Reverse U-to-C editing exceeds C-to-U RNA editing in some ferns - a monilophyte-wide comparison of chloroplast and mitochondrial RNA editing suggests independent evolution of the two processes in both organelles

Insights into U-to-C RNA editing from the lycophyte Phylloglossum drummondii

The lycophyte Phylloglossum drummondii is the sole inhabitant of its genus in the Huperzioideae group and one of a small minority of plants which perform uridine to cytidine RNA editing. We assembled the P. drummondii chloroplast and mitochondrial genomes and used RNA sequence data to build a comprehensive profile of organellar RNA editing events. In addition to many C-to-U editing events in both organelles, we found just four U-to-C editing events in the mitochondrial transcripts cob, nad1, nad5 and rpl2. These events are conserved in related lycophytes in the genera Huperzia and Phlegmariurus. De novo transcriptomes for three of these lycophytes were assembled to search for putative U-to-C RNA editing enzymes. Four putative U-to-C editing factors could be matched to the four mitochondrial U-to-C editing sites. Due to the unusually few numbers of U-to-C RNA editing sites, P. drummondii and related lycophytes are useful models for studying this poorly understood mechanism.

Crosslinking of base-modified RNAs by synthetic DYW-KP base editors implicates an enzymatic lysine as the nitrogen donor for U-to-C RNA editing

Sequence-specific cytidine to uridine (C-to-U) and adenosine to inosine editing tools can alter RNA and DNA sequences and utilize a hydrolytic deamination mechanism requiring an active site zinc ion and a glutamate residue. In plant organelles, DYW-PG domain containing enzymes catalyze C-to-U edits through the canonical deamination mechanism. Proteins developed from consensus sequences of the related DYW-KP domain family catalyze what initially appeared to be uridine to cytidine (U-to-C) edits leading to this investigation into the U-to-C editing mechanism. The synthetic DYW-KP enzyme KP6 was found sufficient for C-to-U editing activity stimulated by the addition of carboxylic acids in vitro. Despite addition of putative amine/amide donors, U-to-C editing by KP6 could not be observed in vitro. C-to-U editing was found not to be concomitant with U-to-C editing, discounting a pyrimidine transaminase mechanism. RNAs containing base modifications were highly enriched in interphase fractions consistent with covalent crosslinks to KP6, KP2, and KP3 proteins. Mass spectrometry of purified KP2 and KP6 proteins revealed secondary peaks with mass shifts of 319 Da. A U-to-C crosslinking mechanism was projected to explain the link between crosslinking, RNA base changes, and the ∼319 Da mass. In this model, an enzymatic lysine attacks C4 of uridine to form a Schiff base RNA-protein conjugate. Sequenced RT-PCR products from the fern Ceratopteris richardii indicate U-to-C base edits do not preserve proteinaceous crosslinks in planta. Hydrolysis of a protonated Schiff base conjugate releasing cytidine is hypothesized to explain the completed pathway in plants.

Is RNA editing truly absent in the complex thalloid liverworts (Marchantiopsida)? Evidence of extensive RNA editing from Cyathodium cavernarum

RNA editing is a crucial modification in plants' organellar transcripts that converts cytidine to uridine (C-to-U; and sometimes uridine to cytidine) in RNA molecules. This post-transcriptional process is controlled by the PLS-class protein with a DYW domain, which belongs to the pentatricopeptide repeat (PPR) protein family. RNA editing is widespread in land plants; however, complex thalloid liverworts (Marchantiopsida) are the only group reported to lack both RNA editing and DYW-PPR protein. The liverwort Cyathodium cavernarum (Marchantiopsida, Cyathodiaceae), typically found in cave habitats, was newly found to have 129 C-to-U RNA editing sites in its chloroplast and 172 sites in its mitochondria. The Cyathodium genus, specifically C. cavernarum, has a large number of PPR editing factor genes, including 251 DYW-type PPR proteins. These DYW-type PPR proteins may be responsible for C-to-U RNA editing in C. cavernarum. Cyathodium cavernarum possesses both PPR DYW proteins and RNA editing. Our analysis suggests that the remarkable RNA editing capability of C. cavernarum may have been acquired alongside the emergence of DYW-type PPR editing factors. These findings provide insight into the evolutionary pattern of RNA editing in land plants.

Profiling of RNA editing events in plant organellar transcriptomes with high-throughput sequencing

RNA editing is a crucial post-transcriptional modification process in plant organellar RNA metabolism. rRNA removal-based total RNA-seq is one of the most common methods to study this event. However, the lack of commercial kits to remove rRNAs limits the usage of this method, especially for non-model plant species. DSN-seq is a transcriptome sequencing method utilizing duplex-specific nuclease (DSN) to degrade highly abundant cDNA species especially those from rRNAs while keeping the robustness of transcript levels of the majority of other mRNAs, and has not been applied to study RNA editing in plants before. In this study, we evaluated the capability of DSN-seq to reduce rRNA content and profile organellar RNA editing events in plants, as well we used commercial Ribo-off-seq and standard mRNA-seq as comparisons. Our results demonstrated that DSN-seq efficiently reduced rRNA content and enriched organellar transcriptomes in rice. With high sensitivity to RNA editing events, DSN-seq and Ribo-off-seq provided a more complete and accurate RNA editing profile of rice, which was further validated by Sanger sequencing. Furthermore, DSN-seq also demonstrated efficient organellar transcriptome enrichment and high sensitivity for profiling RNA editing events in Arabidopsis thaliana. Our study highlights the capability of rRNA removal-based total RNA-seq for profiling RNA editing events in plant organellar transcriptomes and also suggests DSN-seq as a widely accessible RNA editing profiling method for various plant species.

Complete chloroplast genome of Austral king fern Todea barbara (L.) Moore (Osmundaceae)

In this study, we determined the chloroplast genome sequence of the Austral king fern, Todea barbara (L.) Moore. The plastome of T. barbara is a typical circular form composed of 144,208 bp with two inverted repeats (IRs; 10,442 bp), a large single copy (LSC; 101,059 bp), and a small single copy (SSC; 22,265 bp). The complete sequence comprises 131 genes, namely 85 protein-coding genes, eight ribosomal RNAs, and 38 transfer RNAs. The guanine-cytosine (GC) content of the genome was found to be 39.9%. Additionally, U-to-C RNA editing sites were identified in eight genes: atpE, chlB, clpP, matK, rpl20, rpoB, rpoC1, and rpoC2. Phylogenetic analysis using 85 coding gene sequences revealed that the genera Todea and Osmunda form a clade and that the genus Osmundastrum is a sister genus to both.

Plant organellar RNA maturation

Plant organellar RNA metabolism is run by a multitude of nucleus-encoded RNA-binding proteins (RBPs) that control RNA stability, processing, and degradation. In chloroplasts and mitochondria, these post-transcriptional processes are vital for the production of a small number of essential components of the photosynthetic and respiratory machinery-and consequently for organellar biogenesis and plant survival. Many organellar RBPs have been functionally assigned to individual steps in RNA maturation, often specific to selected transcripts. While the catalog of factors identified is ever-growing, our knowledge of how they achieve their functions mechanistically is far from complete. This review summarizes the current knowledge of plant organellar RNA metabolism taking an RBP-centric approach and focusing on mechanistic aspects of RBP functions and the kinetics of the processes they are involved in.

Rickettsial DNA and a trans-splicing rRNA group I intron in the unorthodox mitogenome of the fern Haplopteris ensiformis

Plant mitochondrial genomes can be complex owing to highly recombinant structures, lack of gene syntenies, heavy RNA editing and invasion of chloroplast, nuclear or even foreign DNA by horizontal gene transfer (HGT). Leptosporangiate ferns remained the last major plant clade without an assembled mitogenome, likely owing to a demanding combination of the above. We here present both organelle genomes now for Haplopteris ensiformis. More than 1,400 events of C-to-U RNA editing and over 500 events of reverse U-to-C edits affect its organelle transcriptomes. The Haplopteris mtDNA is gene-rich, lacking only the ccm gene suite present in ancestral land plant mitogenomes, but is highly unorthodox, indicating extraordinary recombinogenic activity. Although eleven group II introns known in disrupted trans-splicing states in seed plants exist in conventional cis-arrangements, a particularly complex structure is found for the mitochondrial rrnL gene, which is split into two parts needing reassembly on RNA level by a trans-splicing group I intron. Aside from ca. 80 chloroplast DNA inserts that complicated the mitogenome assembly, the Haplopteris mtDNA features as an idiosyncrasy 30 variably degenerated protein coding regions from Rickettiales bacteria indicative of heavy bacterial HGT on top of tRNA genes of chlamydial origin.

What can hornworts teach us?

The hornworts are a small group of land plants, consisting of only 11 families and approximately 220 species. Despite their small size as a group, their phylogenetic position and unique biology are of great importance. Hornworts, together with mosses and liverworts, form the monophyletic group of bryophytes that is sister to all other land plants (Tracheophytes). It is only recently that hornworts became amenable to experimental investigation with the establishment of Anthoceros agrestis as a model system. In this perspective, we summarize the recent advances in the development of A. agrestis as an experimental system and compare it with other plant model systems. We also discuss how A. agrestis can help to further research in comparative developmental studies across land plants and to solve key questions of plant biology associated with the colonization of the terrestrial environment. Finally, we explore the significance of A. agrestis in crop improvement and synthetic biology applications in general.

ADAR RNA editing on antisense RNAs results in apparent U-to-C base changes on overlapping sense transcripts

Despite hundreds of RNA modifications described to date, only RNA editing results in a change in the nucleotide sequence of RNA molecules compared to the genome. In mammals, two kinds of RNA editing have been described so far, adenosine to inosine (A-to-I) and cytidine to uridine (C-to-U) editing. Recent improvements in RNA sequencing technologies have led to the discovery of a continuously growing number of editing sites. These methods are powerful but not error-free, making routine validation of newly-described editing sites necessary. During one of these validations on DDX58 mRNA, along with A-to-I RNA editing sites, we encountered putative U-to-C editing. These U-to-C edits were present in several cell lines and appeared regulated in response to specific environmental stimuli. The same findings were also observed for the human long intergenic non-coding RNA p21 (hLincRNA-p21). A more in-depth analysis revealed that putative U-to-C edits result from A-to-I editing on overlapping antisense RNAs that are transcribed from the same loci. Such editing events, occurring on overlapping genes transcribed in opposite directions, have recently been demonstrated to be immunogenic and have been linked with autoimmune and immune-related diseases. Our findings, also confirmed by deep transcriptome data, demonstrate that such loci can be recognized simply through the presence of A-to-I and U-to-C mismatches within the same locus, reflective A-to-I editing both in the sense-oriented transcript and in the cis-natural antisense transcript (cis-NAT), implying that such clusters could be a mark of functionally relevant ADAR1 editing events.

Exploring the RNA Editing Events and Their Potential Regulatory Roles in Tea Plant (Camellia sinensis L.)

RNA editing is a post-transcriptional modification process that alters the RNA sequence relative to the genomic blueprint. In plant organelles (namely, mitochondria and chloroplasts), the most common type is C-to-U, and the absence of C-to-U RNA editing results in abnormal plant development, such as etiolation and albino leaves, aborted embryonic development and retarded seedling growth. Here, through PREP, RES-Scanner, PCR and RT-PCR analyses, 38 and 139 RNA editing sites were identified from the chloroplast and mitochondrial genomes of Camellia sinensis, respectively. Analysis of the base preference around the RNA editing sites showed that in the -1 position of the edited C had more frequent occurrences of T whereas rare occurrences of G. Three conserved motifs were identified at 25 bases upstream of the RNA editing site. Structural analyses indicated that the RNA secondary structure of 32 genes, protein secondary structure of 37 genes and the three-dimensional structure of 5 proteins were altered due to RNA editing. The editing level analysis of matK and ndhD in six tea cultivars indicated that matK-701 might be involved in the color change of tea leaves. Furthermore, 218 PLS-CsPPR proteins were predicted to interact with the identified RNA editing sites. In conclusion, this study provides comprehensive insight into RNA editing events, which will facilitate further study of the RNA editing phenomenon of the tea plant.

A Comprehensive Evolutionary Study of Chloroplast RNA Editing in Gymnosperms: A Novel Type of G-to-A RNA Editing Is Common in Gymnosperms

Although more than 9100 plant plastomes have been sequenced, RNA editing sites of the whole plastome have been experimentally verified in only approximately 21 species, which seriously hampers the comprehensive evolutionary study of chloroplast RNA editing. We investigated the evolutionary pattern of chloroplast RNA editing sites in 19 species from all 13 families of gymnosperms based on a combination of genomic and transcriptomic data. We found that the chloroplast C-to-U RNA editing sites of gymnosperms shared many common characteristics with those of other land plants, but also exhibited many unique characteristics. In contrast to that noted in angiosperms, the density of RNA editing sites in ndh genes was not the highest in the sampled gymnosperms, and both loss and gain events at editing sites occurred frequently during the evolution of gymnosperms. In addition, GC content and plastomic size were positively correlated with the number of chloroplast RNA editing sites in gymnosperms, suggesting that the increase in GC content could provide more materials for RNA editing and facilitate the evolution of RNA editing in land plants or vice versa. Interestingly, novel G-to-A RNA editing events were commonly found in all sampled gymnosperm species, and G-to-A RNA editing exhibits many different characteristics from C-to-U RNA editing in gymnosperms. This study revealed a comprehensive evolutionary scenario for chloroplast RNA editing sites in gymnosperms, and reported that a novel type of G-to-A RNA editing is prevalent in gymnosperms.

Evolution of mitochondrial RNA editing in extant gymnosperms

To unveil the evolution of mitochondrial RNA editing in gymnosperms, we characterized mitochondrial genomes (mitogenomes), plastid genomes, RNA editing sites, and pentatricopeptide repeat (PPR) proteins from 10 key taxa representing four of the five extant gymnosperm clades. The assembled mitogenomes vary in gene content due to massive gene losses in Gnetum and Conifer II clades. Mitochondrial gene expression levels also vary according to protein function, with the most highly expressed genes involved in the respiratory complex. We identified 9132 mitochondrial C-to-U editing sites, as well as 2846 P-class and 8530 PLS-class PPR proteins. Regains of editing sites were demonstrated in Conifer II rps3 transcripts whose corresponding mitogenomic sequences lack introns due to retroprocessing. Our analyses reveal that non-synonymous editing is efficient and results in more codons encoding hydrophobic amino acids. In contrast, synonymous editing, although performed with variable efficiency, can increase the number of U-ending codons that are preferentially utilized in gymnosperm mitochondria. The inferred loss-to-gain ratio of mitochondrial editing sites in gymnosperms is 2.1:1, of which losses of non-synonymous editing are mainly due to genomic C-to-T substitutions. However, such substitutions only explain a small fraction of synonymous editing site losses, indicating distinct evolutionary mechanisms. We show that gymnosperms have experienced multiple lineage-specific duplications in PLS-class PPR proteins. These duplications likely contribute to accumulated RNA editing sites, as a mechanistic correlation between RNA editing and PLS-class PPR proteins is statistically supported.

iPReditor-CMG: Improving a predictive RNA editor for crop mitochondrial genomes using genomic sequence features and an optimal support vector machine

In crops, RNA editing is one of the most important post-transcriptional processes in which specific cytidines (C) in virtually all mitochondrial protein-coding genes are converted to uridines (U). Despite extensive recent research in RNA editing, exploring all of the C-to-U editing events efficiently on the genomic scale remains challengeable. Developing accurate prediction methods for the detection of RNA editing sites would dramatically reduce experimental determination. Therefore, we propose a novel method, iPReditor-CMG (improved predictive RNA editor for crop mitochondrial genomes), to predict crop mitochondrial editing sites using genome sequence and an optimised support vector machine (SVM). We first selected three mitochondrial genomes with known RNA editing sites from Arabidopsis thaliana, Brassica napus and Oryza sativa, released by NCBI, as the training and test sets. The genes and their transcripts from self-sequenced tobacco mitochondrial ATPase were selected as the validation set. The iPReditor-CMG first coded the genome sequences as numerical vectors and then performed an efficient feature selection on the high-dimensional feature space, where the SVM was employed in feature selection and following modelling. The average independent prediction accuracy of intraspecific editing sites across three species was 0.85, and up to 0.91 in A. thaliana, which outperformed the reference models. For the interspecific independent prediction, the prediction accuracy between dicotyledons was 0.78 and the accuracy between dicotyledons and monocotyledons was 0.56, which implies that there might be similarity in the C-to-U editing mechanism in close relatives. Finally, the best model was identified with an independent test accuracy of 0.91 and an AUC of 0.88, which suggested that five unreported feature sequences, i.e. TGACA, ACAAC, GTAGA, CCGTT and TAACA, are closely associated with the editing phenomenon. Multiple tests supported that the iPReditor-CMG could be effectively applied to predict editing sites in crop mitochondria, which may further contribute to understanding the mechanisms of site editing and post-transcriptional events in crop mitochondria.

DEK48 Is Required for RNA Editing at Multiple Mitochondrial Sites and Seed Development in Maize

In flowering plants, C-to-U RNA editing can be critical to normal functions of mitochondrion-encoded proteins. Mitochondrial C-to-U RNA editing is facilitated by many factors from diverse protein families, of which the pentatricopeptide repeat (PPR) proteins play an important role. Owing to their large number and frequent embryo lethality in mutants, functions of many PPRs remain unknown. In this study, we characterized a mitochondrion-localized DYW-type PPR protein, DEK48, functioning in the C-to-U RNA editing at multiple mitochondrial transcripts in maize. Null mutation of Dek48 severely arrests embryo and endosperm development, causing a defective kernel (dek) phenotype, named dek48. DEK48 loss of function abolishes the C-to-U editing at nad3-185, -215, and nad4-376, -977 sites and decreases the editing at 11 other sites, resulting in the alteration of the corresponding amino acids. Consequently, the absence of editing caused reduced assembly and activity of complex I in dek48. Interestingly, we identified a point mutation in dek48-3 causing a deletion of the Tryptophan (W) residue in the DYW motif that abolishes the editing function. In sum, this study reveals the function of DEK48 in the C-to-U editing in mitochondrial transcripts and seed development in maize, and it demonstrates a critical role of the W residue in the DYW triplet motif of DEK48 for the C-to-U editing function in vivo.

DYW domain structures imply an unusual regulation principle in plant organellar RNA editing catalysis

RNA editosomes selectively deaminate cytidines to uridines in plant organellar transcripts–mostly to restore protein functionality and consequently facilitate mitochondrial and chloroplast function. The RNA editosomal pentatricopeptide repeat proteins serve target RNA recognition, whereas the intensively studied DYW domain elicits catalysis. Here we present structures and functional data of a DYW domain in an inactive ground state and activated. DYW domains harbour a cytidine deaminase fold and a C-terminal DYW motif, with catalytic and structural zinc atoms, respectively. A conserved gating domain within the deaminase fold regulates the active site sterically and mechanistically in a process that we termed gated zinc shutter. Based on the structures, an autoinhibited ground state and its activation are cross-validated by RNA editing assays and differential scanning fluorimetry. We anticipate that, in vivo, the framework of an active plant RNA editosome triggers the release of DYW autoinhibition to ensure a controlled and coordinated cytidine deamination playing a key role in mitochondrial and chloroplast homeostasis.

RNA Editing and Its Roles in Plant Organelles

RNA editing, a vital supplement to the central dogma, yields genetic information on RNA products that are different from their DNA templates. The conversion of C-to-U in mitochondria and plastids is the main kind of RNA editing in plants. Various factors have been demonstrated to be involved in RNA editing. In this minireview, we summarized the factors and mechanisms involved in RNA editing in plant organelles. Recently, the rapid development of deep sequencing has revealed many RNA editing events in plant organelles, and we further reviewed these events identified through deep sequencing data. Numerous studies have shown that RNA editing plays essential roles in diverse processes, such as the biogenesis of chloroplasts and mitochondria, seed development, and stress and hormone responses. Finally, we discussed the functions of RNA editing in plant organelles.

The first report of RNA U to C or G editing in the mitochondrial NADH dehydrogenase subunit 5 (Nad5) transcript of wild barley

BACKGROUND

Nad dehydrogenase complex in mtDNA has a significant role in cellular respiration. One of the largest subunits in the complex is subunit 5 (Nad5).

METHODS AND RESULTS

Four cDNAs of the Hordeum vulgare subsp. spontaneum nad5 gene have been characterized and subjected to four phases of 0.5 M salinity, at 0 h (control, accession no. MT235236), after 2 h (acc. no. MT235237), after 12 h (acc. no. MT235238) and after 24 h (acc. no. MT235239). Utilizing raw data from RNA-seq, ten RNA editing sites were reported. Seven sites have common editing from C to U in positions (C1490, C1859, C1895, C1900, C1901, C1916, C1918). A rare editing event U to C was detected in two positions (U1650 and U1652) and a novel editing event U to G was for the first time in positions nad5-U231. The highest editing level was shown in 2 and 12 h after salinity exposure. After 24 h, these edits were disrupted, possibly due to the launch of the programed cell death mechanism. However, the RNA editing in positions U1650, U1652 and U231 was fixed at all exposure times.

CONCLUSIONS

Although study clarified the role of salinity stress in nad5 RNA editing sites, the main achievements are first report of U to G RNA editing in plants at position U231 and first report of U to C editing in the nad5 gene at U1650 and U1652.

Deepred-Mt: Deep representation learning for predicting C-to-U RNA editing in plant mitochondria

In land plant mitochondria, C-to-U RNA editing converts cytidines into uridines at highly specific RNA positions called editing sites. This editing step is essential for the correct functioning of mitochondrial proteins. When using sequence homology information, edited positions can be computationally predicted with high precision. However, predictions based on the sequence contexts of such edited positions often result in lower precision, which is limiting further advances on novel genetic engineering techniques for RNA regulation. Here, a deep convolutional neural network called Deepred-Mt is proposed. It predicts C-to-U editing events based on the 40 nucleotides flanking a given cytidine. Unlike existing methods, Deepred-Mt was optimized by using editing extent information, novel strategies of data augmentation, and a large-scale training dataset, constructed with deep RNA sequencing data of 21 plant mitochondrial genomes. In comparison to predictive methods based on sequence homology, Deepred-Mt attains significantly better predictive performance, in terms of average precision as well as F1 score. In addition, our approach is able to recognize well-known sequence motifs linked to RNA editing, and shows that the local RNA structure surrounding editing sites may be a relevant factor regulating their editing. These results demonstrate that Deepred-Mt is an effective tool for predicting C-to-U RNA editing in plant mitochondria. Source code, datasets, and detailed use cases are freely available at https://github.com/aedera/deepredmt.

A synthetic RNA editing factor edits its target site in chloroplasts and bacteria

Members of the pentatricopeptide repeat (PPR) protein family act as specificity factors in C-to-U RNA editing. The expansion of the PPR superfamily in plants provides the sequence variation required for design of consensus-based RNA-binding proteins. We used this approach to design a synthetic RNA editing factor to target one of the sites in the Arabidopsis chloroplast transcriptome recognised by the natural editing factor CHLOROPLAST BIOGENESIS 19 (CLB19). We show that our synthetic editing factor specifically recognises the target sequence in in vitro binding assays. The designed factor is equally specific for the target rpoA site when expressed in chloroplasts and in the bacterium E. coli. This study serves as a successful pilot into the design and application of programmable RNA editing factors based on plant PPR proteins.

Variation in frequency of plastid RNA editing within Adiantum implies rapid evolution in fern plastomes

PREMISE

Recent studies of plant RNA editing have demonstrated that the number of editing sites can vary widely among large taxonomic groups (orders, families). Yet, very little is known about intrageneric variation in frequency of plant RNA editing, and no study has been conducted in ferns.

METHODS

We determined plastid RNA-editing counts for two species of Adiantum (Pteridaceae), A. shastense and A. aleuticum, by implementing a pipeline that integrated read-mapping and SNP-calling software to identify RNA-editing sites. We then compared the edits found in A. aleuticum and A. shastense with previously published edits from A. capillus-veneris by generating alignments for each plastid gene.

RESULTS

We found direct evidence for 505 plastid RNA-editing sites in A. aleuticum and 509 in A. shastense, compared with 350 sites in A. capillus-veneris. We observed striking variation in the number and location of the RNA-editing sites among the three species, with reverse (U-to-C) editing sites showing a higher degree of conservation than forward (C-to-U) sites. Additionally, sites involving start and stop codons were highly conserved.

CONCLUSIONS

Variation in the frequency of RNA editing within Adiantum implies that RNA-editing sites can be rapidly gained or lost throughout evolution. However, varying degrees of conservation between both C-to-U and U-to-C sites and sites in start or stop codons, versus other codons, hints at the likely independent origin of both types of edits and a potential selective advantage conferred by RNA editing.

Plastid genome evolution in Amazonian açaí palm (Euterpe oleracea Mart.) and Atlantic forest açaí palm (Euterpe edulis Mart.)

The plastomes of E. edulis and E. oleracea revealed several molecular markers useful for genetic studies in natural populations and indicate specific evolutionary features determined by vicariant speciation. Arecaceae is a large and diverse family occurring in tropical and subtropical ecosystems worldwide. E. oleracea is a hyperdominant species of the Amazon forest, while E. edulis is a keystone species of the Atlantic forest. It has reported that E. edulis arose from vicariant speciation after the emergence of the belt barrier of dry environment (Cerrado and Caatinga biomes) between Amazon and Atlantic forests, isolating the E. edulis in the Atlantic forest. We sequenced the complete plastomes of E. edulis and E. oleracea and compared them concerning plastome structure, SSRs, tandem repeats, SNPs, indels, hotspots of nucleotide polymorphism, codon Ka/Ks ratios and RNA editing sites aiming to investigate evolutionary traits possibly affected by distinct environments. Our analyses revealed 303 SNPs, 91 indels, and 82 polymorphic SSRs among both species. Curiously, the narrow correlation among localization of repetitive sequences and indels strongly suggests that replication slippage is involved in plastid DNA mutations in Euterpe. Moreover, most non-synonymous substitutions represent amino acid variants in E. edulis that evolved specifically or in a convergent manner across the palm phylogeny. Amino acid variants observed in several plastid proteins in E. edulis were also identified as positive signatures across palm phylogeny. The higher incidence of specific amino acid changes in plastid genes of E. edulis in comparison with E. oleracea probably configures adaptive genetic variations determined by vicariant speciation. Our data indicate that the environment generates a selective pressure on the plastome making it more adapted to specific conditions.

Deciphering the organelle genomes and transcriptomes of a common ornamental plant Ligustrum quihoui reveals multiple fragments of transposable elements in the mitogenome

Ligustrum quihoui (L. quihoui) is an important hedge material for landscaping and also possesses medicinal value. To generate genomic resources for better understanding the evolutionary history of this important plant, the organelle genomes of L. quihoui are de novo assembled and functionally annotated. Compared with other Oleaceae species, the 163,069 bp chloroplast genome of L. quihoui exhibits a typical quadripartite structure with highly conserved gene content and gene order, while the 848,451 bp mitochondrial genome of L. quihoui exhibits highly divergent genome size and gene content. Codon usage analyses show that genes related with photosynthesis and mitochondrial respiratory chain show inconsistent codon biases. A total of 48,760 bp transposable elements (TEs) fragments and 41,887 bp chloroplast-like sequences are found in the L. quihoui mitochondrial genome. A striking discrepancy of RNA editing between the two organelle genomes is found in L. quihoui, in which 146 mitochondrial editing sites coexist with only 43 such sites in chloroplast. Based on DNA and RNA-Seq data, we propose that GTG may act as the start codon of mitochondrial rpl16 in Oleaceae species. Phylogenetic analysis based on chloroplast genome shows that L. quihoui and L. japonicum form a sister clade within the genus Ligustrum.

Extreme plastid RNA editing may confound phylogenetic reconstruction: A case study of Selaginella (lycophytes)

Cytidine-to-uridine (C-to-U) RNA editing is common in coding regions of organellar genomes throughout land plants. In most cases RNA editing alters translated amino acids or creates new start codons, potentially confounds phylogenetic reconstructions. In this study, we used the spike moss genus Selaginella (lycophytes), which has the highest frequency of RNA editing, as a model to test the effects of extreme RNA editing on phylogenetic reconstruction. We predicted the C-to-U RNA editing sites in coding regions of 18 Selaginella plastomes, and reconstructed the phylogenetic relationships within Selaginella based on three data set pairs consisted of plastome or RNA-edited coding sequences, first and second codon positions, and translated amino acid sequences, respectively. We predicted between 400 and 3100 RNA editing sites of 18 Selaginella plastomes. The numbers of RNA editing sites in plastomes were highly correlated with the GC content of first and second codon positions, but not correlated with the GC content of plastomes as a whole. Contrast phylogenetic analyses showed that there were substantial differences (e.g., the placement of clade B in Selaginella) between the phylogenies generated by the plastome and RNA-edited data sets. This empirical study provides evidence that extreme C-to-U RNA editing in the coding regions of organellar genomes alters the sequences used for phylogenetic reconstruction, and might even confound phylogenetic reconstruction. Therefore, RNA editing sites should be corrected when plastid or mitochondrial genes are used for phylogenetic studies, particularly in those lineages with abundant organellar RNA editing sites, such as hornworts, quillworts, spike mosses, and some seed plants.

Light/heat effects on RNA editing in chloroplast NADH-plastoquinone oxidoreductase subunit 2 (ndhB) gene of Calotropis (Calotropis procera)

Background

RNA editing is common in terrestrial plants, especially in mitochondria and chloroplast. In the photosynthesis process, NAD dehydrogenase plays a very important role. Subunit 2 of NADH-dehydrogenase is one of the major subunits in NAD dehydrogenase complex. Using desert plant Calotropis (Calotropis procera), this study focuses on the RNA editing activity of ndhB based on light time.

Results

NdhB (NADH-dehydrogenase subunit 2) gene accession no. MK144329 was isolated from Calotropis procera genomic data (PRJNA292713). Additionally, using RNA-seq data, the cDNA of the ndhB gene of C. procera was isolated at three daylight periods, i.e., dawn (accession no. MK165161), at midday (accession no. MK165160), and pre-dusk (accession no. MK165159). Seven RNA editing sites have been found in several different positions (nucleotide no. C467, C586, C611, C737, C746, C830, and C1481) within the ndhB coding region. The rate of these alterations was deferentially edited across the three daylight periods. RNA editing rate of ndhB gene was highest at dawn, (87.5, 79.6, 78.5, 76, 68.6, 39.3, and 96.9%, respectively), less in midday (74.8, 54.1, 62.6, 47.4, 45.5, 47.4, and 93.4%, respectively), and less at pre-dusk (67, 52.6, 56.9, 40.1, 40.7, 33.2, and 90%, respectively), also all these sites were validated by qRT-PCR.

Conclusion

The differential editing of chloroplast ndhB gene across light periods may be led to a somehow relations between the RNA editing and control of photosynthesis.

Salinity effects on nad3 gene RNA editing of wild barley mitochondria

Nad complex plays a very important role during cellular respiration. nad3 (nad dehydrogenase subunit 3) is one of the biggest subunits in this complex. Four cDNAs of nad3 gene were characterized in Hordeum vulgare subsp. spontaneum at exposed to four periods of 500 mM salinity, 0 h or control (accession no. MN066165), after 2 h (accession no. MN066166), after 12 h (accession no. MN066167) and after 24 h (accession no. MN066168) using RNA-seq raw data. Seventeen RNA editing sites were found in positions (or nucleotide nos. C5, C39, C44, C61, C62, C79, C80, C147, C185, C190, C191, C208, C209, C275, C317, C344, C349) within the nad3 coding region. These alterations represent differential editing at four exposure times. The maximum editing rate was revealed 2 and 12 h after salinity exposure. However, these edits were disrupted after 24 h probably due to the initiation of program cell death machinery. We found that RNA editing not only improved protein function but also may improve codon bias by altering the nucleotide without any change in amino acid. Characterization of pentatricopeptide repeat-containing protein At4g13650 (PPRSp1) in wild barley helped us to understand the behavior of editing sites C190 and C191 under salinity. Position - 6 in cis-element upstream editing sites of C155, C190 and C191 may be vital to the editing process in these sites by PPRSp1 protein. The differential editing of this gene under salinity led to a relationship between RNA editing and cellular respiration regulation.

Plant organellar RNA editing: what 30 years of research has revealed

The central dogma in biology defines the flow of genetic information from DNA to RNA to protein. Accordingly, RNA molecules generally accurately follow the sequences of the genes from which they are transcribed. This rule is transgressed by RNA editing, which creates RNA products that differ from their DNA templates. Analyses of the RNA landscapes of terrestrial plants have indicated that RNA editing (in the form of C-U base transitions) is highly prevalent within organelles (that is, mitochondria and chloroplasts). Numerous C→U conversions (and in some plants also U→C) alter the coding sequences of many of the organellar transcripts and can also produce translatable mRNAs by creating AUG start sites or eliminating premature stop codons, or affect the RNA structure, influence splicing and alter the stability of RNAs. RNA-binding proteins are at the heart of post-transcriptional RNA expression. The C-to-U RNA editing process in plant mitochondria involves numerous nuclear-encoded factors, many of which have been identified as pentatricopeptide repeat (PPR) proteins that target editing sites in a sequence-specific manner. In this review we report on major discoveries on RNA editing in plant organelles, since it was first documented 30 years ago.

Towards a plant model for enigmatic U-to-C RNA editing: the organelle genomes, transcriptomes, editomes and candidate RNA editing factors in the hornwort Anthoceros agrestis

Hornworts are crucial to understand the phylogeny of early land plants. The emergence of 'reverse' U-to-C RNA editing accompanying the widespread C-to-U RNA editing in plant chloroplasts and mitochondria may be a molecular synapomorphy of a hornwort-tracheophyte clade. C-to-U RNA editing is well understood after identification of many editing factors in models like Arabidopsis thaliana and Physcomitrella patens, but there is no plant model yet to investigate U-to-C RNA editing. The hornwort Anthoceros agrestis is now emerging as such a model system. We report on the assembly and analyses of the A. agrestis chloroplast and mitochondrial genomes, their transcriptomes and editomes, and a large nuclear gene family encoding pentatricopeptide repeat (PPR) proteins likely acting as RNA editing factors. Both organelles in A. agrestis feature high amounts of RNA editing, with altogether > 1100 sites of C-to-U and 1300 sites of U-to-C editing. The nuclear genome reveals > 1400 genes for PPR proteins with variable carboxyterminal DYW domains. We observe significant variants of the 'classic' DYW domain, in the meantime confirmed as the cytidine deaminase for C-to-U editing, and discuss the first attractive candidates for reverse editing factors given their excellent matches to U-to-C editing targets according to the PPR-RNA binding code.

The Expansion and Diversification of Pentatricopeptide Repeat RNA-Editing Factors in Plants

The RNA-binding pentatricopeptide repeat (PPR) family comprises hundreds to thousands of genes in most plants, but only a few dozen in algae, indicating massive gene expansions during land plant evolution. The nature and timing of these expansions has not been well defined due to the sparse sequence data available from early-diverging land plant lineages. In this study, we exploit the comprehensive OneKP datasets of over 1000 transcriptomes from diverse plants and algae toward establishing a clear picture of the evolution of this massive gene family, focusing on the proteins typically associated with RNA editing, which show the most spectacular variation in numbers and domain composition across the plant kingdom. We characterize over 2 250 000 PPR motifs in over 400 000 proteins. In lycophytes, polypod ferns, and hornworts, nearly 10% of expressed protein-coding genes encode putative PPR editing factors, whereas they are absent from algae and complex-thalloid liverworts. We show that rather than a single expansion, most land plant lineages with high numbers of editing factors have continued to generate novel sequence diversity. We identify sequence variations that imply functional differences between PPR proteins in seed plants versus non-seed plants and variations we propose to be linked to seed-plant-specific editing co-factors. Finally, using the sequence variations across the datasets, we develop a structural model of the catalytic DYW domain associated with C-to-U editing and identify a clade of unique DYW variants that are strong candidates as U-to-C RNA-editing factors, given their phylogenetic distribution and sequence characteristics.

Potential of Transcript Editing Across Mitogenomes of Early Land Plants Shows Novel and Familiar Trends

RNA editing alters the identity of nucleotides in an RNA sequence so that the mature transcript differs from the template defined in the genome. This process has been observed in chloroplasts and mitochondria of both seed and early land plants. However, the frequency of RNA editing in plant mitochondria ranges from zero to thousands of editing sites. To date, analyses of RNA editing in mitochondria of early land plants have been conducted on a small number of genes or mitochondrial genomes of a single species. This study provides an overview of the mitogenomic RNA editing potential of the main lineages of these two groups of early land plants by predicting the RNA editing sites of 33 mitochondrial genes of 37 species of liverworts and mosses. For the purpose of the research, we newly assembled seven mitochondrial genomes of liverworts. The total number of liverwort genera with known complete mitogenome sequences has doubled and, as a result, the available complete mitogenome sequences now span almost all orders of liverworts. The RNA editing site predictions revealed that C-to-U RNA editing in liverworts and mosses is group-specific. This is especially evident in the case of liverwort lineages. The average level of C-to-U RNA editing appears to be over three times higher in liverworts than in mosses, while the C-to-U editing frequency of the majority of genes seems to be consistent for each gene across bryophytes.

Extreme variation in rates of evolution in the plastid Clp protease complex

Eukaryotic cells represent an intricate collaboration between multiple genomes, even down to the level of multi-subunit complexes in mitochondria and plastids. One such complex in plants is the caseinolytic protease (Clp), which plays an essential role in plastid protein turnover. The proteolytic core of Clp comprises subunits from one plastid-encoded gene (clpP1) and multiple nuclear genes. TheclpP1 gene is highly conserved across most green plants, but it is by far the fastest evolving plastid-encoded gene in some angiosperms. To better understand these extreme and mysterious patterns of divergence, we investigated the history ofclpP1 molecular evolution across green plants by extracting sequences from 988 published plastid genomes. We find thatclpP1 has undergone remarkably frequent bouts of accelerated sequence evolution and architectural changes (e.g. a loss of introns andRNA-editing sites) within seed plants. AlthoughclpP1 is often assumed to be a pseudogene in such cases, multiple lines of evidence suggest that this is rarely true. We applied comparative native gel electrophoresis of chloroplast protein complexes followed by protein mass spectrometry in two species within the angiosperm genusSilene, which has highly elevated and heterogeneous rates ofclpP1 evolution. We confirmed thatclpP1 is expressed as a stable protein and forms oligomeric complexes with the nuclear-encoded Clp subunits, even in one of the most divergentSilene species. Additionally, there is a tight correlation between amino acid substitution rates inclpP1 and the nuclear-encoded Clp subunits across a broad sampling of angiosperms, suggesting continuing selection on interactions within this complex.

RNA editing in plants: A comprehensive survey of bioinformatics tools and databases

RNA editing is a widespread epitranscriptomic mechanism by which primary RNAs are specifically modified through insertions/deletions or nucleotide substitutions. In plants, RNA editing occurs in organelles (plastids and mitochondria), involves the cytosine to uridine modification (rarely uridine to cytosine) within protein-coding and non-protein-coding regions of RNAs and affects organelle biogenesis, adaptation to environmental changes and signal transduction. High-throughput sequencing technologies have dramatically improved the detection of RNA editing sites at genomic scale. Consequently, different bioinformatics resources have been released to discovery and/or collect novel events. Here, we review and describe the state-of-the-art bioinformatics tools devoted to the characterization of RNA editing in plant organelles with the aim to improve our knowledge about this fascinating but yet under investigated process.

Multifarious Evolutionary Pathways of a Nuclear RNA Editing Factor: Disjunctions in Coevolution of DOT4 and Its Chloroplast Target rpoC1eU488SL

Nuclear-encoded pentatricopeptide repeat (PPR) proteins are site-specific factors for C-to-U RNA editing in plant organelles coevolving with their targets. Losing an editing target by C-to-T conversion allows for eventual loss of its editing factor, as recently confirmed for editing factors CLB19, CRR28, and RARE1 targeting ancient chloroplast editing sites in flowering plants. Here, we report on alternative evolutionary pathways for DOT4 addressing rpoC1eU488SL, a chloroplast editing site in the RNA polymerase β' subunit mRNA. Upon loss of rpoC1eU488SL by C-to-T conversion, DOT4 got lost multiple times independently in angiosperm evolution with intermediate states of DOT4 orthologs in various stages of degeneration. Surprisingly, we now also observe degeneration and loss of DOT4 despite retention of a C in the editing position (in Carica, Coffea, Vicia, and Spirodela). We find that the cytidine remains unedited, proving that DOT4 was not replaced by another editing factor. Yet another pathway of DOT4 evolution is observed among the Poaceae. Although the rpoC1eU488SL edit has been lost through C-to-T conversion, DOT4 orthologs not only remain conserved but also have their array of PPRs extended by six additional repeats. Here, the loss of the ancient target has likely allowed DOT4 to adapt for a new function. We suggest rps3 antisense transcripts as previously demonstrated in barley (Hordeum vulgare) arising from promotor sequences newly emerging in the rpl16 intron of Poaceae as a new candidate target for the extended PPR stretch of DOT4. Altogether, DOT4 and its target show more flexible pathways for evolution than the previously explored editing factors CLB19, CRR28, and RARE1. Certain plant clades (e.g., Amaranthus, Vaccinium, Carica, the Poaceae, Fabales, and Caryophyllales) show pronounced dynamics in the evolution of editing sites and corresponding factors.

Widespread cis-regulation of RNA editing in a large mammal

Post-transcriptional RNA editing may regulate transcript expression and diversity in cells, with potential impacts on various aspects of physiology and environmental adaptation. A small number of recent genome-wide studies in Drosophila, mouse, and human have shown that RNA editing can be genetically modulated, highlighting loci that quantitatively impact editing of transcripts. The potential gene expression and physiological consequences of these RNA-editing quantitative trait loci (edQTL), however, are almost entirely unknown. Here, we present analyses of RNA editing in a large domestic mammal (Bos taurus), where we use whole-genome and high-depth RNA sequencing to discover, characterize, and conduct genetic mapping studies of novel transcript edits. Using a discovery population of nine deeply sequenced cows, we identify 2413 edit sites in the mammary transcriptome, the majority of which are adenosine to inosine edits (98.6%). Most sites are predicted to reside in double-stranded secondary structures (85.1%), and quantification of the rates of editing in an additional 355 cows reveals editing is negatively correlated with gene expression in the majority of cases. Genetic analyses of RNA editing and gene expression highlight 152 cis-regulated edQTL, of which 15 appear to cosegregate with expression QTL effects. Trait association analyses in a separate population of 9989 lactating cows also shows 12 of the cis-edQTL coincide with at least one cosegregating lactation QTL. Together, these results enhance our understanding of RNA-editing dynamics in mammals, and suggest mechanistic links by which loci may impact phenotype through RNA editing mediated processes.

Full plastome sequence of the fern Vandenboschia speciosa (Hymenophyllales): structural singularities and evolutionary insights

We provide here the first full chloroplast genome sequence, i.e., the plastome, for a species belonging to the fern order Hymenophyllales. The phylogenetic position of this order within leptosporangiate ferns, together with the general scarcity of information about fern plastomes, places this research as a valuable study on the analysis of the diversity of plastomes throughout fern evolution. Gene content of V. speciosa plastome was similar to that in most ferns, although there were some characteristic gene losses and lineage-specific differences. In addition, an important number of genes required U to C RNA editing for proper protein translation and two genes showed start codons alternative to the canonical AUG (AUA). Concerning gene order, V. speciosa shared the specific 30-kb inversion of euphyllophytes plastomes and the 3.3-kb inversion of fern plastomes, keeping the ancestral gene order shared by eusporangiate and early leptosporangiate ferns. Conversely, V. speciosa has expanded IR regions comprising the rps7, rps12, ndhB and trnL genes in addition to rRNA and other tRNA genes, a condition shared with several eusporangiate ferns, lycophytes and hornworts, as well as most seed plants.

Molecular and Functional Diversity of RNA Editing in Plant Mitochondria

RNA editing is a fundamental biochemical process relating to the modification of nucleotides in messenger RNAs of functional genes in cells. RNA editing leads to re-establishment of conserved amino acid residues for functional proteins in nuclei, chloroplasts, and mitochondria. Identification of RNA editing factors that contributes to target site recognition increases our understanding of RNA editing mechanisms. Significant progress has been made in recent years in RNA editing studies for both animal and plant cells. RNA editing in nuclei and mitochondria of animal cells and in chloroplast of plant cells has been extensively documented and reviewed. RNA editing has been also extensively documented on plant mitochondria. However, functional diversity of RNA editing factors in plant mitochondria is not overviewed. Here, we review the biological significance of RNA editing, recent progress on the molecular mechanisms of RNA editing process, and function diversity of editing factors in plant mitochondrial research. We will focus on: (1) pentatricopeptide repeat proteins in Arabidopsis and in crop plants; (2) the progress of RNA editing process in plant mitochondria; (3) RNA editing-related RNA splicing; (4) RNA editing associated flower development; (5) RNA editing modulated male sterile; (6) RNA editing-regulated cell signaling; and (7) RNA editing involving abiotic stress. Advances described in this review will be valuable in expanding our understanding in RNA editing. The diverse functions of RNA editing in plant mitochondria will shed light on the investigation of molecular mechanisms that underlies plant development and abiotic stress tolerance.

Complete chloroplast genome sequence of Betula platyphylla: gene organization, RNA editing, and comparative and phylogenetic analyses

BACKGROUND

Betula platyphylla is a common tree species in northern China that has high economic and medicinal value. Our laboratory has been devoted to genome research on B. platyphylla for approximately 10 years. As primary organelle genomes, the complete genome sequences of chloroplasts are important to study the divergence of species, RNA editing and phylogeny. In this study, we sequenced and analyzed the complete chloroplast (cp) genome sequence of B. platyphylla.

RESULTS

The complete cp genome of B. platyphylla was 160,518 bp in length, which included a pair of inverted repeats (IRs) of 26,056 bp that separated a large single copy (LSC) region of 89,397 bp and a small single copy (SSC) region of 19,009 bp. The annotation contained a total of 129 genes, including 84 protein-coding genes, 37 tRNA genes and 8 rRNA genes. There were 3 genes using alternative initiation codons. Comparative genomics showed that the sequence of the Fagales species cp genome was relatively conserved, but there were still some high variation regions that could be used as molecular markers. The IR expansion event of B. platyphylla resulted in larger cp genomes and rps19 pseudogene formation. The simple sequence repeat (SSR) analysis showed that there were 105 SSRs in the cp genome of B. platyphylla. RNA editing sites recognition indicated that at least 80 RNA editing events occurred in the cp genome. Most of the substitutions were C to U, while a small proportion of them were not. In particular, three editing loci on the rRNA were converted to more than two other bases that had never been reported. For synonymous conversion, most of them increased the relative synonymous codon usage (RSCU) value of the codons. The phylogenetic analysis suggested that B. platyphylla had a closer evolutionary relationship with B. pendula than B. nana.

CONCLUSIONS

In this study, we not only obtained and annotated the complete cp genome sequence of B. platyphylla, but we also identified new RNA editing sites and predicted the phylogenetic relationships among Fagales species. These findings will facilitate genomic, genetic engineering and phylogenetic studies of this important species.

Complete chloroplast genome sequence of Dryopteris fragrans (L.) Schott and the repeat structures against the thermal environment

Dryopteris fragrans (L.) Schott is a fern growing on the surface of hot rocks and lava. It is exposed to sunlight directly and bears local hot environment. We sequenced the complete nucleotide sequence of its chloroplast (cp) genome. The cp genome was 151,978 bp in length, consisting of a large single-copy region (85,332 bp), a small single-copy region (31,947 bp) and a pair of inverted repeats (17,314 bp). The cp genome contained 112 genes and 345 RNA editing sites in protein-coding genes. Simple sequence repeats (SSRs) and long repeat structure pairs (30–55 bp) were identified. The number and percent of repeat structures are extremely high in ferns. Thermal denaturation experiments showed its cp genome to have numerous, dispersed and high GC percent repeat structures, which conferred the strongest thermal stability. This repeat-heavy genome may provide the molecular basis of how D. fragrans cp survives its hot environment.

Order-level fern plastome phylogenomics: new insights from Hymenophyllales

PREMISE OF THE STUDY

Filmy ferns (Hymenophyllales) are a highly specialized lineage, having mesophyll one-cell layer thick and inhabiting particularly shaded and humid environments. The phylogenetic placement of Hymenophyllales has been inconclusive, and while over 87 whole fern plastomes have been published, none was from Hymenophyllales. To better understand the evolutionary history of filmy ferns, we sequenced the first complete plastome for this order.

METHODS

We compiled a phylogenomic plastome data set encompassing all 11 fern orders, and reconstructed phylogenies using different data types (nucleotides, codons, and amino acids) and partition schemes (codon positions and loci). To infer the evolution of fern plastome organization, we coded plastome features, including inversions, inverted repeat boundary shifts, gene losses, and tRNA anticodon sequences as characters, and reconstructed the ancestral states for these characters.

KEY RESULTS

We discovered a suite of novel, Hymenophyllales-specific plastome structures that likely resulted from repeated expansions and contractions of the inverted repeat regions. Our phylogenetic analyses reveal that Hymenophyllales is highly supported as either sister to Gleicheniales or to Gleicheniales + the remaining non-Osmundales leptosporangiates, depending on the data type and partition scheme.

CONCLUSIONS

Although our analyses could not confidently resolve the phylogenetic position of Hymenophyalles, the results here highlight the danger of drawing conclusions from "all-in" phylogenomic data set without exploring potential inconsistencies in the data. Finally, our first order-level reconstruction of fern plastome structural evolution provides a useful framework for future plastome research.

Genome-wide organellar analyses from the hornwort Leiosporoceros dussii show low frequency of RNA editing

Because hornworts occupy a pivotal position in early land colonization as sister to other bryophytes, sister to tracheophytes, or sister to all other land plants, a renewed interest has arisen in their phylogenetic diversity, morphology, and genomes. To date, only five organellar genome sequences are available for hornworts. We sequenced the plastome (155,956 bp) and mitogenome (212,153 bp) of the hornwort Leiosporoceros dussii, the sister taxon to all hornworts. The Leiosporoceros organellar genomes show conserved gene structure and order with respect to the other hornworts and other bryophytes. Additionally, using RNA-seq data we quantified the frequency of RNA-editing events (the canonical C-to-U and the reverse editing U-to-C) in both organellar genomes. In total, 109 sites were found in the plastome and 108 in the mitogenome, respectively. The proportion of edited sites corresponds to 0.06% of the plastome and 0.05% of the mitogenome (in reference to the total genome size), in contrast to 0.58% of edited sites in the plastome of Anthoceros angustus (161,162 bp). All edited sites in the plastome and 88 of 108 sites in the mitogenome are C-to-U conversions. Twenty reverse edited sites (U-to-C conversions) were found in the mitogenome (17.8%) and none in the plastome. The low frequency of RNA editing in Leiosporoceros, which is nearly 88% less than in the plastome of Anthoceros and the mitogenome of Nothoceros, indicates that the frequency of RNA editing has fluctuated during hornwort diversification. Hornworts are a pivotal land plant group to unravel the genomic implications of RNA editing and its maintenance despite the evident evolutionary disadvantages.

Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0

Background

Gene expression in plant chloroplasts and mitochondria is affected by RNA editing. Numerous C-to-U conversions, accompanied by reverse U-to-C exchanges in some plant clades, alter the genetic information encoded in the organelle genomes. Predicting and analyzing RNA editing, which ranges from only few sites in some species to thousands in other taxa, is bioinformatically demanding.

Results

Here, we present major enhancements and extensions of PREPACT, a WWW-based service for analysing, predicting and cataloguing plant-type RNA editing. New features in PREPACT’s core include direct GenBank accession query input and options to restrict searches to candidate U-to-C editing or to sites where editing has been documented previously in the references. The reference database has been extended by 20 new organelle editomes. PREPACT 3.0 features new modules “EdiFacts” and “TargetScan”. EdiFacts integrates information on pentatricopeptide repeat (PPR) proteins characterized as site-specific RNA editing factors. PREPACT’s editome references connect into EdiFacts, linking editing events to specific co-factors where known. TargetScan allows position-weighted querying for sequence motifs in the organelle references, optionally restricted to coding regions or sequences around editing sites, or in queries uploaded by the user. TargetScan is mainly intended to evaluate and further refine the proposed PPR-RNA recognition code but may be handy for other tasks as well. We present an analysis for the immediate sequence environment of more than 15,000 documented editing sites finding strong and different bias in the editome data sets.

Conclusions

We exemplarily present the novel features of PREPACT 3.0 aimed to enhance the analyses of plant-type RNA editing, including its new modules EdiFacts integrating information on characterized editing factors and TargetScan aimed to analyse RNA editing site recognition specificities.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2244-9) contains supplementary material, which is available to authorized users.

Towards a comprehensive picture of C-to-U RNA editing sites in angiosperm mitochondria

Our understanding of the dynamic and evolution of RNA editing in angiosperms is in part limited by the few editing sites identified to date. This study identified 10,217 editing sites from 17 diverse angiosperms. Our analyses confirmed the universality of certain features of RNA editing, and offer new evidence behind the loss of editing sites in angiosperms. RNA editing is a post-transcriptional process that substitutes cytidines (C) for uridines (U) in organellar transcripts of angiosperms. These substitutions mostly take place in mitochondrial messenger RNAs at specific positions called editing sites. By means of publicly available RNA-seq data, this study identified 10,217 editing sites in mitochondrial protein-coding genes of 17 diverse angiosperms. Even though other types of mismatches were also identified, we did not find evidence of non-canonical editing processes. The results showed an uneven distribution of editing sites among species, genes, and codon positions. The analyses revealed that editing sites were conserved across angiosperms but there were some species-specific sites. Non-synonymous editing sites were particularly highly conserved (~ 80%) across the plant species and were efficiently edited (80% editing extent). In contrast, editing sites at third codon positions were poorly conserved (~ 30%) and only partially edited (~ 40% editing extent). We found that the loss of editing sites along angiosperm evolution is mainly occurring by replacing editing sites with thymidines, instead of a degradation of the editing recognition motif around editing sites. Consecutive and highly conserved editing sites had been replaced by thymidines as result of retroprocessing, by which edited transcripts are reverse transcribed to cDNA and then integrated into the genome by homologous recombination. This phenomenon was more pronounced in eudicots, and in the gene cox1. These results suggest that retroprocessing is a widespread driving force underlying the loss of editing sites in angiosperm mitochondria.

Organelle Genome Inheritance in Deparia Ferns (Athyriaceae, Aspleniineae, Polypodiales)

Organelle genomes of land plants are predominately inherited maternally but in some cases can also be transmitted paternally or biparentally. Compared to seed plants (>83% genera of angiosperms and >12% genera of gymnosperms), plastid genome (plastome) inheritance has only been investigated in fewer than 2% of fern genera, and mitochondrial genome (mitogenome) from only one fern genus. We developed a new and efficient method to examine plastome and mitogenome inheritance in a fern species-Deparia lancea (Athyriaceae, Aspleniineae, Polypodiales), and found that plastid and mitochondrial DNAs were transmitted from only the maternal parentage to a next generation. To further examine whether both organelle genomes have the same manner of inheritance in other Deparia ferns, we sequenced both plastid and mitochondrial DNA regions of inter-species hybrids, and performed phylogenetic analyses to identify the origins of organellar DNA. Evidence from our experiments and phylogenetic analyses support that both organelle genomes in Deparia are uniparentally and maternally inherited. Most importantly, our study provides the first report of mitogenome inheritance in eupolypod ferns, and the second one among all ferns.

The pentatricopeptide repeat protein EMP9 is required for mitochondrial ccmB and rps4 transcript editing, mitochondrial complex biogenesis and seed development in maize

Pentatricopeptide repeat (PPR) proteins comprise a large family of sequence-specific RNA binding proteins in land plants. Because of its large family size and frequent embryo lethality in the mutants, molecular functions and physiological roles of many PPR proteins are unknown. Through characterization of an empty pericarp9 (emp9) mutant in maize (Zea mays), we defined the functions of EMP9 in mitochondrial RNA editing, respiratory complex formation and seed development. Mu insertions in different regions of Emp9 facilitated dissection of the domain functions of the EMP9. Through genetic and functional analyses of multiple alleles, we showed that deletions of two N-terminal PPR motifs and partial E+ domain do not eliminate the editing function of EMP9. Emp9 encodes an E+ subclass PPR protein that is localized in mitochondria. Loss of EMP9 function abolishes the C-to-U editing of ccmB-43 and rps4-335 sites in mitochondria. The loss of editing at ccmB-43 and rps4-335 affects the maturation of cytochrome c and impairs the biogenesis of mitochondrial respiratory complexes, particularly complex III. This work extends our understanding of PPR-E+ protein in editing function and seed development, and provides insights into the molecular function of mitochondrial CcmB protein in higher plants.

RNA Editing and Its Molecular Mechanism in Plant Organelles

RNA editing by cytidine (C) to uridine (U) conversions is widespread in plant mitochondria and chloroplasts. In some plant taxa, “reverse” U-to-C editing also occurs. However, to date, no instance of RNA editing has yet been reported in green algae and the complex thalloid liverworts. RNA editing may have evolved in early land plants 450 million years ago. However, in some plant species, including the liverwort, Marchantia polymorpha, editing may have been lost during evolution. Most RNA editing events can restore the evolutionarily conserved amino acid residues in mRNAs or create translation start and stop codons. Therefore, RNA editing is an essential process to maintain genetic information at the RNA level. Individual RNA editing sites are recognized by plant-specific pentatricopeptide repeat (PPR) proteins that are encoded in the nuclear genome. These PPR proteins are characterized by repeat elements that bind specifically to RNA sequences upstream of target editing sites. In flowering plants, non-PPR proteins also participate in multiple RNA editing events as auxiliary factors. C-to-U editing can be explained by cytidine deamination. The proteins discovered to date are important factors for RNA editing but a bona fide RNA editing enzyme has yet to be identified.

RNA Editing-Systemic Relevance and Clue to Disease Mechanisms?

Recent advances in sequencing technologies led to the identification of a plethora of different genes and several hundreds of amino acid recoding edited positions. Changes in editing rates of some of these positions were associated with diseases such as atherosclerosis, myopathy, epilepsy, major depression disorder, schizophrenia and other mental disorders as well as cancer and brain tumors. This review article summarizes our current knowledge on that front and presents glycine receptor C-to-U RNA editing as a first example of disease-associated increased RNA editing that includes assessment of disease mechanisms of the corresponding gene product in an animal model.