Whole plastid transcriptomes reveal abundant RNA editing sites and differential editing status in Phalaenopsis aphrodite subsp. formosana

TALE-based organellar genome editing and gene expression in plants

KEY MESSAGE

TALE-based editors provide an alternative way to engineer the organellar genomes in plants. We update and discuss the most recent developments of TALE-based organellar genome editing in plants. Gene editing tools have been widely used to modify the nuclear genomes of plants for various basic research and biotechnological applications. The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 editing platform is the most commonly used technique because of its ease of use, fast speed, and low cost; however, it encounters difficulty when being delivered to plant organelles for gene editing. In contrast, protein-based editing technologies, such as transcription activator-like effector (TALE)-based tools, could be easily delivered, expressed, and targeted to organelles in plants via Agrobacteria-mediated nuclear transformation. Therefore, TALE-based editors provide an alternative way to engineer the organellar genomes in plants since the conventional chloroplast transformation method encounters technical challenges and is limited to certain species, and the direct transformation of mitochondria in higher plants is not yet possible. In this review, we update and discuss the most recent developments of TALE-based organellar genome editing in plants.

Withania somnifera mitochondrial atp4 gene editing alters the ATP synthase b subunit, independent of salt stress

Numerous studies have shown that stress in plant cells and organelles with transport electron chains is related to RNA editing. The ATP synthase complex present in mitochondria plays a crucial role in cellular respiration and consists of several subunits. Among them is the b subunit, which is encoded by the mitochondrial atp4 gene. Computing-based analysis of the effects of RNA editing of the Withania somnifera atp4 gene in mitochondria leading to alterations in the b subunit of ATP synthase. Using the CLC Genomic Workbench 3, RNA editing analysis between the control and salt stress conditions was not significantly different. Depending on RNA editing, the tertiary structure model revealed a change in the states of the b subunit, reflecting differences in the central stalk and F1-catalytic domain. The study found that polar edits in the N-terminus of the b subunit allow for efficient H + ion selectivity and introduce a new coiled-coil alpha-helical structure that may help stabilize the complex. The most noteworthy finding of this study was the strong impact of these editing events on the tertiary structure of the b subunit, which has the potential to affect the ATPase activity and indicate that the editing in this subunit aimed to restore the original active protein and not as a response to salt stress.

Backbone phylogeny and adaptive evolution of Pleurospermum s. l.: New insights from phylogenomic analyses of complete plastome data

Pleurospermum is a taxonomically challenging taxon of Apiaceae, as its circumscription and composition remain controversial for morphological similarities with several related genera, leading to a dispute between Pleurospermum in the broad sense and strict sense. While evidence from previous molecular studies recognized plural branching lineages within the Pleurospermum s. l., it did not support the latest delimitation of Pleurospermum s. str. by only two closely related northern species. So far, no proper delimitation for Pleurospermum has come up, and many of the plural taxa in Pleurospermum s. l. remain unresolved, which may be due to poor phylogenetic resolution yielded barely from ITS sequences. Herein, we newly assembled 40 complete plastomes from 36 species of Pleurospermum s. l. and related genera, 34 of which were first reported and generated a well-resolved backbone phylogeny in a framework of the subfamily Apioideae. From the phylogeny with greatly improved resolution, a total of six well-supported monophyletic lineages within Pleurospermum s. l. were recognized falling in different major clades of Apioideae. Combining morphological characteristics with phylogenetic inference, we suggested to re-delimit the Pleurospermum s. str. by introducing nine species mainly from the Himalayan regions and proposed its boundary features; the remaining species were suggested to be excluded from Pleurospermum to incorporate into their more related taxa being revealed. On this basis, the plastome comparison revealed not only the high conservatism but also the mild differences among lineages in plastome structure and gene evolution. Overall, our study provided a backbone phylogeny essential for further studies of the taxonomically difficult taxa within Pleurospermum s. l.

Polymeric structure of the Cannabis sativa L. mitochondrial genome identified with an assembly graph model

Cannabis sativa L. belongs to the family Cannabaceae in Rosales. It has been widely used as medicines, building materials, and textiles. Elucidating its genome is critical for molecular breeding and synthetic biology study. Many studies have shown that the mitochondrial genomes (mitogenomes) and even chloroplast genomes (plastomes) had complex polymeric structures. Using the Nanopore sequencing platform, we sequenced, assembled, and analyzed its mitogenome and plastome. The resulting unitig graph suggested that the mitogenome had a complex polymeric structure. However, a gap-free, circular sequence was further assembled from the unitig graph. In contrast, a circular sequence representing the plastome was obtained. The mitogenome major conformation was 415,837 bp long, and the plastome was 153,927 bp long. To test if the repeat sequences promote recombination, which corresponds to the branch points in the structure, we tested the sequences around repeats by long-read mapping. Among 208 pairs of predicted repeats, the mapping results supported the presence of cross-over around 25 pairs of repeats. Subsequent PCR amplification confirmed the presence of cross-over around 15 of the 25 repeats. By comparing the mitogenome and plastome sequences, we identified 19 mitochondria plastid DNAs, including seven complete genes (trnW-CCA, trnP-UGG, psbJ, trnN-GUU, trnD-GUC, trnH-GUG, trnM-CAU) and nine gene fragments. Furthermore, the selective pressure analysis results showed that five genes (atp1, ccmB, ccmC, cox1, nad7) had 19 positively selected sites. Lastly, we predicted 28 RNA editing sites. A total of 8 RNA editing sites located in the coding regions were successfully validated by PCR amplification and Sanger sequencing, of which four were synonymous, and four were nonsynonymous. In particular, the RNA editing events appeared to be tissue-specific in C. sativa mitogenome. In summary, we have confirmed the major confirmation of C. sativa mitogenome and characterized its structural features in detail. These results provide critical information for future variety breeding and resource development for C. sativa.

RNA Editing in Chloroplast: Advancements and Opportunities

Many eukaryotic and prokaryotic organisms employ RNA editing (insertion, deletion, or conversion) as a post-transcriptional modification mechanism. RNA editing events are common in these organelles of plants and have gained particular attention due to their role in the development and growth of plants, as well as their ability to cope with abiotic stress. Owing to rapid developments in sequencing technologies and data analysis methods, such editing sites are being accurately predicted, and many factors that influence RNA editing are being discovered. The mechanism and role of the pentatricopeptide repeat protein family of proteins in RNA editing are being uncovered with the growing realization of accessory proteins that might help these proteins. This review will discuss the role and type of RNA editing events in plants with an emphasis on chloroplast RNA editing, involved factors, gaps in knowledge, and future outlooks.

A Transcriptomic Analysis of Tobacco Leaf with the Functional Loss of the Plastid rpoB Operon Caused by TALEN-Mediated Double-Strand Breakage

At least two sets of RNA polymerase (RNAP), nucleus (NEP)- and plastid (PEP)-encoded polymerases, recognizing distinct promoters exist in the plastids of land plants. Most plastid genes are regulated by multiple promoters with different strengths in their response to developmental stages and environmental cues. Recently, we applied chloroplast-targeted transcription activator-like effector nuclease (cpTALEN) technology to site-specifically cause double-strand DNA breaks in the rpoB gene of tobacco, which encodes the β-subunit of PEP. The repair of damaged chloroplast DNA (cpDNA) through microhomology-mediated recombination caused the functional loss of the rpoB operon and resulted in the heterotrophic growth of an albino plant. We conducted a genome-wide analysis of the steady state of gene expression in the leaf tissue of PEP-deficient tobacco by RNA-Seq and compared it with that of wild-type plants. The expression of NEP genes was up-regulated in PEP-deficient tobacco; in particular, the level of RpoT3 transcripts encoding the specifically plastid-targeted NEP was significantly increased. Alongside most housekeeping genes, NEP also plays an important role in the regulation of gene expression involved in photosynthesis. In contrast, alongside the photosynthesis-related genes, PEP also plays an important role in the regulation of gene expression involved in some housekeeping functions. Furthermore, the mitochondrial DNA copy number and the level of most mitochondrial protein-coding transcripts were slightly increased in PEP-deficient tobacco. The disruption of PEP function not only affected plastid gene expression, but also nuclear and mitochondrial gene expression. This study demonstrated the intercompartmental retrograde signaling in the regulation of gene expression.

In-depth analysis of genomes and functional genomics of orchid using cutting-edge high-throughput sequencing

High-throughput sequencing technology has been facilitated the development of new methodologies and approaches for studying the origin and evolution of plant genomes and subgenomes, population domestication, and functional genomics. Orchids have tens of thousands of members in nature. Many of them have promising application potential in the extension and conservation of the ecological chain, the horticultural use of ornamental blossoms, and the utilization of botanical medicines. However, a large-scale gene knockout mutant library and a sophisticated genetic transformation system are still lacking in the improvement of orchid germplasm resources. New gene editing tools, such as the favored CRISPR-Cas9 or some base editors, have not yet been widely applied in orchids. In addition to a large variety of orchid cultivars, the high-precision, high-throughput genome sequencing technology is also required for the mining of trait-related functional genes. Nowadays, the focus of orchid genomics research has been directed to the origin and classification of species, genome evolution and deletion, gene duplication and chromosomal polyploidy, and flower morphogenesis-related regulation. Here, the progressing achieved in orchid molecular biology and genomics over the past few decades have been discussed, including the evolution of genome size and polyploidization. The frequent incorporation of LTR retrotransposons play important role in the expansion and structural variation of the orchid genome. The large-scale gene duplication event of the nuclear genome generated plenty of recently tandem duplicated genes, which drove the evolution and functional divergency of new genes. The evolution and loss of the plastid genome, which mostly affected genes related to photosynthesis and autotrophy, demonstrated that orchids have experienced more separate transitions to heterotrophy than any other terrestrial plant. Moreover, large-scale resequencing provide useful SNP markers for constructing genetic maps, which will facilitate the breeding of novel orchid varieties. The significance of high-throughput sequencing and gene editing technologies in the identification and molecular breeding of the trait-related genes in orchids provides us with a representative trait-improving gene as well as some mechanisms worthy of further investigation. In addition, gene editing has promise for the improvement of orchid genetic transformation and the investigation of gene function. This knowledge may provide a scientific reference and theoretical basis for orchid genome studies.

Repairing TALEN-mediated double-strand break by microhomology-mediated recombination in tobacco plastids generates abundant subgenomic DNA

Transcription activator-like effector nuclease (TALEN) technology has been widely used to edit nuclear genomes in plants but rarely for editing organellar genomes. In addition, ciprofloxacin, commonly used to cause the double-strand break of organellar DNA for studying the repair mechanism in plants, confers no organellar selectivity and site-specificity. To demonstrate the feasibility of TALEN-mediated chloroplast DNA editing and to use it for studying the repair mechanism in plastids, we developed a TALEN-mediated editing technology fused with chloroplast transit peptide (cpTALEN) to site-specifically edit the rpoB gene via Agrobacteria-mediated transformation of tobacco leaf. Transgenic plants showed various degrees of chlorotic phenotype. Repairing damaged plastid DNA resulted in point mutation, large deletion and small inversion surrounding the rpoB gene by homologous recombination and/or microhomology-mediated recombination. In an albino line, microhomology-mediated recombination via a pair of 12-bp direct repeats between rpoC2 and ycf2 genes generated the chimeric ycf2-rpoC2 subgenome, with the level about 3- to 5-fold higher for subgenomic DNA than ycf2. Additionally, the expression of chimeric ycf2-rpoC2 transcripts versus ycf2 mRNA agreed well with the level of corresponding DNA. The ycf2-rpoC2 subgenomic DNA might independently and preferentially replicate in plastids.

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.

Organelle Genomes and Transcriptomes of Nymphaea Reveal the Interplay between Intron Splicing and RNA Editing

Posttranscriptional modifications, including intron splicing and RNA editing, are common processes during regulation of gene expression in plant organelle genomes. However, the intermediate products of intron-splicing, and the interplay between intron-splicing and RNA-editing were not well studied. Most organelle transcriptome analyses were based on the Illumina short reads which were unable to capture the full spectrum of transcript intermediates within an organelle. To fully investigate the intermediates during intron splicing and the underlying relationships with RNA editing, we used PacBio DNA-seq and Iso-seq, together with Illumina short reads genome and transcriptome sequencing data to assemble the chloroplast and mitochondrial genomes of Nymphaea 'Joey Tomocik' and analyze their posttranscriptional features. With the direct evidence from Iso-seq, multiple intermediates partially or fully intron-spliced were observed, and we also found that both cis- and trans-splicing introns were spliced randomly. Moreover, by using rRNA-depleted and non-Oligo(dT)-enrichment strand-specific RNA-seq data and combining direct SNP-calling and transcript-mapping methods, we identified 98 and 865 RNA-editing sites in the plastome and mitogenome of N. 'Joey Tomocik', respectively. The target codon preference, the tendency of increasing protein hydrophobicity, and the bias distribution of editing sites are similar in both organelles, suggesting their common evolutionary origin and shared editing machinery. The distribution of RNA editing sites also implies that the RNA editing sites in the intron and exon regions may splice synchronously, except those exonic sites adjacent to intron which could only be edited after being intron-spliced. Our study provides solid evidence for the multiple intermediates co-existing during intron-splicing and their interplay with RNA editing in organelle genomes of a basal angiosperm.

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.

An integrated DNA and RNA variant detector identifies a highly conserved three base exon in the MAP4K5 kinase locus

RNA variants that emerge from editing and alternative splicing form important regulatory stages in protein signalling. In this report, we apply an integrated DNA and RNA variant detection workbench to define the range of RNA variants that deviate from the reference genome in a human melanoma cell model. The RNA variants can be grouped into (i) classic ADAR-like or APOBEC-like RNA editing events and (ii) multiple-nucleotide variants (MNVs) including three and six base pair in-frame non-canonical unmapped exons. We focus on validating representative genes of these classes. First, clustered non-synonymous RNA edits (A-I) in the CDK13 gene were validated by Sanger sequencing to confirm the integrity of the RNA variant detection workbench. Second, a highly conserved RNA variant in the MAP4K5 gene was detected that results most likely from the splicing of a non-canonical three-base exon. The two RNA variants produced from the MAP4K5 locus deviate from the genomic reference sequence and produce V569E or V569del isoform variants. Low doses of splicing inhibitors demonstrated that the MAP4K5-V569E variant emerges from an SF3B1-dependent splicing event. Mass spectrometry of the recombinant SBP-tagged MAP4K5^V569E and MAP4K5^V569del proteins pull-downs in transfected cell systems was used to identify the protein-protein interactions of these two MAP4K5 isoforms and propose possible functions. Together these data highlight the utility of this integrated DNA and RNA variant detection platform to detect RNA variants in cancer cells and support future analysis of RNA variant detection in cancer tissue.

Complete Plastid and Mitochondrial Genomes of Aeginetia indica Reveal Intracellular Gene Transfer (IGT), Horizontal Gene Transfer (HGT), and Cytoplasmic Male Sterility (CMS)

Orobanchaceae have become a model group for studies on the evolution of parasitic flowering plants, and Aeginetia indica, a holoparasitic plant, is a member of this family. In this study, we assembled the complete chloroplast and mitochondrial genomes of A. indica. The chloroplast and mitochondrial genomes were 56,381 bp and 401,628 bp long, respectively. The chloroplast genome of A. indica shows massive plastid genes and the loss of one IR (inverted repeat). A comparison of the A. indica chloroplast genome sequence with that of a previous study demonstrated that the two chloroplast genomes encode a similar number of proteins (except atpH) but differ greatly in length. The A. indica mitochondrial genome has 53 genes, including 35 protein-coding genes (34 native mitochondrial genes and one chloroplast gene), 15 tRNA (11 native mitochondrial genes and four chloroplast genes) genes, and three rRNA genes. Evidence for intracellular gene transfer (IGT) and horizontal gene transfer (HGT) was obtained for plastid and mitochondrial genomes. ψndhB and ψcemA in the A. indica mitogenome were transferred from the plastid genome of A. indica. The atpH gene in the plastid of A. indica was transferred from another plastid angiosperm plastid and the atpI gene in mitogenome A. indica was transferred from a host plant like Miscanthus siensis. Cox2 (orf43) encodes proteins containing a membrane domain, making ORF (Open Reading Frame) the most likely candidate gene for CMS development in A. indica.

Tight association of genome rearrangements with gene expression in conifer plastomes

BACKGROUND

Our understanding of plastid transcriptomes is limited to a few model plants whose plastid genomes (plastomes) have a highly conserved gene order. Consequently, little is known about how gene expression changes in response to genomic rearrangements in plastids. This is particularly important in the highly rearranged conifer plastomes.

RESULTS

We sequenced and reported the plastomes and plastid transcriptomes of six conifer species, representing all six extant families. Strand-specific RNAseq data show a nearly full transcription of both plastomic strands and detect C-to-U RNA-editing sites at both sense and antisense transcripts. We demonstrate that the expression of plastid coding genes is strongly functionally dependent among conifer species. However, the strength of this association declines as the number of plastomic rearrangements increases. This finding indicates that plastomic rearrangement influences gene expression.

CONCLUSIONS

Our data provide the first line of evidence that plastomic rearrangements not only complicate the plastomic architecture but also drive the dynamics of plastid transcriptomes in conifers.

RNA editing may stabilize membrane-embedded proteins by increasing phydrophobicity: A study of Zanthoxylum piperitum and Z. schinifolium chloroplast NdhG

Most chloroplast genes in Zanthoxylum schinifolium (Korean pepper) and Z. piperitum (Japanese pepper) are subject to neutral or purifying selection (Ka/Ks values < 1); however, NAD(P)H dehydrogenase subunit G (ndhG) has a Ka/Ks value of 1.43, which may indicate positive selection. Here, we modeled the ZsNdhG and ZpNdhG structures by comparing them with the NuoJ subunit of respiratory complex I in Escherichia coli, revealing the locations of four amino acid differences between ZsNdhG and ZpNdhG. As these polymorphisms were located at the end of a membrane-spanning α-helix or in peptide loops external to the membrane, they are not expected to have major effects on the membrane-embedding properties of these proteins. However, we found that C-to-U RNA editing occurred at the ndhG-50 sites of ndhG (uCa to uUa, Ser to Leu) in both species, resulting in changes to an amino acid located in the middle of a membrane-spanning α-helix, which may maintain its hydrophobicity. RNA editing at the ndhG-50 site was conserved in many plant species, and the modeled structures of Anthoceros formosae NdhG and Spirodela polyrhiza NdhB provided further evidence that RNA editing increases the hydrophobicity of membrane-embedded proteins. We also speculate that the polar residues inside membrane-spanning α-helices serve to support the protein structure. This report represents the first RNA-editing site identified in Zanthoxylum and points to the importance of considering RNA editing when identifying positively selected genes based on Ka/Ks values.

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.

The plastomes of Astrocaryum aculeatum G. Mey. and A. murumuru Mart. show a flip-flop recombination between two short inverted repeats

The plastomes of Astrocaryum murumuru and A. aculeatum revealed a lineage-specific structural feature originated by flip-flop recombination, non-synonymous substitutions in conserved genes and several molecular markers. Astrocaryum murumuru Mart. and A. aculeatum G.Mey. are two palm species of Amazon forest that are economically important as source of food, oil and raw material for several applications. Genetic studies aiming to establish strategies for conservation and domestication of both species are still in the beginning given that the exploitation is mostly by extractive activity. The identification and characterization of molecular markers are essential to assess the genetic diversity of natural populations of both species. Therefore, we sequenced and characterized in detail the plastome of both species. We compared both species and identified 32 polymorphic SSR loci, 150 SNPs, 46 indels and eight hotspots of nucleotide diversity. Additionally, we reported a specific RNA editing site found in the ccsA gene, which is exclusive to A. murumuru. Moreover, the structural analysis in the plastomes of both species revealed a 4.6-kb inversion encompassing a set of genes involved in chlororespiration and plastid translation. This 4.6-kb inversion is a lineage-specific structural feature of the genus Astrocaryum originated by flip-flop recombination between two short inverted repeats. Furthermore, our phylogenetic analysis using whole plastomes of 39 Arecaceae species placed the Astrocaryum species sister to Acrocomia within the tribe Cocoseae. Finally, our data indicated substantial changes in the plastome structure and sequence of both species of the genus Astrocaryum, bringing new molecular markers, several structural and evolving features, which can be applied in several areas such as genetic, evolution, breeding, phylogeny and conservation strategies for both species.

Evolutionary Model of Plastidial RNA Editing in Angiosperms Presumed from Genome-Wide Analysis of Amborella trichopoda

Amborella trichopoda is placed close to the base of the angiosperm lineage (basal angiosperm). By genome-wide RNA sequencing, we identified 184C-to-U RNA editing sites in the plastid genome of Amborella. This number is much higher than that observed in other angiosperms including maize (44 sites), rice (39 sites) and grape (115 sites). Despite the high frequency of RNA editing, the biased distribution of RNA editing sites in the genome, target codon preference and nucleotide preference adjacent to the edited cytidine are similar to that in other angiosperms, suggesting a common editing machinery. Consistent with this idea, the Amborella nuclear genome encodes 2-3 times more of the E- and DYW-subclass members of pentatricopeptide repeat proteins responsible for RNA editing site recognition in plant organelles. Among 165 editing sites in plastid protein coding sequences in Amborella, 100 sites were conserved at least in one out of 38 species selected to represent key branching points of the angiosperm phylogenetic tree. We assume these 100 sites represent at least a subset of the sites in the plastid editotype of ancestral angiosperms. We then mapped the loss and gain of editing sites on the phylogenetic tree of angiosperms. Our results support the idea that the evolution of angiosperms has led to the loss of RNA editing sites in plastids.

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.

The implication of plastid transcriptome analysis in petaloid monocotyledons: A case study of Lilium lancifolium (Liliaceae, Liliales)

Transcriptome data provide useful information for studying the evolutionary history of angiosperms. Previously, different genomic events (i.e., duplication, deletion, and pseudogenization) were discovered in the plastid genome of Liliales; however, the effects of these events have not addressed because of the lack of transcriptome data. In this study, we completed the plastid genome (cpDNA) and generated transcriptome data of Lilium lancifolium. Consequently, the cpDNA of L. lancifolium is 152,479 bp in length, which consists of one large single copy (81,888 bp), one small single copy (17,607 bp), and two inverted repeat regions (26,544 bp). The comparative genomic analysis of newly sequenced cpDNA and transcriptome data revealed 90 RNA editing sites of which two positions are located in the rRNA coding region of L. lancifolium. A further check on the secondary structure of rRNA showed that RNA editing causes notable structural changes. Most of the RNA editing contents are C-to-U conversions, which result in nonsynonymous substitutions. Among coding regions, ndh genes have the highest number of RNA editing sites. Our study provided the first profiling of plastid transcriptome analyses in Liliales and fundamental information for further studies on post-transcription in this order as well as other petaloid monocotyledonous species.

High Level of Conservation of Mitochondrial RNA Editing Sites Among Four Populus Species

RNA editing occurs in the endosymbiont organelles of higher plants as C-to-U conversions of defined nucleotides. The availability of large quantities of RNA sequencing data makes it possible to identify RNA editing sites and to quantify their editing extent. We have investigated RNA editing in 34 protein-coding mitochondrial transcripts of four Populus species, a genus noteworthy for its remarkably small number of RNA editing sites compared to other angiosperms. 27 of these transcripts were subject to RNA editing in at least one species. In total, 355 RNA editing sites were identified with high confidence, their editing extents ranging from 10 to 100%. The most heavily edited transcripts were ccmB with the highest density of RNA editing sites (53.7 sites / kb) and ccmFn with the highest number of sites (39 sites). Most of the editing events are at position 1 or 2 of the codons, usually altering the encoded amino acid, and are highly conserved among the species, also with regard to their editing extent. However, one SNP was found in the newly sequenced and annotated mitochondrial genome of P. alba resulting in the loss of an RNA editing site compared to P. tremula and P. davidiana This SNP causes a C-to-T transition and an amino acid exchange from Ser to Phe, highlighting the widely discussed role of RNA editing in compensating mutations.

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.

The complete plastid genomes of Ophrys iricolor and O. sphegodes (Orchidaceae) and comparative analyses with other orchids

Sexually deceptive orchids of the genus Ophrys may rapidly evolve by adaptation to pollinators. However, understanding of the genetic basis of potential changes and patterns of relationships is hampered by a lack of genomic information. We report the complete plastid genome sequences of Ophrys iricolor and O. sphegodes, representing the two most species-rich lineages of the genus Ophrys. Both plastomes are circular DNA molecules (146754 bp for O. sphegodes and 150177 bp for O. iricolor) with the typical quadripartite structure of plastid genomes and within the average size of photosynthetic orchids. 213 Simple Sequence Repeats (SSRs) (31.5% polymorphic between O. iricolor and O. sphegodes) were identified, with homopolymers and dipolymers as the most common repeat types. SSRs were mainly located in intergenic regions but SSRs located in coding regions were also found, mainly in ycf1 and rpoC2 genes. The Ophrys plastome is predicted to encode 107 distinct genes, 17 of which are completely duplicated in the Inverted Repeat regions. 83 and 87 putative RNA editing sites were detected in 25 plastid genes of the two Ophrys species, all occurring in the first or second codon position. Comparing the rate of nonsynonymous (dN) and synonymous (dS) substitutions, 24 genes (including rbcL and ycf1) display signature consistent with positive selection. When compared with other members of the orchid family, the Ophrys plastome has a complete set of 11 functional ndh plastid genes, with the exception of O. sphegodes that has a truncated ndhF gene. Comparative analysis showed a large co-linearity with other related Orchidinae. However, in contrast to O. iricolor and other Orchidinae, O. sphegodes has a shift of the junction between the Inverted Repeat and Small Single Copy regions associated with the loss of the partial duplicated gene ycf1 and the truncation of the ndhF gene. Data on relative genomic coverage and validation by PCR indicate the presence, with a different ratio, of the two plastome types (i.e. with and without ndhF deletion) in both Ophrys species, with a predominance of the deleted type in O. sphegodes. A search for this deleted plastid region in O. sphegodes nuclear genome shows that the deleted region is inserted in a retrotransposon nuclear sequence. The present study provides useful genomic tools for studying conservation and patterns of relationships of this rapidly radiating orchid genus.

Comparative transcriptomic analysis identifies genes responsible for fruit count and oil yield in the oil tea plant Camellia chekiangoleosa

Fruit yield is an important trait for horticultural crops. However, the limited fruit yield of Camellia chekiangoleosa, a novel promising oil tree, restricts the production of oil. The breeding improvement is little due to its long generation time and lack of available genomic sequence. We identified distinct fruit count phenotypes, high-yield (HY) and low-yield (LY). To understand the underlying genetic basis, we focused on global gene discovery and expression levels in floral buds, which affect fruit count. A total of 140,299 de novo assembled unigenes were obtained using RNA-seq technology, and more genes were expressed in HY than in LY. 2395 differentially expressed genes (DEGs) were identified and enriched in membrane, energy metabolism, secondary metabolism, fatty acid biosynthesis and metabolism, and 18 other metabolic pathways. Of the DEGs, twelve identified transcription factors, including AP2, mostly involve in inflorescence and flower development and in hormone networks. Key DEGs in fatty acid biosynthesis (Fab) FabB, FabF, FabZ, and AccD were highly expressed in floral buds and associated with high oil yield in fruits. We hypothesized that a potential link exists between fruit count and its oil yield. These findings help to elucidate the molecular cues affecting fruit count and oil yield.

The complete plastome of macaw palm [Acrocomia aculeata (Jacq.) Lodd. ex Mart.] and extensive molecular analyses of the evolution of plastid genes in Arecaceae

The plastome of macaw palm was sequenced allowing analyses of evolution and molecular markers. Additionally, we demonstrated that more than half of plastid protein-coding genes in Arecaceae underwent positive selection. Macaw palm is a native species from tropical and subtropical Americas. It shows high production of oil per hectare reaching up to 70% of oil content in fruits and an interesting plasticity to grow in different ecosystems. Its domestication and breeding are still in the beginning, which makes the development of molecular markers essential to assess natural populations and germplasm collections. Therefore, we sequenced and characterized in detail the plastome of macaw palm. A total of 221 SSR loci were identified in the plastome of macaw palm. Additionally, eight polymorphism hotspots were characterized at level of subfamily and tribe. Moreover, several events of gain and loss of RNA editing sites were found within the subfamily Arecoideae. Aiming to uncover evolutionary events in Arecaceae, we also analyzed extensively the evolution of plastid genes. The analyses show that highly divergent genes seem to evolve in a species-specific manner, suggesting that gene degeneration events may be occurring within Arecaceae at the level of genus or species. Unexpectedly, we found that more than half of plastid protein-coding genes are under positive selection, including genes for photosynthesis, gene expression machinery and other essential plastid functions. Furthermore, we performed a phylogenomic analysis using whole plastomes of 40 taxa, representing all subfamilies of Arecaceae, which placed the macaw palm within the tribe Cocoseae. Finally, the data showed here are important for genetic studies in macaw palm and provide new insights into the evolution of plastid genes and environmental adaptation in Arecaceae.