develops as a result of a defect in RNA editing of a tobacco-specific editing site in the plastid ATPase alpha-subunit transcript. A plastome-wide analysis of RNA editing in these cytoplasmic hybrids and in plants with a tobacco nucleus and nightshade chloroplasts revealed additional defects in the editing of species-specific editing sites, suggesting that differences in RNA editing patterns in general contribute to the pigment deficiencies observed in interspecific nuclear-plastidial incompatibilities.

Population differentiation and hybrid success in Campanula americana: geography and genome size

Populations within a species may diverge through genetic drift and natural selection. Few studies report on population differentiation in autopolyploids where multiple gene copies and the ratio of cytoplasmic to nuclear genes differ from diploids and may influence divergence. In autotetraploid Campanula americana we created hybrids between populations that differed in geographic proximity and genome size. Differences in genome size (up to 6.5%) did not influence hybrid performance. In contrast, hybrid performance was strongly influenced by population proximity. F1 hybrids between distant populations performed poorly relative to their parents while hybrids between proximate populations outperformed their parents. Outbreeding depression was strongest for juvenile traits. The expression of outbreeding depression often differed between reciprocal hybrids indicating interactions between nuclear and cytoplasmic genes contribute to population differentiation. Because plants were grown under greenhouse conditions, the outbreeding depression was likely due to genetic (underdominance or loss of additive-by-additive epistasis) rather than ecological factors.

Substitutional editing of transcripts from genes of cyanobacterial origin in the dinoflagellate Ceratium horridum

Peridinin-containing dinoflagellates, a group of alveolate organisms, harbour small plasmids called minicircles. As most of these minicircles encode genes of cyanobacterial origin, which are also found in plastid genomes of stramenopiles, they were thought to represent the plastid genome of peridinin-containing dinoflagellates. The analyses of minicircle derived mRNAs and the 16S rRNA showed that extensive editing of minicircle gene transcripts is common for Ceratium horridum. Posttranscriptional changes occur predominantly by editing A into G, but other types of editing including a previously unreported A to C transversion were also detected. This leads to amino acid changes in most cases or, in one case, to the elimination of a stop-codon. Interestingly, the edited mRNAs show higher identities to homologous sequences of other peridinin-containing dinoflagellates than their genomic copy. Thus, our results imply that transcript editing of genes of cyanobacterial origin is species specific in peridinin-containing dinoflagellates and demonstrate that editing of genes of cyanobacterial origin is not restricted to land plants.