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PREMISE OF THE STUDY: Comparative analyses of plastid genomes have suggested that gene order and content are relatively stable across the main groups of land plants, with significant changes rarely reported. We examine plastome organization and RNA editing in ferns and report changes that add valuable information on plastome evolution in land plants. METHODS: Using next‐generation sequencing methods, we fully sequenced plastomes from three species of Schizaeaceae, and compared their plastomes with other groups of land plants to study changes in gene composition, plastome architecture, and putative RNA editing sites. We also performed maximum likelihood and Bayesian inference phylogenetic analyses using 46 plastid‐encoded genes, including 26 ferns, two gymnosperms, and five angiosperms. KEY RESULTS: Within Schizaeaceae, plastomes were similar to each other in gene content and architecture. Striking changes compared with other ferns include the complete loss of ndh genes and reduction of the small single copy. Putative RNA editing was identified in all three plastomes, a characteristic that is shared with other fern groups. The monophyly of Schizaeales and Schizaeaceae was confirmed. CONCLUSIONS: The plastomes of Schizaea are the smallest reported for a fern so far. The loss of the ndh gene suite is associated with the reduction of the small single copy, instead of the inverted repeat as noted for other groups of plants. Putative C‐to‐U and U‐to‐C transitions were observed in several instances in the three plastomes, suggesting that posttranscriptional modification of RNA is likely a common phenomenon in this clade as well.

The 11 plastid ndh genes have hovered frequently on the edge of dispensability, being absent in the plastid DNA of many algae and certain higher plants. We have compared the photosynthetic activity of tobacco (Nicotiana tabacum, cv. Petit Havana) with five transgenic lines (ΔndhF, pr-ΔndhF, T181D, T181A, and ndhF FC) and found that photosynthetic performance is impaired in transgenic ndhF-defective tobacco plants at rapidly fluctuating light intensities and higher than ambient CO2 concentrations. In contrast to wild type and ndhF FC, which reach the maximum photosynthetic rate in less than 1 min when light intensity suddenly increases, ndh defective plants (ΔndhF and T181A) show up to a 5 min delay in reaching the maximum photosynthetic rate at CO2 concentrations higher than the ambient 360 ppm. Net photosynthesis was determined at different CO2 concentrations when sequences of 130, 870, 61, 870, and 130 μmol m(-2) s(-1) PAR sudden light changes were applied to leaves and photosynthetic efficiency and entropy production (Sg) were determined as indicators of photosynthesis performance. The two ndh-defective plants, ΔndhF and T181A, had lower photosynthetic efficiency and higher Sg than wt, ndhF FC and T181D tobacco plants, containing full functional ndh genes, at CO2 concentrations above 400 ppm. We propose that the Ndh complex improves cyclic electron transport by adjusting the redox level of transporters during the low light intensity stage. In ndhF-defective strains, the supply of electrons through the Ndh complex fails, transporters remain over-oxidized (specially at high CO2 concentrations) and the rate of cyclic electron transport is low, impairing the ATP level required to rapidly reach high CO2 fixation rates in the following high light phase. Hence, ndh genes could be dispensable at low but not at high atmospheric concentrations of CO2.

In order to understand the evolution of the orchid plastome, we annotated and compared 124 complete plastomes of Orchidaceae representing all the major lineages in their structures, gene contents, gene rearrangements, and IR contractions/expansions. Forty-two of these plastomes were generated from the corresponding author's laboratory, and 24 plastomes-including nine genera ( , , , , , , , and )-are new in this study. All orchid plastomes, except and have a quadripartite structure consisting of a large single copy (LSC), two inverted repeats (IRs), and a small single copy (SSC) region. The IR region was completely lost in the plastomes. The SSC is lost in the plastome. The smallest plastome size was 19,047 bp, in and the largest plastome size was 178,131 bp, in . The small plastome sizes are primarily the result of gene losses associated with mycoheterotrophic habitats, while the large plastome sizes are due to the expansion of noncoding regions. The minimal number of common genes among orchid plastomes to maintain minimal plastome activity was 15, including the three subunits of (14, 16, and 36), seven subunits of (2, 3, 4, 7, 8, 11, and 14), three subunits of (5, 16, and 23), C-GCA, and P genes. Three stages of gene loss were observed among the orchid plastomes. The first was gene loss, which is widespread in Apostasioideae, Vanilloideae, Cypripedioideae, and Epidendroideae, but rare in the Orchidoideae. The second stage was the loss of photosynthetic genes ( , and ) and gene subunits, which are restricted to and some species of and . The third stage was gene loss related to prokaryotic gene expression ( , , and others), which was observed in , , and In addition, an intermediate stage between the second and third stage was observed in (Vanilloideae). The majority of intron losses are associated with the loss of their corresponding genes. In some orchid taxa, however, introns have been lost in 16 16, and P(2) without their corresponding gene being lost. A total of 104 gene rearrangements were counted when comparing 116 orchid plastomes. Among them, many were concentrated near the IRa/b-SSC junction area. The plastome phylogeny of 124 orchid species confirmed the relationship of {Apostasioideae [Vanilloideae (Cypripedioideae (Orchidoideae, Epidendroideae))]} at the subfamily level and the phylogenetic relationships of 17 tribes were also established. Molecular clock analysis based on the whole plastome sequences suggested that Orchidaceae diverged from its sister family 99.2 mya, and the estimated divergence times of five subfamilies are as follows: Apostasioideae (79.91 mya), Vanilloideae (69.84 mya), Cypripedioideae (64.97 mya), Orchidoideae (59.16 mya), and Epidendroideae (59.16 mya). We also released the first nuclear ribosomal (nr) DNA unit (18S-ITS1-5.8S-ITS2-28S-NTS-ETS) sequences for the 42 species of Orchidaceae. Finally, the phylogenetic tree based on the nrDNA unit sequences is compared to the tree based on the 42 identical plastome sequences, and the differences between the two datasets are discussed in this paper.

Chloroplast genomes are valuable for inferring evolutionary relationships. We report the complete chloroplast genomes of 36 Corydalis spp. and one Fumaria species. We compared these genomes with 22 other taxa and investigated the genome structure, gene content, and evolutionary dynamics of the chloroplast genomes of 58 species, explored the structure, size, repeat sequences, and divergent hotspots of these genomes, conducted phylogenetic analysis, and identified nine types of chloroplast genome structures among Corydalis spp. The ndh gene family suffered inversion and rearrangement or was lost or pseudogenized throughout the chloroplast genomes of various Corydalis species. Analysis of five protein-coding genes revealed simple sequence repeats and repetitive sequences that can be potential molecular markers for species identification. Phylogenetic analysis revealed three subgenera in Corydalis . Subgenera Cremnocapnos and Sophorocapnos represented the Type 2 and 3 genome structures, respectively. Subgenus Corydalis included all types except type 3, suggesting that chloroplast genome structural diversity increased during its differentiation. Despite the explosive diversification of this subgenus, most endemic species collected from the Korean Peninsula shared only one type of genome structure, suggesting recent divergence. These findings will greatly improve our understanding of the chloroplast genome of Corydalis and may help develop effective molecular markers.

The NAD(P)H dehydrogenase complex is encoded by 11 ndh genes in plant chloroplast (cp) genomes. However, ndh genes are truncated or deleted in some autotrophic Epidendroideae orchid cp genomes. To determine the evolutionary timing of the gene deletions and the genomic locations of the various ndh genes in orchids, the cp genomes of Vanilla planifolia , Paphiopedilum armeniacum , Paphiopedilum niveum , Cypripedium formosanum , Habenaria longidenticulata , Goodyera fumata and Masdevallia picturata were sequenced; these genomes represent Vanilloideae, Cypripedioideae, Orchidoideae and Epidendroideae subfamilies. Four orchid cp genome sequences were found to contain a complete set of ndh genes. In other genomes, ndh deletions did not correlate to known taxonomic or evolutionary relationships and deletions occurred independently after the orchid family split into different subfamilies. In orchids lacking cp encoded ndh genes, non cp localized ndh sequences were identified. In Erycina pusilla , at least 10 truncated ndh gene fragments were found transferred to the mitochondrial (mt) genome. The phenomenon of orchid ndh transfer to the mt genome existed in ndh -deleted orchids and also in ndh containing species.

Earlier research has revealed that the ndh loci have been pseudogenized, truncated, or deleted from most orchid plastomes sequenced to date, including in all available plastomes of the two most species-rich subfamilies, Orchidoideae and Epidendroideae. This study sought to resolve deeper-level phylogenetic relationships among major orchid groups and to refine the history of gene loss in the ndh loci across orchids. The complete plastomes of seven orchids, Oncidium sphacelatum (Epidendroideae), Masdevallia coccinea (Epidendroideae), Sobralia callosa (Epidendroideae), Sobralia aff. bouchei (Epidendroideae), Elleanthus sodiroi (Epidendroideae), Paphiopedilum armeniacum (Cypripedioideae), and Phragmipedium longifolium (Cypripedioideae) were sequenced and analyzed in conjunction with all other available orchid and monocot plastomes. Most ndh loci were found to be pseudogenized or lost in Oncidium, Paphiopedilum and Phragmipedium, but surprisingly, all ndh loci were found to retain full, intact reading frames in Sobralia, Elleanthus and Masdevallia. Character mapping suggests that the ndh genes were present in the common ancestor of orchids but have experienced independent, significant losses at least eight times across four subfamilies. In addition, ndhF gene loss was correlated with shifts in the position of the junction of the inverted repeat (IR) and small single-copy (SSC) regions. The Orchidaceae have unprecedented levels of homoplasy in ndh gene presence/absence, which may be correlated in part with the unusual life history of orchids. These results also suggest that ndhF plays a role in IR/SSC junction stability.

The chloroplast (cp) is an autonomous plant organelle with an individual genome that encodes essential cellular functions. The genome architecture and gene content of the cp is highly conserved in angiosperms. The plastome of belongs to the Papaveraceae family, and the genome is comprised of unusual rearrangements and gene content. Thus far, no extensive comparative studies have been carried out to understand the evolution of chloroplast genomes. Therefore, the cp genome was sequenced, and wide-scale comparative studies were conducted using publicly available twenty plastomes. Comparative analyses showed that an extensive genome rearrangement and IR expansion occurred, and these events evolved independently in the species. By contrast, the plastomes of its closely related subfamily Papaveroideae and other Ranunculales taxa are highly conserved. On the other hand, the synapomorphy characteristics of both and the gene loss events happened in the common ancestor of the and sub-clade of the lineage, respectively. The -sub clade species ( lost) are distributed predominantly in the Qinghai-Tibetan plateau (QTP) region. The phylogenetic analysis and divergence time estimation were also employed for the species. The divergence time of the gene in the sub-clade species (44.31 - 15.71 mya) coincides very well with the uplift of the Qinghai-Tibet Plateau in Oligocene and Miocene periods, and maybe during this period, it has probably triggered the radiation of the species. To the best of the authors' knowledge, this is the first large-scale comparative study of plastomes and their evolution. The present study may provide insights into the plastome architecture and the molecular evolution of species.

Background The cactus family (Cactaceae) has been reported to have evolved a minimal photosynthetic plastome size, with the loss of inverted-repeat (IR) regions and NDH gene suites. However, there are very limited genomic data on the family, especially Cereoideae, the largest subfamily of cacti. Results In the present study, we assembled and annotated 35 plastomes, 33 of which were representatives of Cereoideae, alongside 2 previously published plastomes. We analyzed the organelle genomes of 35 genera in the subfamily. These plastomes have variations rarely observed in those of other angiosperms, including size differences (with ~ 30 kb between the shortest and longest), dramatic dynamic changes in IR boundaries, frequent plastome inversions, and rearrangements. These results suggested that cacti have the most complex plastome evolution among angiosperms. Conclusion These results provide unique insight into the dynamic evolutionary history of Cereoideae plastomes and refine current knowledge of the relationships within the subfamily.

Chloroplast genomes (plastomes) are frequently treated as highly conserved among land plants. However, many lineages of vascular plants have experienced extensive structural rearrangements, including inversions and modifications to the size and content of genes. Cacti are one of these lineages, containing the smallest plastome known for an obligately photosynthetic angiosperm, including the loss of one copy of the inverted repeat (∼25 kb) and the gene suite, but only a few cacti from the subfamily Cactoideae have been sufficiently characterized. Here, we investigated the variation of plastome sequences across the second-major lineage of the Cactaceae, the subfamily Opuntioideae, to address (1) how variable is the content and arrangement of chloroplast genome sequences across the subfamily, and (2) how phylogenetically informative are the plastome sequences for resolving major relationships among the clades of Opuntioideae. Our assembly of the plastome recovered an organelle of 150,347 bp in length with both copies of the inverted repeat and the presence of all the gene suite. An expansion of the large single copy unit and a reduction of the small single copy unit was observed, including translocations and inversion of genes, as well as the putative pseudogenization of some loci. Comparative analyses among all clades within Opuntioideae suggested that plastome structure and content vary across taxa of this subfamily, with putative independent losses of the gene suite and pseudogenization of genes across disparate lineages, further demonstrating the dynamic nature of plastomes in Cactaceae. Our plastome dataset was robust in resolving three tribes with high support within Opuntioideae: Cylindropuntieae, Tephrocacteae and Opuntieae. However, conflicting topologies were recovered among major clades when exploring different assemblies of markers. A plastome-wide survey for highly informative phylogenetic markers revealed previously unused regions for future use in Sanger-based studies, presenting a valuable dataset with primers designed for continued evolutionary studies across Cactaceae. These results bring new insights into the evolution of plastomes in cacti, suggesting that further analyses should be carried out to address how ecological drivers, physiological constraints and morphological traits of cacti may be related with the common rearrangements in plastomes that have been reported across the family.

Background The rapidly increasing availability of complete plastomes has revealed more structural complexity in this genome under different taxonomic levels than expected, and this complexity provides important evidence for understanding the evolutionary history of angiosperms. To explore the dynamic history of plastome structure across the subclass Alismatidae, we sampled and compared 38 complete plastomes, including 17 newly assembled, representing all 12 recognized families of Alismatidae. Result We found that plastomes size, structure, repeat elements, and gene content were highly variable across the studied species. Phylogenomic relationships among families were reconstructed and six main patterns of variation in plastome structure were revealed. Among these, the inversion from rbcL to trnV-UAC (Type I) characterized a monophyletic lineage of six families, but independently occurred also in Caldesia grandis . Three independent ndh gene loss events were uncovered across the Alismatidae. In addition, we detected a positive correlation between the number of repeat elements and the size of plastomes and IR in Alismatidae. Conclusion In our study, ndh complex loss and repeat elements likely contributed to the size of plastomes in Alismatidae. Also, the ndh loss was more likely related to IR boundary changes than the adaptation of aquatic habits. Based on existing divergence time estimation, the Type I inversion may have occurred during the Cretaceous-Paleogene in response to the extreme paleoclimate changes. Overall, our findings will not only allow exploring the evolutionary history of Alismatidae plastome, but also provide an opportunity to test if similar environmental adaptations result in convergent restructuring in plastomes.